gebhart/patrepeval huggingface dataset:
The Influence of the Proliferating Cell Nuclear Antigen-interacting Domain of p21 on DNA Synthesis Catalyzed by the Human and Saccharomyces cerevisiae Polymerase δ Holoenzymes (1997)

In eukaryotes, processive DNA synthesis catalyzed by DNA polymerases delta and epsilon (pol delta and epsilon) requires the proliferating cell nuclear antigen (PCNA). It has recently been shown that in humans (h), the PCNA function, required for both DNA replication and nucleotide excision repair, can be inactivated by p21(CIP1) due to a specific interaction between hPCNA and the carboxyl terminus of p21(CIP1). In this report, we show that Saccharomyces cerevisiae (S. cerevisiae) PCNA-dependent pol delta-catalyzed DNA synthesis was inhibited less efficiently than the human system by the intact p21(CIP1) protein and was unaffected by the p21(CIP1) carboxyl-terminal peptide (codons 139-160). This species-specific response of PCNA to p21(CIP1)-mediated inhibition of DNA synthesis results from a marked difference in the ability of h and S. cerevisiae PCNA to interact with p21(CIP1). As shown by binding studies using the surface plasmon resonance technique, hPCNA binds both full-length p21(CIP1) and the p21(CIP1) peptide-(139-160) stoichiometrically with a similar affinity (KD approximately 2.5 nM) while S. cerevisiae PCNA binds p21(CIP1) with approximately 10-fold less affinity and does not interact with the p21(CIP1) peptide-(139-160).
High-Sensitivity X-ray Polarimetry with Amorphous Silicon Active-Matrix Pixel Proportional Counters (2003)

Photoelectric X-ray polarimeters based on pixel micropattern gas detectors (MPGDs) offer order-of-magnitude improvement in sensitivity over more traditional techniques based on X-ray scattering. This new technique places some of the most interesting astronomical observations within reach of even a small, dedicated mission. The most sensitive instrument would be a photoelectric polarimeter at the focus of 2 a very large mirror, such as the planned XEUS. Our efforts are focused on a smaller pathfinder mission, which would achieve its greatest sensitivity with large-area, low-background, collimated polarimeters. We have recently demonstrated a MPGD polarimeter using amorphous silicon thin-film transistor (TFT) readout suitable for the focal plane of an X-ray telescope. All the technologies used in the demonstration polarimeter are scalable to the areas required for a high-sensitivity collimated polarimeter. Leywords: X-ray polarimetry, particle tracking, proportional counter, GEM, pixel readout
Foundational and applied research in access control (2004)

We discuss components of our works in access control here at CERIAS. Our work includes the following:

- A theory for gauging the expressive power of an access control model, and the use of that theory to compare the expressive power of different models,

- Analysis of safety, availability and mutual exclusion properties of access control models, specifically, the hierarchical role based access control model,

- Administrative models for hierarchical role based access control that satisfy both pragmatic and formal requirements. The administrative model we are building scales well with large numbers of users and roles, supports complex role hierarchies and lends itself to automation. It has favorable complexity properties in deciding safety, availability and mutual exclusion, and,

- The relationship of hierarchical role based access control to other models, such as the HRU model (DAC) and Trust Management languages.
On the origin of the 265 nm absorption band in AlN bulk crystals (2012)

Single crystal AlN provides a native substrate for Al-rich AlGaN that is needed for the development of efficient deep ultraviolet light emitting and laser diodes. An absorption band centered around 4.7 eV (∼265 nm) with an absorption coefficient above 1000 cm−1 is observed in these substrates. Based on density functional theory calculations, substitutional carbon on the nitrogen site introduces absorption at this energy. A series of single crystalline wafers were used to demonstrate that this absorption band linearly increased with carbon, strongly supporting the model that CN- is the predominant state for carbon in AlN.
BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure (2017)

Despite current standard of care, the average 5-year mortality after an initial diagnosis of heart failure (HF) is about 40%, reflecting an urgent need for new therapeutic approaches. Previous studies demonstrated that the epigenetic reader protein bromodomain-containing protein 4 (BRD4), an emerging therapeutic target in cancer, functions as a critical coactivator of pathologic gene transactivation during cardiomyocyte hypertrophy. However, the therapeutic relevance of these findings to human disease remained unknown. We demonstrate that treatment with the BET bromodomain inhibitor JQ1 has therapeutic effects during severe, preestablished HF from prolonged pressure overload, as well as after a massive anterior myocardial infarction in mice. Furthermore, JQ1 potently blocks agonist-induced hypertrophy in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). Integrated transcriptomic analyses across animal models and human iPSC-CMs reveal that BET inhibition preferentially blocks transactivation of a common pathologic gene regulatory program that is robustly enriched for NFκB and TGF-β signaling networks, typified by innate inflammatory and profibrotic myocardial genes. As predicted by these specific transcriptional mechanisms, we found that JQ1 does not suppress physiological cardiac hypertrophy in a mouse swimming model. These findings establish that pharmacologically targeting innate inflammatory and profibrotic myocardial signaling networks at the level of chromatin is effective in animal models and human cardiomyocytes, providing the critical rationale for further development of BET inhibitors and other epigenomic medicines for HF.
Soy protein isolate with isoflavones does not prevent estradiol-induced endometrial hyperplasia in postmenopausal women: a pilot trial (2003)

In this pilot study, SPI with isoflavones did not protect the endometrium from E2-induced hyperplasia in postmenopausal women. If higher, long-term doses of isoflavone supplementation are found to be safe for postmenopausal women, then future studies combining E2 with isoflavones may be feasible as an alternative to traditional hormone replacement therapy.
Partition-based path loss analysis for in-home and residential areas at 5.85 GHz (2002)

This paper presents a novel technique for organizing narrowband radio path loss measurements and finding optimal partition-based prediction models. The techniques may be applied to wireless system site planning for indoor, small-cell outdoor, and hybrid indoor-outdoor environments at any frequency. Specifically, this paper develops path loss models using 5.85 GHz continuous-wave (CW) measurements made in and around homes and trees; the resulting models demonstrate how site-specific information will improve path loss prediction. The results are particularly appropriate for site planning in the 5-6 GHz frequency regime for emerging wireless consumer devices that operate in the National Information Infrastructure (in the US) and HIPERLAN (in Europe) bands.
Mice ultrasonic detection and localization in laboratory environment (2016)

The acoustic detection and localization of mice movement by monitoring their ultrasonic vocalization has been demonstrated in laboratory environment using ultrasonic system with three microphones that provides recording of ultrasound up to 120 kHz. The tests were approved by Stony Brook University Institutional Animal Care and Use Committee protocol. Signals were recorded in a set of discrete sequences over several hours. The locomotor activity was characterized by durations up to 3000 ms and wide spectral content, while the syllable vocalization constituted shorter 200 ms events, with a set of identifiable up and down frequency modulated tones between 3 kHz and 55 kHz. The Time Difference of Arrival (TDOA) to various microphones was calculated using cross correlation method and was applied for estimation for mice location. Mice are among the invasive species that have a potential of crossing borders of USA unnoticed in containers. This study demonstrates the feasibility of using acoustic methods for detection of potential rodent intrusions. This work was sponsored by DHS S&T.
Diastereoselective Synthesis of cycloSaligenyl‐Nucleosyl‐Phosphotriesters (2010)

A diastereoselective synthesis of cycloSal-phosphotriesters (cycloSal=cycloSaligenyl) based on chiral auxiliaries has been developed that allows the synthesis of single diastereomers of the cycloSal-pronucleotides. In previously described synthesis routes, the cycloSal-compounds were always obtained as 1:1 diastereomeric mixtures that could be separated in only rare cases. However, it was shown that the diastereomers have different antiviral activity, toxicity, and hydrolysis stabilities. Here, first a chiral thiazoline derivative was used to prepare nonsubstituted and 5-methyl-cycloSal-phosphotriesters in 48 and ≥95% de (de=diastereomeric excess). However, this approach failed to give the important group of 3-substituted cycloSal-nucleotides. Therefore, two other chiral groups were discovered that allowed the synthesis of (R(P))- and (S(P))-3-methyl-cycloSal-phosphotriesters as well. The antiviral activity was found to be five- to 20-fold different between the two individual diastereomers, which proved the importance of this approach.
Carbon nanotubes plastic actuator: Towards lightweight, low-voltage haptic devices (2014)

There is a lack of safe, lightweight, low-voltage actuators that can be used in haptic applications. One of the possible solutions is ionic electroactive polymer actuator - the only one among electroactive polymers that can be operated at low voltage in air. In this paper we present the carbon nanotubes based plastic actuators that we are currently developing as tactors in haptic devices and we will discuss their performance. We show how the use of different types of single-walled carbon nanotubes lead to produce plastic carbon nanotube/ionic liquid based actuators (bucky gel actuators) with different performance. Achieved force for both kinds of non-optimized actuators was two times higher than perceptive capabilities of the human finger. In addition, force-displacement modeling was done in order to rationalize the differences in actuation behavior and to provide design tools to optimize the geometry as a function of the specific requirements.
Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae (2016)

Enhancing xylose utilization has been a major focus in Saccharomyces cerevisiae strain-engineering efforts. The incentive for these studies arises from the need to use all sugars in the typical carbon mixtures that comprise standard renewable plant-biomass-based carbon sources. While major advances have been made in developing utilization pathways, the efficient import of five carbon sugars into the cell remains an important bottleneck in this endeavor. Here we use an engineered S. cerevisiae BY4742 strain, containing an established heterologous xylose utilization pathway, and imposed a laboratory evolution regime with xylose as the sole carbon source. We obtained several evolved strains with improved growth phenotypes and evaluated the best candidate using genome resequencing. We observed remarkably few single nucleotide polymorphisms in the evolved strain, among which we confirmed a single amino acid change in the hexose transporter HXT7 coding sequence to be responsible for the evolved phenotype. The mutant HXT7(F79S) shows improved xylose uptake rates (Vmax = 186.4 ± 20.1 nmol•min(-1)•mg(-1)) that allows the S. cerevisiae strain to show significant growth with xylose as the sole carbon source, as well as partial co-utilization of glucose and xylose in a mixed sugar cultivation.
Method for noncontact measurement of 2DEG mobility and carrier density in AlGaN/GaN on semi-insulating wafers (2021)

Abstract We present a charge-assisted sheet resistance technique for noncontact wafer level determination of two-dimensional electron gas (2DEG) mobility versus sheet carrier density without any test structures or gates. Instead, the electrical biasing of the 2DEG is provided by surface charge deposition, using a corona charging method. Analysis of the sheet resistance versus deposited charge identifies the 2DEG full depletion condition and enables calculation of the 2DEG sheet carrier density required for the mobility. Results for AlGaN/GaN heterostructures on semi-insulating SiC and sapphire substrates show good agreement with Hall results at a zero-bias condition.
An Experimental Investigation of the Bayesian Passive Multi-Target Localization Algorithm (2018)

Passive localization using the time-of-arrival of a wideband signal has the potential to achieve high accuracy at a much smaller cost than active localization solutions, which makes it promising for a variety of applications. However, a major challenge in passive localization involves localizing multiple targets that have the same radar signature, where it is difficult to distinguish between reflections from different targets. This difficulty is compounded if there are an unknown number of targets along with multipath propagation and the possible (statistically dependent) blocking of the direct paths (going from the transmitter and reflecting off a target to the receiver). In this scenario, identifying the direct paths corresponding to each target (known as data association) is non-trivial. In an earlier work, some of the authors investigated this problem using a Bayesian estimation framework, where dependent blocking was modeled as a prior, and proposed the \emph{Bayesian multi-target localization algorithm} as a solution. In this work, we analyze the performance of this algorithm using experimental data, obtained from a commercially available localization testbed. In comparison with the cases where blocking is either completely ignored or assumed to be mutually independent across paths, our results show that for a fixed probability of false-alarm, the detection probability is highest when dependent blocking is taken into account.
Challenges in computer architecture evaluation (2003)

We focus on problems suited to the current evaluation infrastructure. The current limitation and trends in evaluation techniques are troublesome and could noticeably slow the rate of computer system innovation. New research has been recommended to help and make quantitative evaluations of computer systems manageable. We support research in the areas of simulation frameworks, benchmarking methodologies, analytic methods, and validation techniques.
An investigation on the effect of ultra-precision machined patterns in wetting transition (2011)

This paper aims to study the influence of micro patterns on the wetting transition of a hydrophilic material. Surfaces with a designed pattern with various groove widths are machined by ultra-precision raster milling. The impact of different groove widths of the machined patterns on wetting transition will be discussed by studying the spreading of droplets on respective patterns. Contact angle and elongation length were measured using a contact angle goniometer. The present work revealed that machined surfaces on a hydrophilic material with micro patterns can achieve composite solid-liquid-air interfaces when the scales of the machined pattern fall into a critical range. The results from the experiments can provide useful information for designing self-cleaning surfaces.
The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2 (2010)

Gene transcription is controlled by transcriptional regulators acting with specific co-regulators to allow gene activation and repression. Here, we report the identification of the KRAB-containing zinc-finger transcriptional regulator, ZBRK1, as an interaction partner of the SCA2 gene product ataxin-2. Furthermore, we discovered that an elevated ZBRK1 level resulted in increased ataxin-2 levels, whereas interference on transcriptional and protein levels of ZBRK1 yielded reduced ataxin-2 levels, suggesting that a complex comprising ZBRK1 and ataxin-2 regulates SCA2 gene transcription. A bioinformatic analysis utilizing the known ZBRK1 consensus DNA-binding motif revealed ZBRK1-binding sites in the SCA2 promoter. These predicted sites were experimentally validated by chromatin-immunoprecipitation experiments along with luciferase-based promoter analyses corroborating that SCA2 gene transcription is controlled by a ZBRK1/ataxin-2 complex. Finally, we demonstrate that SCA2 gene transcription is significantly reduced in colon tumors possessing low ZBRK1 transcripts. Thus, our results provide first evidence that ataxin-2 acts as a co-regulator of ZBRK1 activating its own transcription, thereby representing the first identified ZBRK1 co-activator.
Human hepatocellular carcinoma cell lines exhibit multidrug resistance unrelated to Mdr1 gene expression (1991)

Multidrug resistance of human cancer cells may result from expression of P-glycoprotein, the product of the MRD1 gene, acting as an energy-dependent drug efflux pump. However, direct evidence that expression of the MDR1 gene contributes to the multidrug resistance of human liver carcinomas has not been established. In this study, we tested five cell lines derived from human hepatocellular carcinomas for sensitivity to a variety of drugs used widely as anticancer agents; these included vinblastine, doxorubicin, actinomycin D, mitomycin C, 5-fluorouracil, 6-mercaptopurine, melphalan, methotrexate, cis-platinum and etoposide (VP-16). All five hepatoma cell lines were resistant at different levels to these chemicals compared to human KB cells. Although it has been demonstrated that resistance to vinblastine, colchicine, doxorubicin and actinomycin D in human multidrug-resistant cells is associated with overexpression of P-glycoprotein, very little expression of P-glycoprotein was found in these human hepatoma cells. Neither verapamil nor quinidine, inhibitors of the drug efflux pump, were able to overcome multidrug resistance in hepatoma cells. These results indicate that the multidrug resistance phenotype in human hepatocellular carcinoma cells cannot be attributed to expression of the MDR1 gene, but that novel mechanisms may account for the resistance of these cancer cells.
Studies of Chain Conformation in Triblock Oligomers and Microblock Copolymers of Ethylene and Ethylene Oxide (2002)

The conformation of ethylene oxide segments has been found to vary when they are incorporated into triblock oligomers [H(CH2)m(CH2CH2O)n(CH2)mH] or microblock copolymers [−(CH2)m(CH2CH2O)n−]x of ethylene (E) and ethylene oxide (EO) depending on the relative length (m vs n) of the sequences. Raman spectroscopy, wide-angle X-ray diffraction, and thermal analysis have been used to investigate these conformational variations. Since both segments crystallize, we have found a profound influence of intermolecular interactions on determining the conformation of the EO segment. In the regime where n < 7 (m = 12−20), the EO segment is found in the planar zigzag conformation similar to that observed in oriented poly(ethylene oxide) (PEO) held under tension. When n > 7 (m = 12−20), the EO segments are found to crystallize in the 7/2 helical conformation similar to that found in PEO. In the case where n = 7 (m = 12−20), both the helical and planar zigzag forms of EO are found depending on the thermal and solution processing history. The helical form can be induced by melt-quenching, but annealing at room temperature for several days produces a gradual return to the planar conformation. A conformational transition caused by solvents also occurs and will be discussed.
An Atypical CNG Channel Activated by a Single cGMP Molecule Controls Sperm Chemotaxis (2009)

Sperm of the sea urchin Arbacia punctulata can respond to a single molecule of chemoattractant released by an egg. The mechanism underlying this extreme sensitivity is unknown. Crucial signaling events in the response of A. punctulata sperm to chemoattractant include the rapid synthesis of the intracellular messenger guanosine 3',5'-monophosphate (cGMP) and the ensuing membrane hyperpolarization that results from the opening of potassium-selective cyclic nucleotide-gated (CNGK) channels. Here, we use calibrated photolysis of caged cGMP to show that approximately 45 cGMP molecules are generated during the response to a single molecule of chemoattractant. The CNGK channel can respond to such small cGMP changes because it is exquisitely sensitive to cGMP and activated in a noncooperative fashion. Like voltage-activated Ca(v) and Na(v) channels, the CNGK polypeptide consists of four homologous repeat sequences. Disabling each of the four cyclic nucleotide-binding sites through mutagenesis revealed that binding of a single cGMP molecule to repeat 3 is necessary and sufficient to activate the CNGK channel. Thus, CNGK has developed a mechanism of activation that is different from the activation of other CNG channels, which requires the cooperative binding of several ligands and operates in the micromolar rather than the nanomolar range.
User engagement in the digital world (2012)

In the online world, user engagement refers to the quality of the user experience that emphasizes the positive aspects of the interaction with a web application and, in particular, the phenomena associated with wanting to use that application longer and frequently. This definition is motivated by the observation that successful web applications are not just used, but they are engaged with. Users invest time, attention, and emotion into them. User engagement is measured in many ways, through methods of self-reporting (e.g., questionnaires), observer methods (e.g., facial expression analysis, speech analysis, desktop actions, etc.), neuro-physiological signal processing methods (e.g., respiratory and cardiovascular accelerations and decelerations, muscle spasms, etc.), and from a web analytics perspective (through online behavior metrics that assess users' depth of engagement with a site). These methods represent various tradeoffs between scale of data and depth of understanding (for instance, surveys are small-scale but deep, whereas clicks are large-scale but shallow in understanding). Little work has been done to integrate these various measures into a coherent understanding of engagement success. We address this problem by combining techniques from web analytics and mining, information retrieval evaluation, and existing works on user engagement coming from the domains of information science, multimodal human computer interaction and cognitive psychology. In this way, we can combine insights from big data with deep analysis of human behavior in the lab or through crowd-sourcing experiment. This research comprises three "inter-woven" parts: (1) Definition of user engagement and its many characteristics. (2) Data-driven approaches looking at user engagement through the development of models that allow for a better representation of how users engage within and across different digital services. (3) How studying affect and cognition is providing additional insights into measuring user engagement.
Three-Dimensional Printed Biopatches With Conductive Ink Facilitate Cardiac Conduction When Applied to Disrupted Myocardium (2019)

We have demonstrated 3-dimensional custom-printed electrically conductive carbon nanotube patches can be surgically manipulated to improve cardiac conduction when passively applied to surgically disrupted epicardial myocardium in canines.