gebhart/patrepeval huggingface dataset:
Abstract A22: Sensitive detection of mutant KRAS in colorectal tissue using the multiplex QuARTS™ assay (2011)

Abstract Background: Colorectal cancer (CRC) is the second leading cause of cancer deaths in the United States, yet it is potentially the most treatable and preventable cancer with effective screening. Exact Sciences has developed a multi-biomarker CRC screening test that targets DNA methylation, DNA mutations, and hemoglobin in stool. The aim of this study was to evaluate the analytical accuracy of a novel assay for the detection of KRAS mutation sequences at Codons 12 and 13 in well-characterized colorectal tissues. Methodology: A multiplexed KRAS assay was designed utilizing QuARTS (Quantitative Allele-specific Real-time Target and Signal amplification), a highly sensitive technology that combines allele-specific DNA amplification with invasive cleavage chemistry to generate signal during each amplification cycle similar to real-time PCR. The assay, which detects seven KRAS mutations and the reference gene β-actin, was used to assess 87 colorectal tissue samples (52 CRCs, 16 adenomas ≥ 1cm, and 19 normal epithelia) as determined by Mayo Clinic Pathology. Samples were obtained by microdissection of fresh frozen tissue biopsies. DNA was extracted by Mayo Clinic using a standardized chloroform/phenol methodology. The genotypes of each sample were established using dye terminator dideoxy sequencing in both the forward and reverse orientations. Copy numbers of KRAS mutations and β-actin were determined by conventional comparison against standard curves. KRAS data are reported as percent mutation and calculated by dividing mutant copies by β-actin copies and multiplying by 100. Results: Based on sequencing data: the 52 CRC samples contained 22 KRAS mutations and 30 wild-type genotypes, the 16 adenomas ≥ 1cm contained 8 mutations and 8 wild-type genotypes, and the 19 normal tissues contained all wild-type genotypes. The QuARTS assay detected 100% of the KRAS mutations in the CRC and adenomas and provided excellent differentiation between wild-type and mutation, with the highest percent KRAS mutation of normal wild-type samples at 0.55% and the lowest percent mutation of KRAS positive samples at 8.34%. Based on this data, this assay has the potential to be more sensitive analytically than standard sequencing. Conclusion: The QuARTS assay detects KRAS mutations in tissue with high sensitivity and specificity. This assay method could provide an accurate and high throughput approach to detection of KRAS mutations in biospecimens for multiple clinical applications. Citation Information: Cancer Prev Res 2011;4(10 Suppl):A22.
Unidirectional Waveguide Grating Antennas for Nanophotonic Phased Arrays (2017)

Unidirectional waveguide grating antennas for nanophotonic phased arrays are demonstrated with over 90% directionality. Unidirectional emission eliminates the fundamental problem of element factor blind spots due to reflections of the antenna radiation within the substrate.
Electrical and structural characterization of 150 nm CNT contacts with Cu damascene top metallization (2012)

This paper discusses the electrical and structural characterization of 150 nm diameter contacts filled with carbon nanotubes (CNTs) and a Cu damascene top metal. We present the first images of CNTs in direct contact with the top metal. A CNT tip clean before metallization reduced the single CNT contact hole resistance from 4.8 kΩ down to 2.8 kΩ (aspect ratio 2.4). The first basic electrical breakdown experiments with Kelvins resulted in high breakdown currents of 5-13 MA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
The C‐terminus of the ssDNA binding protein of phage T7 modulates its ssDNA‐binding activity (2006)

The gene 2.5 (gp2.5), the ssDNA‐binding protein of phage T7, is indispensable for phage growth and a key component of the T7 DNA replication fork. Gp2.5 binds ssDNA, interacts with T7 DNA polymerase, and T7 helicase/primase, and is essential for coordination of leading and lagging strand DNA synthesis. Similar to other prokaryotic ssDNA‐binding proteins, gp2.5 has an acidic C‐terminus that is involved in protein‐protein interactions at the replication fork and in modulation of the ssDNA‐binding properties of the molecule. The presence of an aromatic amino acid as the C‐terminal residue of the protein is essential for gp2.5 function and correlates with its ability to physically interact with the gene 5 DNA polymerase. Moderate shortening the length of the acidic portion of the C‐terminus is tolerated when the aromatic nature of the C‐terminal residue is preserved. Gradual removal of the acidic C‐terminus of gp2.5 results in higher affinities for ssDNA and unmasks dsDNA‐binding ability. Mutant proteins, in which the C‐terminal phenylalanine is replaced with tyrosine and cysteine, bind long oligonucleotides with much higher affinity than the wild type gp2.5, whereas the affinity for short oligonucleotides is comparable. Models for the biological significance of the modulation of gp2.5 DNA binding properties by the acidic C‐terminus are explored. This research is supported from NIH grants GM54397‐41 and F32GM072305.
The 1.6 Å Crystal Structure of Pyranose Dehydrogenase from Agaricus meleagris Rationalizes Substrate Specificity and Reveals a Flavin Intermediate (2013)

Pyranose dehydrogenases (PDHs) are extracellular flavin-dependent oxidoreductases secreted by litter-decomposing fungi with a role in natural recycling of plant matter. All major monosaccharides in lignocellulose are oxidized by PDH at comparable yields and efficiencies. Oxidation takes place as single-oxidation or sequential double-oxidation reactions of the carbohydrates, resulting in sugar derivatives oxidized primarily at C2, C3 or C2/3 with the concomitant reduction of the flavin. A suitable electron acceptor then reoxidizes the reduced flavin. Whereas oxygen is a poor electron acceptor for PDH, several alternative acceptors, e.g., quinone compounds, naturally present during lignocellulose degradation, can be used. We have determined the 1.6-Å crystal structure of PDH from Agaricus meleagris. Interestingly, the flavin ring in PDH is modified by a covalent mono- or di-atomic species at the C(4a) position. Under normal conditions, PDH is not oxidized by oxygen; however, the related enzyme pyranose 2-oxidase (P2O) activates oxygen by a mechanism that proceeds via a covalent flavin C(4a)-hydroperoxide intermediate. Although the flavin C(4a) adduct is common in monooxygenases, it is unusual for flavoprotein oxidases, and it has been proposed that formation of the intermediate would be unfavorable in these oxidases. Thus, the flavin adduct in PDH not only shows that the adduct can be favorably accommodated in the active site, but also provides important details regarding the structural, spatial and physicochemical requirements for formation of this flavin intermediate in related oxidases. Extensive in silico modeling of carbohydrates in the PDH active site allowed us to rationalize the previously reported patterns of substrate specificity and regioselectivity. To evaluate the regioselectivity of D-glucose oxidation, reduction experiments were performed using fluorinated glucose. PDH was rapidly reduced by 3-fluorinated glucose, which has the C2 position accessible for oxidation, whereas 2-fluorinated glucose performed poorly (C3 accessible), indicating that the glucose C2 position is the primary site of attack.
Genetic Transformation, Regeneration and Analysis of Transgenic Peanut (2000)

Conventional breeding has led to the improvement of some peanut traits such as seed yield and drought tolerance. However, many important agronomic traits have yet to be improved. The recent development of transformation and regeneration systems has allowed the introduction of useful genes into peanut germplasm. The understanding of disease resistance mechanisms is becoming increasingly advanced so that it should be possible to apply technologies that have been proven in other species to peanut.In this technical report we describe protocols for the routine regeration of transformed peanut plants of spanish and virginia market types based on microprojectile bombardment of embryogenic callus as well as Agrobacterium-mediated transformation of somatic embryos.
Telomerase and breast cancer (2001)

Current therapies for breast cancer include treatments that are toxic and often result in drug resistance. Telomerase, a cellular reverse transcriptase that maintains the ends of chromosomes (telomeres), is activated in the vast majority of breast cancers (over 90% of breast carcinomas) but not in normal adjacent tissues. Telomerase is thus an attractive target for both diagnosis and therapy because of its distinct pattern of expression. We address the use of telomerase in the diagnostics of breast pathology, as well as the use of telomerase inhibitors in the treatment and prevention of breast cancer.
Adaptive multiphoton and harmonic generation microscopy for developmental biology (2010)

Specimen-induced aberrations often affect microscopes, particularly when high numerical aperture lenses are used to image deep into biological specimens. These aberrations cause a reduction in resolution and focal intensity. This is particularly problematic in multiphoton microscopy, where the non-linear nature of the signal generation process means that the signal level is strongly affected by changes in the focal spot intensity. We have applied the techniques of adaptive optics to correct aberrations in two-photon fluorescence and harmonic generation microscopes, restoring image quality. In particular we have used these microscopes for studies in developmental biology and for the imaging of mammalian embryos.
Chemical synthesis and receptor binding of catfish somatostatin: a disulfide‐bridged β‐d‐Galp‐(1→3)‐α‐d‐GalpNAcO‐glycopeptide* (2000)

The glycopeptide hormone catfish somatostatin (somatostatin-22) has the amino acid sequence H-Asp-Asn-Thr-Val-Thr-Ser-Lys-Pro-Leu-Asn-Cys-Met-Asn-Tyr-Phe-Trp-Lys-Se r-Arg-Thr-Ala-Cys-OH; it includes a cyclic disulfide connecting the two Cys residues, and the major naturally occurring glycoform contains D-GalNAc and D-Gal O-glycosidically linked to Thr5. The linear sequence was assembled smoothly starting with an Fmoc-Cys(Trt)-PAC-PEG-PS support, using stepwise Fmoc solid-phase chemistry. In addition to the nonglycosylated peptide, two glycosylated forms of somatostatin-22 were accessed by incorporating as building blocks, respectively, Nalpha-Fmoc-Thr(Ac3-alpha-D-GalNAc)-OH and Nalpha-Fmoc-Thr(Ac4-beta-D-Gal-(1-->3)-Ac2-alpha-D-GalNAc)-O H. Acidolytic deprotection/cleavage of these peptidyl-resins with trifluoroacetic acid/scavenger cocktails gave the corresponding acetyl-protected glycopeptides with free sulfhydryl functions. Deacetylation, by methanolysis in the presence of catalytic sodium methoxide, was followed by mild oxidation at pH 7, mediated by Nalpha-dithiasuccinoyl (Dts)-glycine, to provide the desired monomeric cyclic disulfides. The purified peptides were tested for binding affinities to a panel of cloned human somatostatin receptor subtypes; in several cases, presence of the disaccharide moiety resulted in 2-fold tighter binding.
The Kindlin Family of Adapter Proteins (2019)

A half century of research and more than 75,000 publications have cemented the foundational role of integrins as major conduits of communication between the extracellular environment and the interior of cells. By serving as cell-surface receptors for numerous extracellular ligands, integrin α and β heterodimers are integrally involved in the physiological and pathophysiological responses of virtually all cell types. Excessive or suppressed ligand binding to integrins are implicated in many diseases, including cancer, inflammation and cardiovascular diseases.
Investigation of the {104} surface of calcite under dry and humid atmospheric conditions with grazing incidence X-ray diffraction (GIXRD) (2006)

Using grazing incidence X-ray diffraction (GIXRD) the three-dimensional surface and interface structure of the {104} calcite surface was investigated under dry and humid atmospheric conditions. The measurement of specular and non-specular crystal truncation rods (CTR) provided information about the periodic order of the vertical and lateral surface structure on atomic scale. The calcite surface is nearly ideally terminated with relaxation of the atoms in the topmost layers down to about 12 A depth. In dry environment the calcite surface structure is dominantly determined by the large shift, rotation and tilt of the surface carbonate groups. In humid atmosphere a laterally ordered monolayer of water is formed on the surface. The truncated coordination site of the surface Ca 2+ ions are filled by a water molecule in a distance of (2.1 ± 0.2) A. The relaxation of the structure is significantly changed, which results in a strong distortion of the Ca-O coordination octahedron. The refinement of water as complete rigid H 2 O species positioned flat on the surface with one rotation parameter resulted in the formation of hydrogen bonds to the adjacent surface carbonate groups. No evidence for a surface reconstruction was found.
Enabling standoff detection of hazardous materials using a fiber optic coupled quantum cascade infrared laser system (2018)

The global defense community requires new approaches for standoff detection of chemical, biological, radiological, nuclear and explosive (CBRNE) threats. Such standoff detection methods must be capable of discriminating the target hazardous materials from the environmental background. Therefore these sensors must exhibit high selectivity. High selectivity detection of CBRNE threats can be accomplished using infrared (IR) spectroscopy, which produces a unique spectral “fingerprint” of the target chemical, enabling discrimination of the target chemical from other chemicals in the background. Standoff detection using IR spectroscopy however requires that enough of the incident source light may be collected at the detector; therefore a high-power source is needed. Commercially available quantum cascade laser (QCL) sources are capable of projecting high power, coherent laser light at targets down range from the source. In order to collect complete IR spectra throughout the entire fingerprint region, the output of multiple QCL modules are combined into a single exit aperture. This is typically achieved using mirrors and other optics which are susceptible to vibrational and temperature misalignments in field systems. In order to provide a more ruggedized solution to combining the beam output of multiple QCL modules, we developed a unique chalcogenide optical fiber beam combiner which combines the output of four commercial QCL modules. This allows for scanning across a spectral range from 6.01 – 11.20 &mu;m encompassing parts of both the IR functional groups and fingerprint regions. We demonstrate the ability of this QCL system to generate high quality IR spectra of hazardous materials.
VAST Challenge 2017: Mystery at the Wildlife Preserve (2017)

The VAST Challenge 2017 offered three mini-challenges and a grand challenge dealing with environmental problems potentially caused by human patterns of life and potentially harmful chemically laden effluent plumes being emitted from factory smokestacks. The data provided included traffic patterns, sensor data though a Preserve, information about the Preserve, multispectral imagery and a map to help an ornithology graduate student particularly concerned with the population decrease of the Rose-Crested Blue Pipit determine who and what might be responsible. Mini-Challenge 1 focused on analysis of vehicles passing through the Preserve over time. Mini-Challenge 2 looked at data collected by air sampling monitors surrounding nearby factories, along with meteorological readings, to understand potential impacts they may be having on the Pipit. Mini-Challenge 3 required investigation into several months of multi-spectral imagery over the area to understand the Preserve's general health. The Grand Challenge asked participants to synthesize across all three mini-challenges to create hypotheses of what is happening and what sensible next steps could be. This year's challenge received 58 submissions and recorded over 1100 unique downloads from 20 countries prior to the submission deadline.
Holographic 3D imaging of microstructures (1999)

A volume holographic matched filter is used for three- dimensional imaging of silicon microstructures. The filter is designed by recording a hologram that is matched to the object depth, allowing confocal imaging of the structure. Confocal imaging of micro devices provides the capability to image the performance of the device, which is not possible in scanning- electron-microscopes (SEM). A matched holographic filter can also provide more information about the device than regular confocal imaging. We present a scanned image of a silicon wafer with micro-fabricated trenches.© (1999) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Practical Methodology for Adding New MANET Routing Protocols to OPNET Modeler (2013)

Optimized Network Engineering Tool (OPNET) Modeler is a comprehensive development environment that enables users to model communication networks and distributed systems by performing discrete event si mulations. The OPNET Modeler accelerates the design and model of Mobile Ad Hoc Network (MANET) routing protocols by providing tools for all phases, including model des ign, simulation, data collection, and data analysis. Usi ng the already defined MANET routing protocols is straightforward, while modifying or extending them is a tricky process that can be time and effort consuming. This paper provides a n overview of OPNET Modeler architecture and describes a practical methodology to add new MANET routing protocols to OPNET Modeler by using the Multi-Aware Cluster Head Maintenance (MACHM) as an implementation example.
Is chronic hepatitis B being undertreated in the United States? (2010)

Chronic infection with the hepatitis B virus (HBV) is a major risk factor for development of end-stage liver disease, including cirrhosis, liver failure and primary liver cancer. There are now seven antiviral agents approved by the United States Food and Drug Administration (FDA) for the management of chronic HBV infection. Despite the fact that there are between 1.4 and 2 million chronic HBV infections in the United States, fewer than 50,000 people per year receive prescriptions for HBV antiviral medications. This report discusses possible explanations for the disparity between the number of people who are chronically infected and the number of people who receive treatment. Explanations for this incongruence include the potentially large number of infected persons who are unscreened and thus remain undiagnosed, and lack of access, including insurance, education and referral to appropriate medical care, particularly for disproportionately infected populations.
Direct measurement of cyclotron coherence times of high-mobility two-dimensional electron gases (2010)

We have observed long-lived (approximately 30 ps) coherent oscillations of charge carriers due to cyclotron resonance (CR) in high-mobility two-dimensional electrons in GaAs in perpendicular magnetic fields using time-domain terahertz spectroscopy. The observed coherent oscillations were fitted well by sinusoids with exponentially-decaying amplitudes, through which we were able to provide direct and precise measures for the decay times and oscillation frequencies simultaneously. This method thus overcomes the CR saturation effect, which is known to prevent determination of true CR linewidths in high-mobility electron systems using Fourier-transform infrared spectroscopy.
Crystal Engineering with DNA* (2020)

The crystallization of microparticles with primarily single-stranded DNA can lead to more ordered structures, in which the flexibility of the DNA design imparts several advantages. The benefits of DNA design 2 translate, to a limited extent, to the crystallization of nanoparticle building blocks. High densities of DNA are beneficial to reorganization into crystalline structures because they increase the probability that a given sticky end can hybridize and decrease the distance that DNA must extend for the building block to engage in multivalent interactions. Crystallization processes in atomic and nanoscale systems benefit from thermal treatments, often described as annealing, to achieve long-range order. Crystal engineering with DNA has enabled the fabrication of superlattices with a high degree of order. Crystal engineering with DNA need not be limited to two-component systems: a single building block may be designed with multiple distinct sticky ends to engage in unique, simultaneous interactions.
Interfacial trap states and improvement of low-temperature mobility by doping in InSb/AlInSb quantum wells (2015)

The effect of doping on InSb/Al0.1In0.9Sb quantum wells (QWs) was investigated, and it was found that doping improves the electron mobility at low temperatures and leads to a weaker dependence of the resistivity with temperature. The dependence of the carrier density on the well width revealed trap states at the interfaces of the QW whose sheet density per interface was estimated to be about 4 × 1010 cm−2. The low mobility of undoped InSb QWs, in particular, at low temperature seems to have been caused by positively ionized impurity scattering at the interfacial trap states. Doping compensates for the trap states and enhances mobility by suppressing ionized impurity scattering. Thus, intentional doping is necessary for developing high-mobility InSb QW devices. The origin of the trap states is qualitatively discussed.
Pellet Digestion: A Simple And Efficient Sample Preparation Technique For Lc–MS/MS Quantification of Large Therapeutic Proteins in Plasma (2011)

This simple sample preparation approach will be beneficial to bioanalytical laboratories engaged in the LC-MS/MS quantification of large therapeutic proteins in biological matrices.
Bidirectional WDM/TDM-PON access networks integrating downstream 10 Gbit/s DPSK and upstream 2.5 Gbit/s OOK on the same wavelength (2006)

WDM-PON and TDM-PON architectures are presented where a remodulation scheme is implemented. The downstream signal is in NRZ-DPSK format and the upstream signal is NRZ-OOK on the same wavelength in a single fiber.
High-Performance Sensorless Force Control Using Superior Wideband and Periodicity-Cancellation Force Observer (2023)

In this paper, a new force observation approach is proposed to realize a superior wideband and periodicity-free sensorless force control system. The proposed force observer is established by the periodicity estimation integrated singular spectrum analysis based disturbance observer. The singular spectrum analysis is designed to significantly separate the essential components of force estimation of the disturbance observer from extreme noise contamination. Accordingly, the bandwidth of the force sensing is considerably broadened at a highly increased pole of the disturbance observer. Additionally, to eliminate the superimposition of the undesired dither periodicity from the force sensation, the periodicity estimation is developed using the least squares method. The proposed method attains a superior widened force sensing bandwidth and high-performance force sensation. The effectiveness validation of the proposed method is performed through the experimental results of force control implemented in a ball-screw system.