gebhart/patrepeval huggingface dataset:
Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones (2016)

Digital single-molecule technologies are expanding diagnostic capabilities, enabling the ultrasensitive quantification of targets, such as viral load in HIV and hepatitis C infections, by directly counting single molecules. Replacing fluorescent readout with a robust visual readout that can be captured by any unmodified cell phone camera will facilitate the global distribution of diagnostic tests, including in limited-resource settings where the need is greatest. This paper describes a methodology for developing a visual readout system for digital single-molecule amplification of RNA and DNA by (i) selecting colorimetric amplification-indicator dyes that are compatible with the spectral sensitivity of standard mobile phones, and (ii) identifying an optimal ratiometric image-process for a selected dye to achieve a readout that is robust to lighting conditions and camera hardware and provides unambiguous quantitative results, even for colorblind users. We also include an analysis of the limitations of this methodology, and provide a microfluidic approach that can be applied to expand dynamic range and improve reaction performance, allowing ultrasensitive, quantitative measurements at volumes as low as 5 nL. We validate this methodology using SlipChip-based digital single-molecule isothermal amplification with λDNA as a model and hepatitis C viral RNA as a clinically relevant target. The innovative combination of isothermal amplification chemistry in the presence of a judiciously chosen indicator dye and ratiometric image processing with SlipChip technology allowed the sequence-specific visual readout of single nucleic acid molecules in nanoliter volumes with an unmodified cell phone camera. When paired with devices that integrate sample preparation and nucleic acid amplification, this hardware-agnostic approach will increase the affordability and the distribution of quantitative diagnostic and environmental tests.
Abstract 5601: Efficient tumor therapy by anthrax toxin fusion proteins that contain cytolethal distending toxin B. (2013)

Abstract Cytolethal distending toxin (Cdt) is produced by several Gram-negative bacterial species. It is composed of three subunits, CdtA, CdtB, and CdtC, with CdtB being the catalytic subunit. We fused CdtB from Haemophilus ducreyi with the N-terminal 254 amino acids of Bacillus anthracis toxin lethal factor (LFn) to produce a novel, potent anti-tumor drug. CdtB is transported into the cytosol of targeted cells via the efficient delivery mechanism of anthrax toxin. The fusion protein efficiently killed various human tumor cell lines by inducing a complete cell cycle arrest in the G2/M phase and subsequently inducing apoptosis. Despite the described role of CdtB as a DNase, we detected a prominent phosphatase activity of CdtB, similar to phosphatase and tensin homolog (PTEN) activity. Animal studies showed very low toxicity of a systemically-applied tumor-specific treatment and impressive anti-tumor effects, resulting in a 90% cure rate. This study demonstrates the great potential of a combination of efficient drug delivery by a modified anthrax toxin system and the enzymatic activity of CdtB, and argues for the continued development of this novel anti-cancer drug. Citation Format: Christopher Bachran, Suzanne Abdelazim, Radka Hasikova, Shihui Liu, Stephen H. Leppla. Efficient tumor therapy by anthrax toxin fusion proteins that contain cytolethal distending toxin B. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5601. doi:10.1158/1538-7445.AM2013-5601
SCNN: An Accelerator for Compressed-sparse Convolutional Neural Networks (2017)

Convolutional Neural Networks (CNNs) have emerged as a fundamental technology for machine learning. High performance and extreme energy efficiency are critical for deployments of CNNs in a wide range of situations, especially mobile platforms such as autonomous vehicles, cameras, and electronic personal assistants. This paper introduces the Sparse CNN (SCNN) accelerator architecture, which improves performance and energy efficiency by exploiting the zero-valued weights that stem from network pruning during training and zero-valued activations that arise from the common ReLU operator applied during inference. Specifically, SCNN employs a novel dataflow that enables maintaining the sparse weights and activations in a compressed encoding, which eliminates unnecessary data transfers and reduces storage requirements. Furthermore, the SCNN dataflow facilitates efficient delivery of those weights and activations to the multiplier array, where they are extensively reused. In addition, the accumulation of multiplication products are performed in a novel accumulator array. Our results show that on contemporary neural networks, SCNN can improve both performance and energy by a factor of 2.7x and 2.3x, respectively, over a comparably provisioned dense CNN accelerator.
Fast and background-free three-dimensional (3D) live-cell imaging with lanthanide-doped upconverting nanoparticles (2015)

We report on the development of a three-dimensional (3D) live-cell imaging technique with high spatiotemporal resolution using lanthanide-doped upconverting nanoparticles (UCNPs). It employs the sectioning capability of confocal microscopy except that the two-dimensional (2D) section images are acquired by wide-field epi-fluorescence microscopy. Although epi-fluorescence images are contaminated with the out-of-focus background in general, the near-infrared (NIR) excitation used for the excitation of UCNPs does not generate any autofluorescence, which helps to lower the background. Moreover, the image blurring due to defocusing was naturally eliminated in the image reconstruction process. The 3D images were used to investigate the cellular dynamics such as nuclear uptake and single-particle tracking that require 3D description.
25 W 2 um broadband polarization-maintaining hybrid Ho- and Tm-doped fiber amplifier (2019)

Current developments in LIDAR and atmospheric sensing experiments highlight the need for multi-watt, large bandwidth, high dynamic range polarization-maintaining optical amplifiers in the eye safe 1.9—2.15 μm band. So far, as an illustration of the previous state of the art for high power devices, multi-watt Tm-doped fiber amplifiers (TDFAs) have been demonstrated by Goodno et al. with an output power of 608 W at a signal wavelength of 2040 nm. As for Ho-doped fiber amplifiers (HDFAs) Hemming et al. have reported output powers of 265 W at 2110 nm. For this HDFA, a double clad Ho-doped fiber pumped by high power fiber lasers made the configuration complex and yielded an optical slope efficiency of 41%. Both of these achievements were with standard (non-polarization-maintaining) fiber.
High performance AlGaN/GaN power switch with HfO2 insulation (2009)

High performance AlGaN/GaN metal-insulator-semiconductor heterostructure field-effect transistor was fabricated using HfO2 as the surface passivation and gate insulator. The gate and drain leakage currents are drastically reduced to tens of nanoamperes before breakdown. Without field plates, for 10 μm of gate-drain spacing, the off-state breakdown voltage is 1035 V with a specific on resistance of 0.9 mΩ cm2. In addition, there is no current slump observed from the pulse measurements. This is the best performance reported on GaN-based power-switching devices on sapphire up to now, which efficiently combines excellent device forward, reverse, and switching characteristics.
Accuracy of Methods for Calculating Postnatal Growth Velocity for Extremely Low Birth Weight Infants (2005)

GV estimates calculated with 3 commonly used models varied widely, compared with actual GVs; however, the exponential model estimates were extremely accurate. The exponential model provides the accuracy and ease of use that are lacking in current methods applied to infant growth research.
Massively parallel processing of signals in dense microphone arrays (2010)

Arrays with large number of microphones can be very effective on audio processing tasks, like denoising, acoustic echo removal, etc. New microphone technologies enable creating large arrays with very low cost per component, but the system can still be very expensive due to costs of transmitting all signals to a single processor, and the computational resources to process the large amount of data. We show how a massively-parallel signal processing approach can solve the cost issues, when applied to the problem of sound source localization. We consider the case where each microphone is coupled to simple processing circuitry, which have full-bandwidth access to data from a few other microphones, while only shared power and low-bandwidth connections are provided between each microphone and a central processor. We discuss implementation issues, and show experimental results obtained in simulations and in microphone array measurements.
Self-Healing Properties of Lignin-Containing Nanocomposite: Synthesis of Lignin-<i>graft</i>-poly(5-acetylaminopentyl acrylate) via RAFT and Click Chemistry (2016)

Lignin can be an important source of synthetic commodity materials owing to its abundance in nature and low production cost. The current use of lignin as a raw material, however, is very limited and focused only on cheap and poorly defined nonfunctional materials. Herein we report a new lignin-containing functional polymer, lignin-graft-poly(5-acetylaminopentyl acrylate) (lignin-graft-PAA), which has been prepared by the covalent linkage of chemically modified lignin with PAA, which is an end-group functionalized polymer. This work makes two significant advances in the study of lignin-containing polymers: (1) lignin-graft-PAA is the first example of lignin being modified by a polymer with sophisticated structure, and (2) lignin-graft-PAA shows a special performance, autonomic self-healing properties, which have not yet been seen in lignin-containing polymers. The key synthetic step in this process utilizes a copper-catalyzed azide–alkyne cycloaddition or “click” reaction in order to join together the lignin and polymer moieties. The polymer, PAA, was itself prepared via reversible addition–fragmentation chain transfer (RAFT) polymerization of monomers containing multiple hydrogen-bonding sites on their pendants in the form of acetylamino functional groups. The selected RAFT agents also resulted in a polymer with an azide group at its terminus, which is necessary for the desired click reaction. Separately, biomass lignin was chemically modified by 5-hexynoic acid to introduce an alkyne functionality onto lignin. The azide terminus of the polymer was joined to the alkyne group of lignin to form a covalent bond. The lignin-graft-PAA possesses a well-dispersed multiphase nanostructure, a rigid lignin phase and a soft-PAA phase, which has a rubber-like flexibility. The mechanical properties of the newly synthesized lignin-graft-PAA can be readily controlled by the mass ratio of lignin and polymer during synthesis. In this study, the mass ratio was varied by either polymer length or weight percentage of lignin. It was revealed that a lignin-graft-PAA composite with 15–20 wt % lignin demonstrated the most optimal rubber-like, flexible property. Thanks to the high degree of hydrogen bonding from the acetylamino functionalities, lignin-graft-PAA also showed self-healing properties, recovering up to 93% of its original maximum stress before fracture.
Impact of LEDGIN treatment during virus production on residual HIV-1 transcription (2019)

LEDGINs present a research tool to study the link between integration and transcription, an essential question in retrovirology. LEDGIN treatment during virus production altered integration of residual provirus in a LEDGF/p75-independent manner, resulting in a reservoir that is refractory to activation.
Resonant optical forces associated with the excitation of whispering gallery modes in microparticles (2014)

The resonant excitation of whispering gallery modes (WGMs) in microparticles can give rise to the appearance of large and highly selective optical forces. The forces can also be viewed as a result of the significant change of the electromagnetic momentum in the system. We compare the forces and their relation to the electromagnetic momentum of the incident radiation in several geometries. The considered geometries include the excitation by a plane wave, focused beam, surface wave, guided mode of a parallel plate waveguide, and by the backward wave of a thin plasma layer.
Aerosol Deposition in Sampling Probes (1992)

Deposition of aerosol particles on the inner walls of sampling probes is of concern in many aerosol sampling applications. Only inertial and gravitational effects have been considered in previous studies of the aerosol deposition; however, the lift force on particles is also of significance. In this investigation, experiments have been conducted to construct a database for aerosol deposition in Willeke-type sampling probes. An empirical correlation has been made between wall losses and the depositional forces of drag, gravity, inertia, and particle lift through the use of dimensionless parameters. Inclusion of the lift effect in this correlation not only helps to better predict particle behavior in the sampling inlet, but it also provides a basis for understanding of the intrinsic deposition phenomenon. The correlation has a geometric standard deviation of 1.13 and a 0.93 correlation coefficient relative to the experimental data.
Optical Characterization Of Radiation-Resistant Fibers (1984)

Various measurements have been made on step index fibers having pure silica cores which are expected to have good radiation hardness properties. These measurements include spec-tral attenuation, numerical aperture, and bandwidth. Values for the preceeding quantities are given for several step index fibers of various diameters including the following: plastic-clad silica (PCS), QSF-AS, Raychem VSC, Dainichi Diaguide, and Ensign-Bickford fiber. Computer-controlled instrumentation was developed for these measurements and is described.
Surface-emitting complex-coupled second-order distributed-feedback lasers for high-power applications (1998)

Theoretical analysis of complex-coupled, surface-emitting distributed feedback (CC-SE-DFB) diode lasers with distributed Bragg reflectors (DBR) is presented. These devices are shown to produce symmetric-mode (single-lobe) surface emission with high efficiency (30%) and uniform near-field in the longitudinal direction. High efficiency and uniform near-field are both necessary for achieving high powers in a single-lobed beam. It is also shown that the device studied here may be combined with a Resonant Optical Waveguide array device which has a uniform near-field in the lateral direction to achieve a two-dimensional surface-emitting device capable of providing greater than 1W CW power in a stable, single-lobed beam.
Characterization of circulating tumor cells in patients with localized high risk prostate cancer, post-prostatectomy. (2017)

e23055 Background: Approximately 15% of men with newly diagnosed prostate cancer (PCa) have high-risk features, which increase the risk of recurrence. Better predictive biomarkers, such as circulating tumor cells (CTCs), could allow for earlier detection of biochemical recurrence. Here, we aim to evaluate the ability to detect CTCs using an enrichment free, unbiased CTC identification technology from men with high risk, localized PCa after radical prostatectomy (RP) and correlate their presence with prospective clinical data. Methods: Blood samples of 31 patients with high risk, localized PCa obtained 2-4 months post RP were shipped to Epic Sciences on an IRB approved protocol. All nucleated cells were subjected to immunofluorescent (IF) staining for cytokeratin (CK), CD45, and AR N terminus. CTCs were identified by fluorescent scanners using algorithmic analysis. CK expressing (CK + ) CTCs were enumerated and analyzed for AR expression and individually sequenced for copy number variation (CNV) and large scale transition (LST, a surrogate of genomic instability). Patients were followed prospectively for biochemical recurrence, defined as detectable PSA. Progression free survival was calculated using Kaplan-Meier and Cox proportional hazards. Results: CTCs were detected in 87.1% (27/31) samples with an average of 5.6 CTCs/ml (range: 0 – 22.87) detected per patient. AR expression was detected in 12.9% (4/31) of patients. Ninety-nine CTCs from 14 patients were amenable to LST and CNV sequencing and analyses. 10.1% (10/99) CTCs from 7 patients exhibited higher ( > = 6) LSTs than control WBCs (95% WBCs had LST < 6). Copy number alterations were identified in CTCs in commonly mutated genes in PCa, including AR, MYC, and TP53 amplification and deletions in PTEN and RB1. Patients with higher CTC burdens exhibited a trend toward shorter PFS (hazard ratio: 1.65; 95% CI: 0.7-3.86; p: 0.13). Conclusions: There was a high incidence of CTC detection after RP in patients with high risk, localized PCa. We observed a trend toward shorter PFS in those with higher CTC burden and genomic alterations detectable in CTCs are consistent with established CNAs in PCa. Tissue genomic correlatives are under analysis.
Fabrication of a high temperature-resistance optical fibre micro pressure sensor (2009)

A micro diaphragm-based Extrinsic Fabry-Perot Interferometric (EFPI) pressure sensor with high temperature immunity is described. The EFPI pressure sensor consists of a single mode silica glass optical fiber, a glass capillary and a glass diaphragm, which are fused together using a conventional fusion splicer. This eliminates the need for the use of other joining materials, e.g. epoxy, allows any thermal mismatch between different materials to be almost completely eliminated and hence the sensor is capable of high temperature operation. In addition, the EFPI pressure sensor is cheap and relatively easy to produce as only splicing, polishing and wet etching are necessary. Moreover, due to its small size, a frequency response of several MHz can be achieved.
Quantum electronic properties of the Na/sub 3/Ga/sub 2/Li/sub 3/F/sub 12/:Cr/sup 3+/ laser (1988)

Few of the existing Cr/sup 3+/ vibronic lasers have achieved the slope efficiency and tuning range expected based on their known spectroscopic properties. To discover the cause of this behavior, the performance of chromium-doped gallium fluoride garnet, Na/sub 3/Ga/sub 2/Li/sub 3/F/sub 12/:Cr/sup 3+/, as a laser material has been investigated experimentally. The data reported include absorption and emission spectra, emission rates, quantum efficiency, laser wavelength tuning range, laser output slope efficiencies, and excited-state absorption spectra. Similar properties of the alexandrite laser material were studied for comparison. The results indicate that the performance of the gallium fluoride garnet laser is severely limited by Cr/sup 3+/ excited-state absorption (ESA). A model is presented to account for the unexpected nature of the ESA, which appears to be a common problem for all Cr/sup 3+/ vibronic lasers. Criteria are suggested for choosing Cr/sup 3+/ hosts for which the effects of ESA will be minimized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Broad and Potent Neutralizing Antibody Responses Elicited in Natural HIV-2 Infection (2011)

Compared with human immunodeficiency virus type 1 (HIV-1), little is known about the susceptibility of HIV-2 to antibody neutralization. We characterized the potency and breadth of neutralizing antibody (NAb) responses in 64 subjects chronically infected with HIV-2 against three primary HIV-2 strains: HIV-2(7312A), HIV-2(ST), and HIV-2(UC1). Surprisingly, we observed in a single-cycle JC53bl-13/TZM-bl virus entry assay median reciprocal 50% inhibitory concentration (IC(50)) NAb titers of 1.7 × 10(5), 2.8 × 10(4), and 3.3 × 10(4), respectively. A subset of 5 patient plasma samples tested against a larger panel of 17 HIV-2 strains where the extracellular gp160 domain was substituted into the HIV-2(7312A) proviral backbone showed potent neutralization of all but 4 viruses. The specificity of antibody neutralization was confirmed using IgG purified from patient plasma, HIV-2 Envs cloned by single-genome amplification, viruses grown in human CD4(+) T cells and tested for neutralization sensitivity on human CD4(+) T target cells, and, as negative controls, env-minus viruses pseudotyped with HIV-1, vesicular stomatitis virus, or murine leukemia virus Env glycoproteins. Human monoclonal antibodies (MAbs) specific for HIV-2 V3 (6.10F), V4 (1.7A), CD4 binding site (CD4bs; 6.10B), CD4 induced (CD4i; 1.4H), and membrane-proximal external region (MPER; 4E10) epitopes potently neutralized the majority of 32 HIV-2 strains bearing Envs from 13 subjects. Patient antibodies competed with V3, V4, and CD4bs MAbs for binding to monomeric HIV-2 gp120 at titers that correlated significantly with NAb titers. HIV-2 MPER antibodies did not contribute to neutralization breadth or potency. These findings indicate that HIV-2 Env is highly immunogenic in natural infection, that high-titer broadly neutralizing antibodies are commonly elicited, and that unlike HIV-1, native HIV-2 Env trimers expose multiple broadly cross-reactive epitopes readily accessible to NAbs.
One-Shot Blind Channel Estimation for OFDM Systems Over Frequency-Selective Fading Channels (2017)

This paper presents a blind channel estimation (BCE) technique for orthogonal frequency division multiplexing communications systems. The proposed system is based on modulating particular pairs of subcarriers using amplitude shift keying and phase shift keying, which enables the realization of a decision-directed one-shot BCE (OSBCE), with complexity and accuracy that are comparable to pilot-based channel estimation techniques. The performance of the proposed estimator is evaluated in terms of the mean squared error (MSE), where an accurate analytical expression is derived and verified using Monte Carlo simulation under various channel conditions. The obtained results show that the MSE of the proposed OSBCE is comparable to pilot-based estimators, which confirms the efficiency of the proposed OSBCE.
Cell manipulation using magnetic nanowires (2002)

The use of magnetic nanowires is demonstrated as a method for the application of force to mammalian cells. Magnetic separations were carried out on populations of NIH-3T3 mouse fibroblast cells using ferromagnetic Ni wires 350 nm in diameter and 35 μm long. Separation purities in excess of 90% and yields of 49% are obtained. The nanowires are shown to outperform magnetic beads of comparable volume.