gebhart/patrepeval huggingface dataset:
Mechanism of Action of Guinea Pig Liver Transglutaminase (1967)

Abstract Evidence is presented that purified guinea pig liver transglutaminase catalyzes the hydrolysis of p-nitrophenyl trimethylacetate. As in the case of the other transglutaminase-catalyzed reactions, calcium ion is required for this esterolysis. This reaction involves the formation of a trimethylacetyl enzyme complex which has been shown by two procedures, burst in p-nitrophenol liberation and incorporation of 14C-trimethylacetyl, to have one trimethylacetyl group per molecule of protein. A trimethylacetyl enzyme complex containing 0.9 eq of trimethylacetyl has been isolated. Incorporation of trimethylacetyl is reflected in a concomitant loss in activity toward p-nitrophenyl acetate and for hydroxylamine incorporation into carbobenzoxy-l-glutaminylglycine. Studies on the inhibition of transglutaminase activity by p-nitrophenyl trimethylacetate and formation of 14C-trimethylacetyl enzyme, both as a function of calcium ion concentration, indicate that the same divalent cation-enzyme complexes are involved in p-nitrophenyl acetate hydrolysis and in p-nitrophenyl trimethylacetate hydrolysis. Thus the apparent dissociation constants for the calcium-transglutaminase complex, as determined by inhibition and by trimethylacetyl enzyme formation at pH 7.0, are 0.37 ± 0.2 x 10-3 m and 0.54 ± 0.2 x 10-3 m, respectively. These values are comparable to the reported activator constant of calcium, 0.4 ± 0.2 x 10-3 m at pH 7.0, determined from the kinetics of p-nitrophenyl acetate hydrolysis. A single radioactive peptide has been separated from a proteolytic digest of 14C-trimethylacetyl transglutaminase. Studies on the isolated peptide indicate that the trimethylacetyl group is bound in thioester linkage to a cysteine —SH group and to the same —SH group in the enzyme with which iodoacetamide reacts to form the inactive carbamidomethyl enzyme. These results are presented in support of a previously suggested cation-controlled mechanism of enzyme action involving the intermediate formation of an acyl enzyme through thioester linkage.
Electrical Detection of Spin Pumping due to the Precessing Magnetization of a Single Ferromagnet (2006)

We report direct electrical detection of spin pumping, using a lateral normal-metal/ferromagnet/normal-metal device, where a single ferromagnet in ferromagnetic resonance pumps spin-polarized electrons into the normal metal, resulting in spin accumulation. The resulting backflow of spin current into the ferromagnet generates a dc voltage due to the spin-dependent conductivities of the ferromagnet. By comparing different contact materials (Al and/or Pt), we find, in agreement with theory, that the spin-related properties of the normal metal dictate the magnitude of the dc voltage.
PCAP: probe choice and analysis package—a set of programs to aid in choosing synthetic oligomers for contig mapping (1993)

In the program, PCAP, we provide a methodology for choosing synthetic oligonucleotide probes to be used in contig mapping experiments. The package serves the purpose of presenting a series of short oligonucleotides (8–12mers) that are chosen based on constraints with respect to frequency of occurrence within a particular genome and the G+C content of the oligonucleotides. The four programs contained within the package: (i) convert GenBank files to a format useable by the package; (ii) calculate trinucleotide and tetranucleotide frequencies in available sequence data on a particular species; (iv) present the user with upper and lower bounds on the frequencies of hybridization sites for oligonucleotide probes of length 8–12, (iv) allow the user to place constraints on site frequency and G+C content and provides a list of short probe sequences that fit these criteria. These sequences can then be synthetically produced and used in hybridization experiments to carry out contig mapping.
HSV Amplicon-Mediated Delivery of LIGHT Enhances the Antigen-Presenting Capacity of Chronic Lymphocytic Leukemia (2002)

Chronic lymphocytic leukemia (CLL) is a B lymphocyte malignancy that remains a largely incurable disease. CLL B cells possess the ability to process and present tumor antigens but lack expression of costimulatory molecules, rendering them inefficient effectors of T-cell activation. We previously demonstrated that helper virus-free preparations of herpes simplex virus (HSV) amplicon vectors encoding CD40L efficiently transduce CLL B cells and render them capable of eliciting specific anti-tumor T-cell responses. LIGHT (TNFSF14), a member of the tumor necrosis factor (TNF) superfamily, efficiently activates both T cells and antigen-presenting cells (APCs). We employed an HSV amplicon vector expressing human LIGHT (hf-HSV-LIGHT) to transduce CLL B cells and compared the immunomodulatory function and T-cell activation induced by hf-HSV-LIGHT transduction to that observed with a CD40L-expressing HSV amplicon (hf-HSV-CD40L). hf-HSV-LIGHT transduction induced expression of endogenous B7.1, B7.2, and ICAM.1 on CLL cells, albeit to a lesser degree than that observed in response to transduction with hf-HSV-CD40L. hf-HSV-LIGHT enhanced the antigen-presenting capacity of CLL B cells, as measured by induction of T-cell proliferation in an allogeneic mixed lymphocyte tumor reaction. Finally, hf-HSV-LIGHT-transduced CLL B cells successfully stimulated the outgrowth of autologous cytotoxic T-lymphocytes in vitro. In aggregate, these data suggest that hf-HSV-LIGHT transduction may be useful for induction of immune responses to CLL and other B-cell lymphoid malignancies.
Iterative decision-feedback differential demodulation of bit-interleaved coded MDPSK for flat Rayleigh fading channels (2001)

A simple receiver structure previously proposed by the authors for convolutional coded M-ary differential phase-shift keying transmission over flat Rayleigh fading channels without channel state information is analyzed in detail. We present a thorough discussion of the iterative decoding procedure, which is referred to as iterative decision-feedback differential demodulation (iterative DF-DM). The convergence behavior of iterative DF-DM is theoretically examined. The analysis supports the observation that the iterative decoding scheme works well for target bit-error rates which are usually of interest. Furthermore, the associated cut-off rate for error-free decision feedback is studied. Judging from this performance parameter, remarkable gains in power efficiency compared to conventional differential demodulation are indicated, while the computational complexity of the decoding remains low. The results from information theory are in good agreement with the given simulation results.
Blocking Lactate Export by Inhibiting the Myc Target MCT1 Disables Glycolysis and Glutathione Synthesis (2013)

Myc oncoproteins induce genes driving aerobic glycolysis, including lactate dehydrogenase-A that generates lactate. Here, we report that Myc controls transcription of the lactate transporter SLC16A1/MCT1 and that elevated MCT1 levels are manifest in premalignant and neoplastic Eμ-Myc transgenic B cells and in human malignancies with MYC or MYCN involvement. Notably, disrupting MCT1 function leads to an accumulation of intracellular lactate that rapidly disables tumor cell growth and glycolysis, provoking marked alterations in glycolytic intermediates, reductions in glucose transport, and in levels of ATP, NADPH, and ultimately, glutathione (GSH). Reductions in GSH then lead to increases in hydrogen peroxide, mitochondrial damage, and ultimately, cell death. Finally, forcing glycolysis by metformin treatment augments this response and the efficacy of MCT1 inhibitors, suggesting an attractive combination therapy for MYC/MCT1-expressing malignancies.
The Smallest Grammar Problem (2005)

This paper addresses the smallest grammar problem: What is the smallest context-free grammar that generates exactly one given string /spl sigma/? This is a natural question about a fundamental object connected to many fields such as data compression, Kolmogorov complexity, pattern identification, and addition chains. Due to the problem's inherent complexity, our objective is to find an approximation algorithm which finds a small grammar for the input string. We focus attention on the approximation ratio of the algorithm (and implicitly, the worst case behavior) to establish provable performance guarantees and to address shortcomings in the classical measure of redundancy in the literature. Our first results are concern the hardness of approximating the smallest grammar problem. Most notably, we show that every efficient algorithm for the smallest grammar problem has approximation ratio at least 8569/8568 unless P=NP. We then bound approximation ratios for several of the best known grammar-based compression algorithms, including LZ78, B ISECTION, SEQUENTIAL, LONGEST MATCH, GREEDY, and RE-PAIR. Among these, the best upper bound we show is O(n/sup 1/2/). We finish by presenting two novel algorithms with exponentially better ratios of O(log/sup 3/n) and O(log(n/m/sup */)), where m/sup */ is the size of the smallest grammar for that input. The latter algorithm highlights a connection between grammar-based compression and LZ77.
Sorbitol dehydration in high temperature liquid water (2011)

Sorbitol dehydration in high temperature liquid water proceeded at 523–573 K without adding any acid catalysts. Anhydrosorbitols (1,4-anhydrosorbitol (1,4-AHSO), 2,5-anhydrosorbitol (2,5-AHSO) and 1,5-anhydrosorbitol (1,5-AHSO)) were produced by the monomolecular dehydration of sorbitol, and isosorbide was produced by the stepwise dehydration of 1,4-AHSO. The formation rates of 1,4-AHSO and 2,5-AHSO (five-membered cyclic ethers) from sorbitol dehydration were much larger than that of 1,5-AHSO (six-membered cyclic ether), and 1,4-AHSO was the main product of the monomolecular dehydration of sorbitol. The dehydration rate of sorbitol to 1,4-AHSO was faster than that of 1,4-AHSO to isosorbide; therefore, 1,4-AHSO could be obtained as an intermediate product. A kinetic analysis of sorbitol dehydration in high temperature liquid water showed that the maximum yield of 1,4-AHSO from the dehydration of sorbitol increased with decreasing reaction temperature (for example, 80% at 500 K) and that the maximum yield of isosorbide was 57% at 590 K for 1 h. 1,4-AHSO and isosorbide could be produced selectively from sorbitol dehydration in high temperature liquid water by controlling both the reaction temperature and reaction time.
Use of a Generalized Stokes Number to Determine the Aerodynamic Capture Efficiency of Non-Stokesian Particles from a Compressible Gas Flow (1982)

The aerodynamic capture efficiency of small but non-diffusing particles suspended in a high-speed stream flowing past a target is known to be influenced by parameters governing (a) small particle inertia, (b) departures from the Stokes drag law (associated with local particle Reynolds numbers greater than unity), and (c) carrier fluid compressibility (at nonnegligible free-stream Mach numbers). By defining an effective Stokes number in terms of the actual (prevailing) particle stopping distance, local fluid viscosity, and inviscid fluid velocity gradient at the target nose, we show that these effects are well correlated in terms of a “standard” (cylindrical collector, Stokes drag, incompressible flow, Re½ ≫ 1) capture efficiency curve. We are thus led to a correlation that (a) simplifies aerosol capture calculations in the parameter range already included in previous numerical solutions, (b) allows rational engineering predictions of deposition in situations not previously specifically calculated, (c) should facilitate the presentation of performance data for gas cleaning equipment and aerosol instruments.
Saliency-enhanced image aesthetics class prediction (2009)

We present a saliency-enhanced method for the classification of professional photos and snapshots. First, we extract the salient regions from an image by utilizing a visual saliency model. We assume that the salient regions contain the photo subject. Then, in addition to a set of discriminative global image features, we extract a set of salient features that characterize the subject and depict the subject-background relationship. Our high-level perceptual approach produces a promising 5-fold cross-validation (5-CV) classification accuracy of 78.8%, significantly higher than existing approaches that concentrate mainly on global features.
Oncogenic but non-essential role of N-myc downstream regulated gene 1 in the progression of esophageal squamous cell carcinoma (2013)

N-myc downstream regulated gene 1 (NDRG1/Cap43/Drg-1) has previously been shown to be dysregulated in esophageal squamous cell carcinoma (ESCC). In this study, we investigated the role of NDRG1 in the neoplastic progression of ESCC using ectopic gain-of-function and loss-of-function approaches. Stable transfectants of the KYSE30 ESCC cell line with altered NDRG1 levels were generated by lentiviral transduction. Although no measurable effects on in vitro cell proliferation were observed with altered NDRG1 expression, the ectopic overexpression of NDRG1 was positively linked to recognized markers of metastasis, angiogenesis and apoptotic evasion. Accordingly, in the nude mouse xenograft model system, NDRG1 overexpression promoted the in vivo growth of KYSE30 derived xenografts, which could be attributed to the reduced apoptotic and enhanced angiogenic activities associated with this gene. These processes were mediated in part by increased NFκB activity in NDRG1 overexpressing cells. Nevertheless, no significant phenotypic changes were observed in response to NDRG1 knock-down, suggesting that this gene might not be essential for the neoplastic progression of ESCC. Taken together, our results suggest that NDRG1 may play positive but dispensable roles in the progression of esophageal squamous cell carcinoma.
Laparoscopic Colon Resection Trends in Utilization and Rate of Conversion to Open Procedure (2012)

There is a trend of increasing utilization of LCR, with acceptable conversion rates, across hospitals in the United States over the recent years. When feasible, attempted LCR had better outcomes than open colectomy in the immediate perioperative period.
Longitudinal Analysis of the Association Between Vasomotor Symptoms and Race/Ethnicity Across the Menopausal Transition: Study of Women’s Health Across the Nation (2006)

Among the risk factors assessed, vasomotor symptoms were most strongly associated with menopausal status. After adjustment for covariates, symptoms were reported most often in all racial/ethnic groups in late perimenopause and nearly as often in postmenopause.
The spectrum of hepatic functional impairment in compensated chronic hepatitis C: results from the Hepatitis C Anti‐viral Long‐term Treatment against Cirrhosis Trial<sup>1</sup> (2008)

Hepatic impairment is common in compensated patients with fibrosis or cirrhosis because of chronic hepatitis C. Cholate shunt, and cholate Cl(oral) and perfused hepatic mass, identify patients at risk for cirrhosis or varices.
Investigation of the silicon beading phenomena during zone-melting recrystallization (1983)

During recrystallization of encapsulated silicon films on SiO2, by the graphite strip heater technique, the silicon sometimes breaks apart and agglomerates into small beads or stripes. By secondary ion mass spectroscopy analysis, it was found that a high concentration of nitrogen at the interface between the silicon and the top SiO2 capping layer is needed to prevent this from occurring. Incorporation of hydrogen into the crystallization ambient was found to cause the beading to occur. The initial stages of the bead formation were investigated by scanning electron cross-section microscopy.
Productive Encystment of Haematococcus pluvialis by Controlling a Specific Irradiation Rate in a Photoautotrophic Induction System for Astaxanthin Production (2006)

A productive photoautotrophic induction system was established for the production of antioxidative astaxanthin by the green microalga Haematococcus pluvialis. During photoautotrophic induction, N-deprived Haematococcus cells were sensitive to the specific irradiation rate (I) on transformation to astaxanthin-rich cyst cells. Compared with the CO2 condition, the optimum specific irradiation rate (Iopt) was confined within narrow limits between light limitation and inhibition. Maximal astaxanthin synthesis in H. pluvialis was promoted under a 5 % CO2 environment and unsynchronized illumination with a specific irradiation rate of 80 µmol photon/g·s, yielding an accumulation rate of 4.3 mg/g·day. This result indicates that a favorable CO2 concentration and controlled specific irradiation rate leads to the productive encystment of H. pluvialis and enhanced astaxanthin synthesis.
Laser Ionization Mass Spectroscopy of Single Aerosol Particles (1995)

We describe an instrument that measures the chemical composition of single aerosol particles. To facilitate detection of volatile species, particles are analyzed less than 0.5 ms after leaving ambient conditions and without touching any surfaces. Particles are introduced into a vacuum through a differentially pumped nozzle, then cross a He-Ne laser beam. The scattered light provides both size information and the trigger for an excimer laser that desorbs and ionizes molecules from the particle. Mass spectra with excellent signal to noise have been obtained from laboratory and ambient particles 0.3 to 16 μm diameter.
Preparation of lignin composite material and its application in ethylene propylene rubber (2009)

Composite material of HBSL/nano-silica is prepared by high boiling solvent lignin and nano-silica,and then characterized.The composite is used as the reinforcing agent in ethylene-propylene rubber,and it can increase the hardness of rubber and improve the resistance to ageing.The elongation at break of the rubber is increased from 165% to 229%,but the tensile strength has reduced slightly.The ratio of nano-silica in the composite is an important factor to the performance of rubber,and the optimum ratio is 5%.
<title>Real-time simulation and visualization of volumetric brain deformation for image-guided neurosurgery</title> (2001)

During neurosurgery, the challenge for the neurosurgeon is to remove as much as possible of a tumor without destroying healthy tissue. This can be difficult because healthy and diseased tissue can have the same visual appearance. To this aim, and because the surgeon cannot see underneath the brain surface, image-guided neurosurgery systems are being increasingly used. However, during surgery, deformation of the brain occurs (due to brain shift and tumor resection), therefore causing errors in the surgical planning with respect to preoperative imaging. In our previous work, we developed software for capturing the deformation of the brain during neurosurgery. The software also allows preoperative data to be updated according to the intraoperative imaging so as to reflect the shape changes of the brain during surgery. Our goal in this paper was to rapidly visualize and characterize this deformation over the course of surgery with appropriate tools. Therefore, we developed tools allowing the doctor to visualize (in 2D and 3D) deformations, as well as the stress tensors characterizing the deformation along with the updated preoperative and intraoperative imaging during the course of surgery. Such tools significantly add to the value of intraoperative imaging and hence could improve surgical outcomes.
Analysis of adaptive streaming for hybrid CDN/P2P live video systems (2011)

Most commercial video streaming systems rely on Content Distribution Networks (CDNs) to distribute video content. HTTP adaptive streaming has been recently adopted by major video streaming providers and is now considered the standard technique used with CDN-based streaming systems. Despite the success of these systems, cost-effective scalability continues to be of concern in their design and deployment. To address this, recent work has proposed the use of hybrid CDN and Peer-to-peer (P2P) live streaming systems. The design of these systems aims to combine the scalability of P2P systems and the desirable performance properties of CDN-based systems. However, the use of adaptive streaming, has not been explored extensively in such hybrid systems. Designing and operating an adaptive hybrid streaming system is very challenging. Two design decisions are very critical in the operation of any such system. The first one is the bitrate adaptation strategy which specifies how different bitrates are assigned to different users while maximizing user satisfaction. The second is defining the operational guidelines for switching the system between the CDN and the P2P modes while efficiently utilizing the available resources. In this paper we present a model and analysis of a hybrid CDN-P2P adaptive live streaming system with the objective of answering these two design questions. We first present a stochastic fluid model to the hybrid streaming system with a single video bitrate and we obtain theoretical results to guide the system operation as described above. We then extend the analysis to the adaptive streaming case with multiple video bitrates. We model adaptive streaming as a linear optimization problem to obtain the best bitrate adaptation strategy. We validate our analysis using simulations. Our conclusion is that adaptive hybrid streaming can significantly improve the ability of the system to satisfy more users with higher video bitrates over CDN-based systems.
AUTOMATIC CLOUD DETECTION FROM MULTI-TEMPORAL SATELLITE IMAGES: TOWARDS THE USE OF PLÉIADES TIME SERIES (2012)

Abstract. Contrary to aerial images, satellite images are often affected by the presence of clouds. Identifying and removing these clouds is one of the primary steps to perform when processing satellite images, as they may alter subsequent procedures such as atmospheric corrections, DSM production or land cover classification. The main goal of this paper is to present the cloud detection approach, developed at the French Mapping agency. Our approach is based on the availability of multi-temporal satellite images (i.e. time series that generally contain between 5 and 10 images) and is based on a region-growing procedure. Seeds (corresponding to clouds) are firstly extracted through a pixel-to-pixel comparison between the images contained in time series (the presence of a cloud is here assumed to be related to a high variation of reflectance between two images). Clouds are then delineated finely using a dedicated region-growing algorithm. The method, originally designed for panchromatic SPOT5-HRS images, is tested in this paper using time series with 9 multi-temporal satellite images. Our preliminary experiments show the good performances of our method. In a near future, the method will be applied to Pléiades images, acquired during the in-flight commissioning phase of the satellite (launched at the end of 2011). In that context, this is a particular goal of this paper to show to which extent and in which way our method can be adapted to this kind of imagery.