gebhart/patrepeval huggingface dataset:
<i>In vivo</i> transposition of <i>mariner</i> -based elements in enteric bacteria and mycobacteria (1999)

mariner family transposons are widespread among eukaryotic organisms. These transposons are apparently horizontally transmitted among diverse eukaryotes and can also transpose in vitro in the absence of added cofactors. Here we show that transposons derived from the mariner element Himar1 can efficiently transpose in bacteria in vivo. We have developed simple transposition systems by using minitransposons, made up of short inverted repeats flanking antibiotic resistance markers. These elements can efficiently transpose after expression of transposase from an appropriate bacterial promoter. We found that transposition of mariner-based elements in Escherichia coli produces diverse insertion mutations in either a targeted plasmid or a chromosomal gene. With Himar1-derived transposons we were able to isolate phage-resistant mutants of both E. coli and Mycobacterium smegmatis. mariner-based transposons will provide valuable tools for mutagenesis and genetic manipulation of bacteria that currently lack well developed genetic systems.
Novel PMD measurement method based on OFDR using a frequency-shifted feedback fiber laser (2001)

We propose a new method to measure polarization mode dispersion (PMD) in optical fibers based on optical frequency domain reflectometry technique. In this method the PMD is directly determined from the beat frequency generated by interference between lights from the Fresnel reflection at the end of the device under test, which makes the measurement at single end of the device possible. An automated PMD measurement system is demonstrated on polarization maintaining fibers with a frequency-shifted feedback fiber laser as a light source.
Nanoscale Optofluidic Sensor Arrays for Dengue virus detection (2008)

Here we present nanoscale optofluidic sensor arrays (NOSAs) for Dengue virus detection, which is an optofluidic architecture for performing label free, highly parallel, detections of biomolecular interactions in aqueous environments with potential for a very low mass limit of detection.
GraphMaps: Browsing Large Graphs as Interactive Maps (2015)

Algorithms for laying out large graphs have seen significant progress in the past decade. However, browsing large graphs remains a challenge. Rendering thousands of graphical elements at once often results in a cluttered image, and navigating these elements naively can cause disorientation. To address this challenge we propose a method called GraphMaps, mimicking the browsing experience of online geographic maps. GraphMaps creates a sequence of layers, where each layer refines the previous one. During graph browsing, GraphMaps chooses the layer corresponding to the zoom level, and renders only those entities of the layer that intersect the current viewport. The result is that, regardless of the graph size, the number of entities rendered at each view does not exceed a predefined threshold, yet all graph elements can be explored by the standard zoom and pan operations. GraphMaps preprocesses a graph in such a way that during browsing, the geometry of the entities is stable, and the viewer is responsive. Our case studies indicate that GraphMaps is useful in gaining an overview of a large graph, and also in exploring a graph on a finer level of detail.
Cryogen Spray Cooling for Spatially Selective Photocoagulation of Hemangiomas: A New Methodology with Preliminary Clinical Reports (1998)

Spatially selective photocoagulation of subsurface-targeted blood vessels by repetitive application of a short cryogen spurt during continuous Nd:YAG laser irradiation has been demonstrated in two human cases. This procedure may be effective for the treatment of thick hemangiomas that require photocoagulation of subsurface blood vessels while protecting the epidermis.
<title>Spatially reduced image extraction from MPEG-2 video: fast algorithms and applications</title> (1997)

The MPEG-2 video standards are targeted for high-quality video broadcast and distribution, and are optimized for efficient storage and transmission. However, it is difficult to process MPEG-2 for video browsing and database applications without first decompressing the video. Yeo and Liu have proposed fast algorithms for the direct extraction of spatially reduced images from MPEG-1 video. Reduced images have been demonstrated to be effective for shot detection, shot browsing and editing, and temporal processing of video for video presentation and content annotation. In this paper, we develop new tools to handle the extra complexity in MPEG-2 video for extracting spatially reduced images. In particular, we propose new classes of discrete cosine transform (DCT) domain and DCT inverse motion compensation operations for handling the interlaced modes in the different frame types of MPEG-2, and design new and efficient algorithms for generating spatially reduced images of an MPEG-2 video. We also describe key video applications on the extracted reduced images.
An adaptive transfer function for deriving the aortic pressure waveform from a peripheral artery pressure waveform (2009)

We developed a new technique to mathematically transform a peripheral artery pressure (PAP) waveform distorted by wave reflections into the physiologically more relevant aortic pressure (AP) waveform. First, a transfer function relating PAP to AP is defined in terms of the unknown parameters of a parallel tube model of pressure and flow in the arterial tree. The parameters are then estimated from the measured PAP waveform along with a one-time measurement of the wave propagation delay time between the aorta and peripheral artery measurement site (which may be accomplished noninvasively) by exploiting preknowledge of aortic flow. Finally, the transfer function with its estimated parameters is applied to the measured waveform so as to derive the AP waveform. Thus, in contrast to the conventional generalized transfer function, the transfer function is able to adapt to the intersubject and temporal variability of the arterial tree. To demonstrate the feasibility of this adaptive transfer function technique, we performed experiments in 6 healthy dogs in which PAP and reference AP waveforms were simultaneously recorded during 12 different hemodynamic interventions. The AP waveforms derived by the technique showed agreement with the measured AP waveforms (overall total waveform, systolic pressure, and pulse pressure root mean square errors of 3.7, 4.3, and 3.4 mmHg, respectively) statistically superior to the unprocessed PAP waveforms (corresponding errors of 8.6, 17.1, and 20.3 mmHg) and the AP waveforms derived by two previously proposed transfer functions developed with a subset of the same canine data (corresponding errors of, on average, 5.0, 6.3, and 6.7 mmHg).
High Surface Area Transparent Conducting Oxide Electrodes with a Customizable Device Architecture (2014)

Herein, we report the development of optically transparent high surface area electrodes (HSEs) made of indium tin oxide (ITO) using a facile, template-free, scalable wet chemical synthetic approach. The transparent HSEs are electronically conductive and physically robust, with tunable electrochemically accessible roughness factors from 1 through ∼100. These transparent HSEs can serve as a broadly functionalizable scaffold ideally suited to bridge the gap between the need to minimize ionic and electronic transport lengths within a device and the need to achieve high loadings of active material per surface area (e.g. for high capacity as needed for batteries or high optical density as required for electrochromics or photovoltaics). This gap currently stands as a major hurdle for the utilization of many nanomaterials in electronic and optoelectronic devices. The synthetic approach described here for ITO is transferable to other transparent conducting oxide (TCO) materials. This is the first report of a large-pore, tunable, high surface area TCO electrode with excellent optical and conductive properties.
Alternating Copolymers of Functional Alkenes with Carbon Monoxide (1996)

The alternating copolymerization of functional alkenes, CH2CH(CH2)xOH (x = 2, 3, 4, 9), CH2CH(CH2)xCOOH (x = 1, 2, 4, 8), and 4-allylanisole, with carbon monoxide was achieved by using [Pd(Me-DUPHOS)(MeCN)2](BF4)2 [Me-DUPHOS = 1,2-bis(2,5-dimethylphospholano)benzene] as the catalyst. The resultant polymers were optically active with isotactic sequences in the backbone. With most alkenes, the polymers had poly(1,4-ketone) and/or “regular” poly(spiroketal) (i.e., 1,6-dioxaspiro[4.4]nonane) enchainments. However, with 4-penten-1-ol and 3-buten-1-ol, the participation of the pendant hydroxyl group in intrachain reactions led to the formation of unusual polycyclic repeating units in the backbone. A comparison of [Pd(Me-DUPHOS)(MeCN)2](BF4)2 with [Pd(DPPP)(MeCN)2](BF4)2 [DPPP = 1,3-bis(diphenylphosphino)propane] indicated that the former was a significantly better catalyst for the alternating copolymerization of alkenols and alkenoic acids with carbon monoxide.
A new high performance field reversed configuration operating regime in the C-2 device (2012)

Large field reversed configurations (FRCs) are produced in the C-2 device by combining dynamic formation and merging processes. The good confinement of these FRCs must be further improved to achieve sustainment with neutral beam (NB) injection and pellet fuelling. A plasma gun is installed at one end of the C-2 device to attempt electric field control of the FRC edge layer. The gun inward radial electric field counters the usual FRC spin-up and mitigates the n = 2 rotational instability without applying quadrupole magnetic fields. Better plasma centering is also obtained, presumably from line-tying to the gun electrodes. The combined effects of the plasma gun and of neutral beam injection lead to the high performance FRC operating regime, with FRC lifetimes up to 3 ms and with FRC confinement times improved by factors 2 to 4.
Orthogonal Comparison of Analytical Methods by Theoretical Reconstruction from Bottom-up Assay Data (2021)

In the never-ending endeavor to produce stable and efficacious protein therapeutics, biopharmaceutical companies often employ numerous analytical techniques to characterize and quantify a drug candidate's stability. Mass spectrometry, due to the information-rich data it produces, is commonly used in its numerous configurations to ascertain chemical and structural stability. At issue is the comparison of the various configurations utilized, that is, comparing bottom-up methods such as proteolytic digest followed by reversed phase LC-MS with intact LC-MS methods. Similar issues also arise when using capillary isoelectric focusing to see how charge variants change over time, that is, monitoring the progression of charge altering modifications like deamidation. To this end, site-specific degradations as quantified from bottom-up methods like peptide mapping can be used to build reconstructions of both theoretical intact mass spectra as well as theoretical electropherograms. The result can then be superimposed over the experimental data to qualitatively, and perhaps quantitatively, evaluate differences. In theory, if both experimental bottom-up data and intact data are accurate, the theoretical reconstruction produced from the bottom-up data should perfectly overlay with that of the experimental data. Valuable secondary information can also be ascertained from reconstructions, such as whether modifications are stochastic, as well as a detailed view of all possible combinations of modifications and their quantities used in the reconstruction. This comparison is also useful in determining unknown mass differences in deconvoluted intact protein spectra that may be a result of multiple modifications in combination. The comparison of data from alternate sources provides a holistic and more comprehensive view of the molecule under study.
Acoustic Emission Method for Monitoring Corrosion Reactions (1976)

There is a continuing need for new test techniques to follow corrosion reaction processes and to predict long-term materials performance in aggressive environments. Additionally, there is a growing awareness of the importance of applying non-destructive inspection to determine the presence of corrosion in non-visible areas of equipment and structures. The possibilities of utilizing acoustic emission for a broad range of applications in the study of these problems were explored. Proprietary methods were developed to follow corrosion reactions and to monitor corrosion of simulated and actual structures. These experiments point out the applicability of acoustic emission as a sensitive new tool for corrosion research and non-destructive testing (NDT) in corrosion prone structures and equipment.
Automated motility and morphology measurement of live spermatozoa (2021)

Automated motility and morphology measurement of single sperm revealed high reproducibility and reliability. The system also achieved a high efficiency for motility and morphology measurement. In addition to the intracytoplasmic sperm injection (ICSI) samples with polyvinylpyrrolidone (PVP), the developed sperm measurement technique is also effective for analyzing semen and washed samples. The system provides a valuable tool for quantitative measurement and selection of single spermatozoa for ICSI. It can also be used for sperm motility and morphology analysis in andrology laboratories.
Association of Longer Telomeres With Better Health in Centenarians (2008)

Prior animal model studies have demonstrated an association between telomere length and longevity. Our study examines telomere length in centenarians in good health versus poor health. Using DNA from blood lymphocytes, telomere length was measured by quantitative polymerase chain reaction in 38 sex- and age-matched centenarians (ages 97-108). "Healthy" centenarians (n = 19) with physical function in the independent range and the absence of hypertension, congestive heart failure, myocardial infarction, peripheral vascular disease, dementia, cancer, stroke, chronic obstructive pulmonary disease, and diabetes were compared to centenarians with physical function limitations and > or =2 of the above conditions (n = 19). Healthy centenarians had significantly longer telomeres than did unhealthy centenarians (p =.0475). Our study demonstrated that investigations of the association between telomere length and exceptional longevity must take into account the health status of the individuals. This raises the possibility that perhaps it is not exceptional longevity but one's function and health that may be associated with telomere length.
Instrumentation for a High Purity Germanium Position Sensing Gamma Ray Detector (1975)

The analysis and design of the instrumentation required to provide spatial and energy information from a high purity germanium, one-dimensional position sensing gamma ray detector is presented. The results of this study demonstrate that the optimum instrumentation system utilizes Gaussian shaping for the energy channel and Gaussian trapezoidal pulse shaping after antisymmetric summation in the spatial channel.
Turbulence compensation of an orbital angular momentum and polarization-multiplexed link using a data-carrying beacon on a separate wavelength (2015)

We investigate the sensing of a data-carrying Gaussian beacon on a separate wavelength as a means to provide the information necessary to compensate for the effects of atmospheric turbulence on orbital angular momentum (OAM) and polarization-multiplexed beams in a free-space optical link. The influence of the Gaussian beacon's wavelength on the compensation of the OAM beams at 1560 nm is experimentally studied. It is found that the compensation performance degrades slowly with the increase in the beacon's wavelength offset, in the 1520-1590 nm band, from the OAM beams. Using this scheme, we experimentally demonstrate a 1 Tbit/s OAM and polarization-multiplexed link through emulated dynamic turbulence with a data-carrying beacon at 1550 nm. The experimental results show that the turbulence effects on all 10 data channels, each carrying a 100 Gbit/s signal, are mitigated efficiently, and the power penalties after compensation are below 5.9 dB for all channels. The results of our work might be helpful for the future implementation of a high-capacity OAM, polarization and wavelength-multiplexed free-space optical link that is affected by atmospheric turbulence.
Performances Of Five Symbol-Lock Detectors (1994)

Report discusses performances of two older and three newer symbol-lock detectors described in Three Alternative Symbol-Lock Detectors (NPO-18521).
High-speed Electro-optic Modulation in Silicon Nitride (2023)

We demonstrate electro-optic modulation up to 15GHz (3dB bandwidth) in a silicon nitride ring resonator by electrically poling the silicon nitride at a high temperature to engineer an electro-optic effect.
Estimating the shell parameters of SonoVue® microbubbles using light scattering (2009)

Experiments were performed to measure the dynamical response of individual SonoVue microbubbles subjected to pulsed ultrasound. Three commonly used bubble dynamic models (i.e., Hoff's, Sarkar's, and linearized Marmottant's models) were compared to determine the most appropriate model for fitting to the experimental data. The models were evaluated against published optical microscopy data. The comparison suggests that it is difficult to rank these models for lipid-shelled microbubbles undergoing small-amplitude oscillations, because under these conditions the shell parameters in these models are closely related. A linearized version of the Marmottant model was used to estimate the shell parameters (i.e., shear modulus and shear viscosity) of SonoVue microbubbles from the experimental light scattering data, as a function of ambient microbubble radius. The SonoVue microbubble shell elasticity and dilatational viscosity increase with ambient bubble radius, in agreement with previously published data. The results suggest that light scattering, used in conjunction with one of several popular bubble dynamics models, is effective at characterizing microbubble response and evaluating shell parameters.
Parameter Estimation by Parameter Signature Isolation in the Time-Scale Domain (2009)

It is shown that output sensitivities of dynamic models can be better delineated in the time-scale domain. This enhanced delineation provides the capacity to isolate regions of the time-scale plane, coined as parameter signatures, wherein individual output sensitivities dominate the others. Due to this dominance, the prediction error can be attributed to the error of a single parameter at each parameter signature so as to enable estimation of each model parameter error separately. As a test of fidelity, the estimated parameter errors are evaluated in iterative parameter estimation in this paper. The proposed parameter signature isolation method (PARSIM) that uses the parameter error estimates for parameter estimation is shown to have an estimation precision comparable to that of the Gauss–Newton method. The transparency afforded by the parameter signatures, however, extends PARSIM’s features beyond rudimentary parameter estimation. One such potential feature is noise suppression by discounting the parameter error estimates obtained in the finer-scale (higher-frequency) regions of the time-scale plane. Another is the capacity to assess the observability of each output through the quality of parameter signatures it provides.
Appearance-based diagnostic system for early assessment of malignant lung nodules (2012)

A novel 2D approach for early assessment of malignant lung nodules based on analyzing the spatial distribution of Hounsfield values for the detected lung nodules is proposed. Spatial distribution of Hounsfield values comprising the malignant nodule appearance is accurately modeled with a new 2D rotationally invariant second-order Markov-Gibbs Random Field (MGRF). Preliminary experiments on 109 lung nodules (51 malignant and 58 benign) show that the proposed method is a promising supplement to current technologies (biopsy-based diagnostic systems) for the early diagnosis of lung cancer.
Breast Cancer MDA-MB-231 Cells Use Secreted Heat Shock Protein-90alpha (Hsp90α) to Survive a Hostile Hypoxic Environment (2016)

Rapidly growing tumours in vivo often outgrow their surrounding available blood supply, subjecting themselves to a severely hypoxic microenvironment. Understanding how tumour cells adapt themselves to survive hypoxia may help to develop new treatments of the tumours. Given the limited blood perfusion to the enlarging tumour, whatever factor(s) that allows the tumour cells to survive likely comes from the tumour cells themselves or its associated stromal cells. In this report, we show that HIF-1α-overexpressing breast cancer cells, MDA-MB-231, secrete heat shock protein-90alpha (Hsp90α) and use it to survive under hypoxia. Depletion of Hsp90α secretion from the tumour cells was permissive to cytotoxicity by hypoxia, whereas supplementation of Hsp90α-knockout tumour cells with recombinant Hsp90α, but not Hsp90β, protein prevented hypoxia-induced cell death via an autocrine mechanism through the LDL receptor-related protein-1 (LRP1) receptor. Finally, direct inhibition of the secreted Hsp90α with monoclonal antibody, 1G6-D7, enhanced tumour cell death under hypoxia. Therefore, secreted Hsp90α is a novel survival factor for certain tumours under hypoxia.
Synthesis of nucleosides of 5‐substituted‐1,2,4‐triazole‐3‐carboxamides (1974)

Abstract Nucleosides of 5‐substituted‐1,2,4‐triazole‐3‐carboxamides were prepared by the acid‐catalyzed fusion procedure and by glycosylation of the appropriate trimethylsilyl derivative. The following nucleosides were obtained in two steps starting from methyl 4‐substituted‐1,2,4‐triazole‐3‐carboxylates: 5‐chloro‐1‐β‐ D ‐ribofuranosyl‐1,2,4‐triazole‐3‐carboxamide ( 6 ), 3‐chloro‐1‐β‐ D ‐ribofuranosyl‐1,2,4‐triazole‐5‐carboxamide ( 5 ), 3‐nitro‐1‐β‐ D ‐ribofuranosyl‐1,2,4‐triazole‐5‐carboxamide ( 12 ), 3‐amino‐1‐β‐ D ‐ribofuranosyl‐1,2,4‐triazole‐5‐carboxamide ( 13 ), 5‐methyl‐1‐β‐ D ‐ribofuranosyl‐1,2,4‐triazole‐3‐carboxamide ( 15 ), and 3‐methyl‐1‐β‐ D ‐ribofuranosyl‐1,2,4‐triazole‐5‐carboxamide ( 16 ). In addition, 5‐amino‐1‐β‐ D ‐ribofuranosyl‐1,2,4‐triazole‐3‐carboxamide ( 7 ), and 1‐β‐ D ‐ribofuranosyl‐1,2,4‐triazole‐3‐carboxamide‐5‐thiol ( 8 ) were prepared from 6 .
Trench schottky rectifiers with non-uniform trench depths (2017)

A design methodology to optimize the drift region doping properties in trench Schottky rectifiers has been presented. Advanced lithography is being used for trench devices that are designed for smaller die sizes in wireless applications. Such devices feature narrow active trenches to maximize active area utilization in combination with a wide termination trench to support the breakdown voltage. Such different trench aspect ratios create a depth mismatch, if they are formed in a single etch step. It has been shown that designing the drift region while accounting for the trench depth difference is vital to properly optimize the device electrical parameters. A new trench architecture has also been proposed which features alternating deeper active trenches. The new trench architecture is shown to have the best performance trade-off at the cost of one additional mask step.