gebhart/patrepeval huggingface dataset:
COGNITION, MECHANISM, AND EVOLUTIONARY RELATIONSHIPS IN AMINOACYL-tRNA SYNTHETASES (1993)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
<i>N</i> -Acetylcysteine and Contrast-Induced Nephropathy in Primary Angioplasty (2006)

Intravenous and oral N-acetylcysteine may prevent contrast-medium-induced nephropathy with a dose-dependent effect in patients treated with primary angioplasty and may improve hospital outcome. (ClinicalTrials.gov number, NCT00237614[ClinicalTrials.gov]).
Cholesteryl ester transfer protein inhibitor (JTT-705) and the development of atherosclerosis in rabbits with severe hypercholesterolaemia (2002)

Cholesteryl ester transfer protein (CETP) is a major determinant of plasma levels of high-density lipoprotein-cholesterol (HDL-C) in humans. The anti-atherogenic effect of lowering CETP levels is dependent not only on HDL-C levels but also on a metabolic background of increased low-density lipoprotein or very-low-density lipoprotein. Here we investigated the effects of JTT-705, a chemical inhibitor of CETP, on the development of atherosclerosis in Japanese white rabbits fed on a high cholesterol diet. After 4 weeks on a diet of 0.25% cholesterol-containing chow, 100 mg/kg (low dose) or 300 mg/kg (high dose) JTT-705 was given, and the animals were monitored at weeks 0, 4, 8 and 12. Aortic atherosclerotic lesions were determined at the end of this period. JTT-705 induced a significant increase in HDL-C in the high-dose group [from 21+/-3 to 50+/-7 mg/dl (mean+/-S.E.M.); P <0.0001] compared with the control group (from 21+/-2 to 27+/-2 mg/dl). The atheromatous area was 60+/-9% in the high-dose group and 58+/-9% in the control group. Moreover, correlation analysis showed that triacylglycerol and non-HDL-C levels had a direct relationship with the development of atherosclerosis, but CETP activity and HDL-C levels did not. Thus the CETP inhibitor JTT-705 alone did not have an anti-atherogenic effect in our rabbit model, of severe hypercholesterolaemia suggesting a relatively minor effect of HDL-elevating therapy as compared with decreases in non-HDL-C (or triacylglycerol) levels in patients with severe hypercholesterolaemia, such as familial hypercholesterolaemia.
Progestin Inhibition of Progesterone Receptor Gene Expression in Human these steroids is determined in part by the cellular Breast Cancer Cells (1989)

The present study was designed to investigate whether inhibition of progesterone receptor (PR) gene transcription and/or regulation of PR mRNA half-life were involved in the progestin-mediated decrease of PR in T-47D human breast cancer cells. Cells were treated with the progestin ORG 2058 and PR mRNA measured by Northern blot analysis of total RNA. A major PR mRNA around 13.5 kilobases and minor species around the 28S ribosomal RNA subunit were decreased upon ORG 2058 treatment. The decrease was not detectable until 2-3 h after treatment and was the same at all ORG 2058 concentrations (1-100 nM) tested. The decrease in PR mRNA was unaffected by actinomycin D in the first 3 h but was inhibited thereafter. There was a partial recovery of PR mRNA levels 24 h after ORG 2058 exposure. Immunoblot analysis showed that immunoreactive PR decreased in parallel with PR mRNA. The rate of protein loss in the first 12 h after progestin treatment was related to the ORG 2058 concentration used. Nuclear run-on experiments showed that ORG 2058 caused a decrease of up to 70% in the transcription rate of the PR gene. The half-life of PR mRNA was shown to be 2-2.5 h by [3H]uridine incorporation, which was much shorter than estimates obtained using actinomycin D, and was unaffected by ORG 2058. In summary, these data have shown that the mechanism by which progestins decrease the concentration of PR includes inhibition of transcription of the PR gene.
<title>Optimization of the optical phase shift in attenuated phase-shifting masks and application to quarter-micrometer deep-UV lithography for logics</title> (1994)

New developments in the field of embedded shifter materials look very promising for defect free phase shifting mask (PSM) manufacturing. Nevertheless, a good control of the shifter parameters (phase shift and absorber transmittance) remains of utmost importance. In this paper, a lithography sensitivity analysis to shifter deviations has been carried out. It was found that dark field masks require different tolerances than light fields. Because of a growing need for an accurate measurement method of the phase shift, an optical technique, based on measurement of the zero diffraction order of diffraction gratings, is investigated. Using this technique, an attenuated PSM manufacturing process has been optimized for deep-UV, in order to demonstrate the possibilities of quarter micron PSM lithography. As a result, 0.3 micrometers contact windows could be printed with sufficient process latitudes. Using modified illumination techniques in combination with the attenuated PSM, considerable gain in process latitudes was found for quarter micron gates as well, although proximity effects are still a concern.
Hybrid Hardware-Software Architecture for Reconfigurable Real-Time Systems (2008)

Recent developments in the field of reconfigurable SoC devices (FPGAs) will enable the development of embedded systems where software tasks, running on a CPU, can coexist with hardware tasks. We devised a real-time computing architecture that can integrate hardware and software executions in a transparent manner, and can support real-time QoS adaptation by means of partial reconfiguration of modern FPGA devices. Tasks are allowed to migrate seamlessly from CPU to FPGA and vice versa to support dynamic QoS adaptation and cope with dynamic workloads. In this paper, we discuss the design and implementation of an on-chip infrastructure, OS extensions and task design methodology that enable hardware-software transparency in the presence of relocation. The overall architecture is suitable to schedule real-time workloads and we derive bounds on relocation overhead. Finally, we show the applicability of our design methodology on a concrete task design case.
Min-Cost Selfish Multicast With Network Coding (2006)

The single-source min-cost multicast problem, which can be framed as a convex optimization problem with the use of network codes and convex increasing edge costs is considered. A decentralized approach to this problem is presented by Lun, Ratnakar for the case where all users cooperate to reach the global minimum. Further, the cost for the scenario where each of the multicast receivers greedily routes its flows is analyzed and the existence of a Nash equilibrium is proved. An allocation rule by which edge cost at each edge is allocated to flows through that edge is presented. We prove that under our pricing rule, the flow cost at user equilibrium is the same as the min-cost. This leads to the construction of a selfish flow-steering algorithm for each receiver, which is also globally optimal. Further, the algorithm is extended for completely distributed flow adaptation at nodes in the network to achieve globally minimal cost in steady state. Analogous results are also presented for the case of multiple multicast sessions
Cell Identification Scheme for OFDM Cellular Systems Based on a New Preamble Structure (2006)

A cell identification scheme for OFDM cellular systems is proposed, which uses only one OFDM symbol with several identical slots as preamble. After performing OFDM timing/frequency synchronization, the UE identifies its cell ID by a novel scheme composed of cell group identification and cell index identification. Each cell group is distinguished from others by a unique subcarrier mask, which is an m-sequence. It activates or deactivates a subset of the subcarriers. Furthermore, cells with different indices in the same cell group load different differentially coded sequences on the adjacent active subcarriers. The UE recognizes the cell-group-specific mask via power detection of the received frequency domain signal. Then it identifies the cell index from differential demodulation and detection of the cell-index-specific sequence. Simulation results show that the proposed scheme is able to support a very large number of cell IDs and it works well even in bad multi-cell environment
Low temperature pulsed etching of large glass substrates (2003)

Glass plates of 20 cm diameter have been etched by SF6 in a pulsed capacitively coupled 13.56 MHz discharge. The plates were mechanically clamped to the cooled substrate holder and allowed to heat due to ion bombardment. The average rf power was set at 220 W and the pulse frequency varied up to 200 kHz for duty cycles between 10% and 100%. For a pressure of 50 mTorr, pulse frequencies around 100 kHz and duty cycles below 30%, the etch rate was about double that of the continuous case and the glass plate temperature was between 90 and 100 °C about 30° below the continuous case. These results show that large plates of glass can be etched rapidly at 0.16 μm per minute at temperatures below the cross linking temperature of a photoresist mask.
On the high-speed VLSI implementation of errors-and-erasures correcting reed-solomon decoders (2002)

Recently a novel algorithm transformation was proposed to reduce the critical path of Berlekamp-Massey algorithm implementation for errors-alone Reed-Solomon decoding. In this paper, we apply the same methodology to transform the Berlekamp-Massey algorithm for errors-and-erasures RS decoding. We present a regular hardware architecture to implement the reformulated Berlekamp-Massey algorithm, which can achieve high throughput. Moreover, an operation scheduling scheme is proposed to further reduce the hardware complexity without loss of throughput.
Gen3 embedded cooling for high power RF components (2017)

Near-junction thermal barriers severely limit the inherent capability of high-quality wide bandgap materials and architectures and necessitate the development of an alternative, Gen3, thermal management paradigm to reach the goals of future high-power RF applications. Recent Gen3 “embedded cooling” efforts in the aerospace industry have focused on reduction of this near-junction thermal resistance, through the use of diamond substrates and efficient removal of the dissipated power with on-chip convective and jet impingement microfluidics. The options, challenges, and techniques associated with the development of embedded thermal management technology are described, with emphasis on the accomplishments and status of efforts related to GaN power amplifiers.
Estimation of operational risk capital charge under parameter uncertainty (2008)

Many banks adopt the loss distribution approach to quantify the operational risk capital charge under Basel II requirements. It is common practice to estimate the capital charge using the 0.999 quantile of the annual loss distribution, calculated using point estimators of the frequency and severity distribution parameters. The uncertainty of the parameter estimates is typically ignored. One of the unpleasant consequences for the banks accounting for parameter uncertainty is an increase in the capital requirement. This paper demonstrates how the parameter uncertainty can be taken into account using a Bayesian framework that also allows for incorporation of expert opinions and external data into the estimation procedure.
A novel genetic engineering platform for the effective management of biological contaminants for the production of microalgae (2016)

Microalgal cultivation that takes advantage of solar energy is one of the most cost-effective systems for the biotechnological production of biofuels, and a range of high value products, including pharmaceuticals, fertilizers and feed. However, one of the main constraints for the cultivation of microalgae is the potential contamination with biological pollutants, such as bacteria, fungi, zooplankton or other undesirable microalgae. In closed bioreactors, the control of contamination requires the sterilization of the media, containers and all materials, which increases the cost of production, whereas open pond systems severely limits the number of species that can be cultivated under extreme environmental conditions to prevent contaminations. Here, we report the metabolic engineering of Chlamydomonas reinhardtii to use phosphite as its sole phosphorus source by expressing the ptxD gene from Pseudomonas stutzeri WM88, which encodes a phosphite oxidoreductase able to oxidize phosphite into phosphate using NAD as a cofactor. Engineered C. reinhardtii lines are capable of becoming the dominant species in a mixed culture when fertilized with phosphite as a sole phosphorus source. Our results represent a new platform for the production of microalgae, potentially useful for both closed photobioreactors and open pond systems without the need for using sterile conditions nor antibiotics or herbicides to prevent contamination with biological pollutants.
Identification of the Smallest Structure Capable of Evoking Opsonophagocytic Antibodies against <i>Streptococcus pneumoniae</i> Type 14 (2008)

ABSTRACT Synthetic overlapping oligosaccharide fragments of Streptococcus pneumoniae serotype 14 capsular polysaccharide (Pn14PS), {6)-[β- d -Gal p -(1→4)-]β- d -Glc p NAc-(1→3)-β- d -Gal p -(1→4)-β- d -Glc p -(1→} n , were conjugated to CRM 197 protein and injected into mice to determine the smallest immunogenic structure. The resulting antibodies were then tested for Pn14PS specificity and for their capacity to promote the phagocytosis of S. pneumoniae type 14 bacteria. Earlier studies have reported that the oligosaccharide corresponding to one structural repeating unit of Pn14PS, i.e., Gal-Glc-(Gal-)GlcNAc, induces a specific antibody response to Pn14PS. The broader study described here, which evaluated 16 oligosaccharides, showed that the branched trisaccharide element Glc-(Gal-)GlcNAc is essential in inducing Pn14PS-specific antibodies and that the neighboring galactose unit at the nonreducing end contributes clearly to the immunogenicity of the epitope. Only the oligosaccharide conjugates that produce antibodies recognizing Pn14PS were capable of promoting the phagocytosis of S. pneumoniae type 14. In conclusion, the branched tetrasaccharide Gal-Glc-(Gal-)GlcNAc may be a serious candidate for a synthetic oligosaccharide conjugate vaccine against infections caused by S. pneumoniae type 14.
Novel three-controller average current mode control of DC-DC PWM converters with improved robustness and dynamic response (2000)

This paper presents a novel average current mode control (ACC) strategy for the control of pulse width modulated (PWM) DC-DC converters, which represents a drastic improvement over conventional ACC. This new method consists of the addition of an auxiliary controller into the control loop, besides the current and voltage regulators. The model-based auxiliary controller can increase the closed loop small-signal bandwidth of Buck derived converters, preserving loop gain crossover frequency and stability margins over significant changes of the power stage passive elements values, the load and the line voltage. Moreover, this control scheme shows much better disturbance rejection properties, i.e., closed loop impedance and audiosusceptibility, than conventional ACC. From a control theory point of view, robust performance is achieved preserving stability. A Buck prototype has been experimentally tested with different LC output filters, line and load conditions, including discontinuous conduction mode. Measurements of the small signal frequency response of the converter have been carried out, showing the improvement achieved by the proposed control scheme. The empirical large signal response of the converter under load steps is also shown in order to validate the concept.
A Phantom Tissue System for the Calibration of Perfusion Measurements (2008)

A convenient method for testing and calibrating surface perfusion sensors has been developed. A phantom tissue model is used to simulate the nondirectional blood flow of tissue perfusion. A computational fluid dynamics (CFD) model was constructed in Fluent(R) to design the phantom tissue and validate the experimental results. The phantom perfusion system was used with a perfusion sensor based on clearance of thermal energy. A heat flux gage measures the heat flux response of tissue when a thermal event (convective cooling) is applied. The blood perfusion and contact resistance are estimated by a parameter estimation code. From the experimental and analytical results, it was concluded that the probe displayed good measurement repeatability and sensitivity. The experimental perfusion measurements in the tissue were in good agreement with those of the CFD models and demonstrated the value of the phantom tissue system.
Cdc25B Phosphatase Inhibitors in Cancer Therapy: Latest Developments, Trends and Medicinal Chemistry Perspective (2008)

The Cdc25 phosphatases (Cdc25A, Cdc25B, and Cdc25C in humans), which are responsible for dephosphorylating specific tyrosine/threonine residues on cyclin dependent kinases (CDKs), function as essential regulators of cell cycle control during normal eukaryotic cell division and as mediators of the checkpoint response in cells with DNA damage. Because overexpression of Cdc25A and Cdc25B has been linked to numerous cancers and often correlates with a poor clinical outcome, both academia and industry have devoted substantial research effort in establishing the basic underlying molecular mechanisms and in identifying novel, specific and potentially useful inhibitors of Cdc25 as potential anticancer drugs. Over the past year, dozens of research papers and patent applications describing new Cdc25 inhibitors belonging to different structural classes have been disclosed. In this review, we give an overview on the current status in the field of medicinal chemistry of Cdc25B inhibitors. In addition, molecular modeling studies aimed to clarify the molecular mechanism of inhibition as well as the pharmacophoric features critical for design of new and selective Cdc25B inhibitors are also discussed.
Non-classical protein secretion in bacteria (2005)

We present a publicly available prediction method capable of discriminating between this group of proteins and other proteins, thus allowing for the identification of novel non-classically secreted proteins. We suggest candidates for non-classically secreted proteins in Escherichia coli and Bacillus subtilis. The prediction method is available online.
Electrical Properties of Prostatic Tissues: I. Single Frequency Admittivity Properties (2009)

The contrast in electrical admittivity properties of different prostate tissues shows promise for distinguishing cancer from benign tissues. Sensitivity and specificity exceed those reported for current prostate specific antigen screening practices at low prostate specific antigen, making this an attractive addition to the clinical armamentarium for identifying prostate cancer.
Evaluation of congestion detection mechanisms for InfiniBand switches (2003)

InfiniBand System Area Networks using link-level flow control can experience congestion spreading, where one bottleneck link causes traffic to block throughout the network. End-to-end congestion control using Explicit Congestion Notification (ECN) packet marking has the potential to solve this problem. In this paper, we develop and evaluate ECN mechanisms for switches with input-buffered configuration (typical for InfiniBand), as opposed to traditional techniques that target output-buffered switches. Our mechanisms vary in two dimensions: the condition that triggers a marking event, and the set of packets marked at such an event. The experimental results show that our approaches avoid congestion spreading while preserving high network throughput. In addition, selective marking of packets at an input buffers on each marking event provides better fairness than a naive mechanism that marks only packets in a full input buffer. Finally, schemes that use state at both input and output ports to trigger marking events can improve fairness over purely input-triggered marking schemes.
Update of gp130 cytokines in multiple myeloma (1998)

Interleukin (IL)-6 plays a major role in the control of the survival and proliferation of myeloma cell lines and primary myeloma cells. The genes of the receptors of IL-6 have been cloned, and the major signaling pathways involved in gp130 IL-6 transducer activation have been identified. In addition, another five cytokines that activate the gp130 IL-6 transducer have been identified. We review the recent data on gp130 cytokines and gp130-mediated signal transduction, their involvement in myeloma cell biology, and we discuss the possible therapeutic applications of this knowledge.
Encoding Predictive Reward Value in Human Amygdala and Orbitofrontal Cortex (2003)

Adaptive behavior is optimized in organisms that maintain flexible representations of the value of sensory-predictive cues. To identify central representations of predictive reward value in humans, we used reinforcer devaluation while measuring neural activity with functional magnetic resonance imaging. We presented two arbitrary visual stimuli, both before and after olfactory devaluation, in a paradigm of appetitive conditioning. In amygdala and orbitofrontal cortex, responses evoked by a predictive target stimulus were decreased after devaluation, whereas responses to the nondevalued stimulus were maintained. Thus, differential activity in amygdala and orbitofrontal cortex encodes the current value of reward representations accessible to predictive cues.
Combining Evidence for Effective Information Filtering (1996)

As part of NIST/ARPA&apos;s TREC Workshop, we used Latent Semantic Indexing (LSI) for filtering 336k incoming documents from diverse sources (newswires, patents technical abstracts) for 50 topics of interest. We developed representations of user interests, or filters, for these topics using two sources of training information. A Word Filter used just the words in the topic statements, and a RelDocs Filter used just the known relevant training documents and ignored the topic statement. Using the relevant training documents (a variant of relevance feedback) was more effective than using a detailed natural language description of interests. Combining these two vectors provided some additional improvements in filtering. On average, 7 of the top 10 documents and 44 of the top 100 documents are relevant using the combined vector method. Data combination using the results of the Word and RelDocs retrieval sets was not generally successful in improving performance compared to the best individual me...
In-Situ Counting of Process-Induced Particles (1992)

A flow-cell-type portable laser particle counter was developed for in-situ counting of process-induced particles. We measured process-induced particles when small amounts of moisture and oxygen were intentionally added to SiH 4 diluted to 10% in argon gas. It was found that there existed a threshold concentration for particle generation caused by the reaction between SiH 4 and moisture/oxygen; i.e., the number of particles was not linearly proportional to the moisture and oxygen concentrations. We also found that the size distribution of generated particles varied due to complex mechanisms such as coagulation of small particles.
Flat 3GPP Evolved Packet Core (2011)

The paper discusses the 3GPP Evolved Packet Core (EPC) as an implementation of a flat data plane architecture. The number of data/user plane nodes might be not minimal in certain situations when multiple connections to different networks are established. Improvements are proposed to achieve an optimal flat network architecture.