gebhart/patrepeval huggingface dataset:
Coded aperture correlation holographic microscope for single-shot quantitative phase imaging with extended field of view (2020)

Recently, a method of recording holograms of coherently illuminated three-dimensional scene without two-wave interference was demonstrated. The method is an extension of the coded aperture correlation holography from incoherent to coherent illumination. Although this method is practical for some tasks, it is not capable of imaging phase objects, a capability that is an important benefit of coherent holography. The present work addresses this limitation by using the same type of coded phase masks in a modified Mach-Zehnder interferometer. We show that by several comparative parameters, the coded aperture-based phase imaging is superior to the equivalent open aperture-based method. As an additional merit of the coded aperture approach, a framework for increasing the system's field of view is formulated and demonstrated for both amplitude and phase objects. The combination of high sensitivity quantitative phase microscope with increased field of view in a single camera shot holographic apparatus, has immense potential to serve as the preferred tool for examination of biological tissues and micro-organisms.
Electron heating mechanisms in helium rf glow discharges: A self-consistent kinetic calculation (1989)

Power dissipation mechanisms in low-pressure helium radio-frequency glow discharges are studied using a model which is able to describe the discharge at the kinetic level with a self-consistent electric field. We find a low average electron energy (&lt;1 eV) in the bulk plasma and a weak electric field (\ensuremath{\approxeq}2 V/cm) that is largely out of phase with the sheath fields. The weak bulk field is shown to be important for heating electrons of all energies.
Evidence supporting WNT2 as an autism susceptibility gene (2001)

We examined WNT2 as a candidate disease gene for autism for the following reasons. First, the WNT family of genes influences the development of numerous organs and systems, including the central nervous system. Second, WNT2 is located in the region of chromosome 7q31-33 linked to autism and is adjacent to a chromosomal breakpoint in an individual with autism. Third, a mouse knockout of Dvl1, a member of a gene family essential for the function of the WNT pathway, exhibits a behavioral phenotype characterized primarily by diminished social interaction. We screened the WNT2 coding sequence for mutations in a large number of autistic probands and found two families containing nonconservative coding sequence variants that segregated with autism in those families. We also identified linkage disequilibrium (LD) between a WNT2 3'UTR SNP and our sample of autism-affected sibling pair (ASP) families and trios. The LD arose almost exclusively from a subgroup of our ASP families defined by the presence of severe language abnormalities and was also found to be associated with the evidence for linkage to 7q from our previously published genomewide linkage screen. Furthermore, expression analysis demonstrated WNT2 expression in the human thalamus. Based on these findings, we hypothesize that rare mutations occur in the WNT2 gene that significantly increase susceptibility to autism even when present in single copies, while a more common WNT2 allele (or alleles) not yet identified may exist that contributes to the disorder to a lesser degree.
STED microscopy visualizes energy deposition of single ions in a solid-state detector beyond diffraction limit (2017)

Fluorescent nuclear track detectors (FNTDs) allow for visualization of single-particle traversal in clinical ion beams. The point spread function of the confocal readout has so far hindered a more detailed characterization of the track spots-the ion's characteristic signature left in the FNTD. Here we report on the readout of the FNTD by optical nanoscopy, namely stimulated emission depletion microscopy. It was firstly possible to visualize the track spots of carbon ions and protons beyond the diffraction limit of conventional light microscopy with a resolving power of approximately 80 nm (confocal: 320 nm). A clear discrimination of the spatial width, defined by the full width half maximum of track spots from particles (proton and carbon ions), with a linear energy transfer (LET) ranging from approximately 2-1016 keV µm<sup>-1</sup> was possible. Results suggest that the width depends on LET but not on particle charge within the uncertainties. A discrimination of particle type by width thus does not seem possible (as well as with confocal microscopy). The increased resolution, however, could allow for refined determination of the cross-sectional area facing substantial energy deposition. This work could pave the way towards development of optical nanoscopy-based analysis of radiation-induced cellular response using cell-fluorescent ion track hybrid detectors.
ChemInform Abstract: Quantitation of Proximity Effects on Rate. A Case Study Involving Dyotropic Hydrogen Migration Within syn‐Sesquinorbornene Disulfones Carrying Central Substituents Having Different Spatial Demands. (1990)

Abstract The known Diels‐Alder adduct (I) is converted to the various derivatives (II) as shown in the scheme.
A GaAs HBT monolithic logarithmic IF (0.5 to 1.5 GHz) amplifier with 60 dB dynamic range and 400 mW power consumption (2003)

A GaAs/AlGaAs HBT (heterojunction bipolar transistor) monolithic successive-detection logarithmic IF amplifier (SDLA) is described which demonstrates significant reduction in size and power consumption over state-of-the-art Si bipolar and GaAs metal-semiconductor field-effect transistor log amps with comparable dynamic range and IF bandwidth. This work was motivated by electronic warfare channelized receiver applications in which size, power, and cost are key drivers. The GaAs HBT SDLA log amp achieves single-chip (1.2*2.4 mm/sup 2/) dynamic range greater than 60 dB (-55 to +5 dBm) with less than +or-1-dB error over 1-GHz IF bandwidth at temperatures up to 125 degrees C while consuming less than 400 mW of power.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Transceiver Design with Low-Precision Analog-to-Digital Conversion : An Information-Theoretic Perspective (2008)

Modern communication receiver architectures center around digital signal processing (DSP), with the bulk of the receiver processing being performed on digital signals obtained after analog-to-digital conversion (ADC). In this paper, we explore Shannon-theoretic performance limits when ADC precision is drastically reduced, from typical values of 8-12 bits used in current communication transceivers, to 1-3 bits. The goal is to obtain insight on whether DSP-centric transceiver architectures are feasible as communication bandwidths scale up, recognizing that high-precision ADC at high sampling rates is either unavailable, or too costly or power-hungry. Specifically, we evaluate the communication limits imposed by low-precision ADC for the ideal real discrete-time Additive White Gaussian Noise (AWGN) channel, under an average power constraint on the input. For an ADC with K quantization bins (i.e., a precision of log2 K bits), we show that the Shannon capacity is achievable by a discrete input distribution with at most K + 1 mass points. For 2-bin (1-bit) symmetric ADC, this result is tightened to show that binary antipodal signaling is optimum for any signal-to-noise ratio (SNR). For multi-bit ADC, the capacity is computed numerically, and the results obtained are used to make the following encouraging observations regarding system design with low-precision ADC : (a) even at moderately high SNR of up to 20 dB, 2-3 bit quantization results in only 10-20% reduction of spectral efficiency, which is acceptable for large communication bandwidths, (b) standard equiprobable pulse amplitude modulation with ADC thresholds set to implement maximum likelihood hard decisions is asymptotically optimum at high SNR, and works well at low to moderate SNRs as well.
A Phase I, Open-label, Dose-escalation, and Cohort Expansion Study to Evaluate the Safety and Immune Response to Autologous Dendritic Cells Transduced With AdGMCA9 (DC-AdGMCAIX) in Patients With Metastatic Renal Cell Carcinoma (2020)

Expression of carbonic-anhydrase IX (CAIX) in clear cell renal cell carcinoma (RCC) makes it an attractive vaccine target. We developed a fusion-gene construct, granulocyte-macrophage (GM) colony-stimulating factor+CAIX, delivered by an adenoviral vector (Ad) into autologous dendritic cells (DCs) in this phase 1 study. The injected immature DCs were expected to stimulate an antigen-specific immune response against CAIX expressing RCC. Three dose-escalation cohorts (5, 15, and 50×10 cells/administration) were injected intradermally q2wk×3 doses based on a 3+3 design. The primary objective was the safety of the injections. Secondary objectives were immune responses using enzyme-linked immunosorbent spot, a serum biomarker panel, and clinical response. Fifteen patients with metastatic RCC were enrolled, and 9 patients received all 3 doses. No serious adverse events were seen. There were 3 (33%) patients with grade 1 fatigue, 1 of whom subsequently experienced grade 2 fatigue. One patient (11%) experienced grade 1-2 leukopenia. Only 1 patient (11%) experienced grade 2 flu-like symptoms. Of the 9 patients who received treatment, 1 expired of progressive disease, 2 patients were lost to follow-up and 6 patients are alive. Of the 6 patients, 5 have progressive disease, and 1 has completed treatment with stable disease at 27 months follow-up. Immune response measurements appeared more robust in higher dose cohorts, which appeared to be related to patients with stable disease at 3 months. These early data show that autologous immature DC-AdGMCAIX can be safely given to metastatic RCC patients without any serious adverse events with CAIX-specific immune response elicited by the treatment. These preliminary data support further study of Ad-GMCAIX, particularly with combination therapies that may enhance clinical activity.
Remote Ischemic Conditioning Reduced Acute Lung Injury After Traumatic Brain Injury in the Mouse (2020)

Traumatic brain injury (TBI) can induce acute lung injury (ALI). The exact pathomechanism of TBI-induced ALI is poorly understood, limiting treatment options. Remote ischemic conditioning (RIC) can mitigate detrimental outcomes following transplants, cardiac arrests, and neurological injuries. In this study, we hypothesized that RIC would reduce TBI-induced ALI by regulating the sphingosine-1-phosphate (S1P)-dependent pathway, a central regulator of endothelial barrier integrity, lymphocyte, and myokine trafficking. Male mice were subjected to either diffuse TBI by midline fluid percussion or control sham injury and randomly assigned among four groups: sham, TBI, sham RIC, or TBI RIC; RIC was performed 1 h prior to TBI. Mice were euthanized at 1-h postinjury or 7 days post-injury (DPI) and lung tissue, bronchoalveolar lavage (BAL) fluid, and blood were collected. Lung tissue was analyzed for histopathology, irisin myokine levels, and S1P receptor levels. BAL fluid and blood were analyzed for cellularity and myokine/S1P levels, respectively. One-hour postinjury, TBI damaged lung alveoli and increased neutrophil infiltration; RIC preserved alveoli. BAL from TBI mice had more neutrophils and higher neutrophil/monocyte ratios compared with sham, where TBI RIC mice showed no injury-induced change. Further, S1P receptor 3 and irisin-associated protein levels were significantly increased in the lungs of TBI mice compared with sham, which was prevented by RIC. However, there was no RIC-associated change in plasma irisin or S1P. At 7 DPI, ALI in TBI mice was largely resolved, with evidence for residual lung pathology. Thus, RIC may be a viable intervention for TBI-induced ALI to preserve lung function and facilitate clinical management.
Integrated Bragg gratings in curved waveguides (2010)

Bragg grating filters with elaborate spectral responses require long structures. We numerically study implementation of Bragg gratings in curved photonic wires to increase their length while minimizing their footprint.
On the Application of Error Backpropagation to the Background Calibration of Time Interleaved ADC for Digital Communication Receivers (2020)

This paper introduces a backpropagation-based technique for the calibration of the mismatch errors of time-interleaved analog to digital converters (TI-ADCs). This technique is applicable to digital receivers such as those used in coherent optical communications. The error at the slicer of the receiver is processed using a modified version of the well known backpropagation algorithm from machine learning. The processed slicer error can be directly applied to compensate the TI-ADC mismatch errors with an adaptive equalizer, or it can be used to digitally estimate and correct said mismatch errors using analog techniques such as delay cells and programmable gain amplifiers (PGA). The main advantages of the technique proposed here compared to prior art are its robustness, its speed of convergence, and the fact that it always works in background mode, independently of the oversampling factor and the properties of the input signal, as long as the receiver converges. Moreover, this technique enables the joint compensation of impairments not addressed by traditional TI-ADC calibration techniques, such as I/Q skew in quadrature modulation receivers. Simulations are presented to demonstrate the effectiveness of the technique, and low complexity implementation options are discussed.
Heparin binding, internalization, and metabolism in vascular smooth muscle cells: I. Upregulation of heparin binding correlates with antiproliferative activity (1995)

Vascular smooth muscle cell (SMC) hyperplasia is an important component in the pathogenesis of arteriosclerotic lesions and is responsible for the failure of many vascular surgical procedures. SMC proliferation is inhibited by the glycosaminoglycan heparin; however, the precise mechanisms of action are still not understood. One important question in this regard is whether binding, internalization, and metabolism of heparin are necessary for the antiproliferative activity. In this study, we have analyzed SMC rendered resistant to the antiproliferative effect of heparin by drug selection and retroviral infection of SMC. We first examined the ability of heparin to bind to SMC. Experiments using [3H]heparin indicate the presence of saturable, heparin-displaceable, protease-sensitive binding sites on both sensitive and resistant SMC. The affinity of heparin binding does not correlate with the antiproliferative response. Using fluorescent and radiolabeled heparin probes, we observed that early heparin internalization kinetics in both sensitive and resistant SMC is similar, indicating that resistance to heparin is not due to changes in the ability of cells to take up heparin. In contrast, we observed during the continuous incubation with heparin that binding to resistant SMC is rapidly downregulated, whereas sensitive cells continue to bind and internalize heparin. These results suggest that upregulation of heparin binding to the SMC surface is required for an antiproliferative response. In an accompanying paper (Letourneur et al. [1995] J. Cell Physiol., 165:687-695, this issue), we describe the degradation and secretion of internalized heparin in both sensitive and resistant SMC.
Decoupling of a neutron interferometer from temperature gradients (2016)

Neutron interferometry enables precision measurements that are typically operated within elaborate, multi-layered facilities which provide substantial shielding from environmental noise. These facilities are necessary to maintain the coherence requirements in a perfect crystal neutron interferometer which is extremely sensitive to local environmental conditions such as temperature gradients across the interferometer, external vibrations, and acoustic waves. The ease of operation and breadth of applications of perfect crystal neutron interferometry would greatly benefit from a mode of operation which relaxes these stringent isolation requirements. Here, the INDEX Collaboration and National Institute of Standards and Technology demonstrates the functionality of a neutron interferometer in vacuum and characterize the use of a compact vacuum chamber enclosure as a means to isolate the interferometer from spatial temperature gradients and time-dependent temperature fluctuations. The vacuum chamber is found to have no depreciable effect on the performance of the interferometer (contrast) while improving system stability, thereby showing that it is feasible to replace large temperature isolation and control systems with a compact vacuum enclosure for perfect crystal neutron interferometry.
Photobleaching and phototoxicity of KillerRed in tumor spheroids induced by continuous wave and pulsed laser illumination (2015)

The purpose of this study was to evaluate photobleaching of the genetically encoded photosensitizer KillerRed in tumor spheroids upon pulsed and continuous wave (CW) laser irradiation and to analyze the mechanisms of cancer cell death after the treatment. We observed the light-dose dependent mechanism of KillerRed photobleaching over a wide range of fluence rates. Loss of fluorescence was limited to 80% at light doses of 150 J/cm(2) and more. Based on the bleaching curves, six PDT regimes were applied for irradiation using CW and pulsed regimes at a power density of 160 mW/cm(2) and light doses of 140 J/cm(2) , 170 J/cm(2) and 200 J/cm(2). Irradiation of KillerRed-expressing spheroids in the pulsed mode (pulse duration 15 ns, pulse repetition rate 10 Hz) induced predominantly apoptotic cell death, while in the case of CW mode the cancer cells underwent necrosis. In general, these results improve our understanding of photobleaching mechanisms in GFP-like proteins and show the importance of appropriate selection of treatment mode for PDT with KillerRed. Representative fluorescence image of two KillerRed-expressing spheroids before and immediately after CW irradiation.
Microencapsulated Hepatocytes Differentiated from Human Induced Pluripotent Stem Cells: Optimizing 3D Culture for Tissue Engineering Applications (2023)

Liver cell therapy and in vitro models require functional human hepatocytes, the sources of which are considerably limited. Human induced pluripotent stem cells (hiPSCs) represent a promising and unlimited source of differentiated human hepatocytes. However, when obtained in two-dimensional (2D) cultures these hepatocytes are not fully mature and functional. As three-dimensional culture conditions offer advantageous strategies for differentiation, we describe here a combination of three-dimensional (3D) approaches enabling the successful differentiation of functional hepatocytes from hiPSCs by the encapsulation of hiPSC-derived hepatoblasts in alginate beads of preformed aggregates. The resulting encapsulated and differentiated hepatocytes (E-iHep-Orgs) displayed a high level of albumin synthesis associated with the disappearance of α-fetoprotein (AFP) synthesis, thus demonstrating that the E-iHep-Orgs had reached a high level of maturation, similar to that of adult hepatocytes. Gene expression analysis by RT-PCR and immunofluorescence confirmed this maturation. Further functional assessments demonstrated their enzymatic activities, including lactate and ammonia detoxification, as well as biotransformation activities of Phase I and Phase II enzymes. This study provides proof of concept regarding the benefits of combining three-dimensional techniques (guided aggregation and microencapsulation) with liver differentiation protocols as a robust approach to generate mature and functional hepatocytes that offer a permanent and unlimited source of hepatocytes. Based on these encouraging results, our combined conditions to produce mature hepatocytes from hiPSCs could be extended to liver tissue engineering and bioartificial liver (BAL) applications at the human scale for which large biomasses are mandatory.
High-output microsized earplug driver system for extreme acoustic environments (2006)

Hearing protection is critical when aircraft flight operations create a high-noise environment (130–150 dB) for aircrew and service members. Untreated aircraft noise causes noise-induced hearing loss (NIHL) and poses risks of similar hearing damage in the future. The authors have developed a new microsized smart material actuator (MSMA), a high-output earplug driver for active noise reduction (ANR) hearing protection, based on highly efficient microstructured acoustic exciters. The MSMA consists of a microscale earplug (MEP) with a proprietary acoustic structure, a protective MEP package, and a compact actuation amplifier easily connected to an external ANR controller. Performance tests show that the system produces over 130 dB into a 1-cc trapped cylindrical volume, 6 mm in diameter by 7 mm long, without significant phase delay or noticeable discontinuities in frequency response.
Hardware-Limited Task-Based Quantization (2019)

Quantization plays a critical role in digital signal processing systems. Quantizers are typically designed to obtain an accurate digital representation of the input signal, operating independently of the system task, and are commonly implemented using serial scalar analog-to-digital converters (ADCs). In this work, we study hardware-limited task-based quantization, where a system utilizing a serial scalar ADC is designed to provide a suitable representation in order to allow the recovery of a parameter vector underlying the input signal. We propose hardware-limited task-based quantization systems for a fixed and finite quantization resolution, and characterize their achievable distortion. We then apply the analysis to the practical setups of channel estimation and eigen-spectrum recovery from quantized measurements. Our results illustrate that properly designed hardware-limited systems can approach the optimal performance achievable with vector quantizers, and that by taking the underlying task into account, the quantization error can be made negligible with a relatively small number of bits.
Restriction of HIV-1 infection in sickle cell trait (2021)

Patients with sickle cell disease (SCD) have a lower risk for HIV-1 infection. We reported restriction of ex vivo HIV-1 infection in SCD peripheral blood mononuclear cells (PBMCs) that was due, in part, to the upregulation of antiviral, inflammatory, and hemolytic factors, including heme oxygenase-1 (HO-1). Here, we investigated whether individuals with sickle cell trait (SCT), who develop mild hemolysis, also restrict HIV-1 infection. Ex vivo infection of SCT PBMCs exhibited an approximately twofold reduction of HIV-1 replication and lower levels of HIV-1 reverse transcription products, 2-long terminal repeat circle, HIV-1 integration, and gag RNA expression. SCT PBMCs had higher HO-1 messenger RNA (mRNA) and protein levels and reduced ribonucleotide reductase 2 (RNR2) protein levels. HO-1 inhibition by tin porphyrin eliminated ex vivo HIV-1 restriction. Among Howard University clinic recruits, higher levels of HO-1 and RNR2 mRNA and lower HIV-1 env mRNA levels were found in SCT individuals living with HIV-1. To determine the population-level effect of SCT on HIV-1 prevalence, we assessed SCT among women living with HIV (WLH) in the WIHS (Women Interagency HIV-1 Study). Among WIHS African-American participants, the prevalence of SCT was lower among women with HIV compared with uninfected women (8.7% vs 14.2%; odds ratio, 0.57; 95% confidence interval, 0.36-0.92; P = .020). WIHS WLH with SCT had higher levels of CD4+/CD8+ ratios over 20 years of follow-up (P = .003) than matched WLH without SCT. Together, our findings suggest that HIV-1 restriction factors, including HO-1 and RNR2, might restrict HIV-1 infection among individuals with SCT and limit the pathogenicity of HIV.