gebhart/patrepeval huggingface dataset:
Synchrotron FTIR imaging of OH in quartz mylonites (2017)

Abstract. Previous measurements of water in deformed quartzites using conventional Fourier transform infrared spectroscopy (FTIR) instruments have shown that water contents of larger grains vary from one grain to another. However, the non-equilibrium variations in water content between neighboring grains and within quartz grains cannot be interrogated further without greater measurement resolution, nor can water contents be measured in finely recrystallized grains without including absorption bands due to fluid inclusions, films, and secondary minerals at grain boundaries.Synchrotron infrared (IR) radiation coupled to a FTIR spectrometer has allowed us to distinguish and measure OH bands due to fluid inclusions, hydrogen point defects, and secondary hydrous mineral inclusions through an aperture of 10 µm for specimens > 40 µm thick. Doubly polished infrared (IR) plates can be prepared with thicknesses down to 4–8 µm, but measurement of small OH bands is currently limited by strong interference fringes for samples < 25 µm thick, precluding measurements of water within individual, finely recrystallized grains. By translating specimens under the 10 µm IR beam by steps of 10 to 50 µm, using a software-controlled x − y stage, spectra have been collected over specimen areas of nearly 4.5 mm2. This technique allowed us to separate and quantify broad OH bands due to fluid inclusions in quartz and OH bands due to micas and map their distributions in quartzites from the Moine Thrust (Scotland) and Main Central Thrust (Himalayas).Mylonitic quartzites deformed under greenschist facies conditions in the footwall to the Moine Thrust (MT) exhibit a large and variable 3400 cm−1 OH absorption band due to molecular water, and maps of water content corresponding to fluid inclusions show that inclusion densities correlate with deformation and recrystallization microstructures. Quartz grains of mylonitic orthogneisses and paragneisses deformed under amphibolite conditions in the hanging wall to the Main Central Thrust (MCT) exhibit smaller broad OH bands, and spectra are dominated by sharp bands at 3595 to 3379 cm−1 due to hydrogen point defects that appear to have uniform, equilibrium concentrations in the driest samples. The broad OH band at 3400 cm−1 in these rocks is much less common. The variable water concentrations of MT quartzites and lack of detectable water in highly sheared MCT mylonites challenge our understanding of quartz rheology. However, where water absorption bands can be detected and compared with deformation microstructures, OH concentration maps provide information on the histories of deformation and recovery, evidence for the introduction and loss of fluid inclusions, and water weakening processes.
Learning Word Representations with Hierarchical Sparse Coding (2014)

We propose a new method for learning word representations using hierarchical regularization in sparse coding inspired by the linguistic study of word meanings. We show an efficient learning algorithm based on stochastic proximal methods that is significantly faster than previous approaches, making it possible to perform hierarchical sparse coding on a corpus of billions of word tokens. Experiments on various benchmark tasks---word similarity ranking, analogies, sentence completion, and sentiment analysis---demonstrate that the method outperforms or is competitive with state-of-the-art methods. Our word representations are available at \url{http://www.ark.cs.cmu.edu/dyogatam/wordvecs/}.
A Framework to Compare Alert Ranking Algorithms (2012)

To improve software quality, rule checkers statically check if a software contains violations of good programming practices. On a real sized system, the alerts (rule violations detected by the tool) may be numbered by the thousands. Unfortunately, these tools generate a high proportion of "false alerts", which in the context of a specific software, should not be fixed. Huge numbers of false alerts may render impossible the finding and correction of "true alerts" and dissuade developers from using these tools. In order to overcome this problem, the literature provides different ranking methods that aim at computing the probability of an alert being a "true one". In this paper, we propose a framework for comparing these ranking algorithms and identify the best approach to rank alerts. We have selected six algorithms described in literature. For comparison, we use a benchmark covering two programming languages (Java and Smalltalk) and three rule checkers (Find Bug, PMD, Small Lint). Results show that the best ranking methods are based on the history of past alerts and their location. We could not identify any significant advantage in using statistical tools such as linear regression or Bayesian networks or ad-hoc methods.
High‐resolution magic angle spinning proton NMR analysis of human prostate tissue with slow spinning rates (2003)

The development of high-resolution magic angle spinning (HR-MAS) NMR spectroscopy for intact tissue analysis and the correlations between the measured tissue metabolites and disease pathologies have inspired investigations of slow-spinning methodologies to maximize the protection of tissue pathology structures from HR-MAS centrifuging damage. Spinning sidebands produced by slow-rate spinning must be suppressed to prevent their complicating the spectral region of metabolites. Twenty-two human prostatectomy samples were analyzed on a 14.1T spectrometer, with HR-MAS spinning rates of 600 Hz, 700 Hz, and 3.0 kHz, a repetition time of 5 sec, and employing various rotor-synchronized suppression methods, including DANTE, WATERGATE, TOSS, and PASS pulse sequences. Among them, DANTE, as the simplest scheme, has shown the most potential in suppression of tissue water signals and spinning sidebands, as well as in quantifying metabolic concentrations.
Changes in endotoxin levels in T2DM subjects on anti-diabetic therapies (2009)

We conclude that sub-clinical inflammation in T2DM may, in part, be mediated by circulating endotoxin. Furthermore, that whilst the endotoxin and adipocytokine profiles of diabetic patients treated with different therapies were comparable, the RSG group demonstrated significant differences in both adiponectin and endotoxin levels. We confirm an association between endotoxin and serum insulin and triglycerides and an inverse relationship with HDL. Lower endotoxin and higher adiponectin in the groups treated with RSG may be related and indicate another mechanism for the effect of RSG on insulin sensitivity.
Efficient processing of k nearest neighbor joins using MapReduce (2012)

k nearest neighbor join ( k NN join), designed to find k nearest neighbors from a dataset S for every object in another dataset R , is a primitive operation widely adopted by many data mining applications. As a combination of the k nearest neighbor query and the join operation, k NN join is an expensive operation. Given the increasing volume of data, it is difficult to perform a k NN join on a centralized machine efficiently. In this paper, we investigate how to perform k NN join using MapReduce which is a well-accepted framework for data-intensive applications over clusters of computers. In brief, the mappers cluster objects into groups; the reducers perform the k NN join on each group of objects separately. We design an effective mapping mechanism that exploits pruning rules for distance filtering, and hence reduces both the shuffling and computational costs. To reduce the shuffling cost, we propose two approximate algorithms to minimize the number of replicas. Extensive experiments on our in-house cluster demonstrate that our proposed methods are efficient, robust and scalable.
Attenuation of cAMP-mediated responses in MA-10 Leydig tumor cells by genetic manipulation of a cAMP-phosphodiesterase (1991)

In order to assess the effect of increased cAMP degradation on the responsiveness on an endocrine cell, we have obtained stable transfectants of MA-10 Leydig tumor cells that overexpress a mammalian cAMP-phosphodiesterase. Two novel cell lines, designated MA-10(P+8) and MA-10(P+29), that express high levels of the transfected enzyme were characterized. Although the basal levels of cAMP in the mutant cell lines are comparable to those of the wild-type cells, the increase in cAMP accumulation elicited by human choriogonadotropin (hCG) is severely blunted. Further studies with MA-10(P+29) show that the ability of hCG to stimulate adenylyl cyclase activity is normal. The failure of MA-10(P+29) cells to accumulate cAMP in response to hCG can be correlated with a similar reduction in hCG-stimulated steroidogenesis. On the other hand, the maximal steroidogenic response of MA-10(P+29) cells to dibutyryl cAMP, a cAMP analogue that is fairly resistant to phosphodiesterase degradation, is normal. We also show that the ability of these cells to respond to hCG with increased cAMP accumulation and steroid synthesis can be restored with a specific phosphodiesterase inhibitor. These results demonstrate that overexpression of a cAMP-phosphodiesterase in MA-10 cells limits the levels of cAMP attained under hCG stimulation and supresses the steroidogenic response of these cells to hCG. Since gonadotropins increase the cAMP-phosphodiesterase activity in their target cells, these findings also provide evidence that this regulation plays a major role in the modulation of cell responsiveness. Last, these new cell lines should be valuable in the study of the actions of cAMP because they express a conditional and reversible cAMP-resistant phenotype.
A Variable Pressure Method for Characterizing Nanoparticle Surface Charge Using Pore Sensors (2012)

A novel method using resistive pulse sensors for electrokinetic surface charge measurements of nanoparticles is presented. This method involves recording the particle blockade rate while the pressure applied across a pore sensor is varied. This applied pressure acts in a direction which opposes transport due to the combination of electro-osmosis, electrophoresis, and inherent pressure. The blockade rate reaches a minimum when the velocity of nanoparticles in the vicinity of the pore approaches zero, and the forces on typical nanoparticles are in equilibrium. The pressure applied at this minimum rate can be used to calculate the zeta potential of the nanoparticles. The efficacy of this variable pressure method was demonstrated for a range of carboxylated 200 nm polystyrene nanoparticles with different surface charge densities. Results were of the same order as phase analysis light scattering (PALS) measurements. Unlike PALS results, the sequence of increasing zeta potential for different particle types agreed with conductometric titration.
A Hyperelastic Approach for Composite Reinforcement Large Deformation Analysis (2009)

A hyperelastic constitutive model is developed for textile composite reinforcement at large strain. A potential is proposed, which is the addition of two tension and one shear energies. The proposed potential is a function of the right Cauchy Green and structural tensor invariants whose choice corresponds to textile composite reinforcement mechanical behavior which exhibits weak elongations in the fiber directions and large angular variations in the fabric plane. The model is implemented in a Vumat user routine of ABAQUS/Explicit. Some elementary tests are performed in order to identify the model and verify its validity. It is then used to simulate the hemispherical punch forming of balanced and unbalanced fabrics. A correct agreement is obtained with experimental forming processes.
The effect of divalent nickel (Ni2+) on in vitro DNA replication by DNA polymerase alpha. (1994)

The effects of the carcinogenic metal nickel on DNA polymerase alpha (pol alpha) activity and fidelity have been analyzed. In the absence of Mg2+, the presence of Ni2+ ions at concentrations below 0.25 mM gave rise to a dose-dependent activation of pol alpha as monitored by [3H]dTMP incorporation into an activated DNA template. The apparent Km for Ni(2+)-dependent pol alpha incorporation of dTTP was estimated to be 25 microM, which was about 10 times higher than the Km for Mg2+ (2.3 microM). Above 0.25 mM, Ni2+ caused a dose-dependent inhibition of pol alpha activity and the Ki was calculated to be 1.5 mM. Scatchard analyses showed that Ni2+ binds to affinity-purified pol alpha and associated proteins at two tight binding sites with a Kd of approximately 50 microM and at eight weak binding sites with a Kd of approximately 4 mM. In the presence of 2 mM Mg2+, the addition of Ni2+ to the reactions caused an inhibition of polymerase activity. The inhibition patterns tended to switch from competitive to mixed-type to noncompetitive as a function of Ni2+ concentration. Lastly, Ni2+ increased the incorporation of the modified nucleotide dideoxy-CMP in reactions using varying ratios of dideoxy-CTP/dCTP.
Photonic chip based tunable and reconfigurable narrowband microwave photonic filter using stimulated Brillouin scattering (2012)

We report the first demonstration of a photonic chip based dynamically reconfigurable, widely tunable, narrow pass-band, high Q microwave photonic filter (MPF). We exploit stimulated Brillouin scattering (SBS) in a 6.5 cm long chalcogenide (As2S3) photonic chip to demonstrate a MPF that exhibited a high quality factor of ~520 and narrow bandwidth and was dynamically reconfigurable and widely tunable. It maintained a stable 3 dB bandwidth of 23 ± 2MHz and amplitude of 20 ± 2 dB over a large frequency tuning range of 2-12 GHz. By tailoring the pump spectrum, we reconfigured the 3 dB bandwidth of the MPF from ~20 MHz to ~40 MHz and tuned the shape factor from 3.5 to 2 resulting in a nearly flat-topped filter profile. This demonstration represents a significant advance in integrated microwave photonics with potential applications in on-chip microwave signal processing for RADAR and analogue communications.
Regulation of a Chitinase Gene Promoter by Ethylene and Elicitors in Bean Protoplasts (1991)

Chitinase gene expression has been shown to be transcriptionally regulated by a number of inducers, including ethylene, elicitors, and pathogen attack. To investigate the mechanism(s) responsible for induction of chitinase gene expression in response to various stimuli, we have developed a transient gene expression system in bean (Phaseolus vulgaris) protoplasts that is responsive to ethylene and elicitor treatment. This system was used to study the expression of a chimeric gene composed of the 5' flanking sequences of a bean endochitinase gene fused to the reporter gene beta-glucuronidase linked to a 3' fragment from nopaline synthase. Addition of 1-aminocyclopropane-1-carboxylic acid, the direct precursor of ethylene, or elicitors such as chitin oligosaccharides or cell wall fragments derived from Colletotrichum lagenarium, to transformed protoplasts resulted in a rapid and marked increase in the expression of the chimeric gene. The kinetics and dose response for these treatments were similar to those observed for the native gene in vivo. Analyses of 5' deletion mutants in the protoplast system indicated that DNA sequences located between -305 and -236 are important for both ethylene and elicitor induction of the reporter gene.
Weighted universal bit allocation: optimal multiple quantization matrix coding (2002)

We introduce a two-stage bit allocation algorithm analogous to the algorithm for weighted universal vector quantization (WUVQ). The encoder uses a collection of possible bit allocations (typically in the form of a collection of quantization matrices) rather than a single bit allocation (or single quantization matrix). We describe both an encoding algorithm for achieving optimal compression using a collection of bit allocations and a technique for designing locally optimal collections of bit allocations. We demonstrate performance on a JPEG style coder using the mean squared error (MSE) distortion measure. On a sequence of medical brain scans, the algorithm achieves up to 2.5 dB improvement over a single bit allocation system, up to 5 dB improvement over a WUVQ with first- and second-stage vector dimensions equal to 16 and 4 respectively, and up to 12 dB improvement over an entropy constrained vector quantizer (ECVQ) using 4 dimensional vectors.
Three-Dimensional Culture of Human Breast Epithelial Cells: The How and the Why (2012)

Organs are made of the organized assembly of different cell types that contribute to the architecture necessary for functional differentiation. In those with exocrine function, such as the breast, cell-cell and cell-extracellular matrix (ECM) interactions establish mechanistic constraints and a complex biochemical signaling network essential for differentiation and homeostasis of the glandular epithelium. Such knowledge has been elegantly acquired for the mammary gland by placing epithelial cells under three-dimensional (3D) culture conditions.Three-dimensional cell culture aims at recapitulating normal and pathological tissue architectures, hence providing physiologically relevant models to study normal development and disease. The specific architecture of the breast epithelium consists of glandular structures (acini) connected to a branched ductal system. A single layer of basoapically polarized luminal cells delineates ductal or acinar lumena at the apical pole. Luminal cells make contact with myoepithelial cells and, in certain areas at the basal pole, also with basement membrane (BM) components. In this chapter, we describe how this exquisite organization as well as stages of disorganization pertaining to cancer progression can be reproduced in 3D cultures. Advantages and limitations of different culture settings are discussed. Technical designs for induction of phenotypic modulations, biochemical analyses, and state-of-the-art imaging are presented. We also explain how signaling is regulated differently in 3D cultures compared to traditional two-dimensional (2D) cultures. We believe that using 3D cultures is an indispensable method to unravel the intricacies of human mammary functions and would best serve the fight against breast cancer.
A study on threat model for federated identities in federated identity management system (2010)

Federated Identity Management (FIM) based on standards allows and facilitates participating federated organizations to share users identity attributes, facilitate authentication and grant or deny service access requests. Using single sign-on facility users authenticates only once to home identity provider and logged into access successive service providing service providers within federation. User's identity theft, misused of user identity information via single sign-on facility in identity providers and service providers, and trustworthiness of subject, identity providers and service providers are active concerns in federated identity management systems. In addition, we had explored trusted computing technology, which covers Trusted Platform Module security features such as Trusted Platform Module Identity, Integrity Measurement and Key certification as well as Trusted Network Connect. In this paper, we presented conceptual threat model for inter-domain web single sign-on in federate identity management system. For this, we set identity theft, misused of identity information, and trust relationship scenarios and in the end, we discussed how trusted computing technology use can effectively resolve identity theft, misused of identity information, and trust relationship concerns in federated identity management system.
Identification of Lactobacillus proteins with different recognition patterns between immune rabbit sera and nonimmune mice or human sera (2016)

The different prevalence of reactions against tested antigens in rabbit, mouse and human sera may indicate significant differences in immune system and commensal cross-talk in these groups. The identification of immunoreactive lactobacilli proteins opens the possibility to use them as an antigens for development of vaccines.
Use of colloidal gold particles in double-labeling immunoelectron microscopy of ultrathin frozen tissue sections. (1981)

Complexes of protein-A with 5 and 16 nm colloidal gold particles (PA/Au5 and PA/Au16) are presented as sensitive and clean immunoprobes for ultrathin frozen sections of slightly fixed tissue. The probes are suitable for indirect labeling and offer the opportunity to mark multiple sites. The best procedure for double labeling was to use the smaller probe first, i.e., antibody 1 - PA/Au5 - antibody 2 - PA/Au16. When this was done, no significant interference between PA/Au5 and PA/Au16 occurred. Using this double-labeling procedure we made an accurate comparison between the subcellular distributions of amylase as a typical secretory protein and of GP-2 a glycoprotein, characteristic for zymogen granule membrane (ZGM) preparations. We prepared two rabbit antibodies against GP-2. One antibody (R x ZGM) was obtained by immunizing with native membrane material. The specificity of R x ZGM was achieved by adsorption with the zymogen granule content subfraction. The other, R x GP-2, was raised against the GP-2 band of the SDS polyacrylamide profile of ZGM. We found that the carbohydrate moiety of GP-2 was involved in the antigenic determinant for R x ZGM, while R x GP-2 was most likely directed against GP-2 polypeptide backbone. THe immunocytochemical observations showed that GP-2, on the one hand, exhibited the characteristics of a membrane protein by its occurrence in the cell membrane, the Golgi membranes, and its association with the membranes of the zymogen granules. On the other hand, GP-2 was present in the contents of the zymogen granules and in the acinar and ductal lumina. Also, a GP-2-like glycoprotein was found in the cannulated pancreatic secretion (Scheffer et al., 1980, Eur. J. Cell Biol. 23:122-128). Hence, GP-2 should be considered as a membrane-associated secretory protein of the rat pancreas.
Chemical and Physical Characterization of Interfacial-Active Lipids from <i>Rhodococcus erythropolis</i> Grown on <i>n</i> -Alkanes (1982)

Lipophilic compounds of the culture suspension containing Rhodococcus erythropolis DSM43215 had surfactant properties when the bacteria were cultivated with n-alkanes as the sole carbon source. Thirteen main components from a dichloromethane-methanol extract of the R. erythropolis cultures were isolated and characterized to specify quantitatively their surfactant properties, e.g., minimum surface and interfacial tensions and critical micelle concentrations. The interfacial activity of the organic extract was dominated by alpha,alpha-trehalose-6,6'-dicorynomycolates which reduced interfacial tension from 44 to 18 mN/m. Phosphatidylethanolamines which were also present in the organic extract reduced the interfacial tension below 1 mN/m. The trehalose corynomycolates had extremely low critical micelle concentrations in high-salinity solutions, and the interfacial properties were stabile in solutions with a wide range of pH and ionic strength.