gebhart/patrepeval huggingface dataset:
Platelet Activating Factor Antagonists (1995)

Platelet Activating Factor (PAF) is a D-glycerol-derived phospholipid which is a potent endogenous mediator of inflammation. PAF is synthesized and released by a variety of cell types and elicits its biological activity by interacting with specific G-protein coupled receptors found on platelets, neutrophils, and other inflammatory cells. The physiological consequences of the interaction of PAF with its receptor includes an increase in vascular permeability, hypotension, bronchoconstriction, and platelet and neutrophil aggregation. These biological effects are consistent with the concept that PAF is involved in a number of inflammatory diseases such as septic shock and asthma. Given the potent pathophysiological effects of PAF, a great deal of effort has been focused on the discovery of agents which block the action of PAF at its receptor. Within the past 10 years, a wide range of structures have been identified as PAF antagonists. These include not only PAF analogs, but also antagonists derived from natural products as well as non-lipid synthetic compounds. Several theories have been proposed to unify these diverse structural classes, but sophisticated molecular models of the receptor have not been widely employed. The discovery of new PAF antagonists has relied heavily on traditional medicinal chemistry approaches. A number of PAF antagonists have advanced to clinical evaluation. While several early compounds demonstrated efficacy in animal models of asthma they have failed to provide benefit for this condition in man. The current generation of potent antagonists are being evaluated as therapies for sepsis, pancreatitis and other disorders.
Photo-physiological variability in phytoplankton chlorophyll fluorescence and assessment of chlorophyll concentration (2011)

Photo-physiological variability of in vivo chlorophyll fluorescence (CF) per unit of chlorophyll concentration (CC) is analyzed using a biophysical model to improve the accuracy of CC assessments. Field measurements of CF and photosystem II (PSII) photochemical yield (PY) with the Advanced Laser Fluorometer (ALF) in the Delaware and Chesapeake Bays are analyzed vs. high-performance liquid chromatography (HPLC) CC retrievals. It is shown that isolation from ambient light, PSII saturating excitation, optimized phytoplankton exposure to excitation, and phytoplankton dark adaptation may provide accurate in vivo CC fluorescence measurements (R2 = 0.90-0.95 vs. HPLC retrievals). For in situ or flow-through measurements that do not allow for dark adaptation, concurrent PY measurements can be used to adjust for CF non-photochemical quenching (NPQ) and improve the accuracy of CC fluorescence assessments. Field evaluation has shown the NPQ-invariance of CF/PY and CF(PY-1-1) parameters and their high correlation with HPLC CC retrievals (R2 = 0.74-0.96), while the NPQ-affected CF measurements correlated poorly with CC (R2 = -0.22).
Phased Array Approach To Retrieve Gases, Liquids, Or Solids From Subsurface And Subaqueous Geologic Or Man-Made Formations (1998)

A method of enhancing the remediation of contaminated soils and ground water, production of oil and gas, and production of any solid, gas, and/or liquid from subsurface geologic and man-made formations including the steps of estimating the geometric boundaries of the region containing the material to be recovered, drilling a recovery well(s) into subsurface in a strategic location to recover the material of interest, establishing multiple sources of acoustical power in an array about and spaced-apart from the surface or at various depths below the surface in a borehole(s) and/or well(s), directing a volume of acoustical excitation from the sources into the region containing the material to be recovered, the excitation in the form of either controllable sinusoidal, square, pulsed, or various combinations of these three waveforms, and controlling the phasing, frequency, power, duration, and direction of these waveforms from the sources to increase and control the intensity of acoustical excitation in the region of the material to be recovered to enhance. the recovery of said material from the recovery well(s). The invention will augment any technology affecting the removal of materials from the subsurface.
A new method of fault detection and treatment in five phase permanent magnet synchronous machine using field reconstruction method (2009)

Permanent magnet synchronous machines (PMSM) are extensively used in industrial applications because of their relatively high power density, negligible rotor losses, high efficiency, ease of control, and being almost maintenance free. In this paper a new method of fault detection and treatment for open circuit faults in 5-phase PMSM has been investigated. In the proposed technique the stator electrical faults are detected and then cleared. As the optimum performance is of great importance in industrial applications the excitation of the remaining healthy phases should be modified to attain the maximum output torque per input phase current. The field reconstruction method has been used in conjunction with optimization methods to find the proper excitation.
Digital spectral separation methods and systems for bioluminescence imaging (2008)

We propose a digital spectral separation (DSS) system and methods to extract spectral information optimally from a weak multi-spectral signal such as in the bioluminescent imaging (BLI) studies. This system utilizes our newly invented spatially-translated spectral-image mixer (SSM), which consists of dichroic beam splitters, a mirror, and a DSS algorithm. The DSS approach overcomes the shortcomings of the data acquisition scheme used for the current BLI systems. Primarily, using our DSS scheme, spectral information will not be filtered out. Accordingly, truly parallel multi-spectral multi-view acquisition is enabled for the first time to minimize experimental time and optimize data quality. This approach also permits recovery of the bioluminescent signal time course, which is useful to study the kinetics of multiple bioluminescent probes using multi-spectral bioluminescence tomography (MSBT).
Antibody-based immunotherapy: targeting CSPG4 on human basal breast cancer stem cells. (2009)

Abstract Abstract #5046 Introduction: Basal-like breast cancer is associated with high grade, poor prognosis, and younger patient age. Because tumors are estrogen receptor (ER) and HER2 negative, effective targeted treatment for basal breast cancer remains elusive. The lack of efficacy of currently used chemotherapies may reflect their inability to eradicate cancer stem cells (CSC) within a basal breast tumor.&#x2028; Chondroitin sulfate proteoglycan 4 (CSPG4), a molecule initially identified in melanoma cells, is a cell surface antigen involved in migration and invasion of tumor cells. The rat homolog of the human CSPG4, named NG2, is expressed by progenitor cells in several types of tissues. Furthermore, NG2 expression is typically maximal when progenitor cells are mitotic and motile. As one important characteristic of cancer stem cells is their ability to migrate and metastasize, and both CSPG4 and NG2 play a role in tumor cell migration, we tested whether CSPG4 is expressed on cells with the CSC phenotype in ER negative/HER2 negative (basal-like) breast cancer, and can thus serve as a target for immunotherapy of breast CSC.&#x2028; Methods and Results: The mRNA levels of CSPG4 in ER- and Her2- breast cancer were compared to ER-/Her2+, ER+/Her2-, and ER+/Her2+ breast cancer using a publicly available, clinically annotated breast cancer data set. The gene expression level of CSPG4 was elevated in the ER- and Her2- subgroup when compared to ER-/Her2+ (Mann Whitney, p=0.03), ER+/Her2- (Mann Whitney, p=0.01), and ER+/Her2+ (Mann Whitney, p=0.06). These results suggest that CSPG4 expression is best correlated with the basal phenotype of breast cancer. Flow cytometric analysis showed that CSPG4 is expressed on CD44+, CD24-/lo cells in the human basal breast cancer cell lines, i.e., MDA-MD-231, MDA-MB-435, HS578T and SUM149, but is not detectable on the luminal breast cancer cell lines, i.e., MCF-7, SK-BR-3 and T-47D. Furthermore CSPG4 is expressed on the cell surface of putative breast CSC identified as lineage-negative (CD2,3,10,16,18,31,45,64,140b), CD44+, CD24-/lo cells in pleural effusions of 12 patients with breast cancer. Further, inoculation of flow cytometric sorted CD44+CD24-/low CSPG4+ cells from the MDA-MB-231-luciferease expressing cell line, to the mammary fat pads of immunodeficient mice, led to the development of tumors detected by whole-body bioluminescent reporter imaging 3 weeks after the injection. In contrast, inoculation of CD44+CD24-/low CSPG4- cells, sorted from the same cell line, did not generate tumors. More importantly, CSPG4-specific mAb significantly inhibited post-surgery tumor recurrence and lung metastases in SCID mice transplanted with the human basal breast cancer cell line MDA-MB-435, which has the putative breast CSC phenotype (CD44+, CD24-/lo) in more than 99% of cells.&#x2028; Conclusion: These results suggest that the CSPG4 is a potential new immunotherapeutic target for basal-like breast cancer and breast CSC. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5046.
Fabrication Technology of Ferroelectric Memories (1997)

Two types of ferroelectric memories have been proposed. One is a 1 transistor and 1 capacitor (1T1C) type and another is an FET (field effect transistor) type. The fabrication technique for fabrication ferroelectric capacitors on polycrystalline Si (poly-Si) was very effective for high density 1T1C ferroelectric memory and metal-ferroelectric-metal-insulator-semiconductor (MFMIS) FET with stable properties. MFMIS FET is one type of FET ferroelectric memory which we proposed. To obtain good ferroelectric capacitors on poly-Si, we used Ir based materials as electrodes of the capacitors. By using Ir based electrodes, the characteristics of Pb(Zi,Ti)O3 (PZT) capacitors on poly-Si were equivalent to those on SiO2. Moreover, the PZT capacitors with Ir based electrodes showed dramatic improvement in fatigue and imprint properties.
Simultaneous lasing of Nd3+:Sr5(PO4)3F at 1.059 and 1.328 µm (1996)

Simultaneous lasing at 1.059 and 1.328 µm has been demonstrated in Nd3+ doped strontium fluorapatite Sr5(PO4)3F or S-FAP, in lamp-pumped operation. More than 1 joule of pulsed output energy has been achieved at each laser line. 589 nm laser emission has been demonstrated through the sum-frequency generation of these two wavelengths.
Chromatic dispersion monitoring technique using sideband optical filtering and clock phase-shift detection (2002)

We propose and demonstrate a novel technique for 40- and 10-Gb/s chromatic dispersion monitoring that uses an optical filter to select the upper and lower vestigial-sideband (VSB) signals in the transmitted optical data and determine the relative clock phase shift caused by dispersion. Without modification of transmitters, this technique provides low cost chromatic dispersion monitoring for WDM systems, <3 ps/nm dispersion resolution for 40-Gb/s data, and greatly reduced sensitivity to the influence of polarization mode dispersion.
MPEG VBR video traffic modeling and classification using fuzzy technique (2001)

We present an approach for MPEG variable bit rate (VBR) video modeling and classification using fuzzy techniques. We demonstrate that a type-2 fuzzy membership function, i.e., a Gaussian MF with uncertain variance, is most appropriate to model the log-value of I/P/B frame sizes in MPEG VBR video. The fuzzy c-means (FCM) method is used to obtain the mean and standard deviation (std) of T/P/B frame sizes when the frame category is unknown. We propose to use type-2 fuzzy logic classifiers (FLCs) to classify video traffic using compressed data. Five fuzzy classifiers and a Bayesian classifier are designed for video traffic classification, and the fuzzy classifiers are compared against the Bayesian classifier. Simulation results show that a type-2 fuzzy classifier in which the input is modeled as a type-2 fuzzy set and antecedent membership functions are modeled as type-2 fuzzy sets performs the best of the five classifiers when the testing video product is not included in the training products and a steepest descent algorithm is used to tune its parameters.
Verifying sequential consistency on shared-memory multiprocessors by model checking (2003)

The memory model of a shared-memory multiprocessor is a contract between the designer and the programmer of the multiprocessor. A memory model is typically implemented by means of a cache-coherence protocol. The design of this protocol is one of the most complex aspects of multiprocessor design and is consequently quite error-prone. However, it is imperative to ensure that the cache-coherence protocol satisfies the shared-memory model. We present a novel technique based on model checking to tackle this difficult problem for the important and well-known shared-memory model of sequential consistency. Surprisingly, verifying sequential consistency is undecidable in general, even for finite-state cache-coherence protocols. In practice, cache-coherence protocols satisfy the properties of causality and data independence. Causality is the property that values of read events flow from values of write events. Data independence is the property that all traces can be generated by renaming data values from traces where the written values are pairwise distinct. We show that, if a causal and data independent system also has the property that the logical order of write events to each location is identical to their temporal order, then sequential consistency is decidable. We present a novel model checking algorithm to verify sequential consistency on such systems for a finite number of processors and memory locations and an arbitrary number of data values.
Wavelength independent grating lens system (1989)

Grating lenses are small, light, and easily mass-produced. However, wavelength variation in the light source causes aberration and changes the focal length of the grating lens. Therefore, it has been difficult to use grating lenses in high-precision focusing optical systems that use a light source with wavelength variations (e.g., a diode laser). To solve this problem, we designed a grating lens system of two grating lenses, which substantially suppresses aberration and keeps the focal length constant at several tens of nanometers of variation. Each grating is made as a concentric circle. These lenses are arranged so that their centers are collinear. Diffraction angle changes due to wavlength variations are compensated for by the second grating. Our calculations confirmed that the allowable wavelength range was +/-15 nm or more for a numerical aperture (N.A.) of 0.5. We made a prototype of this grating lens system by electron beam lithography and confirmed that this lens system was not affected by limited wavelength variations.
Hollow Core Photonic Bandgap fibers for Telecommunications: Opportunities and Potential Issues (2012)

We discuss the potential advantages that hollow core photonic bandgap fibers may ultimately have over conventional all solid fibers and review the state-of-the-art, fundamental physical limits and the many technological challenges to be overcome.
5,5-Disubstituted hydantoins: syntheses and anti-HIV activity (1992)

A series of 5,5-disubstituted hydantoin derivatives was synthesized by alkylating 5,5-bis(mercaptomethyl)-2,4-imidazolidinedione (3) with various halomethylaromatic or halomethylheteroaromatic precursors, or by using the Buchener-Berg procedure on the required ketone. When evaluated for their ability to inhibit HIV-induced cell killing and virus production in CEM or MT-2 cells only compounds 2, 4n, 4o, and 4i demonstrated modest activity, the latter with an IC50 = 53 microM.
Impacts of Menstruation, Community Type, and an Oral Yeast Probiotic on the Vaginal Microbiome (2022)

A healthy state of the vaginal microbiome can prevent vaginal disease and promote successful fertilization and healthy pregnancies. Little is known about the stability of the vaginal microbiome and the influence of factors such as diet and probiotics. While less explored, yeast probiotics have an interesting potential because of their immunomodulatory and pathogen inhibition capacities. In this study, we investigated the impact of the oral yeast probiotic Saccharomyces cerevisiae CNCM I-3856 on the vaginal microbiomes of 52 healthy women using 16S and internal transcribed spacer (ITS) amplicon sequencing and quantitative PCR (qPCR). The vaginal fungal loads remained low, even after oral yeast supplementation, complicating the analysis of the vaginal mycobiome. Lactobacillus crispatus and Lactobacillus iners were the most dominant species in our study population and were found to codominate in 23% of the baseline samples. <i>Bifidobacterium</i>, Streptococcus, and <i>Prevotella</i> were also frequently found. The microbiome profiles were dynamic: 69% of women showed a shift in the dominant community members at least once during the 42-day sampling period. In addition, lower <i>Lactobacillus</i> abundances were observed at the time points after menstruation. Higher relative abundances of <i>Lactobacillus</i> with more L. iners<i>-</i>dominated samples and a trend toward lower relative abundances of <i>Prevotella</i> were observed in the probiotic group, but analyses of the effects of the yeast probiotic were complicated by differences already present at the onset of the study. Thus, our findings especially highlighted that the impact of menstruation and the stratification of women based on the dominant vaginal taxa before randomization and inclusion is important for future research: while the impact of the yeast probiotic on vaginal microbiome in healthy women was limited. <b>IMPORTANCE</b> How to define and promote a healthy state of the vaginal microbiome is not well understood. Knowledge of which underlying factors shape the microbial community composition of the vagina and how to modulate them will contribute to vaginal disease prevention and improve fertility. Here, we found that taking the menstrual cycle into account when designing a microbiome study is highly recommended: menstruation also showed to be poses an interesting time point for intervention because of the drop in the abundance of L. crispatus. Furthermore, the early stratification of groups (e.g., placebo versus treatment) according to the dominant taxa can be of high added value since menstruation impacts vaginal taxa differently, i.e., <i>L. iners</i> remains stable, in contrast to <i>L. crispatus</i>.
Directional, Broad, and Fixed Angle Surface Plasmon Coupled Fluorescence from Iron Thin Films (2009)

Fixed angle surface plasmon coupled fluorescence (SPCF) from iron thin films is demonstrated for the first time. The optimum thickness of the iron thin films was determined to be 15 nm using Fresnel calculations. The angles of minimum reflectivity for light at 496-814 nm were predicted to occur at a fixed and broad range of angles of 60-70°. Experimental corroboration of these predictions were undertaken by employing fluorescein isothiocyanate (emission peak at 517 nm), rhodamine B (580 nm), zinc phthalocyanine (710 nm), and IR 780 dye (814 nm). SPCF emission from all four fluorophores was directional, p-polarized, and observed at a fixed angle of ∼65°.
Freeze-drying for morphological control of high performance semi-interpenetrating polymer networks. III (1991)

The feasibility of using a freeze-drying (solvent removal by sublimation) approach for controlling the morphology of a high-performance semi-IPN is assessed. A high-performance thermoplastic polyimide and commercially available 4,4'-bismaleimide diphenylenemethane were dissolved in a solvent, 1,3,5-trioxane. The solvent was removed from the constituents by freeze-drying. For purposes of comparison, the constituents were dissolved in a high-boiling-point solvent, N,N-dimethylformamide. The solvent was removed from the solution by evaporation. The physical and mechanical properties and phase morphology of the neat resins and composites prepared by freeze-drying and traditional solution methods are presented and compared. It is concluded that the TG is higher and that the magnitude of minor constituent separation is less in the freeze-dry processed materials than for the processed solution.
Cardiac ryanodine receptor N-terminal region biosensors identify novel inhibitors via FRET-based high-throughput screening (2021)

The N-terminal region (NTR) of ryanodine receptor (RyR) channels is critical for the regulation of Ca<sup>2+</sup> release during excitation-contraction (EC) coupling in muscle. The NTR hosts numerous mutations linked to skeletal (RyR1) and cardiac (RyR2) myopathies, highlighting its potential as a therapeutic target. Here, we constructed two biosensors by labeling the mouse RyR2 NTR at domains A, B, and C with FRET pairs. Using fluorescence lifetime (FLT) detection of intramolecular FRET signal, we developed high-throughput screening (HTS) assays with these biosensors to identify small-molecule RyR modulators. We then screened a small validation library and identified several hits. Hits with saturable FRET dose-response profiles and previously unreported effects on RyR were further tested using [<sup>3</sup>H]ryanodine binding to isolated sarcoplasmic reticulum vesicles to determine effects on intact RyR opening in its natural membrane. We identified three novel inhibitors of both RyR1 and RyR2 and two RyR1-selective inhibitors effective at nanomolar Ca<sup>2+</sup>. Two of these hits activated RyR1 only at micromolar Ca<sup>2+</sup>, highlighting them as potential enhancers of excitation-contraction coupling. To determine whether such hits can inhibit RyR leak in muscle, we further focused on one, an FDA-approved natural antibiotic, fusidic acid (FA). In skinned skeletal myofibers and permeabilized cardiomyocytes, FA inhibited RyR leak with no detrimental effect on skeletal myofiber excitation-contraction coupling. However, in intact cardiomyocytes, FA induced arrhythmogenic Ca<sup>2+</sup> transients, a cautionary observation for a compound with an otherwise solid safety record. These results indicate that HTS campaigns using the NTR biosensor can identify compounds with therapeutic potential.