gebhart/patrepeval huggingface dataset:
Macrophage Migration Inhibitory Factor Mediates Hypoxia-Induced Pulmonary Hypertension (2011)

Pulmonary hypertension (PH) is a devastating disease leading to progressive hypoxemia, right ventricular failure, and death. Hypoxia can play a pivotal role in PH etiology, inducing pulmonary vessel constriction and remodeling. These events lead to increased pulmonary vessel wall thickness, elevated vascular resistance and right ventricular hypertrophy. The current study examined the association of the inflammatory cytokine macrophage migration inhibitory factor (MIF) with chronic lung disease and its role in the development of hypoxia-induced PH. We found that plasma MIF in patients with primary PH or PH secondary to interstitial lung disease (ILD) was significantly higher than in the control group (P = 0.004 and 0.007, respectively). MIF involvement with hypoxia-induced fibroblast proliferation was examined in both a human cell-line and primary mouse cells from wild-type (mif⁺/⁺) and MIF-knockout (mif⁻/⁻) mice. In vitro, hypoxia-increased MIF mRNA, extracellular MIF protein accumulation and cell proliferation. Inhibition of MIF inflammatory activity reduced hypoxia-induced cell proliferation. However, hypoxia only increased proliferation of mif⁻/⁻ cells when they were supplemented with media from mif⁺/⁺ cells. This growth increase was suppressed by MIF inhibition. In vivo, chronic exposure of mice to a normobaric atmosphere of 10% oxygen increased lung tissue expression of mRNA encoding MIF and accumulation of MIF in plasma. Inhibition of the MIF inflammatory active site, during hypoxic exposure, significantly reduced pulmonary vascular remodeling, cardiac hypertrophy and right ventricular systolic pressure. The data suggest that MIF plays a critical role in hypoxia-induced PH, and its inhibition may be beneficial in preventing the development and progression of the disease.
Crystal structure of a staphylokinase variant (2002)

Staphylokinase (SAK) is a 15.5-kDa protein from Staphylococcus aureus that activates plasminogen by forming a 1 : 1 complex with plasmin. Recombinant SAK has been shown in clinical trials to induce fibrin-specific clot lysis in patients with acute myocardial infarction. However, SAK elicits high titers of neutralizing antibodies. Biochemical and protein engineering studies have demonstrated the feasibility of generating SAK variants with reduced antigenicity yet intact thrombolytic potency. Here, we present X-ray crystallographic evidence that the SAK(S41G) mutant may assume a dimeric structure. This dimer model, at 2.3-A resolution, could explain a major antigenic epitope (residues A72-F76 and residues K135-K136) located in the vicinity of the dimer interface as identified by phage-display. These results suggest that SAK antigenicity may be reduced by eliminating dimer formation. We propose several potential mutation sites at the dimer interface that may further reduce the antigenicity of SAK.
Photoresist Contact Patterning of Quantum Dot Films (2018)

Scalable and cost-effective protocols to pattern and integrate colloidal quantum dots (QDs) with high resolution have been challenging to establish. While their solubility can facilitate certain processes such as spin-casting into thin films, it also makes them incompatible with many conventional patterning techniques including photolithography that require solution processing. In this work, we present "photoresist (PR) contact patterning", a dry means to pattern QD films over large areas with high resolution while maintaining desired properties. Here, a PR layer on an elastomer substrate is patterned by conventional photolithography and used as a dry contact stamp to selectively peel off QDs in the contact regions, leaving behind a QD film with the negative of the PR pattern. Once patterned, QD films are readily transferred and integrated on foreign substrates by subsequent transfer printing processes. Patterned PR layers can also be transferred from elastomer substrates onto QD films and used as masking layers for subsequent deposition and patterning of additional materials, e. g., patterned metal electrodes or charge transport layers for QD-based devices. The study of the interfacial mechanics and energy of materials associated with PR contact patterning reveals why a lithographically patterned PR is superior for high-resolution QD film patterning. Applicability of PR contact patterning is demonstrated through the fabrication of red, green, and blue (RGB) QD light-emitting diode pixels. PR contact patterning presented in this work not only allows dry patterning of QD films but also enables high-resolution integration of functional multistack structures for future QD-based electronic and optoelectronic devices.
Stable, continuously tunable operation of a diode-pumped doubly resonant optical parametric oscillator (2000)

We demonstrate, for what is the first time to our knowledge, long-term stable, continuously tunable operation of a doubly resonant optical parametric oscillator (OPO) pumped by a single-stripe diode laser without the use of an external semiconductor amplifier. The OPO is based on periodically poled lithium niobate and is pumped by a 150-mW distributed Bragg grating diode laser. 18-mW total output power is generated at 1.3- and 2.3-mum wavelengths. A cavity-length servo system allows continuous signal tuning of 17 GHz and idler tuning of 10 GHz, limited only by the range of a piezoelectric cavity mirror mount. OPO tuning is demonstrated from 1.1 to 1.4 mum and from 2.2 to 3.7 mum.
A Monte-Carlo Calculation of the Neutron Sensitivity of Self-Powered Detectors (1973)

Self-powered (s-p) detectors are useful for incore neutron measurements in nuclear reactors because of their small size, ruggedness and simplicity. In one type of detector, a delayed current results from the beta activity induced in the device by the neutron flux while a second type gives an instantaneous response due to the compton electrons produced by the gammas released following the capture of neutrons in the device. To test these physical models and more importantly, to point the way to improvements in design without having to resort to excessive experimentation, a Monte-Carlo model was constructed to allow computations to be made of the response of both types of detector. The calculations were performed for Rh and V delayed and Co instantaneous detectors with emitter diameters of .051 cm and insulator thickness of .025 cm in all cases. The agreement with experiment was fairly good and the small discrepancies which occur are discussed in the paper.
Quantitative resistance to Botrytis cinerea from Solanum neorickii (2007)

Tomato (Solanum lycopersicum) is susceptible to gray mold (Botrytis cinerea). Quantitative resistance to B. cinerea was previously identified in a wild relative, S. neorickii G1.1601. The 122 F3 families derived from a cross between the susceptible S. lycopersicum cv. Moneymaker and the partially resistant S. neorickii G1.1601 were tested for susceptibility to B. cinerea using a stem bioassay. Three putative quantitative trait loci (pQTL) were detected: pQTL3 and pQTL9 reducing lesion growth (LG) and pQTL4 reducing disease incidence (DI). For each pQTL, a putative homologous locus was identified recently in another wild tomato relative, S. habrochaites LYC4. pQTL3 was confirmed by assessing disease resistance in BC3S1 and BC3S2 progenies of S. neorickii G1.1601. pQTL4 was not statistically confirmed but the presence of the S. neorickii resistance allele reduced DI in all three tested populations. The reduction in LG of pQTL9 was not confirmed but rather, this locus conferred a reduced DI, similar to observations in the QTL study using S. habrochaites. The results are discussed in relation to other disease resistance loci identified in studies with other wild tomato relatives.
PRODIAG: Combined expert system/neural network for process fault diagnosis. Volume 2, Code manual (1995)

We recommend the reader first review Volume 1 of this document, Code Theory, before reading Volume 2. In this volume we make extensive use of terms and concepts described and defined in Volume 1 which are not redefined here to the same extent. To try to reduce the amount of redundant information, we have restricted this volume to the presentation of the expert system code and refer back to the theory described in Volume 1 when necessary. Verification and validation of the results are presented in Volume 3, Application, of this document. Volume 3 also presents the implementation of the component characteristics diagnostic approach through artificial neural networks discussed in Volume 1. We decided to present the component characteristics approach in Volume 3, as opposed to write a separate code manual for it, because the approach, although general, requires a case-by-case analysis. The purpose of this volume is to present the details of the expert system (ES) portion o the PRODIAG process diagnostic program. In addition, we present here the graphical diagnostics interface (GDI) and illustrate the combined use of the ES and GDI with a sample problem. For completeness, we provide the file names of all files, programs and major subroutines of these two systems, ES and GDI, and their corresponding location in the Reactor Analysis Division (RA) computer network and Reactor Engineering Division (RE) computer network as of 30 September 1995.
Improved ground plane detection in real time systems using homography (2014)

Advanced Driver Assistance Systems (ADAS) are used to assist driver by providing real-time information about cross traffic, parking space and so on. Such applications require a fair amount of processing to be done on the incoming video feed. It has been proved that the homography approach is efficient for ground plane detection. But, in the case of Road Plane Detection, the lane markings appear as obstacles when the SAD approach [1] is used. We propose a solution to this problem which involves using a Road Model and applying lane masking. We are able to get an accuracy of 88% to 96%. This technique is suitable for real time applications and we also provide benchmarks on a DSP processor, TMS320C6000 for the key functions used in this algorithm.
The OxiMax System. Nellcor's new platform for pulse oximetry. (2002)

The new OxiMax Pulse Oximetry System includes the Nellcor N-595 Pulse Oximeter and a new line of OxiMax sensor. The main feature of this platform is the digital memory chip inserted within each OxiMax sensor that contains all the calibration and operating characteristics for that individual sensor. It allows an information exchange between the sensor and the monitor improving monitoring performance during difficult acquisition periods. We reviewed several studies showing that the more centrally placed forehead sensor can offer significant advantage over finger sensor when monitoring patient with low pulse perfusion, especially in situation where rapid detection of hypoxemia is critical.
Feature-based compressive signal processing (CSP) measurement design for the pattern analysis of Cognitive Radio spectrum (2013)

Cognitive Radio (CR) can efficiently utilize the licensed wideband spectrum whenever the primary users (PUs) are absent. Spectrum sensing is the first step and an important function to fulfill the CR system. A cyclostationary feature detector can robustly detect the PU's modulated signals even under strong interferences. However this detector needs high signal sampling rate and also puts heavy computation burden on the system. Compressive sensing (CS) can compress the data at the front sampling end but has high overload and delay from the reconstruction side. In this work we generate the compressive CR spectrum measurement by utilizing both the cyclostationary feature and sparsity prior knowledge at the spectrum sensing front end, and we apply the compressive signal processing (CSP) without the need of signal or feature reconstruction. This can significantly shorten the CR spectrum sensing time. Our experimental results have shown the pattern analysis accuracy and efficiency of our CSP scheme.
A Non-Iterative Approach to Reconstruct Face Templates from Match Scores (2006)

Regeneration of biometric templates from match scores has security and privacy implications related to any biometric based authentication system. In this paper, we propose a novel non-iterative scheme to reconstruct face templates from match scores. We use an affine transformation of the images to approximate the behavior of the given face recognition system based on an independent set of face templates termed as "break-in" set. Selected templates from the "break-in" set are matched only once with the enrolled template of the target account and match scores are recorded. These scores are then embedded in the approximating affine space along with break-in set templates to compute the co-ordinates of the target template. The inverse transformation is used to reconstruct the original target template. We present the reconstruction of templates for three different face recognition algorithms: Bayesian intrapersonal/extrapersonal classifier, elastic bunch graph matching (EBGM) algorithm and baseline algorithm used in Face Recognition Grand Challenge (2005). We also report the initial result to break a user's account using the reconstructed template for Bayesian algorithm. Bayesian algorithm was set to operate at 0.1% false acceptance rate and 98% true acceptance rate with 100 enrollments. We observed that with proposed scheme, at most 600 attempts are required to achieve a 0.99 probability of break-in the Bayesian face recognition algorithm
An experimental system for robotic needle biopsy of lung nodules with respiratory motion (2011)

CT-guided needle biopsy is a dominant method of obtaining tissue samples from lung nodules for lung cancer diagnosis. Current practice requires patients to hold their breath during the procedure, which is not applicable to those who have difficulty in holding breath. This paper introduces a CT-guided robotic needle biopsy technique, which adapts to the patient respiratory motion pattern and uses a robot manipulator to drive the biopsy needle towards a target lung nodule with respiratory motion. It enables biopsies on patients who have difficulty in holding breath. An experimental system has been created to facilitate the development and evaluation of the robotic needle placement technique. It consists of three subsystems coordinated by a computer, i.e. a lung nodule phantom subsystem which mimics a lung nodule with respiratory motion, a robotic needle manipulation subsystem which drives the biopsy needle to hit the moving target, and a vision feedback subsystem which tracks the moving lung nodule phantom in real time for controlling the needle placement. The results from a sequence of needle placement tests based on clinically-obtained lung nodule motion paths show that the robotic needle placement technique can provide quick and highly accurate needle placement on moving nodules.
Hypersonic Plasma Particle Deposition of Nanostructured Coatings and Micropatterns (2004)

Nanostructured materials are attractive candidates for advanced friction and wear-resistant coatings due to their potentially enhanced mechanical properties. We have developed a one-step method called hypersonic plasma particle deposition [1] to produce and deposit nanoparticles using a thermal plasma reactor. Particle synthesis is achieved by dissociating vapor phase reactants in the plasma, and quenching the hot gas in a supersonic nozzle expansion. Particles are deposited on a substrate by hypersonic impaction to form a film, or are deposited as micropatterns using a process called focused particle beam deposition [2]. In-situ particle size distribution measurements are performed using a sampling probe interfaced to an extraction/dilution system for measurement by a scanning electrical mobility spectrometer.
54.2: <i>Invited Paper</i> : High Efficiency Polarization Preserving Cinema Projection Screens (2013)

Abstract Conventional polarization preserving cinema projection screens suffer from a number of issues that limit their optical performance. We describe the microscopic structure of these screens and how the different aspects of this structure interact to produce the primary screen properties of gain, viewing angle, stereo contrast, and appearance. We then present an engineered polarization‐preserving projection screen that addresses the limitations associated with conventional silver screens. This screen achieves substantially increased efficiency (brightness), increased stereo contrast, arbitrarily large viewing angle, and matte appearance.
CCL19 as a Chemokine Risk Factor for Posttreatment Lyme Disease Syndrome: a Prospective Clinical Cohort Study (2016)

Approximately 10% to 20% of patients optimally treated for early Lyme disease develop persistent symptoms of unknown pathophysiology termed posttreatment Lyme disease syndrome (PTLDS). The objective of this study was to investigate associations between PTLDS and immune mediator levels during acute illness and at several time points following treatment. Seventy-six participants with physician-documented erythema migrans and 26 healthy controls with no history of Lyme disease were enrolled. Sixty-four cytokines, chemokines, and inflammatory markers were measured at each visit for a total of 6 visits over 1 year. An operationalized definition of PTLDS incorporating symptoms and functional impact was applied at 6 months and 1 year following treatment completion, and clinical outcome groups were defined as the return-to-health, symptoms-only, and PTLDS groups. Significance analysis of microarrays identified 7 of the 64 immune mediators to be differentially regulated by group. Generalized logit regressions controlling for potential confounders identified posttreatment levels of the T-cell chemokine CCL19 to be independently associated with clinical outcome group. Receiver operating characteristic analysis identified a CCL19 cutoff of >111.67 pg/ml at 1 month following treatment completion to be 82% sensitive and 83% specific for later PTLDS. We speculate that persistently elevated CCL19 levels among participants with PTLDS may reflect ongoing, immune-driven reactions at sites distal to secondary lymphoid tissue. Our findings suggest the relevance of CCL19 both during acute infection and as an immunologic risk factor for PTLDS during the posttreatment phase. Identification of a potential biomarker predictor for PTLDS provides the opportunity to better understand its pathophysiology and to develop early interventions in the context of appropriate and specific clinical information.
Improved analysis of the time domain response of scanning force microscope cantilevers (2000)

The snap-to-contact instability encountered in scanning force microscopy-force spectroscopy (SFMFS) limits the range of forces measurable in SFM force–distance experiments. We have generalized the flexural beam theory for SFM cantilevers to include tip interactions that are present in the snap-to-contact region. We compare solutions for the beam theory with the simple harmonic oscillator (SHO) that is often used to approximate SFM cantilevers. The limitations of the SHO model are encountered when large force gradients are present. This causes the beam shape to change leading to error when the SHO is used to reconstruct force curves collected in the snap-to-contact region. We quantify the error introduced into a force–separation curve reconstructed using the SHO approximation by numerical simulation. The force–separation curve reconstructed by the SHO was significantly inaccurate and had distorted separation dependence. This makes physical interpretation of force curves reconstructed using the SHO approximation tenuous when force microscope data from the snap-to-contact region is used.
SU‐FF‐T‐110: Fast Inverse Dose Optimization (FIDO) for IMRT Via Matrix Inversion Without Negative Beamlet Intensities (2005)

Purpose: To optimize an IMRT treatment plan by a matrix inversion method that is very fast, robust and yields a global optimization minimum without negative intensities. Given the availability of online imaging tools, the conformal dose distributions obtained through IMRT and its dynamic delivery features, adaptive radiotherapy becomes an important factor to be considered. A fast and reliable optimization algorithm is crucial not only for designing good radiation treatment plans but also for the successful implementation of future interactive adaptive treatment techniques. Method and Materials: The objective function for the optimization of a large number of beamlets is reformulated such that the optimization problem is reduced to a linear set of equations. The optimal set of intensities is found through a matrix inversion, and negative beamlet intensities are avoided without the need for externally imposed ad‐hoc constraints. The objective function remains quadratic and the optimal result obtained corresponds to a single global minimum. Results: The method has been demonstrated with a test phantom and a few clinical radiotherapy cases using primary photons in the dose calculation only. We have showed that the new method is not only faster but also gives better optimization results. Typical optimization times for a single anatomical slice (2D) (head and neck) using a standard LAPack matrix inversion routine in a single processor desktop computer, are: 0.03 sec. for 500 beamlets; 0.28 sec. for 1,000 beamlets; 3.1 sec. for 2,000 beamlets and 12 sec for 3,000 beamlets. Conclusion: We have developed a fast and robust technique to find a global minimum of an objective function that yields excellent results for the inverse optimization problem for the radiation treatment of tumours with IMRT.
The Anaplasma marginale msp5 gene encodes a 19-kilodalton protein conserved in all recognized Anaplasma species (1992)

Immunization with Anaplasma marginale outer membranes induced immunity against clinical disease which correlated with antibody titer to outer membrane proteins, including a 19-kDa protein (N. Tebele, T. C. McGuire, and G. H. Palmer, Infect. Immun. 59:3199-3204, 1991). This 19-kDa protein, designated major surface protein 5 (MSP-5), was encoded by a single-copy 633-bp gene. The molecular mass of MSP-5, defined in immunoblots by binding to monoclonal antibody ANAF16C1, was conserved among all recognized species of Anaplasma: A. marginale, A. centrale, and A. ovis. Recombinant MSP-5, which absorbed the antibody reactivity of bovine immune serum to native MSP-5, was recognized by anti-A. marginale and anti-A. centrale immune sera in a competitive inhibition assay with monoclonal antibody ANAF16C1. The presence of antibody to the epitope defined by monoclonal antibody ANAF16C1 in all postinfection sera tested indicates that this epitope is a potential diagnostic antigen for use in identifying persistently infected cattle.
Dynamic hardware/software partitioning (2003)

Partitioning an application among software running on a microprocessor and hardware co-processors in on-chip configurable logic has been shown to improve performance and energy consumption in embedded systems. Meanwhile, dynamic software optimization methods have shown the usefulness and feasibility of runtime program optimization, but those optimizations do not achieve as much as partitioning. We introduce a first approach to dynamic hardware/software partitioning. We describe our system architecture and initial on-chip tools, including profiler, decompiler, synthesis, and placement and routing tools for a simplified configurable logic fabric, able to perform dynamic partitioning of real benchmarks. We show speedups averaging 2.6 for five benchmarks taken from Powerstone, NetBench, and our own benchmarks.