gebhart/patrepeval huggingface dataset:
Endogenous morphine: a role in wellness medicine. (2004)

The demonstration of the multiplicity of opiate receptor types has led to the understanding that, depending on their site of action, opioid peptides as well as opiate alkaloids may bind to more than one opiate receptor subtype. In addition to the two main mu opiate receptor subtypes, mu1 and mu2, our laboratory has demonstrated a third mu opiate receptor (mu3) that is selective for opiate alkaloids but insensitive to opioid peptides. Recently, the mu3 opiate receptor subtype has been cloned from human immune, vascular and neural tissues. This mu3 story complements many biochemical reports; demonstrating morphine is an endogenous signaling molecule, functioning in the capacity of a neurotransmitter and hormone. Adding additional evidence to this hypothesis are the findings of morphine precursors in mammalian and invertebrate tissues. The reports published in this issue of MSM complement this story while advancing the hypothesis by placing opiate alkaloid signaling in limbic structures. The pharmacological characteristics of exogenous morphine find a role for explaining morphine action in an "emotional" and belief setting.
End-to-End Automated Synthesis of C(sp<sup>3</sup>)-Enriched Drug-like Molecules <i>via</i> Negishi Coupling and Novel, Automated Liquid–Liquid Extraction (2022)

Herein, we report an end-to-end process including synthesis, work-up, purification, and post-purification with minimal human intervention using Negishi coupling as a key transformation to increase Fsp<sup>3</sup> in bioactive molecules. The main advantages of this protocol are twofold. First, the automated sequential generation of organozinc reagents from readily available alkyl halides offers a large diversity of alkyl groups to functionalize (hetero)aryl halide scaffolds <i>via</i> Pd-catalyzed Negishi coupling in continuous flow. Second, a fully automated liquid-liquid extraction has been developed and successfully applied for unattended operations. The workflow was completed with mass-triggered preparative high-performance liquid chromatography HPLC, providing an efficient production line of compounds with enriched sp<sup>3</sup> character and better drug-like properties. The modular nature allows a smooth adaptation to a wide variety of synthetic methods and protocols and makes it applicable to any medchem laboratory.
Development of a High-Efficiency, Low-Cost Hybrid SOFC/Internal Combustion Engine Power Generator (2021)

The unique and beneficial characteristics of solid oxide fuel cell (SOFC) technology hold much promise for their eventual widespread adoption in numerous residential and commercial building applications. Nevertheless, cost and durability challenges remain that currently limit SOFC technology penetration in stationary energy applications. Under the U.S. DOE ARPA-E INTEGRATE program, the Colorado School of Mines and it partners are developing a novel hybrid stationary power system comprised of an intermediate temperature (600°C), metal-supported solid oxide fuel cell stack (from Ceres Power) integrated with a high efficiency stationary engine and novel balance-of-plant (BOP) equipment. In collaboration with Colorado State University, Kohler Power Systems, and Air-Squared, Inc., the project aims to demonstrate a system that can generate power (125 kW) from natural gas at high electric efficiency (&gt;70%-LHV), and low cost (&lt;900 $/kW). Project development activities on the hybrid SOFC/IC engine system development and requirements are presented and discussed, including experimental results from critical balance-of-plant equipment and techno-economic outlook. Figure 1
Muscle selection and walking performance of multichannel FES systems for ambulation in paraplegia (1997)

A minimal set of muscles (8 to 16) were identified as candidates for implantation in a clinical system to provide walking function to individuals with complete paraplegia using functional electrical stimulation (FES). Three subjects with complete motor and sensory paraplegia had percutaneous intramuscular electrodes implanted in all major muscles controlling the trunk, hips, knees, and ankles. Stimulation patterns for walking with FES were generated for different sets of eight and 16 muscles. The quality and repeatability of the resulting gait produced by walking patterns consisting of various combinations of muscles were determined. Most eight-channel stimulation patterns resulted in scissoring or insufficient hip flexion, preventing forward progression. One eight-channel system allowed a maximum speed of 0.1 m/s with a cadence of 22 steps/min and a stride length less than 0.3 m. Improved walking performance was observed with 16 channels of stimulation. This ranged from slow step- to gait at 0.1 m/s to smooth reciprocal gait at 0.5 m/s. In all three subjects, the favored combination of 16 channels included erector spinae for trunk extension; gluteus maximus, posterior portion of adductor magnus and hamstrings for hip extension; tensor fasciae latae and either sartorius or iliopsoas for hip flexion; vastus lateralis/intermedius for knee extension; and tibialis anterior/peroneous longus for ankle dorsiflexion. In one subject the 16-channel FES system provided repeatable day-to-day gait averaging 0.4 m/s, 58 steps/min and a stride length at 0.8 m. A maximum repeatable walking distance with 16 channels was 34 m. Multiple 34-m trials were possible with minimal rests between walks. Fatigue of both the hip extensors and upper body was a limiting factor. The selection of target muscles for implantation is critical to the performance of FES systems. This study provides guidelines to muscle selection for walking with FES based on objective measures of gait performance. The findings indicate that a 16-channel FES system for total implantation is feasible for repeatable short distance, independent, walker-support walking in paraplegia.
Direct and Standard Injection of Sewage Sludge in a Supercritical Water Gasification System - Optimization of the Energy Efficiency Using Pinch Analysis (2016)

Supercritical Water Gasification is a promising technology to convert wet biomass into syngas. One of the challenges of this technology is the coke formation during heating-up of the wet biomass to its supercritical condition. Literature studies show that coke is the result of polymerization reactions that takes place at sub-critical conditions. It also states that a fast heat up of the wet biomass can minimize this unwanted coke formation. An option to achieve a fast heating rate is by direct injection of the relatively unheated wet biomass feed into supercritical water. Incomplete heating up of the wet biomass increases the waste heat in the product gas which will significantly reduce the energy efficiency. Parametric studies of some operating parameters are done to investigate the influence of this direct injection on the process performance. Results from this investigation show that a SCWG process with direct injection will have an efficiency reduction of approximately 7~16% in comparison to the standard (premixed) injection system. Using a feed with 8 wt% and 20 wt% dry matter at 600 °C and 25MPa, the thermal efficiencies of the system are 13.8 % and 65.5 respectively. Preliminary pinch analysis shows that these numbers can be improved to around 20 % and 70 %.
Bubble Behavior and Nucleate Boiling Heat Transfer in Saturated FC-72 Spray Cooling (2001)

Bubble behavior during saturated FC-72 spray cooling was experimentally investigated. A heater previously used for pool boiling was used to allow direct comparison. The results are analyzed to reveal the interaction between bubbles and impinging droplets. The following are presented: (1) the importance of secondary nuclei entrained by impingement droplets, (2) the role of impinging droplets on bubble parameters such as growth, diameter at puncture, lifetime, life cycle and bubble number density, and (3) the relative contribution of nucleation, especially that of secondary nuclei, to the heat transfer. It is concluded that increasing the droplet flux increases the number of secondary nuclei, helps to lower surface temperature for a given heat flux, increases the overall heat transfer coefficient, and increases heat transfer due to both nucleate boiling and enhanced convection. Increasing the droplet flux also shortens the bubble growth time (i.e., resulting in earlier bubble removal) and life cycle. However, increasing the droplet flux (and, therefore, secondary nucleation) for each of the three heat flux values does not affect the percentage of either nucleate or convection heat transfer. This suggests that both the nucleate and convection heat transfer are enhanced, as a result of increased secondary nuclei and turbulent mixing due to the impinging droplets.
Programmable protein arrays for immunoprofiling HPV‐associated cancers (2016)

Over 600,000 cancers each year are attributed to the human papillomavirus (HPV), including cervical, anogenital and oropharyngeal cancers (OPC). A key challenge in understanding HPV immunobiology is the diversity of oncogenic HPV types and the need for multiplexed display of HPV antigens to measure antibody responses. We have generated custom HPV protein microarrays displaying 98 proteins as C-terminal GST fusion proteins, representing eight antigens of two low-risk HPV types (HPV6 and 11) and ten oncogenic high-risk HPV types (HPV16, 18, 31, 33, 35, 39, 45, 51, 52 and 58). We demonstrate robust and reproducible protein expression of 96/98 of the antigens using a human cell lysate expression system. The target epitopes and specificities of four monoclonal antibodies were identified. Using sera from ten patients with newly diagnosed OPC and ten controls, we demonstrate specific IgG seroreactivity to HPV16 E1, E2, and E7 (a fold increase of 1.52, 2.19 and 1.35 in cases vs. controls, respectively, all p < 0.005), confirming our prior data on an ELISA platform. We also detect HPV52 E7 Abs in serum from a patient with cervical cancer. The HPV protein array has potential for rapid identification of serologic responses to 12 HPV types.
New interface structure for <i>A</i>-type CoSi2/Si(111) (1994)

A new model of a CoSi2/Si(111) interface structure has been generated using images produced by Z-contrast scanning transmission electron microscopy. The images indicate that the top and bottom interfaces between the type-A buried CoSi2 layer and Si(111) both have eightfold coordinated Co atoms. This is accomplished by converting the one interface structure from sevenfold to eightfold coordination by locating a twinned layer of Si at the interface. The preference for this interface over the sevenfold type-A structure is in agreement with theoretical predictions.
Pressure Induced Topological Phase Transitions in Membranes (1992)

Some highly unusual features of a lipid-water liquid crystal are revealed by high pressure x-ray diffraction, light scattering and dilatometric studies of the lamellar (bilayer $L_α$) to nonlamellar inverse hexagonal ($H_{II}$) phase transition. (i) The size of the unit cell of the $H_{II}$ phase increases with increasing pressure. (ii) The transition volume, $ΔV_{bh}$, decreases and appears to vanish as the pressure is increased. (iii) The intensity of scattered light increases as $ΔV_{bh}$ decreases. Data are presented which suggest that this increase is due to the formation of an intermediate cubic phase, as predicted by recent theoretical suggestions of the underlying universal phase sequence.
A Wide Dynamic Range Buck Converter With Sub-nW Quiescent Power (2017)

A buck converter in 65-nm CMOS is optimized for a low quiescent power of 240 pW. It operates with input 1.2-3.3 V and regulates the output from 0.7-0.9 V. Control circuits are designed for low leakage and static current, and scale in power over a hertz to megahertz frequency range, resulting in a wide load current dynamic range of 2×0 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> . With a 2-V input, the converter has a peak efficiency of 89% and delivers load currents of 500 pA to 1 mA with efficiency better than 50%. The peak efficiency is 92% for a 1.2-V input.
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures (2014)

We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5-22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10-25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function.
Supplementary Table 2 from Integrated Profiling Reveals a Global Correlation between Epigenetic and Genetic Alterations in Mesothelioma (2023)

Supplementary Table 2 from Integrated Profiling Reveals a Global Correlation between Epigenetic and Genetic Alterations in Mesothelioma
Endophthalmitis Caused by Gram-negative Organisms (1992)

The medical records of 52 patients (53 eyes) with culture-proven gram-negative endophthalmitis between January 1982 and December 1990 were reviewed. Pseudomonas aeruginosa (23% [12/53]) and Haemophilus influenzae (19% [10/53]) were the most frequent isolates in this series. Overall, 26 (49%) of 53 treated patients achieved 20/400 or better visual acuity. Fifty-two (98%) of the original 53 gram-negative isolates were sensitive to the aminoglycoside antibiotics. To determine their sensitivity to recently developed antibiotics, 35 of the isolates were again grown on culture media and their sensitivities to ceftazidime, ciprofloxacin, and imipenem were obtained. Only ceftazidime demonstrated in vitro efficacy for all the organisms tested.
Peroxiredoxin II is essential for sustaining life span of erythrocytes in mice (2003)

Peroxiredoxins (Prxs) are a family of antioxidant proteins that reduce peroxide levels by using reducing agents such as thioredoxin. These proteins were characterized to have a number of cellular functions, including cell proliferation and differentiation and protection of specific proteins from oxidative damage. However, the physiological roles of the peroxiredoxins have not been determined. To clarify the physiological relevance of this protein type, we generated a mouse model deficient in Prx II, which is abundantly expressed in all types of cells. The Prx II-/- mice were healthy in appearance and fertile. However, they had splenomegaly caused by the congestion of red pulp with hemosiderin accumulation. Heinz bodies were detected in their peripheral blood, and morphologically abnormal cells were elevated in the dense red blood cell (RBC) fractions, which contained markedly higher levels of reactive oxygen species (ROS). The Prx II-/- mice had significantly decreased hematocrit levels, but increased reticulocyte counts and erythropoietin levels, indicative of a compensatory action to maintain hematologic homeostasis in the mice. In addition, a labeling experiment with the thiol-modifying reagent biotinylated iodoacetamide (BIAM) in Prx II-/- mice revealed that a variety of RBC proteins were highly oxidized. Our results suggest that Prx II-/- mice have hemolytic anemia and that Prx II plays a major role in protecting RBCs from oxidative stress in mice.
Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia (2016)

This study represents one of the most comprehensive analyses of whole genome sequence data for Group I and II BoNT-producing strains. Read data and draft genome assemblies generated for 59 isolates will be a resource to the research community. Core genome phylogenies proved to be a powerful tool for differentiating BoNT-producing strains and can provide a framework for the study of these bacteria. Comparative genomic analyses of Clostridia species illustrate the diversity of botulinum-neurotoxin-producing strains and the plasticity of the genomic backgrounds in which bont genes are found.
Addition of a Defibrillation Electrode in the Low Right Atrium to a Right Ventricular Lead Does Not Reduce Ventricular Defibrillation Thresholds (2004)

Transvenous unipolar active can defibrillation systems have proven to be effective in treating ventricular tachyarrhythmias. However, a further reduction of ventricular defibrillation thresholds (V-DFT) would increase the longevity, reduce the size of pulse generators, and help to avoid additional leads in patients with inacceptable high V-DFTs. In a finite difference computer model, the extension of the right ventricular (RV) defibrillation coil into the low right atrium led to a 40% reduction of unipolar V-DFT. To evaluate this finding, we conducted a prospective, randomized study in 11 patients receiving an ICD. Extension of the RV electrode was simulated by adding a second coil placed in the low right atrium with the same polarity. Using a binary search protocol, V-DFT was determined with and without the additional electrode in each patient. Total shock impedance was significantly lower in the two coil (low RA) configuration, compared to the single coil (RV) configuration. Corresponding values were 49.9 +/- 6.7 Ohm and 61.1 +/- 9.3 Ohm, respectively (P < 0.01, paired t-test). However, there was no reduction, but even a nonsignificant increase in V-DFTs. Mean V-DFT in the RV configuration was 12.0 +/- 5.6 J and 16.3 +/- 7.8 J in the low RA configuration (P = 0.09, paired t-test). Despite a reduction in total impedance, the addition of a defibrillation coil in the low right atrium does not reduce ventricular defibrillation thresholds.
Laser photoelectron projection microscopy of an organic conducting polymer (2010)

A conducting organic polymer is visualized on a laser photoelectron projection microscope, which is based on Letokhov’s concept and has a nanometer spatial resolution. Photoelectron images of polyaniline (which is the most promising representative of conducting polymers) with a magnification of ∼105 have been obtained when a 100-nm quartz capillary coated with a film of this material was irradiated by femtosecond laser pulses. The projection photoelectron method using 400- and 800-nm laser radiation has made it possible to directly reveal the existence of the redox heterogeneity of the organic polymer, which is due to the contact of the sections of polyaniline with different oxidation degrees and strongly affects the electric conductivity of the sample.
Performance Limits of a Deep Learning-Enabled Text Semantic Communication under Interference (2023)

Although deep learning (DL)-enabled semantic communication (SemCom) has emerged as a 6G enabler by minimizing irrelevant information transmission -- minimizing power usage, bandwidth consumption, and transmission delay, its benefits can be limited by radio frequency interference (RFI) that causes substantial semantic noise. Such semantic noise's impact can be alleviated using an interference-resistant and robust (IR$^2$) SemCom design, though no such design exists yet. To stimulate fundamental research on IR2 SemCom, the performance limits of a popular text SemCom system named DeepSC are studied in the presence of (multi-interferer) RFI. By introducing a principled probabilistic framework for SemCom, we show that DeepSC produces semantically irrelevant sentences as the power of (multi-interferer) RFI gets very large. We also derive DeepSC's practical limits and a lower bound on its outage probability under multi-interferer RFI, and propose a (generic) lifelong DL-based IR$^2$ SemCom system. We corroborate the derived limits with simulations and computer experiments, which also affirm the vulnerability of DeepSC to a wireless attack using RFI.
Profiling of the Differential Abundance of Drought and Salt Stress-Responsive MicroRNAs Across Grass Crop and Genetic Model Plant Species (2018)

In recent years, it has become readily accepted among interdisciplinary agriculturalists that the current global crop yield to land capability ratio is significantly insufficient to achieve food security for the predicted population of 9.5 billion individuals by the year 2050. This issue is further compounded by the: (1) food versus biofuel debate; (2) decreasing availability of arable land; (3) required reductions to the extensive and ongoing environmental damage caused by either poor agricultural practices or agriculture expansion, and; (4) increasingly unfavorable (duration and severity) crop cultivation conditions that accompany man-made climate change, driven by ever-expanding urbanization and its associated industrial practices. Mounting studies are repeatedly highlighting the critical importance of linking genotypes to agronomically beneficial phenotypes and/or using a molecular approach to help address this global crisis, as “simply” clearing the remaining natural ecosystems of the globe for the cultivation of additional, non-modified crops is not efficient, nor is this practice sustainable. The majority of global food crop production is sourced from a small number of members of the Poaceae family of grasses, namely; maize (Zea mays L.), wheat (Triticum aestivum L.) and rice (Oryza sativa L.). It is, therefore, of significant concern that all three of these Poaceae grass species are susceptible to a range of abiotic stresses, including drought and salt stress. Highly conserved among monocotyledonous and dicotyledonous plant species, microRNAs (miRNAs) are now well-established master regulators of gene expression, influencing all aspects of plant development, mediating defense responses against pathogens and adaptation to environmental stress. Here we investigate the variation in the abundance profiles of six known abiotic stress-responsive miRNAs, following exposure to salt and drought stress across these three key Poaceae grass crop species as well as to compare these profiles to those obtained from the well-established genetic model plant species, Arabidopsis thaliana (L.) Heynh. Additionally, we outline the variables that are the most likely primary contributors to instances of differential miRNA abundance across the assessed species following drought or salt stress exposure, specifically; (1) identifying variations in the experimental conditions and/or methodology used to assess miRNA abundance, and; (2) the distribution of regulatory transcription factor binding sites within the putative promoter region of a MICRORNA (MIR) gene that encodes the highly conserved, stress-responsive miRNA. We also discuss the emerging role that non-conserved, species-specific miRNAs play in mediating a plant’s response to drought or salt stress.