gebhart/patrepeval huggingface dataset:
Platelet transactivation by monocytes promotes thrombosis in heparin-induced thrombocytopenia (2015)

Heparin-induced thrombocytopenia (HIT) is characterized by a high incidence of thrombosis, unlike other antibody-mediated causes of thrombocytopenia. We have shown that monocytes complexed with surface-bound platelet factor 4 (PF4) activated by HIT antibodies contribute to the prothrombotic state in vivo, but the mechanism by which this occurs and the relationship to the requirement for platelet activation via fragment crystallizable (Fc)γRIIA is uncertain. Using a microfluidic model and human or murine blood, we confirmed that activation of monocytes contributes to the prothrombotic state in HIT and showed that HIT antibodies bind to monocyte FcγRIIA, which activates spleen tyrosine kinase and leads to the generation of tissue factor (TF) and thrombin. The combination of direct platelet activation by HIT immune complexes through FcγRIIA and transactivation by monocyte-derived thrombin markedly increases Annexin V and factor Xa binding to platelets, consistent with the formation of procoagulant coated platelets. These data provide a model of HIT wherein a combination of direct FcγRIIA-mediated platelet activation and monocyte-derived thrombin contributes to thrombosis in HIT and identifies potential new targets for lessening this risk.
Toward speaker-independent recognition-by-synthesis (2005)

A system has been designed which abstracts terminal-analog synthesis parameters as sufficient description of the speech signal to be used for talker-independent speech recognition. These parameters are considered descriptors of the articulatory process, obeying the constraints of articulation. These parameters were employed by a very simple statistical-clustering recognition scheme to test their sufficiency for recognition of a small but very difficult vocabulary from a number of different talkers. Results indicate that is, indeed, a very promising approach to speaker-independent recognition by synthesis.
An integrated metasurface filtering cloak for monopole antennas (2015)

A filtering scattering reduction coating is proposed for practical monopole antennas. It retains the radiation properties of the antenna at its own operating frequency band, while reducing its scattering signature as well as the received power at the frequency band of a nearby wireless system. Such a coating contains two layers of concentric anisotropic metasurfaces with distinct electromagnetic responses. While the inner layer is mainly responsible for reducing the received power, both the inner and outer layers provide the scattering reduction such that the coated monopole does not block the radiation of the nearby source. Full-wave simulation results are presented, which validate the proposed idea.
The Evolution of Dip‐Pen Nanolithography. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Glutaminyl Cyclases as Novel Targets for the Treatment of Septic Arthritis (2012)

The compounds investigated here represent a novel class of small molecular antiarthritic inhibitors. In our studies, they exerted strong antiinflammatory actions, and therefore they might be suited for disease-modifying treatment of infectious arthritis.
Superfluidity of indirect biexcitons in superlattices (1999)

The instability of the ground state of a system of two-dimensional spatially indirect excitons interacting in a slab of superlattice with alternating electron and hole layers is established. The stable system of spatially indirect quasi–two-dimensional biexcitons, consisting in spatially indirect excitons with opposite directed dipole moments is considered. The radius and the binding energy of spatially indirect biexciton are calculated. The collective spectrum of a low-density system of two-dimensional spatially indirect biexcitons, interacting as electrical quadrupoles, is studied. The density of the superfluid component ns(T) and the Kosterlitz-Thouless phase transition to the superfluid state in this system are analyzed.
Self-Disinfecting Polymeric Coatings (2020)

A novel derivative of a previously-published polymeric material has been synthesized and developed into an easily-sprayable coating. Surface characterization of coatings confirm correct elemental presence, and viral assays reveal quantitative elimination of MS2 bacteriophage and Phi6 bacteriophage, surrogates used for SARS-CoV-2, in as little as 5 minutes upon contact. Furthermore, an N95 mask was dip-coated in the polymer solution and analyzed through microscopy and filtration efficacy testing. Though coating was successful, electrostatic interactions between mask layers and polymer reduced filtration efficacy significantly. As such, we expect the current results of this work to be applicable on non-respiratory PPE and on solid substrates of commonly-touched surfaces for rapid self-decontamination.
3D computational cannula fluorescence microscopy enabled by artificial neural networks (2020)

Computational cannula microscopy (CCM) is a high-resolution widefield fluorescence imaging approach deep inside tissue, which is minimally invasive. Rather than using conventional lenses, a surgical cannula acts as a lightpipe for both excitation and fluorescence emission, where computational methods are used for image visualization. Here, we enhance CCM with artificial neural networks to enable 3D imaging of cultured neurons and fluorescent beads, the latter inside a volumetric phantom. We experimentally demonstrate transverse resolution of ∼6µm, field of view ∼200µm and axial sectioning of ∼50µm for depths down to ∼700µm, all achieved with computation time of ∼3ms/frame on a desktop computer.
Antimicrobial peptides and uses therefore (2023)

Materials and methods for making and using cationic anti-microbial peptides (CAMPs), and compositions containing such peptides.
Time-reversed ultrasound (1997)

Time-reversal invariance is a very powerful concept in classical and quantum mechanics. However, simple experimental evidence of this concept is difficult to obtain. In the field of acoustic waves, where time reversal invariance also occurs, time-reversal experiments may be achieved simply with large ultrasonic piezoelectric transducer arrays. Time-reversal mirrors (TRMs) are made of such reversible acoustic retina, allowing an incident acoustic field to be sampled, recorded, time-reversed, and re-emitted. Time reversal of acoustic fields allows an optimal approach to focus pulsed ultrasonic waves through inhomogeneous media in the sense that it realizes the matched filter in both the spatial and temporal dimensions to the inhomogeneous propagation transfer function. In the field of acoustics, the ability to work directly in the time domain, with piezoelectric retina, allows pulse echo mode processing in an iterative mode. In multitarget media, such an iterative process converges on the most reflective target. In the case of an extended elastic target, automatic resonances of vibration modes can be achieved. TRMs are also innovative tools in the field of fundamental physics. They may be used to study inverse scattering problems, multiple scattering processes, chaotic scattering as well as scattering by turbulent media. Several experiments illustrating these areas will be presented. Applications of TRMs will also be described and include medical applications (kidney stone destruction and hyperthermia) as well as nondestructive testing of solid media. Experimental results illustrating these applications will be presented.
Synthesis of Novel γ-Aminobutyric Acid (GABA) Uptake Inhibitors. 5. Preparation and Structure−Activity Studies of Tricyclic Analogues of Known GABA Uptake Inhibitors (2001)

On the basis of the SAR of a series of known gamma-aminobutyric acid (GABA) uptake inhibitors, including 4 (SKF 89976), new tricyclic analogues have been prepared. These novel compounds are derivatives of nipecotic acid, guvacine, and homo-beta-proline, substituted at the nitrogen of these amino acids by various lipophilic moieties such as (10,11-dihydro-5H-dibenz[b,f]azepin-5-yl)alkoxyalkyl or (10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-ylidene)alkoxyalkyl. The in vitro values for inhibition of [(3)H]-GABA uptake in rat synaptosomes was determined for each compound in this new series, and it was found that several of the novel compounds showed a high potency comparable with that of the reference compounds 4, 5 (tiagabine), and 6 (CI-966). Several of the novel compounds were also evaluated for their ability in vivo to inhibit clonic seizures induced by a 15 mg/kg (ip) dose of methyl 6,7-dimethoxy-4-ethyl-beta-carboline-3-carboxylate (DMCM). One compound, (R)-1-(2-(2-(10,11-dihydro-5H-dibenz[b,f]azepin-5-yl)ethoxy)ethyl)-3-piperidinecarboxylic acid (23), was selected for further biological investigations and showed a protective index comparable to or slightly better than that of the recently launched anticonvulsant product 5 ((R)-1-(4,4-bis(3-methyl-2-thienyl)-3-butenyl)-3-piperidinecarboxylic acid).
Systemic inhibition of tissue-nonspecific alkaline phosphatase alters the brain-immune axis in experimental sepsis (2019)

Tissue-nonspecific alkaline phosphatase (TNAP) is a ubiquitous enzyme present in many cells and tissues, including the central nervous system. Yet its functions at the brain-immune axis remain unclear. The goal of this study was to use a novel small molecular inhibitor of TNAP, SBI-425, to interrogate the function of TNAP in neuroimmune disorders. Following intraperitoneal (IP) administration of SBI-425, mass spectrometry analysis revealed that the SBI-425 does not cross the blood-brain barrier (BBB) in healthy mice. To elucidate the role of TNAP at the brain-immune axis, mice were subjected to experimental sepsis and received either vehicle or SBI-425 (25 mg/kg, IP) daily for 7 days. While SBI-425 administration did not affect clinical severity outcomes, we found that SBI-425 administration suppressed CD4 + Foxp3+ CD25- and CD8 + Foxp3+ CD25- splenocyte T-cell populations compared to controls. Further evaluation of SBI-425's effects in the brain revealed that TNAP activity was suppressed in the brain parenchyma of SBI-425-treated mice compared to controls. When primary brain endothelial cells were treated with a proinflammatory stimulus the addition of SBI-425 treatment potentiated the loss of barrier function in BBB endothelial cells. To further demonstrate a protective role for TNAP at endothelial barriers within this axis, transgenic mice with a conditional overexpression of TNAP were subjected to experimental sepsis and found to have increased survival and decreased clinical severity scores compared to controls. Taken together, these results demonstrate a novel role for TNAP activity in shaping the dynamic interactions within the brain-immune axis.
Early Address Prediction (2021)

Achieving low load-to-use latency with low energy and storage overheads is critical for performance. Existing techniques either prefetch into the pipeline (via address prediction and validation) or provide data reuse in the pipeline (via register sharing or L0 caches). These techniques provide a range of tradeoffs between latency, reuse, and overhead. In this work, we present a pipeline prefetching technique that achieves state-of-the-art performance and data reuse without additional data storage, data movement, or validation overheads by adding address tags to the register file. Our addition of register file tags allows us to forward (reuse) load data from the register file with no additional data movement, keep the data alive in the register file beyond the instruction’s lifetime to increase temporal reuse, and coalesce prefetch requests to achieve spatial reuse. Further, we show that we can use the existing memory order violation detection hardware to validate prefetches and data forwards without additional overhead. Our design achieves the performance of existing pipeline prefetching while also forwarding 32% of the loads from the register file (compared to 15% in state-of-the-art register sharing), delivering a 16% reduction in L1 dynamic energy (1.6% total processor energy), with an area overhead of less than 0.5%.
Achieving utility arbitrarily close to the optimal with limited energy (2000)

Energy is one of the limited resources for modern systems, especially the battery-operated devices and personal digital assistants. The backlog in new technologies for more powerful battery is changing the traditional system design philosophies. For example, due to the limitation on battery life, it is more realistic to design for the optimal benefit from limited resource rather than design to meet all the applications' requirement. We consider the following problem: a system achieves a certain amount of utility from a set of applications by providing them certain levels of quality of service(QoS). We want to allocate the limited system resources to get the maximal system utility. We formulate this utility maximization problem, which is NP-hard in general, and propose heuristic algorithms that are capable of finding solutions provably arbitrarily close to the optimal. We have also derived explicit formulae to guide the allocation of resources to actually achieve such solutions. Simulation shows that our approach can use 99.9% of the given resource to achieve 25.6% and 32.17% more system utilities over two other heuristics, while providing QoS guarantees to the application program.
Versailles Project on Advanced Materials and Standards interlaboratory study on intensity calibration for x-ray photoelectron spectroscopy instruments using low-density polyethylene (2020)

We report the results of a Versailles Project on Advanced Materials and Standards interlaboratory study on the intensity scale calibration of x-ray photoelectron spectrometers using low-density polyethylene (LDPE) as an alternative material to gold, silver, and copper. An improved set of LDPE reference spectra, corrected for different instrument geometries using a quartz-monochromated Al Kα x-ray source, was developed using data provided by participants in this study. Using these new reference spectra, a transmission function was calculated for each dataset that participants provided. When compared to a similar calibration procedure using the NPL reference spectra for gold, the LDPE intensity calibration method achieves an absolute offset of ∼3.0% and a systematic deviation of ±6.5% on average across all participants. For spectra recorded at high pass energies (≥90 eV), values of absolute offset and systematic deviation are ∼5.8% and ±5.7%, respectively, whereas for spectra collected at lower pass energies (<90 eV), values of absolute offset and systematic deviation are ∼4.9% and ±8.8%, respectively; low pass energy spectra perform worse than the global average, in terms of systematic deviations, due to diminished count rates and signal-to-noise ratio. Differences in absolute offset are attributed to the surface roughness of the LDPE induced by sample preparation. We further assess the usability of LDPE as a secondary reference material and comment on its performance in the presence of issues such as variable dark noise, x-ray warm up times, inaccuracy at low count rates, and underlying spectrometer problems. In response to participant feedback and the results of the study, we provide an updated LDPE intensity calibration protocol to address the issues highlighted in the interlaboratory study. We also comment on the lack of implementation of a consistent and traceable intensity calibration method across the community of x-ray photoelectron spectroscopy (XPS) users and, therefore, propose a route to achieving this with the assistance of instrument manufacturers, metrology laboratories, and experts leading to an international standard for XPS intensity scale calibration.
Mass Spectrometry-based Diagnostics: The Upcoming Revolution in Disease Detection (2003)

Advances in mass spectrometry-based diagnostics could ignite a revolution in the field of molecular medicine. This platform has the potential to become the practical clinical analyzer of the future for nucleic acids and proteins. Mass spectrometry-based diagnostics are an example of a “disruptive” or “nonlinear” technology (1)(2). Such disruptive technologies are by their very nature polarizing, causing a dynamic dichotomy of excitement (3) as well as anxiety(4) in the clinical diagnostic community because this technology can potentially outperform traditional measurement and detection systems. In this issue of Clinical Chemistry , Bonk et al. (5) demonstrate the advantages of mass spectrometry compared with traditional electrophoretic methodologies. Bonk et al. used mass spectrometry as a “sensor” to detect the amplified product from a PCR amplification reaction. The ultimate clinical application for this study is the early detection of colon cancer, a topic of obvious public health importance.

Although major advances have been made in elucidating the genetic underpinnings of cancer, especially colorectal cancer, diagnostic methodologies for routine clinical detection and monitoring of important cancer genetic derangements have lagged behind. Microsatellite instability (MSI), caused by mismatch repair gene silencing, is predicted to be an important early event in cancer progression (6)(7)(8).

In this issue, Bonk et al. (5) report on a study in which they use time-of-flight-based mass spectrometry to detect MSI. Unlike previous studies, in which chromatography, electrophoresis, and traditional DNA sequencing methodologies were used to detect the presence of MSI, these authors have chosen …
A Note on Detecting Dominant Points (1989)

Detecting dominant points is a crucial preprocessing step for shape recognition and point-based motion estimation. Polygonal approximation has been a commonly used approach to detecting dominant points. This paper presents two alternatives which detect stable dominant points.
A Comparison of Alternating Current and Direct Current Electrospray Ionization for Mass Spectrometry (2014)

A series of studies comparing the performance of alternating current electrospray ionization (AC ESI) mass spectrometry (MS) and direct current electrospray ionization (DC ESI) MS have been conducted, exploring the absolute signal intensity and signal-to-background ratios produced by both methods using caffeine and a model peptide as targets. Because the high-voltage AC signal was more susceptible to generating gas discharges, the operating voltage range of AC ESI was significantly smaller than that for DC ESI, such that the absolute signal intensities produced by DC ESI at peak voltages were one to two orders of magnitude greater than those for AC ESI. Using an electronegative nebulizing gas, sulfur hexafluoride (SF6), instead of nitrogen (N2) increased the operating range of AC ESI by ~50%, but did not appreciably improve signal intensities. While DC ESI generated far greater signal intensities, both ionization methods produced comparable signal-to-background noise, with AC ESI spectra appearing qualitatively cleaner. A quantitative calibration analysis was performed for two analytes, caffeine and the peptide MRFA. AC ESI utilizing SF6 outperforms all other techniques for the detection of MRFA, producing chromatographic limits of detection nearly one order of magnitude lower than that of DC ESI utilizing N2, and one-half that of DC ESI utilizing SF6. However, DC ESI outperforms AC ESI for the analysis of caffeine, indicating that improvements in spectral quality may benefit certain compounds or classes of compounds, on an individual basis.
Quantitative Trait Loci for Chloride Tolerance in ‘Osage’ Soybean (2017)

Salt is a severe abiotic stress that reduces soybean [ Glycine max (L.) Merr.] yield by &gt;20% in saline soils and irrigated fields. Marker‐assisted selection (MAS) is an efficient method to identify salt‐tolerant soybean lines. ‘Osage’ is a salt‐tolerant and high‐yielding cultivar in the Mid‐South of the United States and is a distant progeny tracing five generations back to ‘S‐100’. The objective of this study was to determine the inheritance of salt tolerance in Osage soybean by identifying the quantitative trait loci (QTL) controlling the trait. A chloride (Cl − ) includer, ‘RA‐452’, was crossed with Cl − excluder, Osage, to develop an F 4:6 mapping population. The F 4:6 lines were genotyped by 5403 single nucleotide polymorphism (SNP) markers spanning 20 chromosomes (Chr.), of which, 1269 were polymorphic. The salt stress response of F 4:6 lines, along with parental genotypes, was evaluated in the greenhouse in April and June 2013. Three different treatments (120 mM NaCl, 120 mM KCl, and water) were initiated at V1 stage and continued for ∼18 to 21 d. The leaf Cl − contents were quantified by inductively coupled plasma optical emission spectroscopy. Composite interval mapping analysis indicated that a major Cl − –tolerant QTL was confirmed and narrowed down on Chr. 3 in both NaCl and KCl treatments, a novel Cl − –tolerant QTL on Chr. 15 was identified in NaCl treatment, and a novel Cl − –tolerant QTL on Chr. 13 was identified in the KCl treatment. Two annotated genes, Glyma.13G161800 and Glyma.15G091600 , were proposed to be the candidate gene conferring the Cl − tolerance within QTL region on Chr. 13 and 15, respectively. A total of 27 SNP markers were significantly associated with Cl − tolerance, which could be used for MAS in breeding salt‐tolerant soybean lines.
Cytometry and Velocimetry on a Microfluidic Chip Using Polyelectrolytic Salt Bridges (2005)

This paper reports a polyelectrolytic salt bridge-based electrode (PSBE), which is a key embedded unit in a microchip device that can size-selectively count microparticles and measure their velocities. The construction of salt bridges at specific locations within a microfluidic chip enables dc-driven electrical detection to be performed successfully. This is expected to be a competitive alternative to the optical methods currently used in conventional cell sorters. The PSBEs were fabricated by irradiating ultraviolet light over a patterned mask on the parts of interest, which were filled with an aqueous monomer solution containing diallyldimethylammonium chloride. A pair of such PSBEs was easily formed at the two lateral branches perpendicular to the main microchannel and was found to be very useful for dc impedometry. The human blood cells as well as the fluorescent microbeads passing between the two PSBEs produced impedance signals in proportional to their size. The information about the velocity of a microparticle was extracted from a doublet of the dc impedance signals, which were generated when cells or microbeads sequentially passed through two PSBE pairs separated from each other by a fixed distance. The plot of peak amplitude versus velocity of the moving microbeads and cells indicated only a slight correlation between the size and the velocity, which means that the peak amplitude of the dc impedance signals alone can provide information about the size of the cells in a mixture. The experimental results showed a screening rate of over 1000 cells s(-1) and a velocity of the cells of over 100 mm s(-1). Compared with the previously suggested electrical detection system based on metal electrodes, the sensitivity and selectivity in cell detection were remarkably improved. In addition, the detection unit including the operating circuit became innovatively simple and the whole device could be miniaturized.
Supplementary Table 1 from <i>De Novo</i> Design of a Tumor-Penetrating Peptide (2023)

&lt;p&gt;PDF file - 382K, Peptide description. ID and sequence in single letter amino acid code of each peptide is shown&lt;/p&gt;