gebhart/patrepeval huggingface dataset:
Effect of Biological Alterations of Type I 5'Deiodinase Activity on Affinity Labeled Membrane Proteins in Rat Liver and Kidney* (1990)

Type I iodothyronine 5'deiodinase (5'D-I) is a membrane-bound enzyme catalyzing the deiodination of T4 to T3. The affinity label, N-bromoacetyl-thyroxine (BrAcT4), has previously been used to characterize a 27 kilodalton protein (p27) from rat liver and kidney microsomes with characteristics of the catalytic subunit of the 5'D-I. We examined the effect of physiological conditions, known to alter 5'D-I activity, on affinity-labeled proteins in rat liver and kidney microsomes. To confirm that the affinity labeled protein was associated with the deiodinase, we treated rats with the active site directed enzyme inhibitor, propylthiouracil (PTU), in the absence and presence of 100-fold excess methimazole (MMI), an antithyroid drug which blocks PTU inhibition of 5'D-I in vivo. In addition, we used the affinity label as a probe to measure 5'D-I levels in membrane preparations from short and long term fasted rats. Rats were treated ip with PTU (50 micrograms/100 g BW) or MMI (5 mg/100 g BW); in a second experiment, groups of rats were fasted for 4 days (4 D), 1 day (1 D), or fed ad lib (C) and hepatic and kidney microsomes were prepared. 5'D-I activity and 5'D-I content, as judged by specific incorporation of the affinity label into p27, were determined. PTU decreased both 5'D-I activity and BrACT incorporation into p27 by 60-65%. Coadministration of MMI attenuated the effect of PTU on 5'D-I activity and p27 affinity labeling. No other affinity labeled proteins were affected. In fasting experiments, the changes in affinity labeling of p27 paralleled the changes in 5'D-I activity. 5'D-I activity was significantly decreased in hepatic microsomes obtained from 4 D-fasted rats as compared to C rats, but was unchanged in hepatic microsomes from 1 D-fasted rats or in kidney microsomes from 1 D or 4 D-fasted rats as compared to C. Maximal BrAcT4 incorporation into p27 decreased by 45% in hepatic microsomes from 4 D-starved rats as compared to C (6.7 +/- 0.9 vs. 11.9 +/- 1.5 pmol BrAcT4 incorporated/mg microsomal protein, respectively). There was no change in p27 content in hepatic microsomes from 1 D-starved rats (11.2 +/- 1.1). Starvation failed to alter the BrAcT4 labeling of kidney microsomes (16.7 +/- 4.4, 16.2 +/- 6.6, and 14.8 +/- 3.2 pmol BrAcT4 in 4 D, 1 D, and C rats, respectively). In this study, we have demonstrated that alterations in biological activity of 5'D-I correspond to alterations in affinity labeling of p27.
Enhanced interpolation-based interference rejection combining for black-space cognitive radio in time-varying channels (2020)

Abstract In this paper, we investigate multi-antenna interference rejection combing (IRC)-based black-space cognitive radio (BS-CR) operation in time-varying channels. The idea of BS-CR is to transmit secondary user (SU) signal in the same frequency band with the primary user (PU) such that SU’s power spectral density is clearly below that of the PU, and no significant interference is inflicted on the PU receivers. We explore the effects of interpolation and mobility on the novel blind IRC technique which allows such operation mode for effective reuse of the PU spectrum for relatively short-distance CR communication. We assume that both the PU system and the BS-CR use orthogonal frequency division multiplexing (OFDM) waveforms with common numerology. In this case, the PU interference on the BS-CR signal is strictly flat-fading at subcarrier level. Sample covariance matrix-based IRC adaptation is applied during silent gaps in CR operation. We evaluate the effect of the gap length on the link performance, using known PU channel-based interference covariance estimation as reference. We also propose an interpolation-based scheme for tracking the spatial covariance in time-varying channels, demonstrating significantly improved robustness compared to the earlier scheme. The performance of the proposed IRC scheme is tested considering terrestrial digital TV broadcasting (DVB-T) as the primary service. Also joint PU and co-channel CR interference cancellation is included in the study. The resulting interference suppression capability is evaluated with different PU interference power levels, silent gap durations, data block lengths, and CR device mobilities.
Direct Observation of G-protein Binding to the Human δ-Opioid Receptor Using Plasmon-Waveguide Resonance Spectroscopy (2003)

Using a recently developed method (Salamon, Z., Macleod, H. A., and Tollin, G. (1997) Biophys. J. 73, 2791-2797), plasmon-waveguide resonance spectroscopy, we have been able, for the first time, to directly measure the binding between the human brain delta-opioid receptor (hDOR) and its G-protein effectors in real-time. We have found that the affinity of the G-proteins toward the receptor is highly dependent on the nature of the ligand pre-bound to the receptor. The highest affinity was observed when the receptor was bound to an agonist ( approximately 10 nm); the lowest when receptor was bound to an antagonist ( approximately 500 nm); and no binding at all was observed when the receptor was bound to an inverse agonist. We also have found direct evidence for the existence of an additional G-protein binding conformational state that corresponds to the unliganded receptor, which has a G-protein binding affinity of approximately 60 nm. Furthermore, GTP binding to the receptor.G-protein complex was only observed when the agonist was pre-bound. Similar studies were carried out using the individual G-protein subtypes for both the agonist and the unliganded receptor. Significant selectivity toward the different G-protein subtypes was observed. Thus, the unliganded receptor had highest affinity toward the Galphao (Kd approximately 20 nm) and lowest affinity toward the Galphai2 ( approximately 590 nm) subtypes, whereas the agonist-bound state had highest affinity for the Galphao and Galphai2 subtypes (Kd approximately 9 nm and approximately 7 nm, respectively). GTP binding was also highly selective, both with respect to ligand and G-protein subtype. We believe that this methodology provides a powerful new way of investigating transmembrane signaling.
Cytomegalovirus Infection after Liver Transplantation– Incidence, risks and benefit of prophylaxis (2009)

Introduction: Cytomegalovirus (CMV) infection and related disease is a feared complication after liver transplantation. Depending on CMV status of donor and recipient and individual risk profile antiviral prophylaxis is recommended in clinical practice guidelines.
Safety Assessment of Broadband Laser Exposure in µOCT (2021)

Abstract Micro-optical coherence tomography (µOCT) improves the spatial resolution of in vivo OCT imaging by utilizing sophisticated focusing schemes and broadband illumination. This study explores the safety of coronary and trachea tissue exposure to µOCT illumination. © 2021 The Authors
THE FRANK STINCHFIELD AWARD: Muscle Damage after Total Hip Arthroplasty Done with the Two-incision and Mini-posterior Techniques (2005)

Some surgeons have suggested that a minimally invasive two-incision approach allows total hip arthroplasty to be done without cutting or damaging any muscle or tendon. To our knowledge that claim has not been supported by any published clinical or basic science data. Our purpose in doing this study was to quantify the extent and location of damage to the abductor and external rotator muscles and tendons after two-incision and mini-posterior total hip arthroplasty. Ten cadavers (20 hips) were studied. In each cadaver one hip randomly was assigned to the two-incision group and the contralateral hip was assigned to the mini-posterior group. After inserting the total hip arthroplasty components the muscle damage was assessed using a technique described previously. Damage to the muscle of the gluteus medius and gluteus minimus was substantially greater with the two-incision technique than with the mini-posterior technique. Every two-incision total hip replacement caused measurable damage to the abductors, the external rotators, or both. Every mini-posterior hip replacement caused the external rotators to detach during the exposure and had additional measurable damage to the abductor muscles and tendon. We do not support the contention that a two-incision total hip arthroplasty is done without cutting muscle or tendon. None of the two-incision hip replacements were done without cutting, reaming, or damaging the gluteus medius or gluteus minimus muscle or external rotators.
Hardware instancing for real-time realistic forest rendering (2011)

Real-time rendering of vegetation is important in many applications, such as video games, internet graphics applications, landscape design and visualization. However, the visualization of large-scale forests has always been a challenge not only due to the high geometric complexity but also due to the small batch problem. Moreover, generating real-time shadows for forests will heavily increase the burden. The batch problem is caused by a large number of graphics API draw calls launched in every frame. Normally, rendering a tree model requires at least one graphics API draw call. As a forest usually consists of thousands of trees and the graphics API invocation is a relatively high cost for CPU, the large-scale forest rendering is often CPU bound.
Gain Measurements in Dy3+ -doped LaCl3: A potential 1.3 μm optical amplifier for telecommunications (1996)

A number of Dy3+-doped crystals have been studied and spectroscopic and theoretical data suggests that Dy3+:chlorides are promising candidates for amplification of the 1.3 μm signal used by the telecommunications network. In particular, LaCl3:Dy3+ has an emission band centered around 1.3 μm with a radiative lifetime greater than one millisecond which is consistent with a quantum yield above 70% (compared to 3% for Pr:ZBLAN). Gain data from pump-probe experiments at 1.319 μm and 1338 μm resulted in a net gain of 13% and ~14%, respectively.
Treatment of Advanced Human Immunodeficiency Virus Type 1 Disease with the Viral Entry Inhibitor PRO 542 (2004)

Viral entry inhibitors represent an emerging mode of therapy for human immunodeficiency virus type 1 (HIV-1) infection. PRO 542 (CD4-immunoglobulin G2) is a tetravalent CD4-immunoglobulin fusion protein that broadly neutralizes primary HIV-1 isolates. PRO 542 binds to the viral surface glycoprotein gp120 and blocks attachment and entry of virus into CD4(+) cells. Previously, PRO 542 demonstrated antiviral activity without significant toxicity when tested at single doses ranging to 10 mg/kg. In this study, 12 HIV-infected individuals were treated with 25-mg/kg single-dose PRO 542 and then monitored for safety, antiviral effects, and PRO 542 pharmacokinetics for 6 weeks. The study examined two treatment cohorts that differed in the extent of HIV-1 disease progression. PRO 542 at 25 mg/kg was well tolerated and demonstrated a serum half-life of 3 days. Statistically significant acute reductions in HIV-1 RNA levels were observed across all study patients, and greater antiviral effects were observed in the cohort of patients with more advanced HIV-1 disease. In advanced disease (HIV-1 RNA > 100,000 copies/ml; CD4 lymphocytes < 200 cells/mm(3)), PRO 542 mediated an 80% response rate and statistically significant approximately 0.5 log(10) mean reductions in viral load for 4 to 6 weeks posttreatment. Similar findings were obtained in an analysis of all (n = 11) advanced disease patients treated to date with single doses of PRO 542 ranging from 1 to 25 mg/kg. In addition, a significant correlation was observed between antiviral effects observed in vivo and viral susceptibility to PRO 542 in vitro. The findings support continued development of PRO 542 for salvage therapy of advanced HIV-1 disease.
Stochastic fairness queueing (2002)

A class of algorithms called stochastic fairness queuing is presented. The algorithms are probabilistic variants of fairness queuing. They do not require an exact mapping and thus are suitable for high-speed software or firmware implementation. The algorithms span a broad range of CPU, memory, and fairness tradeoffs. It is shown that the worst-case execution-speed stochastic fairness queuing is faster than the best-case execution speed of all of the implementations of fair queuing presented. This advantage is larger for protocols with longer addresses, e.g. the ISO protocol suite.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Determination of the Total Phenolics Content and Antioxidant Activity of Extracts from Parts of Plants from the Greek Island of Crete (2023)

Oxidative damages are responsible for many adverse health effects and food deterioration. The use of antioxidant substances is well renowned, and as such, much emphasis is placed on their use. Since synthetic antioxidants exhibit potential adverse effects, plant-derived antioxidants are a preferable solution. Despite the myriads of plants that exist and the fact that numerous studies have been carried out so far, there are many species that have not been examined so far. Many plants under research exist in Greece. Trying to fill this research gap, the total phenolics content and antioxidant activity of seventy methanolic extracts from parts of Greek plants were evaluated. The total phenolics content was measured by the Folin-Ciocalteau assay. Their antioxidant capacity was calculated by the 2,2-Diphenyl-1-picrylhydrazyl (DPPH) scavenging test, the Rancimat method based on conductometric measurements, and the thermoanalytical method DSC (Differential Scanning Calorimetry). The tested samples were obtained from several parts of fifty-seven Greek plant species belonging to twenty-three different families. Both a remarkably high phenolic content (with gallic acid equivalents varying between 311.6 and 735.5 mg/g of extract) and radical scavenging activity (IC<sub>50</sub> values ranged from 7.2 to 39.0 μg/mL) were found in the extract of the aerial parts of <i>Cistus</i> species (<i>C. creticus</i> subsp. <i>creticus</i>, <i>C. creticus</i> subsp. <i>eriocephalus</i>, <i>C. monspeliensis</i>, <i>C. parviflorus</i> and <i>C. salviifolius</i>), <i>Cytinus</i> taxa (<i>C. hypocistis</i> subsp. <i>hypocistis</i>, <i>C. hypocistis</i> subsp. <i>orientalis</i> and <i>C. ruber</i>), and <i>Sarcopoterium spinosum</i>. Furthermore, the sample of <i>Cytinus ruber</i> showed the highest protection factor (PF = 1.276) regarding the Rancimat method, which was similar to that of butylated hydroxytoluene (BHT) (PF = 1.320). The results indicated that these plants are rich in antioxidant compounds, potentiating their use either as food additives to enhance the antioxidant properties of food products, or protect them from oxidation, or as sources for the preparation of food supplements with antioxidant properties.
Metamaterials-based broadband generation of orbital angular momentum carrying vector beams (2013)

We propose a simple approach to broadband generation of orbital angular momentum (OAM) carrying vector beams based on compact metamaterials. It consists of two concentric rings in a gold film, where each ring is composed of subwavelength rectangular apertures with gradually varied orientation. The subwavelength rectangular aperture serves as a localized spatial polarizer. We show the generation of different OAM-carrying vector beams with OAM charge number and polarization order varying from -3 to +3 using a 11.2×11.2 μm device. The extinction ratio can exceed 20 dB, and the operation bandwidth (1500 nm) can cover from 1000 to 2500 nm (from near-infrared to mid-infrared). The device provides three degrees of freedom (polarization order l, polarization of input beam σ, and initial orientation angle α(0)) to flexibly generate different OAM-carrying vector beams. We can use a single device to generate two OAM-carrying vector beams with opposite charge sign of OAM by simply controlling the polarization of the input beam. We further study the performance dependence of the designed metamaterials on the offset of the initial orientation angle, length, and width of the rectangular apertures. The obtained results indicate favorable fabrication tolerance.
Supplementary Figures from Sodium Channel Subunit SCNN1B Suppresses Gastric Cancer Growth and Metastasis via GRP78 Degradation (2023)

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Kinematic chip to chip bonding (2023)

The various technologies presented herein relate to integrating an IC having at least one waveguide incorporated therein with a v-groove array IC such that an optical fiber located in a v-groove is aligned relative to a waveguide in the IC maximizing optical coupling between the fiber and the waveguide. The waveguide IC and the v-groove array IC are bonded in a stacked configuration. Alignment of the waveguide IC and the array IC in the stacked configuration enables advantage to be taken of lithographic accuracy of features formed with respect to the Z-direction. Further, kinematic pins and sockets are utilized to provision accuracy in the X- and Z-directions, wherein advantage is taken of the placement accuracy and fabrication tolerance(s) which can be utilized when forming the and sockets. Accordingly, automated alignment of the waveguide IC and the array IC is enabled, facilitating accurate alignment of the respective waveguides and fibers.
Organic hard masks utilizing fullerene derivatives (2015)

We have developed a series of fullerene containing materials for use as organic hard masks. Films with a thickness of up to 250 nm were deposited via spin coating. After a crosslinking bake the films exhibit good thermal stability – in the best case a mass loss of less than 3% at 400 °C is seen. Etch resistance of the different formulations are presented and hig-hresolution patterning is demonstrated. During the transfer into silicon no adverse “wiggling” is observed at high resolution. We attribute this to the low levels of aliphatic hydrogen present in the materials.
Optimization of carbon and energy utilization through differential translational efficiency (2018)

Control of translation is vital to all species. Here we employ a multi-omics approach to decipher condition-dependent translational regulation in the model acetogen Clostridium ljungdahlii. Integration of data from cells grown autotrophically or heterotrophically revealed that pathways critical to carbon and energy metabolism are under strong translational regulation. Major pathways involved in carbon and energy metabolism are not only differentially transcribed and translated, but their translational efficiencies are differentially elevated in response to resource availability under different growth conditions. We show that translational efficiency is not static and that it changes dynamically in response to mRNA expression levels. mRNAs harboring optimized 5'-untranslated region and coding region features, have higher translational efficiencies and are significantly enriched in genes encoding carbon and energy metabolism. In contrast, mRNAs enriched in housekeeping functions harbor sub-optimal features and have lower translational efficiencies. We propose that regulation of translational efficiency is crucial for effectively controlling resource allocation in energy-deprived microorganisms.
Cytidine deaminase protects pancreatic cancer cells from replicative stress and drives resistance to DNA-targeting drugs (2021)

ABSTRACT Chronic DNA replication stress and genome instability are two hallmarks of cancer that fuel oncogenesis and tumor diversity. Therapeutic approaches aimed to leverage tumor-specific replication stress to intolerable levels or to expose vulnerabilities for synthetic lethality purposes have recently gained momentum, especially for pancreatic cancer, a disease with no cure. However, the current knowledge regarding the molecular mechanisms involved in the replication stress response in pancreatic tumors is limited. Cytidine deaminase (CDA) is involved in the pyrimidine salvage pathway for DNA and RNA synthesis. Loss of CDA induces genomic instability in Bloom Syndrome, and CDA protects tumor cells from chemotherapy with pyrimidine analogs. Here, we show that CDA is overexpressed in genetically unstable pancreatic tumors, associates with a DNA replication signature, and is instrumental for experimental tumor growth. In cancer cells, CDA promotes DNA replication, increases replication fork speed, and controls replication stress and genomic stability levels. CDA expression is predictive of DNA-damaging drug efficacy and targeting CDA relieves resistance to chemotherapy in patients models, both in vitro and in vivo . Our findings shed new light on the mechanisms by which pancreatic cancer cells control replication stress, and highlight targeting of CDA as a potential therapeutic strategy to defeat tumor resistance to treatment.
Simple automated continuous filament winding system for fibre reinforced composites (1990)

A simple, automated continuous filament winding system has been developed and fabricated which is capable of producing composite components in both hoop and helical winding modes. Automation was achieved by means of a closed-loop controlling system employing an incremental encoder with a BALDOR controller card. The program software developed is capable of effecting both a closed circuit and a repeating lamina pattern for the helical winding mode.
“On‐Droplet” Chemistry: The Cycloaddition of Diethyl Azodicarboxylate and Quadricyclane (2017)

Sharpless and co-workers previously studied the [2σ+2σ+2π] cycloaddition of diethyl azodicarboxylate (DEAD) and quadricyclane and reported that the addition of water to the neat reagents caused an acceleration in the reaction rate, giving birth to what has been called "on-water" chemistry. We have examined the same reaction in aqueous microdroplets (ca. 5 μm diameter) and find that the cycloaddition reaction is accelerated even further (by a factor of 10<sup>2</sup> ) compared to that of the "on-water" reaction reported previously. The trends of acceleration in solvents other than water demonstrated by Sharpless and colleagues were replicated in the corresponding microdroplet experiments. We also find that DEAD reacts with itself to form a variety of hydrazine carboxylates and intercept intermediates of this reaction in microdroplets to validate a mechanism proposed herein. We suggest that "on-droplet" chemistry, similar to "on-water" chemistry, may be a general process of synthetic interest.
A Critique of the Intraoperative Use of Jugular Venous Bulb Catheters During Neurosurgical Procedures (1995)

MATTA, BASIL F.; LAM, ARTHUR M.; MAYBERG, TERESA S.; SHAPIRA, YORAM; WINN, H. RICHARD Author Information