gebhart/patrepeval huggingface dataset:
Efficient Method for the Synthesis of Hetarenoindanones Based on 3-Arylhetarenes and Their Conversion into Hetarenoindenes (2004)

A series of hetarenoindanones have been prepared by direct double metalation of the appropriate 3-phenylhetarene with butyllithium in the presence of TMEDA followed by treatment of the resulting dilithium compound with ethyl N,N-dimethylcarbamate. All hetarenoindanones were reduced according to Wolff-Kishner by hydrazine in the presence of KOH to the corresponding hetarenoindenes.
A Herpes Simplex Virus Type 1 Mutant Expressing a Baculovirus Inhibitor of Apoptosis Gene in Place of Latency-Associated Transcript Has a Wild-Type Reactivation Phenotype in the Mouse (2005)

The latency-associated transcript (LAT) is essential for the wild-type herpes simplex virus type 1 (HSV-1) high-reactivation phenotype since LAT- mutants have a low-reactivation phenotype. We previously reported that LAT can decrease apoptosis and proposed that this activity is involved in LAT's ability to enhance the HSV-1 reactivation phenotype. The first 20% of the primary 8.3-kb LAT transcript is sufficient for enhancing the reactivation phenotype and for decreasing apoptosis, supporting this proposal. For this study, we constructed an HSV-1 LAT- mutant that expresses the baculovirus antiapoptosis gene product cpIAP under control of the LAT promoter and in place of the LAT region mentioned above. Mice were ocularly infected with this mutant, designated dLAT-cpIAP, and the reactivation phenotype was determined using the trigeminal ganglion explant model. dLAT-cpIAP had a reactivation phenotype similar to that of wild-type virus and significantly higher than that of (i) the LAT- mutant dLAT2903; (ii) dLAT1.5, a control virus containing the same LAT deletion as dLAT-cpIAP, but with no insertion of foreign DNA, thereby controlling for potential readthrough transcription past the cpIAP insert; and (iii) dLAT-EGFP, a control virus identical to dLAT-cpIAP except that it contained the enhanced green fluorescent protein open reading frame (ORF) in place of the cpIAP ORF, thereby controlling for expression of a random foreign gene instead of the cpIAP gene. These results show that an antiapoptosis gene with no sequence similarity to LAT can efficiently substitute for the LAT function involved in enhancing the in vitro-induced HSV-1 reactivation phenotype in the mouse.
Code Combining--A Maximum-Likelihood Decoding Approach for Combining an Arbitrary Number of Noisy Packets (1985)

It is well known that if the data rate is chosen below the available channel capacity, error-free communication is possible. Furthermore, numerous practical error-correction coding techniques exist which can be chosen to meet the user's reliability constraints. However, a basic problem in designing a reliable digital communication system is still the choice of the actual code rate. While the popular rate-1/2 code rate is a reasonable, but not optimum, choice for additive Gaussian noise channels, its selection is far from optimum for channels where a high percentage of the transmitted bits are destroyed by interference. Code combining represents a technique of matching the code rate to the prevailing channel conditions. Information is transmitted in packet formats which are encoded with a relatively high-rate code, e.g., rate 1/2, which can be repeated to Obtain reliable communications when the redundancy in a rate-1/2 code is not sufficient to overcome the channel interference. The receiver combines noisy packets (code combining) to obtain a packet with a code rate which is low enough such that reliable communication is possible even for channels with extremely high error rates. By combining the minimum number of packets needed to overcome the channel conditions, the receiver optimizes the code rate and minimizes the delay required to decode a given packet. Thus, the receiver adapts to the actual jammer-to-signal <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(J/S)</tex> ratio which is critical when the level of interference <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">J</tex> is not known a priori.
Optical crosstalk accumulation in WDM networks (1998)

Probability theory is used to model crosstalk accumulation in WDM networks, from the same source and different sources at the same nominal wavelength, as a function of link utilisation, number of wavelength channels, nodal connectivity and routing algorithms. BER performance and power penalty are assessed as a function of optical crosstalk by approximating the noise statistics as Gaussian.
Secure localization algorithms for wireless sensor networks (2008)

In the military and emergency preparedness class of applications, wireless sensor networks have a number of desirable characteristics, such as being autonomous systems that can be deployed in a remote - possibly hostile - environment and can perform tasks like battlefield surveillance or enemy tracking, as well as monitor the security of military facilities. One of the main challenges in this kind of application is security. Due to their key role in WSNs and also their fragility, localization systems can be the target of an attack that could compromise the entire functioning of a WSN and lead to incorrect military plans and decision making, among other problems. In this article we show how current localization systems are vulnerable to these security attacks, and how existing techniques can be used to prevent or impede these attacks in WSNs.
Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows (2009)

Much of modern biology relies on the strategic manipulation of molecules for creating ordered arrays prior to high throughput molecular analysis. Normally, DNA arrays involve deposition on surfaces, or confinement in nanochannels; however, we show that microfluidic devices can present stretched molecules within a controlled flow in ways complementing surface modalities, or extreme confinement conditions. Here we utilize pressure-driven oscillatory shear flows generated in microchannels as a new way of stretching DNA molecules for imaging "arrays" of individual DNA molecules. Fluid shear effects both stretch DNA molecules and cause them to migrate away from the walls becoming focused in the centerline of a channel. We show experimental findings confirming simulations using Brownian dynamics accounting for hydrodynamic interactions between molecules and channel-flow boundary conditions. Our findings characterize DNA elongation and migration phenomena as a function of molecular size, shear rate, oscillatory frequency with comparisons to computer simulation studies.
Effect of ornithine and lactate on urea synthesis in isolated hepatocytes (1976)

1. In hepatocytes isolated from 24 h-starved rats, urea production from ammonia was stimulated by addition of lactate, in both the presence and the absence of ornithine. The relationship of lactate concentration to the rate of urea synthesis was hyperbolic. 2. Other glucose precursors also stimulated urea production to varying degrees, but none more than lactate. Added oleate and butyrate did not stimulate urea synthesis. 3. Citrulline accumulation was largely dependent on ornithine concentration. As ornithine was increased from 0 to 40 mM, the rate of citrulline accumulation increased hyperbolically, and was half-maximal when ornithine was 8-12 mM. 4. The rate of citrulline accumulation was independent of the presence of lactate, but with pyruvate the rate increased. 5. The rate of urea production continued to increase as ornithine was varied from 0 to 40 mM. 6. It was concluded that intermediates provided by both ornithine and lactate are limiting for urea production from ammonia in isolated liver cells. It was suggested that the stimulatory effect of lactate lies in increased availability of cytosolic aspartate for condensation with citrulline.
Prediction of MHC class I binding peptides, using SVMHC (2002)

Prediction of MHC class I binding peptides using Support Vector Machines, shows high performance and is easy to apply to a large number of MHC class I types. As more peptide data are put into MHC databases, SVMHC can easily be updated to give prediction for additional MHC class I types. We suggest that the number of binding peptides needed for SVM training is at least 20 sequences.
Signal transduction by activated mNotch: importance of proteolytic processing and its regulation by the extracellular domain. (1996)

Previous studies imply that the intracellular domain of Notch1 must translocate to the nucleus for its activity. In this study, we demonstrate that a mNotch1 mutant protein that lacks its extracellular domain but retains its membrane-spanning region becomes proteolytically processed on its intracellular surface and, as a result, the activated intracellular domain (mNotchIC) is released and can move to the nucleus. Proteolytic cleavage at an intracellular site is blocked by protease inhibitors. Intracellular cleavage is not seen in cells transfected with an inactive variant, which includes the extracellular lin-Notch-glp repeats. Collectively, the studies presented here support the model that mNotch1 is proteolytically processed and the cleavage product is translocated to the nucleus for mNotch1 signal transduction.
The role of ATP citrate lyase, malic enzyme and fatty acid synthase in the regulation of lipid accumulation in Cunninghamella sp. 2A1 (2010)

Identification of enzymes involved in the regulation of lipid biosynthesis in Cunninghamella sp. 2A1 was carried out by observing specific activity profile of seven lipogenic enzymes during lipid accumulation phase until cessation of lipogenesis occurred. Activities of all enzymes, 6-phosphogluconate dehydrogenase (6-PGDH), glucose-6-phosphogluconate dehydrogenase (G-6-PDH), NADP+:isocitrate dehidrogenase (NADP+:ICDH), malic enzyme (ME), ATP citrate lyase (ACL) and fatty acid synthase (FAS), increased when lipogenesis occurred after exhaustion of nitrogen in the culture. The enzymes remained active until the end of the experiment (79 h) except for ACL, ME and FAS which showed marked decreases (84, 72 and 59% respectively) in activity after 48 h. This decrease in activity coincided with the cessation of lipid accumulation at 48 h, although glucose was still present. This observation suggests that the three enzymes play a vital role in the down-regulation of lipid accumulation in Cunninghamella sp. 2A1. When 1 g/l ammonium tartrate was reintroduced into the culture at 60 h, the activity of ACL, ME and FAS was restored. This suggests that the decrease in ACL, ME and FAS activities was due to the depletion of nitrogen in the culture medium. The probable involvement of feedback inhibition in this observation is discussed.
Analysis of protein interactions on protein arrays by a wavelength interrogation‐based surface plasmon resonance biosensor (2004)

We have investigated whether surface plasmon resonance (SPR) sensors based on the wavelength interrogation are able to analyze protein interactions on protein arrays. The spectral SPR sensor was self-constructed and its detection limit, expressed as the minimal refractive index variation, was calculated to be 6.6x10(-5) with the signal fluctuation of 1.0x10(-5). The protein array surface was modified by a mixed thiol monolayer to immobilize proteins. Protein arrays were analyzed by the line-scanning mode of the SPR sensor, which scanned every 100 microm along the central line of array spots and the scanned results were presented by color spectra from blue to red. Glutathione S-transferase (GST)-rac1 caused a concentration-dependent increase of SPR wavelength shift on protein arrays. The surface structure of the protein arrays was analyzed by atomic force microscopy. Specific interactions of antigens with antibodies were analyzed on the protein arrays by using three antibodies and eight proteins. These results suggest that the wavelength interrogation-based SPR sensor can be used as the biosensor for the high-throughput analysis of protein interactions on protein arrays.
Polyaniline as a transparent electrode for polymer light-emitting diodes: Lower operating voltage and higher efficiency (1994)

We demonstrate that by using polyaniline (PANI) or a combination of (PANI) and indium/tin oxide (ITO) as the transparent anode of a polymer light-emitting diode with poly[2-methoxy-5-(2′-ethyl- hexyloxy)-1,4-phenylene vinylene] (MEH-PPV), as the active layer, device performance can be significantly improved. The operating voltage can be reduced by ∼30%–50% and the quantum efficiency can be increased by ∼30%–40% with respect to the devices using ITO alone as the hole-injecting anode. The barrier height at the PANI/MEH-PPV interface is estimated to be ∼0.08–0.12 eV, approximately half of that at the ITO/MEH-PPV interface.
Vascular evaluation of the problem diabetic foot. (1998)

Ischemia plays a pivotal role in the management of the problem diabetic foot. Prompt revascularization offers the patient with diabetes with lower-extremity ischemia the best hope for limb salvage and normal ambulation. The true vascular status of the diabetic foot may be difficult to assess by clinical examination. Because of the dangers of missing correctable vascular disease, noninvasive vascular testing plays an important role in the evaluation of the problem diabetic foot. The laboratory should have documented reliability, and its results must be interpreted in the context of the patient's clinical progress. The most common laboratory error is overestimating the blood supply to the foot because of technical problems with mural calcification. Algorithms for the use of the vascular laboratory for common foot problems are presented. The vascular laboratory, although helpful, is no substitute for clinical judgement. When ischemia is suspected or when response to conservative care is poor, early vascular surgical consultation is prudent.
Integrated photonic inverter with gain (2001)

Photonic integrated circuits (PICs) require inverting gates with gain greater than one to enable logic functionality with fanout and cascade. Optically modulated semiconductor laser technology is speed-limited by the photon cavity lifetime and, therefore, can provide high speed, integrable, digital logic gates. If semiconductor lasers can be configured as photonic inverters with gain exceeding one, then photonic clocks, oscillators, and logic gates would be possible at high data rates. This letter reports the demonstration of a semiconductor laser photonic inverter with an integrated dielectric input waveguide and gain greater than one.
Visual model structures and synchrony constraints for audio-visual speech recognition (2006)

This paper presents the design and evaluation of a speaker-independent audio-visual speech recognition (AVSR) system that utilizes a segment-based modeling strategy. The audio and visual feature streams are integrated using a segment-constrained hidden Markov model, which allows the visual classifier to process visual frames with a constrained amount of asynchrony relative to proposed acoustic segments. The core experiments in this paper investigate several different visual model structures, each of which provides a different means for defining the units of the visual classifier and the synchrony constraints between the audio and visual streams. Word recognition experiments are conducted on the AV-TIMIT corpus under variable additive noise conditions. Over varying acoustic signal-to-noise ratios, word error rate reductions between 14% and 60% are observed when integrating the visual information into the automatic speech recognition process.
Ruthenium‐Indenylidene Complexes: Scope in Cross‐Metathesis Transformations (2008)

Abstract A comparative study examining the catalytic activity of a series of five indenylidene‐containing ruthenium complexes in olefin cross‐metathesis reactions is presented. Results reveal the greater efficiency of precatalyst 5 , highlighting the key role of the N,N′ ‐bis(2,6‐diisopropylphenyl)imidazol‐2‐ylidene (IPr) ligand for this transformation. The scope of this precatalyst was investigated and several microwave experiments were carried out allowing for catalyst loadings as low as 0.1 mol%. Overall, cross‐metathesis products were isolated in moderate to excellent yields with high stereoselectivity.
Hybridization protection assay: a rapid, sensitive, and specific method for detection of Philadelphia chromosome-positive leukemias (1991)

The Philadelphia (Ph1) chromosome is present in greater than 90% of patients with chronic myelogenous leukemia (CML) and in 2% to 20% of those with acute leukemias, for which it is an important prognostic marker too. The chimeric BCR-ABL mRNAs resulting from the translocation encode either a 210-Kd or a 190-Kd protein. The techniques used to detect Ph1 chromosome include karyotyping, Southern analysis to demonstrate bcr rearrangement, and polymerase chain reaction to amplify the BCR-ABL transcripts. However, the routine performance of these methods by clinical laboratories is cumbersome, time consuming, and exposes laboratory personnel to radioisotopes. We describe here the clinical application of a new method, the hybridization protection assay (HPA), which uses chemiluminescent acridinium-ester-labeled probes in conjunction with PCR for detection of the amplified BCR-ABL sequences. The method is sensitive, specific, and can reliably distinguish between the transcripts for P190BCR-ABL and P210BCR-ABL. In contrast to the 2 days or longer required for conventional hybridization, HPA analysis can be completed in less than 30 minutes. We have successfully used this method to analyze 60 leukemia samples (34 from Ph1-negative acute leukemias; 6 from Ph1-positive acute leukemias; and 20 from CML) with complete correlation (of BCR-ABL positivity or negativity) with the results of karyotype or Southern Blot analysis of genomic DNA for bcr rearrangement. Therefore, the HPA, in conjunction with PCR, appears to provide a rapid and reliable test for the diagnosis of Ph1-positivity.
Taxonomic Study of Viridans Streptococci: Description of Streptococcus gordonii sp. nov. and Emended Descriptions of Streptococcus sanguis (White and Niven 1946), Streptococcus oralis (Bridge and Sneath 1982), and Streptococcus mitis (Andrewes and Horder 1906) (1989)

We examined a collection of 151 strains of the viridans type of streptococci, which were isolated mainly from human oral cavities and included several reference strains, in an attempt to revise and improve the taxonomy of this group of bacteria. Our examinations included determinations of a high number of biochemical and physiological characteristics and serological reactivity. The resulting data revealed several hitherto unrecognized characters of taxonomic significance, and several of the species can now be more accurately defined. A diagnostic key to the taxa is presented. Strains previously identified as Streptococcus sanguis could be divided into two clearly distinct species, Streptococcus sanguis sensu stricto (type strain, ATCC 10556) and a new species, Streptococcus gordonii (type strain, ATCC 10558). Streptococcus mitis was divided into two biovars, consisting of strains possessing group O antigens and strains possessing group K antigen. The group of strains assigned to Streptococcus anginosus was biochemically and serologically heterogeneous, but the data did not allow natural subdivisions. Based on the results of this study, emended descriptions of the species Streptococcus oralis, S. mitis, and S. sanguis are provided. The classification resulting from this study is in complete agreement with previously published genetic data.
A Predominantly Clonal Multi-Institutional Outbreak ofClostridium difficile–Associated Diarrhea with High Morbidity and Mortality (2005)

A strain of C. difficile that was resistant to fluoroquinolones and had binary toxin and a partial deletion of the tcdC gene was responsible for this outbreak of C. difficile-associated diarrhea. Exposure to fluoroquinolones or cephalosporins was a risk factor.
Visual dysfunction in Alzheimer's disease: Relation to normal aging (1991)

In patients with Alzheimer's disease (AD), compared with age-matched and young healthy control subjects, visual deficits in the following functions were observed: color, stereoacuity, contrast sensitivity, and backward masking (homogeneous and pattern). Critical flicker fusion thresholds were normal, relative to age-matched healthy subjects. For color, the majority of the errors were tritanomalous (blue axis). Color and stereoacuity deficits were unrelated to severity of dementia, in accordance with models of vision that describe these functions as modular rather than diffuse for cortical localization. Although contrast sensitivity was depressed throughout the frequency range in AD, more patients were impaired at low than at high spatial frequencies, contrasting with the observed normal aging pattern of high-frequency loss. Healthy elderly subjects showed depressed critical flicker fusion thresholds and reduced contrast sensitivity at high frequencies, relative to the young group; differences between these groups were not found for the other vision tests. A subset of the AD group received detailed neuro-ophthalmological examination, and no abnormalities were found. This finding, taken together with normal thresholds for critical flicker fusion, suggests that the widespread visual dysfunction reported here is more likely to be related to known pathological changes in primary visual and association cortex in AD than to changes in the retina or optic nerve.
Reversible Surface Oxidation and Efficient Luminescence Quenching in Semiconductor Single-Wall Carbon Nanotubes (2004)

We have investigated reversible single-wall carbon nanotube (SWNT) oxidation by quantitative analysis of the oxide-induced absorption bleaching and luminescence quenching at low pH. These data, in combination with DFT structure calculations, suggest that the nanotube oxide is a 1,4-endoperoxide. At low pH, the endoperoxide protonates to create a hydroperoxide carbocation, introducing a hole in the SWNT valence band. Nanotube luminescence is extremely sensitive to quenching by hole-doping, while the absorption is relatively robust.
Immune Suppression in the Tumor Microenvironment (2006)

The identification of tumor-expressed antigens that can be recognized by specific T lymphocytes has made it possible both to study the properties of T cells participating in anti-tumor immune responses in patients and also to develop antigen-specific immunotherapies as a treatment modality. Interestingly, moves toward intervention have proceeded at a faster pace than have investigations toward understanding. In melanoma in particular, many clinical trials of active immunization have been performed, and many of these have shown increases in tumor antigen-specific T cells circulating in the blood. However, clinical responses have been infrequent, arguing that mechanisms of resistance downstream from initial T cell priming may be dominant in many cases. In fact, may patients show spontaneous generation of immune effector cells and/or antibodies, implying that the priming phase has occurred already in such individuals even without vaccination. Recent attention has turned toward mechanisms of immune evasion at the effector phase of the anti-tumor immune response, predominantly within the tumor microenvironment. Evidence is accumulating that T cell-intrinsic hyporesponsiveness or anergy, extrinsic suppression by regulatory cell populations, inhibitory ligands such as PD-L1, soluble factors such as TGF-beta, and the activity of nutrient-catabolizing enzymes such as indoleamine 2,3-dioxygenase (IDO), may contribute to immune escape in different settings. Murine preclinical models have shown that interfering with each of these processes can translate into T cell-mediated tumor control. Clinical studies to estimate the frequency of specific immune evasion mechanisms in individual patients, to correlate specific events with clinical outcome, and to develop strategies to counter resistance mechanisms should receive a high priority.