gebhart/patrepeval huggingface dataset:
An <em>In Vitro</em> Enzymatic Assay to Measure Transcription Inhibition by Gallium(III) and H<sub>3</sub> 5,10,15-tris(pentafluorophenyl)corroles (2015)

Chemotherapy often involves broad-spectrum cytotoxic agents with many side effects and limited targeting. Corroles are a class of tetrapyrrolic macrocycles that exhibit differential cytostatic and cytotoxic properties in specific cell lines, depending on the identities of the chelated metal and functional groups. The unique behavior of functionalized corroles towards specific cell lines introduces the possibility of targeted chemotherapy. Many anticancer drugs are evaluated by their ability to inhibit RNA transcription. Here we present a step-by-step protocol for RNA transcription in the presence of known and potential inhibitors. The evaluation of the RNA products of the transcription reaction by gel electrophoresis and UV-Vis spectroscopy provides information on inhibitive properties of potential anticancer drug candidates and, with modifications to the assay, more about their mechanism of action. Little is known about the molecular mechanism of action of corrole cytotoxicity. In this experiment, we consider two corrole compounds: gallium(III) 5,10,15-(tris)pentafluorophenylcorrole (Ga(tpfc)) and freebase analogue 5,10,15-(tris)pentafluorophenylcorrole (tpfc). An RNA transcription assay was used to examine the inhibitive properties of the corroles. Five transcription reactions were prepared: DNA treated with Actinomycin D, triptolide, Ga(tpfc), tpfc at a [complex]:[template DNA base] ratio of 0.01, respectively, and an untreated control. The transcription reactions were analyzed after 4 hr using agarose gel electrophoresis and UV-Vis spectroscopy. There is clear inhibition by Ga(tpfc), Actinomycin D, and triptolide. This RNA transcription assay can be modified to provide more mechanistic detail by varying the concentrations of the anticancer complex, DNA, or polymerase enzyme, or by incubating the DNA or polymerase with the complexes prior to RNA transcription; these modifications would differentiate between an inhibition mechanism involving the DNA or the enzyme. Adding the complex after RNA transcription can be used to test whether the complexes degrade or hydrolyze the RNA. This assay can also be used to study additional anticancer candidates.
Supplementary Table S2 from GLI2 Knockdown Using an Antisense Oligonucleotide Induces Apoptosis and Chemosensitizes Cells to Paclitaxel in Androgen-Independent Prostate Cancer (2023)

Supplementary Table S2 from GLI2 Knockdown Using an Antisense Oligonucleotide Induces Apoptosis and Chemosensitizes Cells to Paclitaxel in Androgen-Independent Prostate Cancer
Biologically based strategies to augment rotator cuff tears (2012)

Lesions of the rotator cuff (RC) are among the most frequent tendon injuries. In spite of the developments in both open and arthroscopic surgery, RC repair still very often fails. In order to reduce the failure rate after surgery, several experimental in vitro and in vivo therapy methods have been developed for biological improvement of the reinsertion. This article provides an overview of the current evidence for augmentation of RC reconstruction with growth factors. Furthermore, potential future therapeutic approaches are discussed. We performed a comprehensive search of the PubMed database using various combinations of the keywords "tendon," "rotator cuff," "augmentation," "growth factor," "platelet-rich fibrin," and "platelet-rich plasma" for publications up to 2011. Given the linguistic capabilities of the research team, we considered publications in English, German, French, and Spanish. We excluded literature reviews, case reports, and letters to the editor.
Limits of Mn detection in vivo: Spatial segregation of relaxation behavior (2010)

Toxic effects of photochemical smog on ponderosa and Jeffrey pines in the San Bernardino Mountains were discovered in the 1950s. It was revealed that ozone is the main cause of foliar injury manifested as chlorotic mottle and premature needle senescence. Various morphological, physiological and biochemical alterations in the affected plants have been reported over a period of about 40 years of multidisciplinary research. Recently, the focus of research has shifted from studying the effects of ozone to multiple pollutant effects. Recent studies have indicated that the combination of ozone and nitrogen may alter biomass allocation in pines towards that of deciduous trees, accelerate litter accumulation, and increase carbon sequestration rates in heavily polluted forests. Further study of the effects of multiple pollutants, and their long-term consequences on the mixed conifer ecosystem, cannot be adequately done using the original San Bernardino Mountains Air Pollution Gradient network. To correct deficiencies in the design, the new site network is being configured for long-term studies on multiple air pollutant concentrations and deposition, physiological and biochemical changes in trees, growth and composition of over-story species, biogeochemical cycling including carbon cycling and sequestration, water quality, and biodiversity of forest ecosystems. Eleven sites have been re-established. A comparison of 1974 stand composition with data from 2000 stand composition indicate that significant changes in species composition have occurred at some sites with less change at other sites. Moist, high-pollution sites have experienced the greatest amount of forest change, while dryer low-pollution sites have experienced the least amount of stand change. In general, ponderosa pine had the lowest basal area increases and the highest mortality across the San Bernardino Mountains.
Mechanistic Approaches of PHE and PPF Columns for Separation of Rasberry Ketone and Caffeine (2015)

High-Performance Liquid Chromatography (HPLC) separation mechanisms of raspberry ketone and caffeine on phenyl columns (PhE and PPF) are described. The π–π interactions played major role in separation phenomenon. PhE column resulted into better separation than PPF due poor π–π interactions in later column. Fast, reproducible, selective, and effective HPLC method was developed for analyses of ketone and caffeine in pharmaceutical preparation. The columns used were Sunniest PhE (phenyl) (250 × 4.6 mm, 5.0 µm) and Sunshell PFP (100 × 4.6 mm, 2.6 µm) of Chromanik Japan. The mobile phase used was water–acetonitrile (60:40, v/v, at different pH values) at 1.0 mL/min flow rate. The detection was at 280 nm with 27 ± 1°C as working temperature. The ranges of capacity (k), separation (α), and resolution (Rs) factors at different pH values on both columns were 2.60–5.10, 1.32–1.60, and 3.22–4.28, respectively. The values of limit of detection (LOD) and limit of quantitation (LOQ) of raspberry ketone and caffeine on both columns ranged from 5.0 to 20.0 and 7.0 to 25.0, respectively. The developed mechanistic aspect is useful for designing separation strategies of other molecules on these phenyl columns. The reported method may be used for quality control in industries and government organizations. Besides, fast analyses may be carried out in various food products.
A Quantitative and Qualitative Assessment of Automatic Text Summarization Systems (2015)

Text summarization is the process of automatically creating a shorter version of one or more text documents. This paper presents a qualitative and quantitative assessment of the 22 state-of-the-art extractive summarization systems using the CNN corpus, a dataset of 3,000 news articles.
Ultra-low-power and high sensitivity resonant micromechanical receiver (2017)

This paper describes the proposed architecture and the analytical optimization of an ultra-low-power and high sensitivity Resonant Micromechanical Receiver (RMR) to be used in wake-up radios. The proposed radio frequency (RF) system is composed of three different stages: (1) a piezoelectric resonator that provides for passive voltage amplification, impedance matching, and high-Q filtering; (2) a MEMS resonant demodulator that acts as an efficient envelope detector of the modulated RF signal; and (3) a low power trans-impedance amplifier (TIA) that amplifies the output current of the demodulator and triggers a latch rectifier. All the RF components except for the CMOS are passive, which drastically reduce the power required to detect the RF signature. The CMOS components are constrained to operate with a maximum power consumption of 10 nW, approximately equivalent to the leakage rate of a battery. We analyze the performance of the proposed system for input frequencies ranging between 50 MHz and 400 MHz, and a modulation frequency (equal to the frequency of the MEMS demodulator) of 20-100 kHz. Our investigation shows that by using high performance acoustic resonators based on thin-films of lithium niobate [1] operating around 100 MHz in conjunction with narrow-gap MEMS demodulators [2], our proposed RMR can attain a sensitivity of at least -80 dBm for a 50% OOK signal and consume only 10 nW.
High-sensitivity interferometric schemes for ML2 micromirror calibrations (2006)

This paper presents an interferometric method with high sensitivity and good linearity for calibration of micromirror arrays used in maskless lithography. An analytic model based on electric-field perturbation is developed to quantify the influences of mirror configuration and defocus on calibration sensitivity. With the analytic model, two optimization strategies to achieve the highest sensitivity are developed. For a 5-by-5 sub-array with a pixel size of 0.5&#955;/NA, the sensitivity is improved from 0.0078 <i>I</i>/° when the surrounding pixels are not actuated, to 0.02286 <i>I</i>/° and 0.0347 <i>I</i>/° when the pixels are arranged in optimized schemes at defocus of 0.0RU and 1.5RU, respectively. The typical improvement is about 3X to 4X when the optimized calibration schemes are used.
Microwave-Assisted Concise Total Syntheses of Quinazolinobenzodiazepine Alkaloids (2005)

[reactions: see text] One-pot total syntheses of the quinazolinobenzodiazepine alkaloids sclerotigenin (1), (+/-)-circumdatin F (2), and (+/-)-asperlicin C (3) via novel microwave-assisted domino reactions were achieved in 55%, 32%, and 20% yields, respectively, from commercially available starting materials. A two-step total synthesis of (+/-)-benzomalvin A (4) was accomplished with an overall yield of 16%. Additionally, analogues of circumdatin E were synthesized via the three-component one-pot sequential reactions promoted by microwave irradiation. Finally, a two-step formal total synthesis of (+/-)-asperlicin E (5) was also realized by using this microwave-assisted protocol.
A theoretical analysis of feedback flow control (1990)

Congestion is a longstanding problem in datagram networks. One congestion avoidance technique is feedback flow control, in which sources adjust their transmission rate in response to congestion signals sent (implicitly or explicitly) by network gateways. The goal is to design flow control algorithms which provide time-scale invariant, fair, stable, and robust performance. In this paper we introduce a simple model of feedback flow control, in which sources make synchronous rate adjustments based on the congestion signals and other local information, and apply it to a network of Poisson sources and exponential servers. We investigate two different styles of feedback, aggregate and individual, and two different gateway service disciplines, FIFO and Fair Share. The purpose of this paper is to identify, in the context of our simple model, which flow control design choices allow us to achieve our performance goals . Aggregate feedback flow control, in which congestion signals reflect only the aggregate congestion at the gateways, can provide time-scale invariant and stable performance, but not fair or robust performance. The properties of individual feedback flow control, in which the congestion signals reflect the congestion caused by the individual source, depend on the service discipline used in the gateways. Individual feedback with FIFO gateways can provide time-scale invariant, fair, and stable performance, but not robust performance. Individual feedback with Fair Share gateways can achieve all four performance goals. Furthermore, its stability properties are superior to those of the other two design choices. By making robust and more stable performance possible, gateway service disciplines play a crucial role in realizing effective flow control .
Stably Transmitted Triple-Promoter Retroviral Vectors and Their Use in Transformation of Primary Mammalian Cells (1988)

Retroviral vectors were constructed which coexpressed three inserted genes from independent transcriptional promoters in singly infected cells. Several such triple-promoter vectors were constructed with various combinations of oncogenes and selectable drug resistance genes. All expressed three mRNAs of the expected size in infected cells. One vector expressing the v-Ha-ras, v-myc, and neo genes was characterized in detail. This retrovirus did not undergo rearrangement during the process of infection, as judged by Southern analysis, and infection of primary rat embryo fibroblasts demonstrated that ras-myc-cotransformed cells could be selected in G418. This demonstration that retroviral vectors can be used to express three cistrons independently increases their value as gene transfer vehicles, particularly for studies involving oncogene cooperation in primary cells.
P4C-4 In Vitro Investigation of Thrombosis Dissolution with Microbubble-Induced Continuous Acoustic Activities (2007)

The effectiveness of sustained cavitation in vitro in the presence of a lipid-encapsulated microbubble contrast agent has been investigated in order to maximize sonothrombolysis effect. Sustained cavitation is indicated by broadband scattered signals received continuously by a passive acoustic detector. Percent clot mass loss increased from 1.9% plusmn 3.0% (control) to 13.4% plusmn 4.0% with ultrasound alone. The loss is further increased to 19.5% plusmn 6.7% with the combination of the microbubbles and therapeutic ultrasound. The presence of sustained cavitation appears to play an important role in the enhancement of thrombolysis.
Synaptic Integration Mediated by Striatal Cholinergic Interneurons in Basal Ganglia Function (2000)

The physiological role of striatal cholinergic interneurons was investigated with immunotoxin-mediated cell targeting (IMCT). Unilateral cholinergic cell ablation caused an acute abnormal turning behavior. These mice showed gradual recovery but displayed abnormal turning by both excess stimulation and inhibition of dopamine actions. In the acute phase, basal ganglia function was shifted to a hyperactive state by stimulation and suppression of striatonigral and striatopallidal neurons, respectively. D1 and D2 dopamine receptors were then down-regulated, relieving dopamine-predominant synaptic perturbation but leaving a defect in controlling dopamine responses. The acetylcholine-dopamine interaction is concertedly and adaptively regulated for basal ganglia synaptic integration.
Identity-Based Linkable Ring Signatures From Lattices (2021)

Linkable ring signatures is a useful cryptographic tool for constructing applications such as ones relative to electronic voting (e-voting), digital cashes (e-cashes) as well as cloud computing. Equipped with linkable ring signatures, e-voting, e-cash systems can simultaneously enjoy the privacy and the unreusability properties thanks to the anonymity and the linkability of linkable ring signatures. Likewise, cloud servers can enjoy a privacy-preserving ability, a flexible access control and an efficient security management with linkable ring signatures. Moreover, linkable ring signatures built in the identity-based setting would help to remove the expense of using the conventional public key infrastructure and also could be applied to the user management. This primitive hence would be suitable for huge-scale applications. In this paper, we present the first identity-based linkable ring signatures (IdLRS) in both integer lattice and ideal lattice setting. The proposed IdLRS is proved secure in the random oracle model and based on the hardness of the short integer solution and ring short integer solution assumption. We also implement the proposed idLRS as a proof of concept and then do some experiments to evaluate the running times and the sizes.
Delayed vaginal SHIV infection in VRC01 and anti-α4β7 treated rhesus macaques (2019)

VRC01 protects macaques from vaginal SHIV infection after a single high-dose challenge. Infusion of a simianized anti-α4β7 mAb (Rh-α4β7) just prior to, and during repeated vaginal exposures to SIVmac251 partially protected macaques from vaginal SIV infection and rescued CD4+ T cells. To investigate the impact of combining VRC01 and Rh-α4β7 on SHIV infection, 3 groups of macaques were treated with a suboptimal dosing of VRC01 alone or in combination with Rh-α4β7 or with control antibodies prior to the initiation of weekly vaginal exposures to a high dose (1000 TCID50) of SHIVAD8-EO. The combination Rh-α4β7-VRC01 significantly delayed SHIVAD8-EO vaginal infection. Following infection, VRC01-Rh-α4β7-treated macaques maintained higher CD4+ T cell counts and exhibited lower rectal SIV-DNA loads compared to controls. Interestingly, VRC01-Rh-α4β7-treated macaques had fewer IL-17-producing cells in the blood and the gut during the acute phase of infection. Moreover, higher T cell responses to the V2-loop of the SHIVAD8-EO envelope in the VRC01-Rh-α4β7 group inversely correlated with set point viremia. The combination of suboptimal amounts of VRC01 and Rh-α4β7 delayed infection, altered antiviral immune responses and minimized CD4+ T cell loss. Further exploration of the effect of combining bNAbs with Rh-α4β7 on SIV/HIV infection and antiviral immune responses is warranted and may lead to novel preventive and therapeutic strategies.
Investigation of defects and striations in as-grown Si crystals by SEM using Schottky diodes (1975)

As-grown silicon crystals are investigated in the scanning electron microscope using Schottky barrier diodes in the electron-beam-induced current mode. Dislocations, A- and B-type swirl defects, as well as dopant striations are detected. In high-resistivity crystals (∼1000 Ω cm) variations in dopant concentration of 1012 cm−3 are readily revealed. Hydrogen doping is found to eliminate preferential recombination at microdefects. It is established that bulk stresses due to carbon striations have no detectable electrical effect.
Study of SF6/N2O Microwave Plasma for Surface Texturing of Multicrystalline (<150 µm) Solar Substrates (2012)

Surface texturing is an imperative process to reduce the reflection of the incident light on solar cells, by enhancing sunlight diffusion into the silicon solar cells for photon generation. As a result, the current generation can be increased. In this study, the plasma texturing process with linear microwave plasma sources has been benchmarked with the industrial acidic iso-texturing process on 156×156 mm2 multicrystalline substrates. By optimizing the plasma texturing parameters, the absolute solar cells efficiency can be increased by 4.9% for 150 µm thickness silicon substrate. The proposed process offers a significant advantage over the standard acidic iso-texturing without major modification in the existing industrial solar cells manufacturing sequence. In order to explain plasma-induced surface morphology changes, the Kardar–Parisi–Zhang (KPZ), Pétri–Brault, and Jason–Drotar models are used.
Statistical image recovery: A message-passing perspective (2015)

Abstract—We review MAP and MMSE-based approaches to image recovery and their implementation via generalized approximate message-passing (GAMP), highlighting recent results on GAMP convergence for general measurement operators. We consider the recovery of image x ∈ CN from noisy outputs y ∈ CM of known linear measurement operator Φ ∈ CM×N. The “statistical ” approach to image recovery models the image x as a realization of random x ∼ px and the measurements as a realization of random y whose statistics are governed by a likelihood function of the form py|z(y|Φx̂). Here, py|z is the pdf of y conditioned on the (hidden) transform outputs z = Φx and x ̂ is a hypothesis of the image. For clarity, we denote random quantities in san-serif font. In the maximum a posteriori (MAP) approach to statistical image recovery, one computes the most probable estimate of x given y, i.e., x̂MAP = argmaxx ̂ px|y(x̂|y) = argmaxx ̂ py|x(y|x̂)px(x̂)/py(y) = argmin x̂ − log py|z(y|Φx̂) − log px(x̂)
<title>Fuzzified genetic algorithm with prefiltering for adaptive optimization</title> (1997)

Genetic algorithm performance has been improved by adaptively modifying genetic operators, and by filtering out recurring chromosomes from the fitness evaluation process. The enhanced genetic algorithm has been applied to neural network topology selection and function optimization. The performance of the algorithm was evaluated in multiple function and problem domains, where it showed superior convergence speed.
Quenched phases in strongly coupled laser cavities (2017)

Strongly coupled dissipative optical cavities with nonlinear interactions give new opportunities to explore symmetry breaking phenomena and phase transitions, Josephson dynamics and quantum criticality. Among the different experimental realizations, photonic crystal coupled nanocavities operating in the laser regime are outstanding systems since nonlinearity, gain/dissipation and intercavity coupling can be judiciously tailored. Complex photon statistics is inherent to the nature of nanolasers due to the presence of strong spontaneous emission noise. Yet, although most common scenarios emerge from quasi-dynamical equilibrium where the gain nearly compensates for losses, little is known about far out-of-equilibrium statistics resulting, for instance, from short pulsed pumping. Here we show that bimodal nanolasers under pulsed pump generically display quenched phases which, when projected onto the nonlasing mode, exhibit superthermal light. Such a mechanism is akin to the fast cooling of a suspension of Brownian particles under gravity, with the intracavity intensity playing the role of the inverse temperature. We implement a simple experimental technique to access the probability density functions, that enabled quantifying the distance from thermal equilibrium --and hence the degree of residual order-- via the Gibbs entropy. This allowed us to further detect mixing of thermal states with coherent broken parity phases, thus paving the road for investigating far nonequilibrium thermodynamics with semi-classical multimode optical oscillators.
Experimental Test of Bell’s Inequality for Temporal Orders (2018)

Bell’s inequality has been violated using different physical systems, but never for the temporal order between events. Here we present such a Bell inequality and experimentally violate it by entangling the temporal order between events.
Correction: An indenocarbazole-based host material for solution processable green phosphorescent organic light emitting diodes (2021)

[This corrects the article DOI: 10.1039/D1RA04855D.].
Design and evaluation of a hybrid passive/active ripple filter with voltage injection (2003)

Active ripple filters can substantially attenuate power converter ripple, allowing considerable reduction in passive filter component size. Investigated here is a hybrid passive/active filter topology that achieves ripple reduction by injecting a compensating voltage ripple across a series filter element. Both ripple feedforward and feedback are employed. The design of sensor, amplifier, and injector circuitry for this application is explored. The experimental results demonstrate the feasibility and high performance of the new approach, and illustrate its potential benefits. It is demonstrated that the proposed approach is most effective in cases where it is desirable to minimize the amount of capacitance in the filter.