gebhart/patrepeval huggingface dataset:
Antagonism of the mu-delta opioid receptor heterodimer enhances opioid antinociception by activating Src and calcium/calmodulin-dependent protein kinase II signaling (2021)

The opioid receptors are important regulators of pain, reward, and addiction. Limited evidence suggests the mu and delta opioid receptors form a heterodimer (MDOR), which may act as a negative feedback brake on opioid-induced analgesia. However, evidence for the MDOR in vivo is indirect and limited, and there are few selective tools available. We recently published the first MDOR-selective antagonist, D24M, allowing us to test the role of the MDOR in mice. We thus cotreated CD-1 mice with D24M and opioids in tail flick, paw incision, and chemotherapy-induced peripheral neuropathy pain models. D24M treatment enhanced oxymorphone antinociception in all models by 54.7% to 628%. This enhancement could not be replicated with the mu and delta selective antagonists CTAP, naltrindole, and naloxonazine, and D24M had a mild transient effect in the rotarod test, suggesting this increase is selective to the MDOR. However, D24M had no effect on morphine or buprenorphine, suggesting that only specific opioids interact with the MDOR. To find a mechanism, we performed phosphoproteomic analysis on brainstems of mice. We found that the kinases Src and CaMKII were repressed by oxymorphone, which was restored by D24M. We were able to confirm the role of Src and CaMKII in D24M-enhanced antinociception using small molecule inhibitors (KN93 and Src-I1). Together, these results provide direct in vivo evidence that the MDOR acts as an opioid negative feedback brake, which occurs through the repression of Src and CaMKII signal transduction. These results further suggest that MDOR antagonism could be a means to improve clinical opioid therapy.
Recognition of repetitive sequential human activity (2009)

We present a novel framework for recognizing repetitive sequential events performed by human actors with strong temporal dependencies and potential parallel overlap. Our solution incorporates sub-event (or primitive) detectors and a spatiotemporal model for sequential event changes. We develop an effective and efficient method to integrate primitives into a set of sequential events where strong temporal constraints are imposed on the ordering of the primitives. In particular, the combination process is approached as an optimization problem. A specialized Viterbi algorithm is designed to learn and infer the target sequential events and handle the event overlap simultaneously. To demonstrate the effectiveness of the proposed framework, we report detailed quantitative analysis on a large set of cashier checkout activities in a retail store.
Parallelizing Data Processing on FPGAs with Shifter Lists (2015)

Parallelism is currently seen as a mechanism to minimize the impact of the power and heat dissipation problems encountered in modern hardware. Data parallelism—based on partitioning the data—and pipeline parallelism—based on partitioning the computation—are the two main approaches to leverage parallelism on a wide range of hardware platforms. Unfortunately, not all data processing problems are susceptible to either of those strategies. An example is the skyline operator [Börzsönyi et al. 2001], which computes the set of Pareto-optimal points within a multidimensional dataset. Existing approaches to parallelize the skyline operator are based on data parallelism. As a result, they suffer from a high overhead when merging intermediate results because of the lack of a global view of the problem inherent to partitioning the input data. In this article, we show how to combine pipeline with data parallelism on a Field-Programmable Gate Array (FPGA) for a more efficient utilization of the available hardware parallelism. As we show in our experiments, skyline computation using our proposed technique scales linearly with the number of processing elements, and the performance we achieve on a rather small FPGA is comparable to that of a 64-core high-end server running a state-of-the-art data parallel implementation of skyline [Park et al. 2009]. The proposed approach to parallelize the skyline operator can be generalized to a wider range of data processing problems. We demonstrate this through a novel, highly parallel data structure, a shifter list , that can be efficiently implemented on an FPGA. The resulting template is easy to parametrize to implement a variety of computationally intensive operators such as frequent items , n -closest pairs , or K-means .
Sequence analysis of a yeast genomic DNA fragment sharing homology with the human c-myc gene (1988)

Journal Article Sequence analysis of a yeast genomic DNA fragment sharing homology with the human c-myc gene Get access Jacob Sarid, Jacob Sarid Search for other works by this author on: Oxford Academic PubMed Google Scholar Philip Leder Philip Leder 1The Howard Hughes Medical InstituteBoston, MA 02115, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 10, 25 May 1988, Page 4725, https://doi.org/10.1093/nar/16.10.4725 Published: 25 May 1988 Article history Accepted: 08 April 1988 Published: 25 May 1988
Evidence of Aromaticity-Specific Maltene NMR Relaxation Enhancement Promoted by Semi-immobilized Radicals (2016)

The broad distribution of NMR proton relaxation times in crude oil is a consequence not only of the overlap of a multitude of different constituents, but also of interactions of different strength with asphaltene aggregates, which was found to be influenced by the maltenes’ aromaticity. The so-called dispersion, or frequency dependence, of the longitudinal relaxation time T1(ω), and the ratio T1/T2 as a related parameter, becomes more pronounced for aromatic solvent molecules, in particular for fluorine-containing tracers, and is assumed to be a consequence of either or both the nuclear-electron interaction with the asphaltenes’ radical component or geometric trapping of maltenes within the asphaltene aggregates in crude oil. In this work, we seek proof for this assumption by investigating the concentration dependence of relaxation properties in solutions of asphaltenes, and by comparing the relaxation properties to a number of simplified model solutions possessing either similar geometry or radical concentration. The notion of an enhanced interaction strength is further supported by dynamic nuclear polarization experiments of native crude oil doped with selected tracer molecules.
8 × 10 Gb/s, 1.3-m WDM unrepeatered transmission system with Raman post- and preamplifiers and a fiber span of 141 km (1997)

A total transmission distance of 141 km has been demonstrated in a WDM system experiment for 8 channels of 10 Gb/s with wavelengths ranging from 1305.8 nm to 1311.6 nm. Raman post- and pre-amplifiers facilitate the 45.1-dB power budget.
Graphical Ranking of Divisors to Get the Most out of a Resolution-Enhanced Kendrick Mass Defect Plot (2018)

Resolution-enhanced Kendrick Mass Defect (KMD) analysis using the new concept of fractional base units (repeating unit R divided by integer X; R/ X as a mathematical moiety) is now a powerful data-processing tool to unravel complex mass spectra of polymers. It enhances regular KMD analysis using the chemical moiety, R, to compute mass defects with unprecedented separation of ion series differing by their isotopic or comonomeric contents, end-groups, or charge states in highly visual KMD plots. The value of the divisor, X, dictates the gain of separating power from the regular to the resolution-enhanced KMD plot, and its choice strongly affects the ease and speed of data interpretation. A simple tool to help select the best values of X depending on the users' needs is mandatory to rationalize the analysis and avoid a time-consuming trial-and-error methodology. We propose two graphical representations intuitively ranking the well-suited divisors for the appropriate separation of isotopes or co-oligomers for copolymeric mass-spectral data. Rankings are extended to any type of data set from homopolymeric blends to terpolymers by generalizing the formulas with three variables beyond the specific separation of isotopes. The RANK functions are now available in commercial or homemade spreadsheets (available upon request) to interactively select divisors and compute the associated KMD plots.
Outer membranes of gram-negative bacteria. XIX. Isolation from Pseudomonas aeruginosa PAO1 and use in reconstitution and definition of the permeability barrier (1978)

A method for separating the outer and inner membranes of Pseudomonas aeruginosa PAO1 in the absence of added ethylenediaminetetraacetic acid was devised. The method yields two outer membrane fractions which show the same protein pattern on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but differ substantially in their relative contents of phospholipids. One of these outer membrane fractions and the inner membrane fraction are less than 4% cross-contaminated, as judged by the content of typical inner and outer membrane markers. The outer membrane contains four major protein bands with apparent molecular weights of 37,000, 35,000, 21,000 and 17,000. Vesicles reconstituted from lipopolysaccharide and phospholipids were impermeable to all saccharides included in the vesicles during vesicle formation. When the vesicles contained outer membrane proteins, they fully retained only those saccharides of greater than 9,000 molecular weight, suggesting that the exclusion limit of the outer membrane of P. aeruginosa for saccharides is substantially larger than the figure (500 to 600 daltons) obtained for certain enteric bacteria. The advantages and potential disadvantages of having an outer membrane with a higher exclusion limit for hydrophilic substances are discussed.
Monitoring Earth's shortwave reflectance: GEO instrument concept (2015)

In this paper we present a GEO instrument concept dedicated to monitoring the Earth's global spectral reflectance with a high revisit rate.Based on our measurement goals, the ideal instrument needs to be highly sensitive (SNR>100) and to achieve global coverage with spectral sampling (::S1Onm) and spatial sampling (::Slkm) over a large bandwidth (380-2510 nm) with a revisit time (3x/day) sufficient to fully measure the spectral-radio metric-spatial evolution of clouds and confounding factor during daytime. After a brief study of existing instruments and their capabilities, we choose to use a GEO constellation of up to 6 satellites as a platform for this instrument concept in order to achieve the revisit time requirement with a single launch. We derive the main parameters of the instrument and show the above requirements can be fulfilled while retaining an instrument architecture as compact as possible by controlling the telescope aperture size and using a passively cooled detector.
Comparison of the LTQ‐Orbitrap Velos and the Q‐Exactive for proteomic analysis of 1–1000 ng RAW 264.7 cell lysate digests (2012)

The Q-Exactive outperformed the LTQ-Orbitrap Velos for shotgun proteomics analysis of 1 to 1000 ng RAW 264.7 cell lysate digests in terms of obtained peptide and protein group IDs.
Capsulation of carbon nanotubes on top of colloidally templated and electropolymerized polythiophene arrays (2011)

We describe the capsulation of colloidally templated polythiophene (P3-TAA) arrays with multi-walled carbon nanotubes (MWNTs) after colloidal template electropolymerization. The dissolution of the polystyrene (PS) particle templates, which were assembled via the Langmuir-Blodgett (LB)-like technique, allowed the formation of hollow-shell Janus type arrays.
From the Pharmacokinetics to the Intracellular Dynamic Phase &#8212; Direct Introduction of Nanoparticles into Cytoplasm of Living Cells (2006)

We developed a technology to directly introduce nanoparticles into the cytoplasm of living cells at one time without using a micromanipulator. Moreover, we confirmed that antisense oligonucleotides as a model drug can be released slowly in cytoplasm from these particles.
The effect of concomitant fields in fast spin echo acquisition on asymmetric MRI gradient systems (2017)

We demonstrate that the zeroth/first-order CFs specific to asymmetric gradients can cause substantial artifacts, including signal loss and dark bands for brain imaging. These effects can be corrected using real-time compensation. Magn Reson Med 79:1354-1364, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Automated analysis of immunohistochemical images based on curve evolution approaches (2013)

The HER2/neu oncogene is notable both for its role in the pathogenesis of breast cancer and its role as a target of treatment. Qualitative or quantitative protein evaluation has been achieved using immunohistochemistry (IHC) on frozen and archival tissues, a widely adopted technique due to the standardization of the internal procedural steps and its easy and low-cost applicability to any laboratory. The goal of the present study is to introduce an efficient tool for the automated detection of HER2 protein overexpression in tissues, providing accurate, instant, yet objective interpretation outcomes through a formalized procedure. The comparison of results with classifications by specialists who evaluated the same tissue samples dataset confirms the efficiency and prospect of the methodology.
Synthesis and characterization of Thermally Rearranged (TR) polymers: influence of ortho-positioned functional groups of polyimide precursors on TR process and gas transport properties (2012)

Aromatic polyimides bearing various ortho-functional groups (i.e., acetate group and pivalic acetate group) were prepared via acetylation of a poly(hydroxyimide) containing ortho-positioned hydroxy groups using acetic anhydride or pivalic anhydride. The completeness of acetylation was confirmed by 1H NMR and FTIR. Chemically derivatized polyimides were used as precursors for an imide-to-benzoxazole thermal rearrangement (TR) process. The influence of various ortho-functionalities on the TR process and gas transport properties of the resulting TR polymers was studied. Differing from the –OH groups in a poly(hydroxyimide), the acetate groups of acetylated polyimide precursors degrade at elevated temperatures, and the degradation process interplays with imide-to-benzoxazole conversion. The acidic degradation product, as detected by 1H NMR, is suspected to have some catalytic effect on the TR process, which along with the protecting function of the acetate groups, resulted in a lower onset TR conversion temperature, the ability to conduct the TR process in air, and a higher TR conversion level. Gas permeation properties greatly depend on the ortho-functionality of polyimide precursors as well. The precursor films containing larger functional groups are much more permeable with comparable gas selectivities. Similarly, the resulting TR polymers formed from polyimides with larger leaving groups also showed much higher gas permeabilities despite similar degrees of TR conversion. The incorporation of bulkier functional groups in the TR precursors provides an effective way to significantly improve the gas transport performance, particularly the gas permeabilities of both the polyimide precursors and the resulting TR polymers.
Supplementary Figures 2-8 from Genome-Wide DNA Methylation Profiling of CpG Islands in Breast Cancer Identifies Novel Genes Associated with Tumorigenicity (2023)

Supplementary Figures 2-8 from Genome-Wide DNA Methylation Profiling of CpG Islands in Breast Cancer Identifies Novel Genes Associated with Tumorigenicity
Functional properties of a rat monoclonal IgE antibody specific for Schistosoma mansoni. (1987)

A rat monoclonal antibody of IgE isotype (B48-14) raised against Schistosoma mansoni has been generated by the fusion of mesenteric lymph node cells from LOU/M rats immunized with a preparation of adult schistosome worms and IR973F nonsecreting rat myeloma cells. Investigation of the in vitro effector functions of this IgE antibody showed a high level of cytotoxicity against S. mansoni schistosomula in the presence of eosinophils, macrophages, and platelets. A significant level of protection (40 to 60%) against a challenge infection with S. mansoni cercariae was achieved by passive transfer experiment of B48-14 IgE to naive recipient rats. By immunoprecipitation, B48-14 IgE antibodies were shown to react with an antigen of 26 kDa present in excretion-secretion products of schistosomula, previously described as a potential immunogen eliciting a protective IgE response against schistosomiasis.
Wavefront Preservation in Soft X-Ray Beamlines for the Advanced Light Source Upgrade (2021)

In the 4th generation of X-ray light sources, including Free-Electron Lasers (FEL) and Diffraction-Limited Storage Rings (DLSR), the emittance of the electron beam is small or negligible compared to the emittance of the photon beam produced by insertion devices, thus generating coherent beams of light. Over the next few years, several lightsource facilities will be built or upgraded to produce X-ray beams of unprecedented coherent flux. Delivering these exceptional beams to the sample chambers requires beamline optical systems that are designed to preserve the wavefront properties. Our goal in the Advanced Light Source upgrade project (ALS-U) is to create a new class of beamlines that reach diffraction-limited X-ray optical quality through tightly integrated, efficient optical systems, diagnostics, and adaptive mirrors, thus providing users with new scientific capabilities offered by coherent X-ray light interactions with matter. Herein we describe aspects of the beamlines’ design as they enter the project’s final design phase.
S2F: Slow-to-Fast Interpolator Flow (2017)

We introduce a method to compute optical flow at multiple scales of motion, without resorting to multi-resolution or combinatorial methods. It addresses the key problem of small objects moving fast, and resolves the artificial binding between how large an object is and how fast it can move before being diffused away by classical scale-space. Even with no learning, it achieves top performance on the most challenging optical flow benchmark. Moreover, the results are interpretable, and indeed we list the assumptions underlying our method explicitly. The key to our approach is the matching progression from slow to fast, as well as the choice of in-terpolation method, or equivalently the prior, to fill in regions where the data allows it. We use several off-the-shelf components, with relatively low sensitivity to parameter tuning. Computational cost is comparable to the state-of-the-art.
Controlled deposition of plasma‐polyaniline thin film by PECVD: Understanding the influence of aniline to argon ratio (2022)

Abstract Low pressure capacitively coupled radiofrequency plasmas operated in a mixture of aniline vapor and argon are used for the deposition of thin films on silicon substrates. The influence of the aniline vapor fraction in the gas mixture upon the plasma properties and the characteristics of the deposited thin film is analyzed. Plasmas diagnostics are carried out using mass spectrometry and optical emission spectroscopy and the thin films are characterized by means of Fourier transform infrared spectroscopy, X‐ray photoelectron spectroscopy, and near‐edge X‐ray absorption fine‐structure spectroscopy. Experiments highlight that the use of a low aniline/argon ratio leads to the deposition of an amorphous film whereas high‐aniline/argon ratios allow the synthesis of a plasma polymer similar to polyaniline. The properties of such plasmas and the mechanisms involved in the deposition process are discussed in detail.
ChemInform Abstract: Comparison of Microbiologically and Enzymatically Mediated Baeyer‐ Villiger Oxidations: Synthesis of Optically Active Caprolactones. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Position and mode dependent coupling of terahertz quantum cascade laser fields to an integrated diode (2013)

A Schottky diode integrated into a terahertz quantum cascade laser waveguide couples directly to the internal laser fields. In a multimode laser, the diode response is correlated with both the instantaneous power and the coupling strength to the diode of each lasing mode. Measurements of the rectified response of diodes integrated in two quantum cascade laser cavities at different locations indicate that the relative diode position strongly influences the laser-diode coupling.
Synthesis of Novel N-Halamine Biocidal Polymers (1999)

Two new water-insoluble polymeric biocides have been synthesized: poly[3-chloro-2,2,5,5-tetramethyl-1-(4'-vinylbenzyl)imidazolidin-4-one] (Poly-p-VBD-Cl) and poly[acrylonitrile-co-(1,3-dichloro-5-methyl-5-(4'-vinylbenzyl)barbituric acid)] (Poly-AN-Barb-Cl). The polymer and copolymer were tested for longevity of the bactericidal activity against Staphylococcus aureus. Not only did this test reveal significant bactericidal activity by these materials, but also good stability in dry storage. These new biocidal polymers could be used in cartridge filters for the disinfection of recreational and potable water.
Visualization of the Electron-solid Interaction Volume in Dielectric Materials Under Variable Pressure Conditions (2006)

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2006
THE USE OF NONTRADITIONAL ASSAYS IN AN INTEGRATED ENVIRONMENTAL ASSESSMENT OF CONTAMINATED GROUND WATER (1997)

The toxic potential of ground water contaminated with several probable carcinogenic heavy metals and halogenated solvents was evaluated using an integrated environmental assessment approach. A number of assays, which included acute toxicity, short-term chronic toxicity, genotoxicity, developmental toxicity and carcinogenicity, were used to assist in a hazard assessment. Comprehensive analytical chemistry was performed throughout the 9-month exposure to document the chemical characteristics of the ground water. An initiation-promotion protocol using a non-neoplastic concentration of diethylnitrosamine as an initiator in a 9-month chronic exposure of Japanese medaka (Oryzias latipes) was used to evaluate potential carcinogenicity of the ground water. The fish were exposed to groundwater concentrations of 1% and 10% ground water by volume. No significant lesions were found in the Japanese medaka exposed to groundwater concentrations at 1% or 10% ground water by volume. Likewise, no genotoxicity, developmental toxicity, acute toxicity or short-term chronic toxicity, were found at concentrations of ≤10% ground water by volume. The negative results obtained in this study show that the potential hazard posed by low concentrations of a complex mixture containing suspect carcinogens may not be manifested at environmentally relevant concentrations.
Program transformation strategies for memory size and power reduction of pseudoregular multimedia subsystems (1998)

A program transformation strategy is presented that is able to reduce the buffer size and power consumption for a relatively large class of (pseudo)regular data-dominated signal processing algorithms. Our methodology is targeted toward an implementation on programmable processors, but most of the principles remain valid for a custom processor implementation. As power and area cost are crucial in the context of embedded multimedia applications, this strategy can be very valuable. The feasibility of our approach is demonstrated on a representative high-speed video processing algorithm for which we obtain a substantial reduction of the area and power consumption compared to the classical approaches.