gebhart/patrepeval huggingface dataset:
Different promoter affinities account for specificity in MYC-dependent gene regulation (2016)

Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells.
Facial Age Estimation using Deep neural networks: A Survey (2019)

Facial age estimation techniques are extensively used in vitality applications nowadays; however, they are a time-consuming task. Compared to other methods, deep learning algorithms showed a superior performance to solve face related age estimation problem. The current surveys are incomplete, not up-to-date and are not concerned with deep learning in particular. In this paper, a comprehensive updated summary of the deep age estimation frameworks are introduced. We review the previous research efforts in deep age estimation systems and present the popular datasets. Convolution Neural Networks (CNN) are introduced with their models. The performance criteria widely used in evaluation are declared. Finally, the challenges and the future directions are discussed to reach a robust facial age estimation system.
Metal-on-metal hip resurfacing: what have we learned? (2007)

Surface hip arthroplasty has many attractive features for young, active patients, particularly because of the conservative nature of this treatment and its ability to preserve femoral bone. It is more anatomic and physiologic than stem-type hip replacements, and it represents a truly minimally osteoinvasive procedure, with no penetration into the femoral intramedullary canal. In addition, the construct has increased stability because of the near-normal diameter of the femoral component compared with most conventional hip replacement components. Although the short- to midterm clinical results for metal-on-metal hybrid hip resurfacing implants are definitely superior to those of earlier generations of resurfacing implants, the results of conventional total hip replacement using contemporary designs and bearing materials have also improved. As a result, it is imperative to assess what is known about the safety and efficacy of resurfacing to refine the indications and technique to improve the overall results and durability.
Cleavage of <i>N ‘</i>,<i>N ‘</i>-Dialkylhydrazides with PhI(OH)OTs (2000)

N',N'-Dimethylhydrazides are efficiently cleaved to give the carboxylic acid upon treatment with PhI(OH)OTs in water or water/CH(2)Cl(2) mixtures. The reaction occurs with the evolution of a gas.
A low-power wide-dynamic-range readout IC for breath analyzer system (2013)

We present a low-power wide-dynamic-range readout circuit that directly interfaces a selective metal-oxide gas sensor. The proposed novel readout architecture implements an adaptive baseline compensation and limits the sensor current. The readout IC can interface the sensors with the baseline resistance from 1 kΩ to 100 MΩ and measures the gas induced resistance change in the range from 0.05% to 10% of the baseline resistance. The simulations demonstrate the 166 dB dynamic range of the readout circuit and 113 μW power consumption amenable to the sensors that can operate at room temperature for the application of the proposed system in portable breath analyzers.
Human XPA and RPA DNA repair proteins participate in specific recognition of triplex-induced helical distortions (2002)

Nucleotide excision repair (NER) plays a central role in maintaining genomic integrity by detecting and repairing a wide variety of DNA lesions. Xeroderma pigmentosum complementation group A protein (XPA) is an essential component of the repair machinery, and it is thought to be involved in the initial step as a DNA damage recognition and/or confirmation factor. Human replication protein A (RPA) and XPA have been reported to interact to form a DNA damage recognition complex with greater specificity for damaged DNA than XPA alone. The mechanism by which these two proteins recognize such a wide array of structures resulting from different types of DNA damage is not known. One possibility is that they recognize a common feature of the lesions, such as distortions of the helical backbone. We have tested this idea by determining whether human XPA and RPA proteins can recognize the helical distortions induced by a DNA triple helix, a noncanonical DNA structure that has been shown to induce DNA repair, mutagenesis, and recombination. We measured binding of XPA and RPA, together or separately, to substrates containing triplexes with three, two, or no strands covalently linked by psoralen conjugation and photoaddition. We found that RPA alone recognizes all covalent triplex structures, but also forms multivalent nonspecific DNA aggregates at higher concentrations. XPA by itself does not recognize the substrates, but it binds them in the presence of RPA. Addition of XPA decreases the nonspecific DNA aggregate formation. These results support the hypothesis that the NER machinery is targeted to helical distortions and demonstrate that RPA can recognize damaged DNA even without XPA.
Floodwater detection on roadways from crowdsourced images (2018)

This work proposes an image processing pipeline for detecting floodwater extent on inundated roadways from image data captured and generated by mobile consumer devices, such as smartphones. A sample data-set collected from actual nuisance flooding events in Norfolk, VA and location-matched reference images are used to demonstrate the proposed approach. The highly variable nature of crowdsourced data manifests as discrepancies in location-matched dry/flooded condition image pairs, making extracting inundation information more challenging. These discrepancies may include differences in resolution, lighting and environmental conditions. Scenes may include dynamic objects, such as vehicles and pedestrians, on the roadway. In the proposed pipeline, images go through a set of pre-processing operations consisting of water edge detection, image inpainting and contrast correction. A Region-Based Convolutional Neural Network (R-CNN) is trained, tested and deployed for vehicle detection. An inpainting procedure removes vehicles detected by the R-CNN. The images are registered using the Scale Invariant Feature Transform flow algorithm. Boundaries of the flooded area are detected. Reflections of landmarks and sky/clouds also pose an important challenge to detection of inundated areas. Reflections from nearby landmarks are first identified, then used as a seed for identifying the remaining water body, including reflections of sky/clouds, through saturation channel processing. The result is further processed with the detected water edge lines. False positives are removed. The proposed method is applied to real-world images and its accuracy is evaluated. The results show that the method produces satisfactory results despite the complexities of the crowdsourced image data and dynamic environment.
Metronomic photodynamic therapy (mPDT) -- headlights to lead the way forward: technical feasibility and rationale in brain tumor (2003)

The concept of metronomic photodynamic therapy (mPDT) is presented, in which both the photosensitizer and light are deliverd continuously at low rates over extended periods in order to increase selective tumor cell kill through apoptosis. The focus of the present work is on mPDT treatment of malignant brain tumors, in which selectivity between damage to tumor cells versus normal brain tissue is critical. Previous studies have shown taht low-dose PDT using aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) can induce apoptosis in tumor cells within causing nectrosis in either tumor or normal brain tissue or apoptosis in teh latter. In order to produce enough tumor cell kill to be an effective therapy, multiple PDT treatments, such as hyperfractionation or metronomic delivery, are likely required, based on the levels of apoptosis achieved and model calculations of tumor growth rates. mPDT poses two substantial technical challenges: extended delivery of ALA and implantation of interstitial devices for extended light delivery while allowing free movement. In rat models ALAL administration via the drinking water has been accomplished at significant doesse (up to 10 times therapeutic dose) for up to 10 days, and ex vivo spectrofluorimetry of tumor, normal brain and other tissues post mortem demonstrates a 3-4 increase in the tumor-to-brain concentration of PpIX, without toxicity. Prototype light sources and delivery devices are also shown to be practical, either using laser diode or light emitting diode (LED) coupled to an implanted optical fiber in the case of the rat model or a directly-implanted LED in rabbits. The combined delivery of both drug and light over an extended period, with survival of the animls, is demonstrated. Preliminary evidence of selective aopotosis of tumor under these conditions is presented.
Developing control strategies to mitigate injury after falling backward with a lower limb exoskeleton (2017)

Powered lower limb exoskeletons (LLEs) are wearable robotic aids that provide mobility assistance for people with mobility impairments. Despite their advanced design, LLEs are still far from being effective assistive devices that can be used to perform activities of daily living. The main challenge in the operation of a LLE is to ensure that balance is maintained. However, maintaining an upright stance is not always achievable and regardless of the quality of user skill and training, inevitably falls will occur. Currently, there is no control strategy developed or implemented in LLEs that help reduce the user’s risk of injury in the case of an unexpected fall. In this thesis, an optimization methodology was developed and used to create a safer strategy for exoskeletons falling backwards in a simulation environment. Due to the data available regarding the biomechanics of human falls, the optimization methodology was first developed to study falls with simulation parameters characteristic of healthy people. The resulting optimal fall strategy in this study had similar kinematic and dynamic characteristics to the findings of previous studies on human falls. Rapid knee flexion at the onset of the fall, and knee extension prior to ground contact are examples of these characteristics. Following this, the optimization methodology was extended to include the characteristics of an exoskeleton. The results revealed that the hip impact velocity was reduced by 58% when the optimal fall strategy was employed compared to the case where the exoskeleton fell with locked joints. It was also shown that in both cases of optimal human and human-exoskeleton falls, the models contacted the ground with an upright trunk with a near-zero trunk angular velocity to avoid head impact. These results achieved the thesis goal of developing an effective safe fall control strategy. This strategy was then implemented in a prototype exoskeleton test device. The experimental results validated the simulation outcomes and support the feasibility of implementing this control strategy. Future studies are needed to further examine the effectiveness of applying this strategy in an actual LLE.
Cytokines and Pain (2011)

Cytokines have an important role in pain through different mechanisms in several sites of pain transmission pathways.
Towards reliable traffic sign recognition (2009)

The demand for reliable traffic sign recognition (TSR) increases with the development of safety driven advanced driver assistance systems (ADAS). Emerging technologies like brake-by-wire or steer-by-wire pave the way for collision avoidance and threat identification systems. Obviously, decision making in such critical situations requires high reliability of the information base. Especially for comfort systems, we need to take into account that the user tends to trust the information provided by the ADAS. In this paper, we present a robust system architecture for the reliable recognition of circular traffic signs. Our system employs complementing approaches for the different stages of current TSR systems. This introduces the application of local SIFT features for content-based traffic sign detection along with widely applied shape-based approaches. We further add a technique called contracting curve density (CCD) to refine the localization of the detected traffic sign candidates and therefore increase the performance of the subsequent classification module. Finally, the recognition stage based on SIFT and SURF descriptions of the candidates executed by a neural net provides a robust classification of structured image content like traffic signs. By applying these steps we compensate the weaknesses of the utilized approaches, and thus, improve the system's performance.
High-Power Thyratron-Type Switch For Laser Applications (1989)

A review of recent progress in the development of the low-pressure (~27 Pa H2) glow discharge pulsed high-power (10~30kV) switch, the Back-Lighted Thyratron (BLT), is to be presented. The BLT operates with a glow discharge and utilizes a simple device geometry. New data on peak current capability, current rise rate, current reversal ability, life, repetition rate operation, and trigger efficiency and comparisons of delay and jitter with different trigger methods (flash-triggered, laser-triggered and electrically-triggered) are reported.
Kinetic‐energy‐sensitive mass spectrometry for separation of different ions with the same <i>m</i>/<i>z</i> value (2008)

A double-focusing mass spectrometer (MS) equipped with a superconducting-tunnel-junction (STJ) detector has been applied to measure relative ionization cross-sections for the production of ions that are accompanied by different ion species with the same mass-to-charge (m/z) value. The STJ detector fabricated for this study enables kinetic energy (E) measurement of incoming individual ions at a counting rate of up to approximately 100 k ions/s and an energy resolution (DeltaE/E) of 15%. Both high counting rate and high-energy resolution are necessary to independently determine both m and z and not the m/z value only in ion-counting MS experiments. Ions such as (14)N(2) (2+) and (14)N(+) with the same m/z value can be clearly discriminated using a kinetic-energy-sensitive MS. This fine discrimination capability allows direct determination of relative ionization cross-sections of the homonuclear diatomic ions (14)N(2) (2+)/(14)N(2) (+) and (16)O(2) (2+)/(16)O(2) (+), which are difficult to measure due to the strong interference by the signals of their dissociated atomic ions with noticeably large ionization cross-sections. The new instrument requires no low-abundance heteronuclear diatomic molecules of the forms (14)N(15)N or (16)O(17)O to carry out ionization studies and thus, is expected to be useful in fields such as atmospheric science, interstellar science, or plasma physics.
Use of Ethidium Bromide for Separation and Determination of Nucleic Acids of Various Conformational Forms and Measurement of Their Associated Enzymes (1971)

This chapter contains sections titled: Introduction Summary of the Properties of the Ethidium Bromide Preparation and Separation of Covalently Closed Circular DNAs Fluorometric Determination of Nucleic Acids in Different Fluorometric Assay of Nucleic Acid Associated Enzymes Miscellaneous Applications of Ethidium Bromide to the Nucleic Acids Methodology
The Catalytic Dehydrogenation of Alcohols with Reduced Copper under Ultraviolet Light (1971)

Abstract In order to investigate whether or not the dehydrogenation activity of the reduced copper is affected by ultraviolet light, the reaction of such alcohols as ethanol, 1-propanol, 2-propanol, and 1-butanol was carried out with reduced copper and ultraviolet light at 250°C. It was found that the conversion of alcohols and the yield of aldehydes were larger with the reduced copper under ultraviolet light than without the light, and that aldol condensation for the ethanol reaction was recognizable when the reduced copper catalyst was used without ultraviolet light.
Influence of basic fibroblast growth factor on the growth of HeLa cells and the expression of angiogenin (2009)

Basic fibroblast growth factor (bFGF) is closely involved in angiogenesis and tumor growth of various cancers, but its role in cervical cancer remains to be defined. We investigated the effects of bFGF on HeLa cell growth and studied its influence on the expression of angiogenin. We transfected the bFGF gene in the sense and antisense orientation into HeLa cells, and obtained stable bFGF underexpressing and overexpressing transfectants. In our experiments, we demonstrated that inhibition of bFGF gene and protein expression in the bFGF antisense transfectants induced increased protein expression of angiogenin. In contrast, in the bFGF sense transfectants the expression of angiogenin decreased. Delivery of recombinant angiogenin into transfected and control cells led to increased proliferation in the bFGF antisense transfectants and the control cells. However, the cell proliferation had no change in the bFGF sense transfectants. In conclusion, we demonstrated that besides its angiogenic activity, bFGF and angiogenin also directly contribute to HeLa cell proliferation. Furthermore, endogenous bFGF affects the expression of angiogenin in HeLa cells. These findings suggest that inhibition of bFGF alone is not a promising strategy to inhibit angiogenesis.
Implementability restrictions of the beta-CMOS artificial neuron (2003)

The paper is focused on the functional possibilities, parameter stability and learnability of the artificial learnable neuron implemented on the base of CMOS /spl beta/-driven threshold element. A neuron /spl beta/-comparator circuit is suggested with a very high sensitivity to input current change that allows us to sharply increase the threshold value of the functions. The SPICE simulation results confirm that the neuron is learnable to realize threshold functions of 10, 11 and 12 variables with maximum values of threshold 89, 144 and 233 respectively. A number of experiments were conducted to determine the limits in which the working parameters of the neuron can change providing its stable functioning after learning the functions for each of these threshold values. MOSIS BSIM3v3.1 0.8 /spl mu/m transistor models were used in the SPICE simulation.
A new method for a self-calibrating capacitive sensor (2002)

In this paper a new method for a self-calibrating capacitive sensor for threshold liquid level measurement is presented. The basic theoretical ideas are described and illustrated. The theoretical results are proven by field simulations. For practical experiments, a container was manufactured and special electronic circuits were developed. The values of the capacitors are measured, converted into digital values and transferred to the computer. Experimental results are depicted.
Production of monospecific antibodies to rat liver ornithine decarboxylase and their use in turnover studies. (1977)

Two forms of ornithine decarboxylase (L-ornithine carboxy-lyase, EC 4.1.1.17) were purified from the livers of rats which had been treated with thioacetamide for 16 h (for details, see miniprint to Obenrader, M.F., and Prouty, W. F. (1977) J. Biol. Chem. 252, 2860-2865). The enzyme was purified over 7,000-fold from liver cytosol with an overall yield of 8%. Enzyme activity was eluted finally in two distinct fractions by chromatography on activated thiol-Sepharose 4B. Both forms appear to be dimeric proteins having molecular weights of approximately 100,000 by equilibrium sedimentation and analysis on a calibrated Sephadex G-200 column. The apparent subunits are approximately 50,000 daltons as determined by electrophoresis on polyacrylamide gels in the presence of sodium dodecyl sulfate. Since electrophoresis in the presence of detergent is the only method used here to indicate subunits, the possibility that conditions of sample preparation resulted in splitting of a labile protein cannot be excluded from consideration. Ornithine decarboxylase has a very broad pH-activity curve with an optimum that shifts from pH 7.0 to pH 7.8 as the enzyme is purified. The apparent Km values for a highly purified mixture of the two forms of enzyme for L-ornithine and pyridoxal 5'-phosphate were determined to be 0.13 mM and 0.25 micronM, respectively. Both sodium and potassium chloride were shown to inhibit enzymatic activity; 50% inhibition occurred at 270 mM for each when Km amounts or ornithine were used. Rat liver ornithine decarboxylase antiserum was prepared in rabbits using Form I of the enzyme as the antigen. The antibody was shown to precipitate quantitatively the ornithine decarboxylase activity isolated from induced rat liver and rat ventral prostate. The specificity of the antiserum was demonstrated by rocket immunoelectrophoresis and by gel electrophoresis in the presence of sodium dodecyl sulfate using immunoprecipitates obtained from enzyme preparations labeled either in vivo, with [3H]leucine, or in vitro, by reductive methylation using formaldehyde and sodium [3H]borohydride. The antibody preparation has been used in a titration method to assess the half-life of antigen in livers of rats induced for ornithine decarboxylase by injection of thioacetamide. In two experiments, the t1/2 of activity at the height of induction, following injection of cycloheximide, was 19 and 24 min, while the t1/2 of disappearance of antigen was 28 and 33 min, respectively. In each experiment the t1/2 for antigen was significantly longer than the t1/2 for loss of enzyme activity. Enzyme levels appear to be modulated primarily by synthesis and degradation of antigen. Furthermore, the observation that enzyme activity is lost with a shorter t1/2 than antigen is consistent with the idea that denaturation is an initial step in the degradation of this enzyme...