gebhart/patrepeval huggingface dataset:
Sparsely cross‐linked “nanogels” for microchannel DNA sequencing (2003)

We have developed sparsely cross-linked "nanogels", sub-colloidal polymer structures composed of covalently linked, linear polyacrylamide chains, as novel DNA sequencing matrices for capillary electrophoresis. The presence of covalent cross-links affords nanogel matrices with enhanced network stability relative to standard, linear polyacrylamide (LPA), improving the separation of large DNA fragments. Nanogels were synthesized via inverse emulsion (water-in-oil) copolymerization of acrylamide and N,N-methylenebisacrylamide (Bis). In order to retain the fluidity necessary in a replaceable polymer matrix for capillary array electrophoresis (CAE), a low percentage of the Bis cross-linker (< 10(-4) mol%) was used. Nanogels were characterized by multiangle laser light scattering and rheometry, and were tested for DNA sequencing by CAE with four-color laser-induced fluorescence (LIF) detection. The properties and performance of nanogel matrices were compared to those of a commercially available LPA network, which was matched for both weight-average molar mass (Mw) and extent of interchain entanglements (c/c*). Nanogels presented in this work have an average radius of gyration of 226 nm and a weight-average molar mass of 8.8 x 10(6) g/mol. At concentrations above the overlap threshold, nanogels form a clear, viscous solution, similar to the LPA matrix (Mw approximately 8.9 x 10(6) g/mol). The two matrices have similar flow and viscosity characteristics. However, because of the physical network stability provided by the internally cross-linked structure of the nanogels, a substantially longer read length ( approximately 63 bases, a 10.4% improvement) is obtained with the nanogel matrix at 98.5% accuracy of base-calling. The nanogel network provides higher-selectivity separation of ssDNA sequencing fragments longer than 375 bases. Moreover, nanogel matrices require 30% less polymer per unit volume than LPA. This is the first report of a sequencing matrix that provides better performance than LPA, in a side-by-side comparison of polymer matrices matched for Mw and extent of interchain entanglements.
TGF-β1 programmed myeloid-derived suppressor cells (MDSC) acquire immune-stimulating and tumor killing activity capable of rejecting established tumors in combination with radiotherapy (2018)

Cancer-induced myeloid-derived suppressor cells (MDSC) play an important role in tumor immune evasion. MDSC programming or polarization has been proposed as a strategy for leveraging the developmental plasticity of myeloid cells to reverse MDSC immune suppressive functions, or cause them to acquire anti-tumor activity. While MDSC derived <i>ex vivo</i> from murine bone marrow precursor cells with tumor-conditioned medium efficiently suppressed T cell proliferation, MDSC derived from conditioned medium in presence of TGF-β1 (TGFβ-MDSC) acquired a novel immune-stimulatory phenotype, losing the ability to inhibit T cell proliferation and acquiring enhanced antigen-presenting capability. Altered immune function was associated with SMAD-2 dependent upregulation of maturation and costimulatory molecules, and downregulation of inducible nitric oxide synthase (iNOS), an effector mechanism of immunosuppression. TGFβ-MDSC also upregulated FAS-ligand expression, leading to FAS-dependent killing of murine human papillomavirus (HPV)-associated head and neck cancer cells and tumor spheroids <i>in vitro</i> and anti-tumor activity <i>in vivo</i>. Radiation upregulated FAS expression on tumor cells, and the combination of radiotherapy and intratumoral injection of TGFβ-MDSC strongly enhanced class I expression on tumor cells and induction of HPV E7 tetramer-positive CD8 + T cells, leading to clearance of established tumors and long-term survival. TGFβ-MDSC derived from human PBMC with tumor conditioned medium also lost immunosuppressive function and acquired tumor-killing activity. Thus, TGFβ1 mediated programming of nascent MDSC leads to a potent anti-tumor phenotype potentially suitable for adoptive immunotherapy.
Trace gas detection in ambient air with cw and pulsed QC lasers (2000)

Summary form only given.Recently developed quantum-cascade lasers' have been shown to be useful tunable single-frequency light sources for laser-based absorption spectroscopy in the important mid-IR region. In this work, we demonstrate the application of cw and pulsed single-frequency quantum cascade (QC) DFB lasers to the sensitive detection of CH/sub 4/, N/sub 2/O, C/sub 2/H/sub 5/OH (ethanol) and different isotopic species of H/sub 2/O in ambient air will be reported. In order to determine the ethanol concentration from its dense infrared spectrum, a new approach based on a linear correlation technique was applied.
<title>Optically programmable assembly of ordered bead arrays: a novel technology for on-chip biochemical analysis</title> (1999)

We describe an optically programmable bead array assembly process and its efficient implementation. Invoking our core technology of light-controlled electrokinetic assembly of particles near surfaces, this process enables the on-demand assembly and real-time manipulation of planar arrays of microparticles (`beads') within a small reaction chamber in response to electric fields and in accordance with computer- generated patterns of illumination. We are integrating this array fabrication process with proprietary microfluidics and image acquisition in a palmtop bioanalytical microlab to provide a general-purpose platform for a highly parallel assay format in which tens to thousands of biochemical tests (`assays') can be performed simultaneously on the surface of a semiconductor chip. Applications include the quantitative analysis of protein-protein interactions and DNA hybridization as well as cellular analysis.
<i>In Vitro</i>Combination of Anti-Cytomegalovirus Compounds Acting through Different Targets: Role of the Slope Parameter and Insights into Mechanisms of Action (2013)

Conventional therapy for human cytomegalovirus (CMV) relies on inhibition of the viral DNA polymerase. Ganciclovir (GCV) is the first-line therapy, but when GCV-resistant strains emerge, alternative therapies are extremely limited and are associated with significant toxicities. Combination of anti-CMV agents that act on different targets or stages of virus replication has not been well studied, mostly because of the limited number of anti-CMV agents. We report our investigation of combinations of agents that inhibit CMV by targeting the viral DNA polymerase, cellular kinases, or other cell/virus mechanisms yet to be discovered. The selected compounds differed by the slopes of their dose-response curve: compounds with a slope of 1 (GCV) representing one target or noncooperativity and compounds with high slopes indicating positive cooperativity. Analysis of anti-CMV drug combinations using the Bliss model (which accounts for the slope parameter) distinguished between combinations with synergistic, antagonistic, and additive activities. The combination of GCV and foscarnet was slightly synergistic; strong synergism was found when GCV was used with artemisinin-derived monomers or dimers or the MEK inhibitor U0126. The combination of GCV and cardiac glycosides (digoxin, digitoxin, and ouabain) was additive. The monomeric artemisinin artesunate was synergistic when combined with U0126 or the multikinase inhibitor sunitinib. However, the combination of artemisinin-derived dimers (molecular weights, 606 and 838) and U0126 or sunitinib was antagonistic. These results demonstrate that members of a specific drug class show similar patterns of combination with GCV and that the slope parameter plays an important role in the evaluation of drug combinations. Lastly, antagonism between different classes of CMV inhibitors may assist in target identification and improve the understanding of CMV inhibition by novel compounds.
Exploiting non-volatile memory in disks for write caching (1994)

The I/O subsystem in a computer system is becoming the bottleneck as a result of recent dramatic improvements in processor speeds. Disk caches have been effective in closing this gap but the benefit is restricted to the read operations as the write I/Os are usually committed to disk to maintain consistency and to allow for crash recovery. As a result, write I/O traffic is becoming dominant and solutions to alleviate this problem are becoming increasingly important. A simple solution which can easily work with existing file systems is to use non-volatile disk caches together with a write-behind strategy. In this study, we look at the issues around managing such a cache using a detailed trace driven simulation. Traces from three different commercial sites are used in the analysis of various policies for managing the write cache. We observe that even a simple write-behind policy for the write cache is effective in reducing the total number of writes by over 50%. We further obser...
Detection sensitivity of laser feedback interferometry using a terahertz quantum cascade laser (2019)

We report on the high detection sensitivity of a laser feedback interferometry scheme based on a terahertz frequency quantum cascade laser (QCL). We show that variations on the laser voltage induced by optical feedback to the laser can be resolved with the reinjection of powers as low as ∼-125 dB of the emitted power. Our measurements demonstrate a noise equivalent power of ∼1.4 pW/√Hz, although, after accounting for the reinjection losses, we estimate that this corresponds to only ∼1 fW/√Hz being coupled to the QCL active region.
Assessment of Aortic Valve Opening During Rotary Blood Pump Support Using Pump Signals (2013)

During left ventricular support by rotary blood pumps (RBPs), the biomechanics of the aortic valve (AV) are altered, potentially leading to adverse events like commissural fusion, valve insufficiency, or thrombus formation. To avoid these events, assessment of AV opening and consequent adaptation of pump speed seem important. Additionally, this information provides insight into the heart-pump interaction. The aim of this study was to develop a method to assess AV opening from the pump flow signal. Data from a numerical model of the cardiovascular system and animal experiments with an RBP were employed to detect the AV opening from the flow waveform under different hemodynamic conditions. Three features calculated from the pump flow waveform were used to classify the state of the AV: skewness, kurtosis, and crest factor. Three different classification algorithms were applied to determine the state of the AV based on these features. In the model data, the best classifier resulted in a percentage of correctly identified beats with a closed AV (specificity) of 99.9%. The percentage of correctly identified beats with an open AV (sensitivity) was 99.5%. In the animal experiments, specificity was 86.8% and sensitivity reached 96.5%. In conclusion, a method to detect AV opening independently from preload, afterload, heart rate, contractility, and degree of support was developed. This algorithm makes the evaluation of the state of the AV possible from pump data only, allowing pump speed adjustment for a frequent opening of the AV and providing information about the interaction of the native heart with the RBP.
Characterization of Particle Flow in a Free-Falling Solar Particle Receiver (2015)

Falling particle receivers are being evaluated as an alternative to conventional fluid-based solar receivers to enable higher temperatures and higher efficiency power cycles with direct storage for concentrating solar power applications. This paper presents studies of the particle mass flow rate, velocity, particle-curtain opacity and density, and other characteristics of free-falling ceramic particles as a function of different discharge slot apertures. The methods to characterize the particle flow are described, and results are compared to theoretical and numerical models for unheated conditions.
The Murine IL-13 Receptor α2: Molecular Cloning, Characterization, and Comparison with Murine IL-13 Receptor α1 (1998)

Abstract Two components of a receptor complex for IL-13, the IL-4R and a low affinity IL-13-binding chain, IL-13Rα1, have been cloned in mice and humans. An additional high affinity binding chain for IL-13, IL-13Rα2, has been described in humans. We isolated a cDNA from the thymus that encodes the murine orthologue of the human IL-13Rα2. The predicted protein sequence of murine IL-13Rα2 (mIL-13Rα2) has 59% overall identity to human IL-13Rα2 and is closely related to the murine low affinity IL-13-binding subunit, IL-13Rα1. The genes for both mIL-13-binding chains map to the X chromosome. A specific interaction between mIL-13Rα2.Fc protein and IL-13 was demonstrated by surface plasmon resonance using a BIACORE instrument. Ba/F3 cells that were transfected with mIL-13Rα2 expressed 5000 molecules per cell and bound IL-13 with a single Kd of 0.5 to 1.2 nM. However, these cells did not proliferate in response to IL-13, and the IL-4 dose response was unaffected by high concentrations of IL-13. In contrast, the expression of mIL-13Rα1 by Ba/F3 cells resulted in a sensitive proliferative response to IL-13. Consistent with its lower affinity for IL-13, IL-13Rα1.Fc was 100-fold less effective than IL-13Rα2.Fc in neutralizing IL-13 in vitro. These results show that mIL-13Rα2 and mIL-13Rα1 are not functionally equivalent and predict distinct roles for each polypeptide in IL-13R complex formation and in the modulation of IL-13 signal transduction.
Regional correlation of biochemical measures of amyloid and tau phosphorylation in the brain (2020)

Alzheimer's disease (AD) neuropathologic change is characterized by amyloid plaques and neurofibrillary tangles (NFTs) that consist of aggregated amyloid beta (Abeta) and hyperphosphorylated tau proteins (p-tau), respectively. Although the global relationship between Abeta and p-tau has been studied for decades, it is still unclear whether a regional correlation exists between Abeta and p-tau in the human brain. Recent studies in cerebrospinal fluid (CSF) have suggested that tau phosphorylation at specific sites such as T217 is modified at an early stage of AD when amyloid plaques become detectable. We applied biochemical and mass spectrometry methods in human brain samples with and without Abeta plaque pathology to measure site-specific phosphorylation occupancies in soluble and insoluble tau. Our quantitative results identified multiple residues specifically hyper-phosphorylated in AD, including at sites T111, T153, S184 (or S185), T205, S208, T217, S262, and S285 in brain soluble tau. In contrast, the most enriched phosphorylated residues in brain insoluble tau were T111, S113, T153, T181, S199, S202, T205, T217, T231, S262, and S396. Tau phosphorylation occupancies in the insoluble fraction were relatively constant across brain regions, suggesting that tau has a consistent phosphorylation pattern once it has aggregated into NFTs. We did not find regional association between Abeta42 and insoluble tau. However, the phosphorylation profile of soluble tau in AD brain was highly correlated to that in AD CSF, which was analyzed in a previous study. We also found a higher regional association between total Abeta42 and soluble tau phosphorylation occupancy at residues T111, T153 and T217 in the brain. This study provides insights into regional interactions between amyloidosis and specific tau phosphorylated residues in the human brain and may explain the specific increases of tau species phosphorylation observed in AD CSF.
Naive ray-tracing (2011)

We present an efficient ray-tracing algorithm which, for the first time, does not store any data structures when performing spatial subdivisions, and directly computes intersections inside the scene. This new algorithm is often faster than comparable ray-tracing methods at rendering dynamic scenes, and has a similar level of performance when compared to static ray-tracers. Memory management is made minimal and deterministic, which simplifies ray-tracing engineering, as spatial subdivision data structures are no longer considered in the graphics pipeline. This is possible with a modification of Whitted's naive ray-tracing algorithm by using a divide-and-conquer approach, and by having a sufficient collection of rays in order to reduce the complexity of naive ray-tracing. In particular, the algorithm excels at spontaneously solving large Ray/Primitive intersection problems.
Development of novel Ni-based single crystal superalloys for power-generation gas turbines (2007)

In advanced industrial gas-turbine systems, there has been a great demand for new single crystal (SC) superalloys with an excellent combination of high-temperature creep strength, hot-corrosion resistance and oxidation resistance. In this study, 12 nickel-based SC superalloys were designed with the aid of the d-electrons concept. Their chemical compositions were in the range of 1.2–1.5%Ti, 3.8–6.5%Cr, 11%Co, 0–1.4%Mo, 0–3.0%Ru, 6.5–7.4%Ta, 5.0–6.4%W, 3.6–5.4%Re, 5.1–5.5%Al, 0.12–0.14%Hf and balanced Ni in wt%. A series of experiments such as creep rupture tests, burner rig tests and cyclic oxidation tests were conducted with the heat-treated SC specimens of these alloys. Almost all the designed alloys were found to be superior in creep rupture life to a second generation superalloy currently used in the world. For hot-corrosion resistance, estimated from the burner rig tests, any of the designed alloys were comparable or even superior to a second generation superalloy. The oxidation resistance was very different among the designed alloys, but some of them showed better resistance than the second generation superalloy. Thus the SC alloys containing about 4–5 wt%Re had about 30°C or more higher temperature capability than the second generation superalloy, while exhibiting excellent hot-corrosion resistance and good oxidation resistance.
Generalizing Boolean Satisfiability III: Implementation (2005)

This is the third of three papers describing ZAP, a satisfiability engine that substantially generalizes existing tools while retaining the performance characteristics of modern high-performance solvers. The fundamental idea underlying ZAP is that many problems passed to such engines contain rich internal structure that is obscured by the Boolean representation used; our goal has been to define a representation in which this structure is apparent and can be exploited to improve computational performance. The first paper surveyed existing work that (knowingly or not) exploited problem structure to improve the performance of satisfiability engines, and the second paper showed that this structure could be understood in terms of groups of permutations acting on individual clauses in any particular Boolean theory. We conclude the series by discussing the techniques needed to implement our ideas, and by reporting on their performance on a variety of problem instances.
GM-CSF-Induced Regulatory T cells Selectively Inhibit Anti-Acetylcholine Receptor-Specific Immune Responses in Experimental Myasthenia Gravis (56.1) (2012)

Abstract We and others have demonstrated the ability of granulocyte-macrophage colony-stimulating factor (GM-CSF) to suppress autoimmunity by increasing the number of CD4+CD25+ regulatory T cells (Tregs). In the current study, we have explored the critical role of induced antigen specific Tregs in the therapeutic effects of GM-CSF in murine experimental autoimmune myasthenia gravis (EAMG). Specifically, we show that Tregs from GM-CSF treated EAMG mice (GM-CSF/AChR-induced-Tregs) adoptively transferred into animals with EAMG suppressed clinical disease more potently than equal numbers of Tregs from either GM-CSF untreated EAMG mice or healthy mice treated with GM-CSF. In addition, GM-CSF/AChR-induced-Tregs selectively suppressed antigen specific T cell proliferation induced by AChR relative to that induced by an irrelevant self antigen, (thyroglobulin) and failed to significantly alter T cell proliferation in response to an exogenous antigen (ovalbumin). These results are consistent with the hypothesized mechanism of action of GM-CSF involving the mobilization of tolerogenic dendritic cell precursors which, upon antigen (AChR) capture, suppress the anti-AChR immune response through the induction/expansion of AChR-specific Tregs.
Total Synthesis of Bryostatin 9 (2011)

The total synthesis of bryostatin 9 was accomplished using a uniquely step-economical and convergent Prins-driven macrocyclization strategy. At 25 linear and 42 total steps, this is currently the most concise and convergent synthesis of a potent bryostatin.
Silica based erbium doped fiber extending the L-band to 1620+ nm (2002)

A fiber has been developed for use in extended L-band amplifiers, utilizing the wavelength range from 1565 to 1620 nm. The fiber is silica based and has low splice loss to standard telecommunication fiber. The quantum conversion efficiency is >60%.
Fatigue-Resistant Photochromic Plastics (1989)

The optical switching properties of a photochromic spirooxazine compound in retrofit polyester film and in poly (vinyl butyral) have been measured. The light fatigue resistance of these two optical switching elements were tested by an accelerated method. The length of photochromic activity of the optical switching elements can be improved by various organonickel and hindered amine light stabilizers. The effectiveness and optimal concentration for each light stabilizer in these host materials has been determined. These two types of light stabilizers act synergistically in improving the light fatigue resistance of the optical switching elements significantly.
Identification of multiple HIV-1 cytotoxic T-cell epitopes presented by human leukocyte antigen B35 molecules. (1996)

In addition to the four HLA-B35-restricted HIV-1 CTL epitopes that have been previously reported, nine HLA-B35-restricted HIV-1 CTL epitopes were identified in the present study. These multiple epitopes will be useful in studies for immunopathogenesis of AIDS.
Field Application of a Novel Core-Based In-Situ Stress Estimation Technique (2002)

Abstract In this paper, we present the first field application of a novel method to estimate in-situ rock stress. This technique, which we have baptized "PKM (Pestman-Kenter-vanMunster) method", uses Acoustic Emission-controlled polyaxial reloading of core in the laboratory. The method works analogous to the Kaiser effect that is observed when reloading along a single stress axis. Contrary to other Acoustic Emission methods, our novel approach is likely to measure present-day stresses, even if the core has been subjected to paleo-stresses that are higher than the present day stresses1. Proof of concept of the method has been provided using extensive experimental work on outcrop sandstone2 (which was subjected to a stress path simulating burial, coring and core retrieval to surface), a simple analytic model3 and numerical simulations using a 3D discrete particle method4. Recently, the method was applied for the first time on real core material, a preserved sandstone core from the Munnekezijl field (onshore gas) of NAM (Nederlandsche Aardolie Maatschappij) in The Netherlands. An advantage of first application of the technique to this field was that there was availability of good quality stress estimates (for the same layer as where our core was taken) obtained from other methods. A study including hydraulic frac data and borehole breakout shape had been performed in the past to estimate the magnitudes of the major and minor horizontal effective stress. Hence, the results of our method could be compared to other good quality data. Three samples have been cut from core taken at a depth of some 4000 m [13000 ft] in the Munnekezijl field, for application of our PKM method. Only the weakest sample showed a clear stress memory effect, and was used for stress estimation using our method. The results compared very satisfactorily with the estimates from the hydraulic frac data and borehole breakout analysis. Although this is only the first application, and further validation is needed, these results show a clear promise of the PKM method.