gebhart/patrepeval huggingface dataset:
Ligand-Induced Folding of a Two-Component Signaling Receiver Domain (2015)

To survive and adapt to environmental changes, bacteria commonly use two-component signaling systems. Minimally, these pathways use histidine kinases (HKs) to detect environmental signals, harnessing these to control phosphorylation levels of receiver (REC) domains of downstream response regulators that convert this signal into physiological responses. Studies of several prototypical REC domains suggest that phosphorylation shifts these proteins between inactive and active structures that are globally similar and well-folded. However, it is unclear how globally these findings hold within REC domains in general, particularly when they are considered within full-length proteins. Here, we present EL_LovR, a full-length REC-only protein that is phosphorylated in response to blue light in the marine α-proteobacterium, Erythrobacter litoralis HTCC2594. Notably, EL_LovR is similar to comparable REC-only proteins used in bacterial general stress responses, where genetic evidence suggests that their potent phosphatase activity is important to shut off such systems. Size exclusion chromatography, light scattering, and solution NMR experiments show that EL_LovR is monomeric and unfolded in solution under conditions routinely used for other REC structure determinations. Addition of Mg(2+) and phosphorylation induce progressively greater degrees of tertiary structure stabilization, with the solution structure of the fully activated EL_LovR adopting the canonical receiver domain fold. Parallel functional assays show that EL_LovR has a fast dephosphorylation rate, consistent with its proposed function as a phosphate sink that depletes the HK phosphoryl group, promoting the phosphatase activity of this enzyme. Our findings demonstrate that EL_LovR undergoes substantial ligand-dependent conformational changes that have not been reported for other RRs, expanding the scope of conformational changes and regulation used by REC domains, critical components of bacterial signaling systems.
Plasma inhibitory activity (PIA): a pharmacodynamic assay reveals insights into the basis for cytotoxic response to FLT3 inhibitors (2006)

We have developed a useful surrogate assay for monitoring the efficacy of FLT3 inhibition in patients treated with oral FLT3 inhibitors. The plasma inhibitory activity (PIA) for FLT3 correlates with clinical activity in patients treated with CEP-701 and PKC412. Using the PIA assay, along with in vitro phosphorylation and cytotoxicity assays in leukemia cells, we compared PKC412 and its metabolite, CGP52421, with CEP-701. While both drugs could effectively inhibit FLT3 in vitro, CEP-701 was more cytotoxic to primary samples at comparable levels of FLT3 inhibition. PKC412 appears to be more selective than CEP-701 and therefore less effective at inducing cytotoxicity in primary acute myeloid leukemia (AML) samples in vitro. However, the PKC412 metabolite CGP52421 is less selective than its parent compound, PKC412, and is more cytotoxic against primary blast samples at comparable levels of FLT3 inhibition. The plasma inhibitory activity assay represents a useful correlative tool in the development of small-molecule inhibitors. Our application of this assay has revealed that the metabolite CGP52421 may contribute a significant portion of the antileukemia activity observed in patients receiving oral PKC412. Additionally, our results suggest that nonselectivity may constitute an important component of the cytotoxic effect of FLT3 inhibitors in FLT3-mutant AML.
Content-Based Brain Tumor Retrieval for MR Images Using Transfer Learning (2019)

This paper presents an automatic content-based image retrieval (CBIR) system for brain tumors on T1-weighted contrast-enhanced magnetic resonance images (CE-MRI). The key challenge in CBIR systems for MR images is the semantic gap between the low-level visual information captured by the MRI machine and the high-level information perceived by the human evaluator. The traditional feature extraction methods focus only on low-level or high-level features and use some handcrafted features to reduce this gap. It is necessary to design a feature extraction framework to reduce this gap without using handcrafted features by encoding/combining low-level and high-level features. Deep learning is very powerful for feature representation that can depict low-level and high-level information completely and embed the phase of feature extraction in self-learning. Therefore, we propose a deep convolutional neural network VGG19-based novel feature extraction framework and apply closed-form metric learning to measure the similarity between the query image and database images. Furthermore, we adopt transfer learning and propose a block-wise fine-tuning strategy to enhance the retrieval performance. The extensive experiments are performed on a publicly available CE-MRI dataset that consists of three types of brain tumors (i.e., glioma, meningioma, and pituitary tumor) collected from 233 patients with a total of 3064 images across the axial, coronal, and sagittal views. Our method is more generic, as we do not use any handcrafted features; it requires minimal preprocessing, tested as robust on fivefold cross-validation, can achieve a fivefold mean average precision of 96.13%, and outperforms the state-of-the-art CBIR systems on the CE-MRI dataset.
Microstructure, Plasticity and Ductility of a TNM+ Alloy Densified by Spark Plasma Sintering (2022)

This work presents a study of the microstructure and mechanical properties of a TNM+ alloy (Ti-43.5Al-4Nb-1Mo-0.1B-0.3C-0.3Si, in at.%) densified by Spark Plasma Sintering (SPS), in comparison to the as-SPSed TNM alloy, which contains neither carbon nor silicon. Tensile tests at room temperature and 800 °C, as well as creep tests at 800 °C and 200 MPa, were performed. The microstructures and the fracture surfaces of deformed samples were studied by scanning and transmission electron microscopies, as well as by X-ray diffraction. The deformation mechanisms were investigated by means of in situ straining experiments and post-mortem analyses of deformed samples, both performed by transmission electron microscopy. Contrary to the TNM alloy, the as-SPSed microstructure of the TNM+ alloy does not contain β/βo phase due to the incorporation of carbon. At room temperature, the TNM+ alloy exhibits a yield stress of 520 MPa but a poor ductility of less than 0.1% of plastic strain. The incorporation of carbon and silicon leads to an increase in the creep resistance of the alloy at 800 °C. Despite the fact that iron inclusions are responsible for the premature failure of some samples during tensile tests, the TNM+ alloy is found to be able to deform plastically at room temperature by the glide of ordinary dislocations and by twinning.
Advanced Multi-Product Coal Utilization By-Product Processing Plant (2006)

The objective of the project is to build a multi-product ash beneficiation plant at Kentucky Utilities 2,200-MW Ghent Generating Station, located in Carroll County, Kentucky. This part of the study includes an investigation of the secondary classification characteristics of the ash feedstock excavated from the lower ash pond at Ghent Station. The market study for the products of the processing plant (Subtask 1.6), conducted by Cemex, is reported herein. The study incorporated simplifying assumptions and focused only on pozzolan and ultra fine fly ash (UFFA). It found that the market for pozzolan in the Ghent area was oversupplied, with resultant poor pricing structure. Reachable export markets for the Ghent pozzolan market were mostly locally served with the exception of Florida. It was concluded that a beneficiated material for that market may be at a long term disadvantage. The market for the UFFA was more complex as this material would compete with other beneficiated ash and potential metakaolin and silica fume as well. The study concluded that this market represented about 100,000 tons of sales per year and, although lucrative, represented a widely dispersed niche market.
A SILICON PHOTODIODE ARRAY DETECTOR COVERING A LARGE SOLID ANGLE FOR FLUORESCENCE EXAFS MEASUREMENTS FROM 2 TO 25 keV (1986)

A Si-photodiode array detector operated in the photovoltaic mode is shown to offer several advantages over other fluorescence detectors : high efficiency, perfect linearity of the response, vacuum compatibility for soft X-ray measurements, absence of gas and voltage supplies. Low temperature cooling down to - 120°C is needed in order to decrease the dark current and thermal noise of the shunt resistance.Typica1 spectra recorded on a dilute cytochrome c solution and on a liquid which is strongly absorbing in the soft X-ray range i.e. C2Cl4[MATH] are presented.
PRIMARY FROZEN SHOULDER, THE UNTOLD STORY! (2006)

The purpose of the study was to test the hypothesis that cellular mechanisms of fibroblasts derived from primary frozen shoulder (PFS) exhibit similar activity in terms of contraction, response to cytokine transforming growth factor-beta1 (TGF beta1) and mechanical stimulation similar to that generated by fibroblasts derived from dupuytren's disease. Frozen shoulder has been postulated to be Dupuytren's disease of the shoulder with an association inferred since 1936. Primary explant cultures of fibroblasts from seven patients with PFS and five control patients were obtained using standard tissue culture techniques. Fibroblasts were seeded in 3-D collagen constructs and contraction force generated over 24 hours measured using a culture force monitor (CFM) in real time. Increasing concentrations of TGF-beta1 were added to cell seeded gels and force generated measured using the CFM over 24 hours. These mechanical output data were statistically compared to data available from Dupuytren's disease. Compared to Dupuytren's fibroblasts, PFS fibroblasts showed a statistically reduced ability to contract a 3-D collagen gel over 24 hours (p&lt;0.01). In Dupuytren's disease, fibroblasts derived from nodules and cords generate peak forces of 140 dynes and 110 dynes respectively, while PFS fibroblasts generated peak force of 8 dynes The response to TGF-beta1 stimulation, which has been shown to enhance peak force contraction in Dupuytren's fibroblasts had no effect on PFS fibroblasts and this was statistically significant (p&lt;0.01). These data suggest intrinsic differences in cellular activity and mechanisms between Dupuytren's and Primary Frozen Shoulder even though clinically they both manifest with a contracted extracellular matrix affecting function and requiring surgical intervention. This may explain increased post surgical recurrence in Dupuytren's as compared to Primary Frozen Shoulder release.
H3K9 Histone Methyltransferase, KMT1E/SETDB1, Cooperates with the SMAD2/3 Pathway to Suppress Lung Cancer Metastasis (2014)

Aberrant histone methylation is a frequent event during tumor development and progression. KMT1E (also known as SETDB1) is a histone H3K9 methyltransferase that contributes to epigenetic silencing of both oncogenes and tumor suppressor genes in cancer cells. In this report, we demonstrate that KMT1E acts as a metastasis suppressor that is strongly downregulated in highly metastatic lung cancer cells. Restoring KMT1E expression in this setting suppressed filopodia formation, migration, and invasive behavior. Conversely, loss of KMT1E in lung cancer cells with limited metastatic potential promoted migration in vitro and restored metastatic prowess in vivo. Mechanistic investigations indicated that KMT1E cooperates with the TGFβ-regulated complex SMAD2/3 to repress metastasis through ANXA2. Together, our findings defined an essential role for the KMT1E/SMAD2/3 repressor complex in TGFβ-mediated lung cancer metastasis.
Universal Amplification and Analysis of Pathogen 16S rDNA for Classification and Identification of Mycoplasmalike Organisms (1993)

Regions representing about 80% of the 16S rDNA sequences of 40 mycoplasmalike organism (MLO) strains from North America, Asia, and Europe were amplified by polymerase chain reaction (PCR) using a primer pair designed on the basis of an MLO 16S rRNA gene. This primer pair detected every MLO examined from infected periwinkle (Catharanthus roseus) and some other plants. No PCR products were obtained in samples containing DNA extracted from healthy plants. The partial 16S rDNA sequences amplified from these various MLOs were compared through restriction fragment length polymorphism (RFLP) analyses [...]
Price based protocols for fair resource allocation: convergence time analysis and extension to Leontief utilities (2008)

We analyze several distributed, continuous time protocols for a fair allocation of bandwidths to flows in a network (or resources to agents). Our protocols converge to an allocation which is a logarithmic approximation, simultaneously, to all canonical social welfare functions (i.e. functions which are symmetric, concave, and non-decreasing). These protocols can be started in an arbitrary state. While a similar protocol was known before, it only applied to the simple bandwidth allocation problem, and its stability and convergence time was not understood. In contrast, our protocols also apply to the more general case of Leontief utilities, where each user may place a different requirement on each resource. Further, we prove that our protocols converge in polynomial time. The best convergence time we prove is), where n is the number of agents in the O(n log ncmaxamax cminamin network, cmax and cmin are the maximum and minimum capacity of the links, and amax, amin are the largest and smallest Leontief coefficients, respectively. This time is achieved by a simple MIMD (multiplicative increase, multiplicative decrease) protocol which had not been studied before in this setting. We also identify combinatorial properties of these protocols that may be useful in proving stronger convergence bounds. The final allocations by our protocols are supported by usage-sensitive dual prices which are fair in the sense that they shield light users of a resource from the impact of heavy users. Thus our protocols can also be thought of as efficient distributed schemes for computing fair prices. 1
Well-Log and Seismic Data Integration for Reservoir Characterization: A Signal Processing and Machine-Learning Perspective (2018)

Reservoir characterization (RC) is a process of finding petrophysical properties of the subsurface mainly from the seismic and well-log data. The nonlinear and heterogeneous nature of the subsurface is the major bottleneck in estimating the reservoir properties. In the past two decades, the RC has eventually turned out to be an interdisciplinary field of research involving computational science, signal processing, geostatistics, and geophysics. This article provides the interdisciplinary perspective in RC focusing on the applications of signal processing and machine learning (ML). We provide an account of various state-of-the-art algorithms while categorizing them into three stages in an RC framework: preprocessing, prediction, and postprocessing. RC has been known to be a highly data-driven problem. Huge volumes of seismic and well-log data are cleverly integrated by experts to decipher the subsurface properties. Some of the anomalies may lead to the existence of a potential reservoir. The signal processing tools are primarily required for information matching, preprocessing for noise and artifacts, and postprocessing for removing irregularities in the prediction, whereas the ML tools are required to map the seismic data to well logs. This article provides a comprehensive study on the recent advances in RC involving seismic volumes and well logs.
On Blocking Collisions between People, Objects and other Robots (2018)

Intentional or unintentional contacts are bound to occur increasingly more often due to the deployment of autonomous systems in human environments. In this paper, we devise methods to computationally predict imminent collisions between objects, robots and people, and use an upper-body humanoid robot to block them if they are likely to happen. We employ statistical methods for effective collision prediction followed by sensor-based trajectory generation and real-time control to attempt to stop the likely collisions using the most favorable part of the blocking robot. We thoroughly investigate collisions in various types of experimental setups involving objects, robots, and people. Overall, the main contribution of this paper is to devise sensor-based prediction, trajectory generation and control processes for highly articulated robots to prevent collisions against people, and conduct numerous experiments to validate this approach.
Hypothesis test for synchronization: Twin surrogates revisited (2009)

The method of twin surrogates has been introduced to test for phase synchronization of complex systems in the case of passive experiments. In this paper we derive new analytical expressions for the number of twins depending on the size of the neighborhood, as well as on the length of the trajectory. This allows us to determine the optimal parameters for the generation of twin surrogates. Furthermore, we determine the quality of the twin surrogates with respect to several linear and nonlinear statistics depending on the parameters of the method. In the second part of the paper we perform a hypothesis test for phase synchronization in the case of experimental data from fixational eye movements. These miniature eye movements have been shown to play a central role in neural information processing underlying the perception of static visual scenes. The high number of data sets (21 subjects and 30 trials per person) allows us to compare the generated twin surrogates with the "natural" surrogates that correspond to the different trials. We show that the generated twin surrogates reproduce very well all linear and nonlinear characteristics of the underlying experimental system. The synchronization analysis of fixational eye movements by means of twin surrogates reveals that the synchronization between the left and right eye is significant, indicating that either the centers in the brain stem generating fixational eye movements are closely linked, or, alternatively that there is only one center controlling both eyes.
ChemInform Abstract: Isolation of a Putative Biogenetic Taxane Precursor from Taxus Canadensis Needles. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Synthesis of silicon carbide by carbothermal reduction of quartz in H2-Ar gas mixtures (2015)

The slogan of our fourteenth Congress is ‘Energy efficiency and environmental friendliness are the future of the global Ferroalloy industry’, and we hope that this will be the key approach in the Congress subject area to be discussed within plenary meetings and workshops in the days to come. The same topic will be raised during such events as traditional Technical exhibition and tech tours to leading ferroalloy plants of Ukraine. The present book contains 102 reports which will be heard during 2 plenary sessions and 24 break-out sessions of 14 sections of the Congress. All reports have been peer-reviewed, for this purpose the large team of international experts has been involved. Program and Organizing committees express sincere thanks to all authors and reviewers for their work.
Draft Whole-Genome Sequences of Seven Listeria monocytogenes Strains with Variations in Virulence and Stress Responses (2018)

Listeria monocytogenes is an important foodborne pathogen that causes listeriosis. Here, we report the draft genome sequences of seven L. monocytogenes strains isolated from food, environmental, and clinical sources. Sequence differences at the genome level may help in understanding why these strains displayed different virulence and stress response characteristics.
Insecticidal and repellent properties of nine volatile constituents of essential oils against the American cockroach,Periplaneta americana(L.) (1998)

The toxic and repellent properties of nine major constituents of essential oils, comprising benzene derivatives and terpenes, were evaluated against Periplaneta americana (L.). Contact and fumigant toxicities to adult females and repellency to nymphs were determined. The decreasing order of knockdown activity via contact was methyl-eugenol>isosafrole=eugenol>safrole. The killing effect via contact was in the order eugenol=methyl-eugenol=isosafrole>safrole. Fumigant toxicity was only observed for safrole and isosafrole, with safrole being the more potent. Isoeugenol and the tested terpenes had neither contact nor fumigant toxic effect. The decreasing order of repellency to nymphs was safrole>isosafrole>methyl-eugenol=α-pinene> eugenol>isoeugenol. The benzene derivatives were generally more toxic and repellent to P. americana than the terpenes. The distance of the side chain double bond from the aromatic ring and the substitution of a methoxy group to these compounds appeared to be important determinants of their toxicity and repellency. © 1998 Society of Chemical Industry
NBS time to the Western Hemisphere by satellite (1979)

As a complement to the present time and frequency services of WWV, WWVH, and WWVB, the National Bureau of Standards (NBS) is now providing a satellite‐disseminated time code using the Geostationary Operational Environmental Satellites (Goes) of the National Oceanic and Atmospheric Administration (NOAA). The time code is referenced to the NBS time scale, giving coordinated universal time (UTC). In addition to the usual information of day of year, hours, minutes, seconds, and the UTl correction the time code contains the satellite's current position for use in path delay calculations. The time signals are relayed to the entire Western Hemisphere from two geostationary satellites on a full‐time basis except during brief periods of solar eclipses occurring during the vernal and autumnal equinoxes. The time code, originally intended for use by environmental monitoring platforms, is easily accessible by anyone using relatively simple, commercially available equipment. Physically small antennas (30 cm × 30 cm × 1cm) are typical. The generation, satellite relay, and recovery of these signals is discussed. Results obtained with commercial receiving equipment are included.
Integrated terahertz transmitters and receivers (2004)

Through a US Army sponsored SBIR project we are developing terahertz components based on integrated GaAs Schottky diodes for the frequency range from 200 - 700 GHz. These new components are inherently broadband and therefore require no mechanical tuners. Rather, they can be electronically swept across significant frequency bands and are therefore useful for chemical and biological spectroscopy. This talk will focus on our demonstration of a terahertz frequency Transmit / Receive capability which may be of use for CB detection and secure communications.