gebhart/patrepeval huggingface dataset:
Lung cancer biomarkers, targeted therapies and clinical assays. (2015)

Until recently, the majority of genomic cancer research has been in discovery and validation; however, as our knowledge of tumor molecular profiling improves, the idea of genomic application in the clinic becomes increasingly tangible, paralleled with the drug development of newer targeted therapies. A number of profiling methodologies exist to identify biomarkers found within the patient (germ-line DNA) and tumor (somatic DNA). Subsequently, commercially available clinical assays to test for both germ-line and somatic alterations that are prognostic and/or predictive of disease outcome, toxicity or treatment response have significantly increased. This review aims to summarize clinically relevant cancer biomarkers that serve as targets for therapy and their potential relationship to lung cancer. In order to realize the full potential of genomic cancer medicine, it is imperative that clinicians understand these intricate molecular pathways, the therapeutic implication of mutations within these pathways, and the availability of clinical assays to identify such biomarkers.
DNA Polymerase λ Inactivation by Oxidized Abasic Sites (2013)

Base excision repair (BER) plays a vital role in maintaining genomic integrity in mammalian cells. DNA polymerase λ (Pol λ) is believed to play a backup role to DNA polymerase β (Pol β) in base excision repair. Two oxidized abasic lesions that are produced by a variety of DNA-damaging agents, including several antitumor antibiotics, the C4'-oxidized abasic site following Ape1 incision (pC4-AP), and 5'-(2-phosphoryl-1,4-dioxobutane) (DOB), irreversibly inactivate Pol β and Pol λ. The interactions of DOB and pC4-AP with Pol λ are examined in detail using DNA substrates containing these lesions at defined sites. Single-turnover kinetic experiments show that Pol λ excises DOB almost 13 times more slowly than a 5'-phosphorylated 2-deoxyribose (dRP). pC4-AP is excised approximately twice as fast as DOB. The absolute rate constants are considerably slower than those reported for Pol β for the respective reactions, suggesting that Pol λ may be an inefficient backup in BER. DOB inactivates Pol λ approximately 3-fold less efficiently than it does Pol β, and the difference can be attributed to a higher K(I) (33 ± 7 nM). Inactivation of Pol λ's lyase activity by DOB also prevents the enzyme from conducting polymerization following preincubation of the protein and DNA. Mass spectral analysis of GluC-digested Pol λ inactivated by DOB shows that Lys324 is modified. There is inferential support for the idea that Lys312 may also be modified. Both residues are within the Pol λ lyase active site. When acting on pC4-AP, Pol λ achieves approximately four turnovers on average before being inactivated. Lyase inactivation by pC4-AP is also accompanied by loss of polymerase activity, and mass spectrometry indicates that Lys312 and Lys324 are modified by the lesion. The ability of DOB and pC4-AP to inactivate Pol λ provides additional evidence that these lesions are significant sources of the cytotoxicity of DNA-damaging agents that produce them.
Modified implant surfaces show different biofilm compositions under <i>in vivo</i> conditions (2009)

A coating of glass surfaces with ZrN significantly reduced the species richness in early bacterial colonization but the diversity was not significantly changed. In consideration of the results obtained by this and former studies a ZrN coating appears to rather modify the quantity of early bacterial adherence than the quality of the microbial community structure.
Spectrum analysis of dynamic scattering light measured via a low-coherence interferometer (2003)

Power spectrum of dynamically scattered light measured via a low-coherence interferometer is theoretically studied. It is shown that low-coherence interferometer is available for measuring a path-length-resolved spectrum and a path-length distribution of light multiply scattered from a dense suspension.
A 14-bit Digitally Self-Calibrated Pipelined ADC With Adaptive Bias Optimization for Arbitrary Speeds Up to 40 MS/s (2006)

This paper presents a 14-bit digitally self-calibrated pipelined analog-to-digital converter (ADC) featuring adaptive bias optimization. Adaptive bias optimization controls the bias currents of the amplifiers in the ADC to the minimum amount required, depending on the sampling speed, environment temperature, and power-supply voltage, as well as the variations in chip fabrication. It utilizes information from the digital calibration process and does not require additional analog circuits. The prototype ADC occupies an area of 0.5/spl times/2.3 mm/sup 2/ in a 0.18-/spl mu/m dual-gate CMOS technology; with a power supply of 2.8 V, it consumes 19.2, 33.7, 50.5, and 72.8 mW when operating at 10, 20, 30, and 40 MS/s, respectively. The peak differential nonlinearity (DNL) is less than 0.5 least significant bit (LSB) for all the sampling speeds with temperature variation up to 80/spl deg/C. When operated at 20 MS/s with 1-MHz input, the ADC achieves 72.1-dB SNR and 71.1-dB SNDR.
Capillary electrophoresis and liquid chromatography in the analysis of some quaternary ammonium salts used in lozenges as antibacterial agents. (1999)

A comparison is made of the relative merits of high-performance liquid chromatography and capillary electrophoresis, both using direct UV detection, for the determination of three quaternary ammonium compounds used as the active antibacterial ingredient in lozenge formulations. While both techniques are capable of separating the compounds cetylpyridinium chloride, dequalinium chloride, and benzalkonium chlorides, the liquid chromatographic method involving ion pairing and using a 5-micron cyanopropyl stationary phase, was unable to resolve the benzalkonium chlorides from the lozenge excipients and quantitation was not possible. The capillary electrophoresis method using a 205-mm 50-micron-i.d. capillary with a running buffer of 50% vol/vol 50 mM phosphate buffer at pH 3 provided superior resolution of the three antibacterials in all lozenge formulations. This system was also capable of resolving impurities in the dequalinium chloride both in the standard and in lozenges containing this compound. On the basis of quantitative results previously published, both methods have adequate validation parameters since the relative insensitivity of capillary electrophoresis compared with liquid chromatography is not important at the concentration required to be determined following a single simple sample pretreatment.
Thermal conductivity measurements of high and low thermal conductivity films using a scanning hot probe method in the 3ω mode and novel calibration strategies (2015)

This work discusses measurement of thermal conductivity (k) of films using a scanning hot probe method in the 3ω mode and investigates the calibration of thermal contact parameters, specifically the thermal contact resistance (R(th)C) and thermal exchange radius (b) using reference samples with different thermal conductivities. R(th)C and b were found to have constant values (with b = 2.8 ± 0.3 μm and R(th)C = 44,927 ± 7820 K W(-1)) for samples with thermal conductivity values ranging from 0.36 W K(-1) m(-1) to 1.1 W K(-1) m(-1). An independent strategy for the calibration of contact parameters was developed and validated for samples in this range of thermal conductivity, using a reference sample with a previously measured Seebeck coefficient and thermal conductivity. The results were found to agree with the calibration performed using multiple samples of known thermal conductivity between 0.36 and 1.1 W K(-1) m(-1). However, for samples in the range between 16.2 W K(-1) m(-1) and 53.7 W K(-1) m(-1), calibration experiments showed the contact parameters to have considerably different values: R(th)C = 40,191 ± 1532 K W(-1) and b = 428 ± 24 nm. Finally, this work demonstrates that using these calibration procedures, measurements of both highly conductive and thermally insulating films on substrates can be performed, as the measured values obtained were within 1-20% (for low k) and 5-31% (for high k) of independent measurements and/or literature reports. Thermal conductivity results are presented for a SiGe film on a glass substrate, Te film on a glass substrate, polymer films (doped with Fe nano-particles and undoped) on a glass substrate, and Au film on a Si substrate.
AMMONIA VOLATILIZATION FROM DIFFERENT FERTILIZER SOURCES AND EFFECTS OF TEMPERATURE AND SOIL pH1 (1999)

Improved understanding of nitrogen sources, environmental factors, and nitrification effects on NH3 volatilization is needed for optimal management of nitrogen in crop production systems. In the laboratory, a sponge-trapping and KCl-extraction method was modified for measuring NH3 volatilization from different N sources as affected by temperature and soil pH. The kinetics of NH3 volatilization from four N sources surface applied to an Alfisol (a Riviera fine sand, pH 7.9) followed an initial rapid reaction, and then a slow reaction, which was adequately described by a Langmuir kinetic model. The potential maximum NH3 volatilization (qm) under the experimental conditions, as predicted by the Langmuir equation, decreased in the order: NH4HCO3 (23.2% of applied NH4-N) > (NH4)2SO4 (21.7%) > CO(NH2)2 (21.4%) > NH4NO3 (17.6%). With an increase in NH4-N application rate, NH3 volatilization increased significantly for (NH4)2SO4, CO(NH2)2, and NH4HCO3 but decreased for NH4NO3. Ammonia volatilization was minimal at the initial soil pH of 3.5 and increased rapidly with increasing pH up to 8.5. The potential maximum NH3 volatilization increased by 2- and 3-fold, respectively, with an increase in the incubation temperature from 5 to 25 °C, and from 25 to 45 °C, respectively. The greatly enhanced NH3 volatilization at 45 °C, compared with that at 25 °C, was related to the inhibition of nitrification at the high temperature, which increased the availability of NH4 for NH3 volatilization over a prolonged period of time.
A Single-Molecule Barcoding System using Nanoslits for DNA Analysis (2009)

Single DNA molecule approaches are playing an increasingly central role in the analytical genomic sciences because single molecule techniques intrinsically provide individualized measurements of selected molecules, free from the constraints of bulk techniques, which blindly average noise and mask the presence of minor analyte components. Accordingly, a principal challenge that must be addressed by all single molecule approaches aimed at genome analysis is how to immobilize and manipulate DNA molecules for measurements that foster construction of large, biologically relevant data sets. For meeting this challenge, this chapter discusses an integrated approach for microfabricated and nanofabricated devices for the manipulation of elongated DNA molecules within nanoscale geometries. Ideally, large DNA coils stretch via nanoconfinement when channel dimensions are within tens of nanometers. Importantly, stretched, often immobilized, DNA molecules spanning hundreds of kilobase pairs are required by all analytical platforms working with large genomic substrates because imaging techniques acquire sequence information from molecules that normally exist in free solution as unrevealing random coils resembling floppy balls of yarn. However, nanoscale devices fabricated with sufficiently small dimensions fostering molecular stretching make these devices impractical because of the requirement of exotic fabrication technologies, costly materials, and poor operational efficiencies. In this chapter, such problems are addressed by discussion of a new approach to DNA presentation and analysis that establishes scaleable nanoconfinement conditions through reduction of ionic strength; stiffening DNA molecules thus enabling their arraying for analysis using easily fabricated devices that can also be mass produced. This new approach to DNA nanoconfinement is complemented by the development of a novel labeling scheme for reliable marking of individual molecules with fluorochrome labels, creating molecular barcodes, which are efficiently read using fluorescence resonance energy transfer techniques for minimizing noise from unincorporated labels. As such, our integrative approach for the realization of genomic analysis through nanoconfinement, named nanocoding, was demonstrated through the barcoding and mapping of bacterial artificial chromosomal molecules, thereby providing the basis for a high-throughput platform competent for whole genome investigations.
Erythromycin Enhances<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mtext>CD4</mml:mtext><mml:mtext>+</mml:mtext></mml:msup></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mtext>Foxp3</mml:mtext><mml:mtext>+</mml:mtext></mml:msup></mml:math>Regulatory T-Cell Responses in a Rat Model of Smoke-Induced Lung Inflammation (2012)

Heavy smoking can induce airway inflammation and emphysema. Macrolides can modulate inflammation and effector T-cell response in the lungs. However, there is no information on whether erythromycin can modulate regulatory T-cell (Treg) response. This study is aimed at examining the impact of erythromycin on Treg response in the lungs in a rat model of smoking-induced emphysema. Male Wistar rats were exposed to normal air or cigarette smoking daily for 12 weeks and treated by gavage with 100 mg/kg of erythromycin or saline daily beginning at the forth week for nine weeks. The lung inflammation and the numbers of inflammatory infiltrates in bronchoalveolar lavage fluid (BALF) were characterized. The frequency, the number of Tregs, and the levels of Foxp3 expression in the lungs and IL-8, IL-35, and TNF-α in BALF were determined by flow cytometry, RT-PCR and ELISA, respectively. Treatment with erythromycin reduced smoking-induced inflammatory infiltrates, the levels of IL-8 and TNF-α in the BALF and lung damages but increased the numbers of CD4+Foxp3+ Tregs and the levels of Foxp3 transcription in the lungs, accompanied by increased levels of IL-35 in the BALF of rats. Our novel data indicated that erythromycin enhanced Treg responses, associated with the inhibition of smoking-induced inflammation in the lungs of rats.
Resistance to cancer immunotherapy mediated by apoptosis of tumor-infiltrating lymphocytes (2017)

Despite impressive clinical success, cancer immunotherapy based on immune checkpoint blockade remains ineffective in many patients due to tumoral resistance. Here we use the autochthonous TiRP melanoma model, which recapitulates the tumoral resistance signature observed in human melanomas. TiRP tumors resist immunotherapy based on checkpoint blockade, cancer vaccines or adoptive T-cell therapy. TiRP tumors recruit and activate tumor-specific CD8<sup>+</sup> T cells, but these cells then undergo apoptosis. This does not occur with isogenic transplanted tumors, which are rejected after adoptive T-cell therapy. Apoptosis of tumor-infiltrating lymphocytes can be prevented by interrupting the Fas/Fas-ligand axis, and is triggered by polymorphonuclear-myeloid-derived suppressor cells, which express high levels of Fas-ligand and are enriched in TiRP tumors. Blocking Fas-ligand increases the anti-tumor efficacy of adoptive T-cell therapy in TiRP tumors, and increases the efficacy of checkpoint blockade in transplanted tumors. Therefore, tumor-infiltrating lymphocytes apoptosis is a relevant mechanism of immunotherapy resistance, which could be blocked by interfering with the Fas/Fas-ligand pathway.
Breakdown quenching in high electron mobility transistor by using body contact (2001)

In this paper, the effect of a body contact (BC) to quench breakdown effects and increase the breakdown voltage in high-electron mobility transistors (HEMTs) is theoretically investigated. The body contact is formed by a highly p-type doped substrate connected to an ohmic back contact. By means of a two-dimensional (2-D) self consistent Monte Carlo simulator we show that the BC prevents holes generated by impact ionization (II) from accumulating in the channel and in the buffer, thus inhibiting the parasitic bipolar effect (PBE). This improves the breakdown behavior and extends the range of the usable drain voltages.
Spatial resolution of a noninvasive measurement of the arterial and venous input function using a wrist monitor (2004)

The current method for measuring the input function of a PET tomograph is by withdrawing arterial blood from a patient's wrist In this study, the possibility of making a noninvasive measurement of the arterial blood is explored to determine the feasibility of using a planar set of detectors situated around the wrist. The arterial measurement was simulated using a peristaltic pump and an anatomically correct wrist phantom with attenuation. A step function was used to measure the activity flowing through arterial and venous tubing in the phantom. The detector was tested for spatial resolution and counting efficiency. The results showed the detector was able to discriminate the arterial and venous flows from noise when using planar coincidence images.
New technologies for advanced LCD‐TV performance (2004)

Abstract— Samsung intends to be the world leader in LCD‐TV through a combination of superior product technology, advanced process execution, and aggressive capitalization. This paper explores and updates Samsung's latest developments toward its goal of ultimate LCD‐TV performance and market leadership. Samsung's development of Super PVA (S‐PVA) represents a key performance achievement. S‐PVA is a new technology which enables screen quality advantages over S‐IPS and MVA, including high transmittance, >1000:1 contrast ratio, and wide angle of view with no off‐axis image inversion. This new technology is described in detail. This paper also addresses the other remaining performance issues facing LCD‐TV, including Samsung's plans for addressing these challenges. Until recently, inter‐gray response time and associated motion blur were significant issues for achieving quality LCD‐TV images. Samsung has invented DCC‐II technology to achieve sub‐10‐msec response time, and this achievement is described. Other technology advancements, including next‐generation color performance and ultra‐low black performance, are discussed. Samsung has announced the development of a 57‐in. full‐HD (1920 × 1080) LCD‐TV panel, the world's largest, based on S‐PVA technology. This product represents the culmination of many technical breakthroughs, and is discussed herein. Samsung's LCD manufacturing strategy, which includes the world's first generation 7 LCD fab, is also described.
Optimal Selection of Basis Functions for Minimum-Effort Tracking Control of Nonminimum Phase Systems Using Filtered Basis Functions (2019)

Abstract Accurate tracking of nonminimum phase (NMP) systems is well known to require large amounts of control effort. It is, therefore, of practical value to minimize the effort needed to achieve a desired level of tracking accuracy for NMP systems. There is growing interest in the use of the filtered basis functions (FBF) approach for tracking the control of linear NMP systems because of distinct performance advantages it has over other methods. The FBF approach expresses the control input as a linear combination of user-defined basis functions. The basis functions are forward filtered through the dynamics of the plant, and the coefficients are selected such that the tracking error is minimized. There is a wide variety of basis functions that can be used with the FBF approach, but there has been no work to date on how to select the best set of basis functions. Toward selecting the best basis functions, the Frobenius norm of the lifted system representation (LSR) of dynamics is proposed as an excellent metric for evaluating the performance of linear time varying (LTV) discrete-time tracking controllers, like FBF, independent of the desired trajectory to be tracked. Using the metric, an optimal set of basis functions that minimize the control effort without sacrificing tracking accuracy is proposed. The optimal set of basis functions is shown in simulations and experiments to significantly reduce control effort while maintaining or improving tracking accuracy compared to popular basis functions, like B-splines.
Dynamic Warpage Analysis of QFP Packages During Soldering Reflow Process and Thermal Cycle (2018)

The mechanical reliability of thin plastic packages during soldering reflow process on circuit board and thermal cycle becomes one of the most critical aspect in device mounting and operation. When a package is subjected to thermal loadings, deformation and deviation from an ideal uniform planar flatness usually result. Package warpage leads to thermo-mechanical issues at those sites of weak adhesion in the structure. The estimation of warpage is necessary for increasing package reliability. This paper deals with in-situ characterization of temperature-induced package warpage by adopting fringe pattern projection principle. The experimental analysis allows to evaluate real-time dynamic warpage at different target temperatures. In addition, numerical modeling is employed to identify the most critical material interface when a package is subjected to thermal loads. Simulation results are in good agreement with standard reliability trials on packages mounted on board.
Very high-mobility organic single-crystal transistors with in-crystal conduction channels (2007)

Very high-mobility organic transistors are fabricated with purified rubrene single crystals and high-density organosilane self-assembled monolayers. The interface with minimized surface levels allows carriers to distribute deep into the crystals by more than a few molecular layers under weak gate electric fields, so that the inner channel plays a significant part in the transfer performance. With the in-crystal carriers less affected by scattering mechanisms at the interface, the maximum transistor mobility reaches 18cm2∕Vs and the contact-free intrinsic mobility turned out to be 40cm2∕Vs as the result of four-terminal measurement. These are the highest values ever reported for organic transistors.
Multiple height calibration reference for nano-metrology (2015)

Modern nano-metrology instruments require calibration references with nanometer accuracy in the x, y, and z directions. A common problem is the accurate calibration in the z direction (height). For example, it is generally not difficult to obtain accurate x- and y- calibration references for a Scanning Probe Microscope (SPM). It is, however, much more difficult to obtain accurate z-axis results. It is difficult to control z-axis piezo dynamics because during scanning in the xy-plane the x-and y-axes move at a constant rate whiles the z axis does not. Furthermore due to the high cost of producing calibration standards, the microscope is often calibrated at only one height. However, if the relationship between the measured z height and the actual z height is not linear, then the height measurements will not be correct. In this paper, we will present a method for the fabrication of calibration references with: (i) sub-10 nm features and (ii) multiple step heights on one reference, allowing for better calibration of the non-linearity in the z direction.