gebhart/patrepeval huggingface dataset:
Formulation and implementation of a phase-resolved fluorescence technique for latent-fingerprint imaging: theoretical and experimental analysis (2005)

A theoretical and experimental study of the imaging of latent fingerprints by a phase-resolved fluorescence technique along with associated signal-processing analysis is described. The system configuration is optimized by incorporation of a novel approach of homodyne-assisted even-step phase shifting in a signal-processing concept. The excitation laser source and gain of the detection device, which are modulated at megahertz frequency followed by sensitive signal-processing concepts, are employed to separate the fingerprint fluorescence from background fluorescence. Experiments are carried out with fingerprints deposited upon different types of substrate surfaces. Later, a quantitative image-quality assessment is carried out, which confirms the improvement in the quality of the phase-resolved fingerprint image. Imaging of older fingerprints with better contrast is also carried out with the proposed novel technique.
Photonic Crystal Biosensors (2005)

Photonic crystals have been used to produce a general-purpose disposable plastic biosensor platform for performing many types of biochemical and cellular assays without the use of fluorescent labels for applications in pharmaceutical research.
An HIV Reverse Transcriptase-Selective Nucleoside Chain Terminator (2002)

The synthesis of a 2',3'-dideoxynucleoside cytidine analogue, but one that lacks the O2-carbonyl, is described from 2-aminopyridine in an overall yield of 60%. The synthesis of the 2-pyridone C-nucleoside relies upon the use of a Heck-type coupling between an appropriately protected sugar glycal and the 5-iodo derivative of 2-aminopyridone. Upon conversion of the dideoxynucleoside to the corresponding 5'-triphosphate, the analogue ddNTP is observed to be a reasonable substrate with HIV reverse transcriptase (for a template dG residue), but is not a substrate for calf thymus DNA polymerase alpha or for human DNA polymerase beta. With the human mitochondrial DNA polymerase the analogue functions as a poor substrate. The observed polymerase selectivities appear to arise from the absence of the O2-carbonyl, which either results in a destabilized Watson-Crick base pair or represents a critical contact for some polymerases.
Affinity-purified Varicella-Zoster Virus Glycoprotein gp1/gp3 Stimulates the Production of Neutralizing Antibody (1985)

Varicella-zoster virus glycoprotein gp1/gp3 was purified by affinity chromatography using anti-gp1/gp3 monoclonal antibody 19.1 linked to CNBr-activated Sepharose CL-4B. Rabbits immunized with purified glycoprotein gp1/gp3 developed mono-specific neutralizing antibody.
Packed-bed bioreactor synthesis of feruloylated monoacyl- and diacylglycerols: clean production of a “green” sunscreen (2003)

A biocatalytic process for covalent incorporation of ferulic acid onto the glycerol backbone of vegetable oil proceeds efficiently, although rather slowly, with Candida antarctica lipase B in a packed-bed reactor. The bioreactor shows considerable long-term stability. Product yield is influenced by the water content of the fluid phase and enzyme support. The enzyme support modulates substrate concentrations through adsorption and subsequent release of reactants over the course of the reaction. The resulting product has excellent UVA/UVB absorbing properties, making it a potential substitute for conventional petroleum-based sunscreen active agents.
Ion-Ion Interactions in Charge Detection Mass Spectrometry (2019)

Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined by simultaneously measuring their mass-to-charge ratio (m/z) and charge. Ions are usually trapped inside an electrostatic linear ion trap (ELIT) where they oscillate back and forth through a detection cylinder, generating a periodic signal that is analyzed by fast Fourier transforms. The oscillation frequency is related to the ion's m/z, and the magnitude is related to the ion's charge. In early work, multiple ion trapping events were discarded because there was a question about whether ion-ion interactions affected the results. Here, we report trajectory calculations performed to assess the influence of ion-ion interactions when multiple highly charged ions are simultaneously trapped in an ELIT. Ion-ion interactions cause trajectory and energy fluctuations that lead to variations in the oscillation frequencies that in turn degrade the precision and accuracy of the m/z measurements. The peak shapes acquire substantial high and low m/z tails, and the average m/z shifts to a higher value as the number of trapped ions increases. The effects of the ion-ion interactions are proportional to the product of the charges and the square root of the number of trapped ions and depend on the ions' m/z distribution. For the ELIT design examined here, ion-ion interactions limit the m/z resolving power to several hundred for a typical homogeneous ion population.
Squared channel matrix prediction for CSI reporting in Rayleigh fading channels (2015)

The need for accurate and relevant CSI feedback is one of the pillars for the efficiency of cellular systems. However, one problem facing CSI reporting is the effect of CSI aging such that the reported CSI information is obsolete when data is scheduled based on it. CSI may instead be predicted in order to mitigate some of the aging loss. In doing so two things need to be considered. First, the CSI prediction needs to have low bias also for cases where prediction is hard, such as short channel coherence time or infrequent CSI reporting. Second, it is desirable not to predict the interference part of the channel quality, as the interference is in the control of the network and hence there is no need for the UE to predict it. This paper addresses the CSI prediction problem taking these two aspects into consideration and proposes a method based on squared channel matrix prediction.
Nanobeam photonic crystal cavity light-emitting diodes (2011)

We present results on electrically driven nanobeam photonic crystal cavities formed out of a lateral p-i-n junction in gallium arsenide. Despite their small conducting dimensions, nanobeams have robust electrical properties with high current densities possible at low drive powers. Much like their two-dimensional counterparts, the nanobeam cavities exhibit bright electroluminescence at room temperature from embedded 1250 nm InAs quantum dots. A small room temperature differential gain is observed in the cavities with minor beam self-heating suggesting that lasing is possible. These results open the door for efficient electrical control of active nanobeam cavities for diverse nanophotonic applications.
Oral administration of Lactobacillus and Bifidobacterium strains of intestinal and vaginal origin to healthy human females: Re-isolation from faeces and vagina (2005)

The healthy vaginal ecosystem is maintained by the interaction of the vaginal epithelium and the microflora, where lactobacilli and occasionally bifidobacteria play an important role. Imbalances in the dominance of lactobacilli may lead to bacterial vaginosis or yeast vaginitis. Probiotics may be a means to secure a favourable microbial balance in the vagina and, as the normal vaginal flora ascends from the rectal mucosa, a convenient form of administration may be via the oral gastrointestinal route. Ten healthy women of different ages were orally administered a blend of 12 selected Lactobacillus strains and three Bifidobacterium strains originating from the intestine and the vagina. The daily dose of each Lactobacillus strain was 1-3x10 9 CFU and 1x10 8 to 1x10 9 CFU for each Bifidobacterium strain, and the doses were given in an oatmilk/blueberry drink. The treatment went on for 10 days. Samples of faeces and vaginal fluid were taken immediately before the administration was started, after 10 days of administration and 7 days after the termination of the administration. Five strains were recovered from faeces and three from the vagina after treatment. The test strains could be found in 9 of the 10 volunteers. L. plantarum strains, originally isolated from intestinal mucosa, were recovered from the vagina of five subjects after treatment. The L. plantarum strains, together with one strain of L. crispatus and one L . gasseri strain, were recovered from faeces. Key words: Probiotics , Lactobacillus, vagina , oral administration , Bifidobacterium
Active Thermography for the Detection of Defects in Powder Metallurgy Compacts (2007)

Active thermography is an established NDE technique that has become the method of choice in many industrial applications which require non‐contact access to the parts under test. Unfortunately, when conducting on‐line infrared (IR) inspection of powder metallic compacts, complications can arise due the generally low emissivity of metals and the thermally noisy environment typically encountered in manufacturing plants. In this paper we present results of an investigation that explores the suitability of active IR imaging of powder metallurgy compacts for the detection of surface and sub‐surface defects in the pre‐sinter state and in an on‐line manufacturing setting to ensure complete quality assurance. Additional off‐line tests can be carried out for statistical quality analyses. In this research, the IR imaging of sub‐surface defects is based on a transient instrumentation approach that relies on an electric control system which synchronizes and monitors the thermal response due to an electrically generated heat source. Preliminary testing reveals that this newly developed pulsed thermography system can be employed for the detection of subsurface defects in green‐state parts. Practical measurements agree well with theoretical predictions. The inspection approach being developed can be used for the testing of green‐state compacts as they exit the compaction press at speeds of up to 1,000 parts per hour.
Code Thumbnails: Using Spatial Memory to Navigate Source Code (2006)

Modern development environments provide many features for navigating source code, yet studies show the developers still spend a tremendous amount of time just navigating. Since existing navigation features rely heavily on memorizing symbol names, we present a new design, called code thumbnails, intended to allow a developer to navigate source code by forming a spatial memory of it. To aid intra-file navigation, we add a thumbnail image of the file to the scrollbar, which makes any part of the file one click away. To aid interfile navigation, we provide a desktop of file thumbnail images, which make any part of any file one click away. We did a formative evaluation of the design with eleven experienced developers and present the results
Therapeutic targeting of casein kinase 1δ in breast cancer (2015)

Identification of specific drivers of human cancer is required to instruct the development of targeted therapeutics. We demonstrate that CSNK1D is amplified and/or overexpressed in human breast tumors and that casein kinase 1δ (CK1δ) is a vulnerability of human breast cancer subtypes overexpressing this kinase. Specifically, selective knockdown of CK1δ, or treatment with a highly selective and potent CK1δ inhibitor, triggers apoptosis of CK1δ-expressing breast tumor cells ex vivo, tumor regression in orthotopic models of triple-negative breast cancer, including patient-derived xenografts, and tumor growth inhibition in human epidermal growth factor receptor 2-positive (HER2(+)) breast cancer models. We also show that Wnt/β-catenin signaling is a hallmark of human tumors overexpressing CK1δ, that disabling CK1δ blocks nuclear accumulation of β-catenin and T cell factor transcriptional activity, and that constitutively active β-catenin overrides the effects of inhibition or silencing of CK1δ. Thus, CK1δ inhibition represents a promising strategy for targeted treatment in human breast cancer with Wnt/β-catenin involvement.
Development of generic raman models for a GS‐KO <sup>TM</sup> CHO platform process (2018)

The monitoring and control of bioprocesses is of the utmost importance in order to provide a consistent, safe, and high-quality product for consumers. Current monitoring and control schemes rely on infrequent and time consuming offline sampling methods, which inherently leads to some variability in the process which may impact the product quality profile. As part of Lonza's dedication to process analytical technology (PAT) initiatives this study evaluated the ability to generate generic calibration models, which are independent of the cell line, using Raman probes to monitor changes in glucose, lactate, glutamate, ammonium, viable cell concentration (VCC), total cell concentration (TCC) and product concentration. Calibration models were developed from cell culture using two different CHOK1SV GS-KO<sup>TM</sup> cell lines producing different monoclonal antibodies (mAbs). Developed predictive models, measured changes in glucose, lactate, ammonium, VCC, and TCC with average prediction errors of 0.44, 0.23, 0.03 g L<sup>-1</sup> , 1.90 × 10<sup>6</sup> cells mL<sup>-1</sup> , and 1.85 × 10<sup>6</sup> cells mL<sup>-1</sup> , respectively over the course of cell culture with minimal cell line dependence. The development of these generic models allows the application of spectroscopic PAT techniques in clinical and commercial manufacturing environments, where processes are typically run once or twice in GMP manufacturing based on a common platform process. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:730-737, 2018.
On providing blocking probability and throughput guarantees in a multi‐service environment (2002)

Abstract As the Internet evolves from a packet network supporting a single best effort service class towards an integrated infrastructure supporting several service classes—some with QoS guarantees—there is a growing interest in the introduction of admission control and in devising bandwidth sharing strategies, which meet the diverse needs of QoS‐assured and elastic services. In this paper we show that the extension of the classical multi‐rate loss model is possible in a way that makes it useful in the performance analysis of a future admission control based Internet that supports traffic with peak rate guarantee as well as elastic traffic. After introducing the model, it is applied for the analysis of a single link, where it sheds light on the trade‐off between blocking probability and throughput . For the investigation of this trade‐off, we introduce the throughput‐threshold constraint, which bounds the probability that the throughput of a traffic flow drops below a predefined threshold. Finally, we use the model to determine the optimal parameter set of the popular partial overlap link allocation policy: we propose a computationally efficient algorithm that provides blocking probability‐ and throughput guarantees. We conclude that the model and the numerical results provide important insights in traffic engineering in the Internet. Copyright © 2002 John Wiley & Sons, Ltd.
Accuracy of least squares designed spatial FIR filters for segmentation of images of fluorescence stained cell nuclei (1996)

A method for accurate, real-time image segmentation is needed for the development of a fully automated image cytometer that combines the speed and case-of-use of flow cytometry with the detailed morphometry of imaging. Object intensity variation and inherent optical blur make real-time segmentation challenging. The best spatial finite impulse response (FIR) filter, implemented as a convolution, was tested for sharpening edges and creating the required contrast. The filter and threshold segmentation steps were treated as a two-category linear classifier. Best 3 x 3 through 25 x 25 filters were designed utilizing the perceptron criterion and nonlinear least squares, and tested on ten montage images of a combined 1,070 manually segmented DAPI stained cell nuclei. The resulting image contrast, or class separation, led to simple automatic thresholding via the histogram intermodal minimum. Image segmentation accuracy began to plateau at 7 x 7 filters and did not increase above 15 x 15. Little loss in accuracy occurred with application to the images not used for design. This segmentation method provides a systematic, fast and accurate means of creating binary object maps useful for subsequent measurement, processing and cell classification.
Chicken Avidin Exhibits Pseudo-catalytic Properties (2001)

Avidin and its bacterial analogue streptavidin exhibit similarly high affinities toward the vitamin biotin. The extremely high affinity of these two proteins has been utilized as a powerful tool in many biotechnological applications. Although avidin and streptavidin have similar tertiary and quaternary structures, they differ in many of their properties. Here we show that avidin enhances the alkaline hydrolysis of biotinyl p-nitrophenyl ester, whereas streptavidin protects this reaction even under extreme alkaline conditions (pH > 12). Unlike normal enzymatic catalysis, the hydrolysis reaction proceeds as a single cycle with no turnover because of the extremely high affinity of the protein for one of the reaction products (i.e. free biotin). The three-dimensional crystal structures of avidin (2 A) and streptavidin (2.4 A) complexed with the amide analogue, biotinyl p-nitroanilide, as a model for the p-nitrophenyl ester, revealed structural insights into the factors that enhance or protect the hydrolysis reaction. The data demonstrate that several molecular features of avidin are responsible for the enhanced hydrolysis of biotinyl p-nitrophenyl ester. These include the nature of a decisive flexible loop, the presence of an obtrusive arginine 114, and a newly formed critical interaction between lysine 111 and the nitro group of the substrate. The open conformation of the loop serves to expose the substrate to the solvent, and the arginine shifts the p-nitroanilide moiety toward the interacting lysine, which increases the electron withdrawing characteristics and consequent electrophilicity of the carbonyl group of the substrate. Streptavidin lacked such molecular properties, and analogous interactions with the substrate were consequently absent. The information derived from these structures may provide insight into the action of artificial protein catalysts and the evolution of catalytic sites in general.
Fast nondamageable laser-pulse detector using gaseous plasma (1980)

We investigated pulsed laser radiation detectors in which the emf is generated by the plasma formed when the radiation is focused onto a solid metal surface. We report on measurements made with 10.6-μn laser pulses at peak power levels up to 100 MW. For an evacuated detector, we obtained signals ≳1 kV and subnanosecond rise times into a 50-Ω load. Detector performance is strongly modified with the introduction of a background gas. With one atmosphere of air, the detector produces signals on the order of 1 V and nanosecond response for pulse trains lasting 100 ns, and is thus a good qualitative beam monitor. With argon, krypton, or xenon at pressures on the order of 10 Torr, the detector generates ’’trigger pulses’’ of 250-V amplitude and &lt;0.2-ns rise times. These detectors are indestructable.
The protective effect of the anti-Toll-like receptor 9 antibody against acute cytokine storm caused by immunostimulatory DNA (2017)

Toll-like Receptor 9 (TLR9) is an innate immune receptor recognizing microbial DNA. TLR9 is also activated by self-derived DNA, such as mitochondrial DNA, in a variety of inflammatory diseases. We show here that TLR9 activation in vivo is controlled by an anti-TLR9 monoclonal Ab (mAb). A newly established mAb, named NaR9, clearly detects endogenous TLR9 expressed in primary immune cells. The mAb inhibited TLR9-dependent cytokine production in vitro by bone marrow-derived macrophages and conventional dendritic cells. Furthermore, NaR9 treatment rescued mice from fulminant hepatitis caused by administering the TLR9 ligand CpGB and D-(+)-galactosamine. The production of proinflammatory cytokines induced by CpGB and D-(+)-galactosamine was significantly impaired by the mAb. These results suggest that a mAb is a promising tool for therapeutic intervention in TLR9-dependent inflammatory diseases.
Flux-focusing eddy current probe and rotating probe method for flaw detection (1994)

A flux-focusing electromagnetic sensor which uses a ferromagnetic flux-focusing lens simplifies inspections and increases detectability of fatigue cracks about circular fasteners and other circular inhomogeneities in high conductivity material. The unique feature of the device is the ferrous shield isolating a high-turn pick-up coil from an excitation coil. The use of the magnetic shield is shown to produce a null voltage output across the receiving coil in the presence of an unflawed sample. A redistribution of the current flow in the sample caused by the presence of flaws, however, eliminates the shielding condition and a large output voltage is produced, yielding a clear unambiguous flaw signal. By rotating the probe in a path around a circular fastener such as a rivet while maintaining a constant distance between the probe and the center of a rivet, the signal due to current flow about the rivet can be held constant. Any further changes in the current distribution, such as due to a fatigue crack at the rivet joint, can be detected as an increase in the output voltage above that due to the flow about the rivet head.
Abstract 236: Biphasic Reprogramming of Ventricular Cardiomyocytes to Pacemaker Cells by Tbx18 (2019)

Background: We have previously demonstrated that an embryonic transcription factor, TBX18, suffices to reprogram postnatal ventricular cardiomyocytes to induced pacemaker cells. Here, we sought to gain finer understanding of the reprogramming process by investigating genotype/phenotype of the de novo pacemaker cells in multiple temporal domains. Methods: TBX18-induced pacemaker cells (TBX18-iPMs) were created in vitro by somatic gene transfer of Adeno-TBX18 into neonatal rat ventricular myocytes (NRVMs). Control ventricular myocytes were transduced with Adeno- GFP. To investigate in vivo reprogramming, we delivered AAV9-TBX18 via tail vein of Hcn4(+/eGFP) heterozygous transgenic mice, which expresses eGFP under the Hcn4 promoter, so as to lineage-trace de novo pacemaker cells in the ventricular myocardium. Results: The automaticity of TBX18-iPMs was higher than that of GFP-NRVMs during D1-D3, decreased after D3 and rebound by D14. Monolayers of the iPMs revealed multiple foci of spontaneous field potentials with lower spike amplitude, spike slope, and conduction velocity, demonstrating phenotypic reprogramming to the iPMs by D14. RNAseq and qPCR revealed two distinct phases of reprogramming; an early phase that showed loss of expression of ventricular myocyte-related gene program and a late phase that showed gain of expression of nodal gene program which plateaued by D14. For example, Hcn4 gene expression began increasing during week 1 and continued the pattern during week 2. By week 3, Hcn4-positive TBX18-iPMs appeared in clusters of NRVM monolayers while GFP-NRVMs were spread evenly throughout the monolayers. We lineage-traced de novo, TBX18-reprogrammed pacemaker cells in vivo by delivering AAV9-TBX18 via tail-vein of Hcn4(+/eGFP) mice. In line with our in vitro data, in vivo pacemaker cell lineage tracing experiments indicated a progressive loss of ventricular gene program followed by gain of nodal gene program. Conclusions: Our data indicate that TBX18-induced reprogramming of ventricular myocytes to nodal pacemaker cells undergoes progressive changes in gene expression shedding ventricular gene/phenotype first, and then gaining nodal pacemaker genotype/phenotype, establishing fully functional nodal pacemaker by D14.