gebhart/patrepeval huggingface dataset:
A Biomimetic, One-Step Transformation of Simple Indolic Compounds to Malassezia-Related Alkaloids with High AhR Potency and Efficacy (2019)

<i>Malassezia furfur</i> isolates from diseased skin preferentially biosynthesize compounds which are among the most active known aryl-hydrocarbon receptor (AhR) inducers, such as indirubin, tryptanthrin, indolo[3,2-<i>b</i>]carbazole, and 6-formylindolo[3,2-<i>b</i>]carbazole. In our effort to study their production from <i>Malassezia</i> spp., we investigated the role of indole-3-carbaldehyde (I3A), the most abundant metabolite of <i>Malassezia</i> when grown on tryptophan agar, as a possible starting material for the biosynthesis of the alkaloids. Treatment of I3A with H<sub>2</sub>O<sub>2</sub> and use of catalysts like diphenyldiselenide resulted in the simultaneous one-step transformation of I3A to indirubin and tryptanthrin in good yields. The same reaction was first applied on simple indole and then on substituted indoles and indole-3-carbaldehydes, leading to a series of mono- and bisubstituted indirubins and tryptanthrins bearing halogens, alkyl, or carbomethoxy groups. Afterward, they were evaluated for their AhR agonist activity in recombinant human and mouse hepatoma cell lines containing a stably transfected AhR-response luciferase reporter gene. Among them, 3,9-dibromotryptanthrin was found to be equipotent to 2,3,7,8-tetrachlorodibenzo-<i>p</i>-dioxin (TCDD) as an AhR agonist, and 3-bromotryptanthrin was 10-times more potent than TCDD in the human HG2L7.5c1 cell line. In contrast, 3,9-dibromotryptanthrin and 3-bromotryptanthrin were ∼4000 and >10,000 times less potent than TCDD in the mouse H1L7.5c3 cell line, respectively, demonstrating that they are species-specific AhR agonists. Involvement of the AhR in the action of 3-bromotryptanthrin was confirmed by the ability of the AhR antagonists CH223191 and SR1 to inhibit 3-bromotryptanthrin-dependent reporter gene induction in human HG2L7.5c1 cells. In conclusion, I3A can be the starting material used by <i>Malassezia</i> for the production of both indirubin and tryptanthrin through an oxidation mechanism, and modification of these compounds can produce some highly potent, efficacious and species-selective AhR agonists.
High-Sensitivity Phased Array Receivers for Radio Astronomy (2016)

Phased arrays have a long history in radio astronomy. Large, sparse synthesis arrays have been in use for decades to capture high-resolution images of deep space objects. More recent work has extended the range of applications to other types of arrays, including aperture arrays (AAs) and phased array feeds (PAFs) for multibeam reflector antennas. The extreme sensitivity required for astronomical instrumentation is driving advances in numerical electromagnetic modeling, design optimization of large arrays, low noise amplifiers, minimization of receiver noise, cryogenic PAFs, array calibration, optimal beamforming, interferometric imaging, and array signal processing algorithms for radio-frequency interference mitigation. We give an overview of research progress, current and planned array-based instruments, and open challenges in these areas related to the new generation of sparse arrays, PAFs, and AAs that are in development for astronomical observatories around the world.
Improving RSSI-Based Path-Loss Models Accuracy for Critical Infrastructures: A Smart Grid Substation Case-Study (2017)

IoT is rapidly expanding to all productive sectors; however, as thousands of devices are envisioned to be deployed, a careful study of the radio spectrum (and its interferences) must be considered to predict and improve the network performance. In this sense, radio-channel characterization is essential; in particular, path-loss characterization allows to mathematically predict the propagation behavior and interferences of IoT devices with precision. In this paper, we show that by means of a set of mathematical corrections and measuring procedures, we can soundly employ the received signal strength indicator (RSSI), available in most IoT motes, to derive accurate path-loss models of industrial infrastructures. Experimental results reveal that the proposed scheme substantially improves the characterization accuracy of a real smart grid environment. This, in turn, is proven to have a measurable positive impact on the planning stage of an IoT network, whose life-of-time and cost analysis can be better anticipated.
Novel Peptide Therapeutic Approaches for Cancer Treatment (2021)

Peptides are increasingly being developed for use as therapeutics to treat many ailments, including cancer. Therapeutic peptides have the advantages of target specificity and low toxicity. The anticancer effects of a peptide can be the direct result of the peptide binding its intended target, or the peptide may be conjugated to a chemotherapy drug or radionuclide and used to target the agent to cancer cells. Peptides can be targeted to proteins on the cell surface, where the peptide-protein interaction can initiate internalization of the complex, or the peptide can be designed to directly cross the cell membrane. Peptides can induce cell death by numerous mechanisms including membrane disruption and subsequent necrosis, apoptosis, tumor angiogenesis inhibition, immune regulation, disruption of cell signaling pathways, cell cycle regulation, DNA repair pathways, or cell death pathways. Although using peptides as therapeutics has many advantages, peptides have the disadvantage of being easily degraded by proteases once administered and, depending on the mode of administration, often have difficulty being adsorbed into the blood stream. In this review, we discuss strategies recently developed to overcome these obstacles of peptide delivery and bioavailability. In addition, we present many examples of peptides developed to fight cancer.
Research contributions in human-computer interaction (2016)

column Share on Research contributions in human-computer interaction Authors: Jacob O. Wobbrock University of Washington University of WashingtonView Profile , Julie A. Kientz University of Washington University of WashingtonView Profile Authors Info & Claims InteractionsVolume 23Issue 3May + June 2016 pp 38–44https://doi.org/10.1145/2907069Published:26 April 2016Publication History 102citation22,398DownloadsMetricsTotal Citations102Total Downloads22,398Last 12 Months6,719Last 6 weeks342 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
LuxT is a Global Regulator of Low-Cell Density Behaviors Including Type III Secretion, Siderophore Production, and Aerolysin Production in Vibrio harveyi (2021)

Abstract Quorum sensing (QS) is a chemical communication process in which bacteria produce, release, and detect extracellular signaling molecules called autoinducers. Via combined transcriptional and post-transcriptional regulatory mechanisms, QS allows bacteria to collectively alter gene expression on a population-wide scale. Recently, the TetR-family transcriptional regulator LuxT was shown to control V. harveyi qrr 1, encoding the Qrr1 small RNA that functions at the core of the QS regulatory cascade. Here, we use RNA-Sequencing to reveal that, beyond control of qrr 1, LuxT is a global regulator of 414 V. harveyi genes including those involved in type III secretion, siderophore production, and aerolysin toxin biosynthesis. Importantly, LuxT directly represses swrZ, encoding a GntR-family transcriptional regulator, and LuxT control of type III secretion, siderophore, and aerolysin genes occurs by two mechanisms, one that is SwrZ-dependent and one that is SwrZ-independent. All of these target genes specify QS-controlled behaviors that are enacted when V. harveyi is at low cell density. Thus, LuxT and SwrZ function in parallel with QS to drive particular low cell density behaviors. Phylogenetic analyses reveal that luxT is highly conserved among Vibrionaceae, but swrZ is less well conserved. In a test case, we find that in Aliivibrio fischeri, LuxT also represses swrZ . SwrZ is a repressor of A. fischeri siderophore production genes. Thus, LuxT repression of swrZ drives activation of A. fischeri siderophore gene expression. Our results indicate that LuxT is a major regulator among Vibrionaceae, and, in the species that also possess swrZ , LuxT functions with SwrZ to control gene expression. Importance Bacteria precisely tune gene expression patterns to successfully react to changes that occur in the environment. Defining the mechanisms that enable bacteria to thrive in diverse and fluctuating habitats, including in host organisms, is crucial for a deep understanding of the microbial world and also for development of effective applications to promote or to combat particular bacteria. In this study, we show that a regulator called LuxT controls over 400 genes in the marine bacterium Vibrio harveyi and, moreover, that LuxT is highly conserved among Vibrionaceae species, ubiquitous marine bacteria that often cause disease. We characterize the mechanisms by which LuxT controls genes involved in virulence and nutrient acquisition. We show that LuxT functions in parallel with a set of regulators of the bacterial cell-to-cell communication process called quorum sensing to promote V. harveyi behaviors at low cell density.
Knowledge-based transformation ordering (2002)

Transformations have been widely used in VLSI design, high level synthesis and DSP. We propose a two-step approach for transformation ordering which combines the use of optimization-intensive CAD techniques with knowledge-based user-driven search strategy. The first step is the development of basic building blocks which target small sets of transformations which are well suited for optimization intensive CAD treatment. Next, transformation orderings are developed using knowledge about mathematical laws, an application domain, and the relationship among transformations. Transformation ordering scripts combine several building blocks to form effective approaches for optimization of several design metrics in many common computational structures. As the highlight of the approach, we developed a method which efficiently simultaneously optimizes the throughput, latency, power, and area of linear computations.
Novel molecularly hybridized polyethylene/silica composite materials: Polymerization of ethylene with supported titanocenes by mesoporous silicates (2000)

A novel molecularly hybridized polyethylene/silica composite thin film was obtained by the gas-phase polymerization of ethylene with a titanocene-mounted mesoporous silica layer on a mica plate with mesoscopic pores arranged on the film surface. However, the use of titanocene-mounted hexagonal domains of mesoporous silica on a glass plate for the gas-phase polymerization of ethylene resulted in the formation of an islanded polyethylene/silica hybridized material. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 4821–4825, 2000
Lateral Flow Immunoassay for Diagnosis of Trypanosoma cruzi Infection with High Correlation to the Radioimmunoprecipitation Assay (2009)

The incidence of blood donors seropositive for Trypanosoma cruzi in North America has increased with population migration and more rigorous surveillance. The United States, considered nonendemic for T. cruzi, could therefore be at risk to exposure to parasite transmission through blood or organ donations. Current tests show variable reactivity, especially with Central American sera. Here we describe the development of a lateral flow immunoassay for the rapid detection of T. cruzi infection that has a strong correlation to the radioimmunoprecipitation assay (RIPA) "gold standard" in the United States. Such a test could have utility in small blood banks for prescreening donors, as well as in cardiac transplantation evaluation. T. cruzi consensus and/or RIPA-positive sera from Central and South America were evaluated in enzyme immunoassays (EIAs). These included commercial panels from Boston Biomedica, Inc. (BBI) (n = 14), and HemaBio (n = 21). Other sources included RIPA-positive sera from the American Red Cross (ARC) (n = 42), as well as from Chile. Sera were tested with the multiepitope recombinant TcF. All but one of the BBI samples were positive and 7 of 21 HemaBio samples and 6 of 42 ARC samples were low positive or negative. This observation indicated the need for additional antigens. To complement TcF reactivity, we tested the sera with peptides 30, 36, SAPA, and 1.1, 1.2, and 1.3 His fragments of 85-kDa trans-sialidase. We identified a promising combination of the tested antigens and constructed a single recombinant protein, ITC6, that enhanced the relative sensitivity in U.S. blood donor sera compared to that of TcF. The data on its evaluation using RIPA-confirmed positive sera in EIA and lateral flow immunoassay studies are presented, along with an additional recombinant protein, ITC8.2, with two additional sequences for peptide 1 and Kmp-11. The latter, when evaluated in a dipstick assay with consensus positive sera, had a sensitivity of 99.2% and a specificity of 99.1%.
CMOS Compatible Guided-Wave Tunable Optical Equalizer (2007)

A compact 4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> -order pole-zero optical filter fabricated entirely in a silicon complementary metal-oxide semiconductor foundry is configured as a tunable optical equalizer. Equalization of a bandwidth-limited 10-Gb/s signal is demonstrated with a single voltage control.
A 0.3 &#x2013; 3GHz reconfigurable digital transmitter with multi-bit envelope &#x0394;&#x03A3; modulator using phase modulated carrier clock for wireless sensor networks (2012)

A reconfigurable digital transmitter for wireless sensors using phase-modulated-carrier-clocking multi-bit envelope ΔΣ modulation is presented. The prototype IC designed in 90 nm CMOS process covers UHF, 2.4GHz ISM and 3GPP frequency bands up to 3 GHz in conformity with IEEE 802.11g, W-CDMA and LTE in 5 MHz-mode. The IC dissipates 10 mW for 0.3 GHz and 8.0 mW for 1.95 GHz WCDMA signal, and occupies 0.26 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Evaluation of Kidney Histological Images Using Unsupervised Deep Learning (2021)

The proposed approach could successfully extract features that were related to the clinical variables from the kidney biopsy images along with the visualization for interpretability. The approach could aid in the quantified evaluation of renal histopathology.
Faculty Opinions recommendation of Molecular dissection of Neurospora Spore killer meiotic drive elements. (2012)

Meiotic drive is a non-Mendelian inheritance phenomenon in which certain selfish genetic elements skew sexual transmission in their own favor. In some cases, progeny or gametes carrying a meiotic drive element can survive preferentially because it causes the death or malfunctioning of those that do not carry it. In Neurospora, meiotic drive can be observed in fungal spore killing. In a cross of Spore killer (Sk) × WT (Sk-sensitive), the ascospores containing the Spore killer allele survive, whereas the ones with the sensitive allele degenerate. Sk-2 and Sk-3 are the most studied meiotic drive elements in Neurospora, and they each theoretically contain two essential components: a killer element and a resistance gene. Here we report the identification and characterization of the Sk resistance gene, rsk (resistant to Spore killer). rsk seems to be a fungal-specific gene, and its deletion in a killer strain leads to self-killing. Sk-2, Sk-3, and naturally resistant isolates all use rsk for resistance. In each killer system, rsk sequences from an Sk strain and a resistant isolate are highly similar, suggesting that they share the same origin. Sk-2, Sk-3, and sensitive rsk alleles differ from each other by their unique indel patterns. Contrary to long-held belief, the killer targets not only late but also early ascospore development. The WT RSK protein is dispensable for ascospore production and is not a target of the spore-killing mechanism. Rather, a resistant version of RSK likely neutralizes the killer element and prevents it from interfering with ascospore development. PMID: 22753473
Optimal Transthoracic Targeting of Liver Tumors Using Dual-mode Ultrasound Arrays: A numerical and experimental study (2010)

The targets of therapeutic ultrasound are often located behind strongly scattering objects and layered tissue. These inhomogeneities can degrade the intended foci and misdirect acoustic energy causing unwanted hot spots or failure to meet the therapeutic endpoint at the target. We have previously shown the capabilities of dual‐mode ultrasound arrays (DMUAs) in imaging strongly scattering objects in the path of the HIFU beam and, consequently, refocusing the beam to optimize the power deposition at the target while minimizing direct exposure to the obstacles. This capability may be a key to successful transthoracic targeting of abdominal tumors. We have experimentally verified the efficacy of this approach in improving the quality of the therapeutic focus and minimizing collateral damage to critical tissue structures in the path of the HIFU beam. In order to study the phenomena associated with transthoracic focusing more thoroughly, we have developed a finite‐difference time‐domain simulation capable of characterizing the transient propagation of the therapeutic beam through inhomogeneous, attenuating media. This simulation is shown to provide the necessary information for aberration correction of deep seated foci as well as control over the acoustic field at select points. In addition, the FDTD simulation allows for computation of the temperature rise throughout the therapeutic region as governed by the transient bioheat transfer equation. We have validated the predictive abilities of our simulation with hydrophone measurements as well as thermocouple readings from within tissue mimicking phantoms. The experimental validation of the simulation model allows for its use as a key component in treatment planning of thermal therapy using HIFU. Experimental and simulation results demonstrating the role of the advantages of incorporation of the computational model in optimizing the quality of HIFU beams will be presented and discussed.
Graph- and finite element-based total variation models for the inverse problem in diffuse optical tomography (2019)

Total variation (TV) is a powerful regularization method that has been widely applied in different imaging applications, but is difficult to apply to diffuse optical tomography (DOT) image reconstruction (inverse problem) due to unstructured discretization of complex geometries, non-linearity of the data fitting and regularization terms, and non-differentiability of the regularization term. We develop several approaches to overcome these difficulties by: i) defining discrete differential operators for TV regularization using both finite element and graph representations; ii) developing an optimization algorithm based on the alternating direction method of multipliers (ADMM) for the non-differentiable and non-linear minimization problem; iii) investigating isotropic and anisotropic variants of TV regularization, and comparing their finite element (FEM)- and graph-based implementations. These approaches are evaluated on experiments on simulated data and real data acquired from a tissue phantom. Our results show that both FEM and graph-based TV regularization is able to accurately reconstruct both sparse and non-sparse distributions without the over-smoothing effect of Tikhonov regularization and the over-sparsifying effect of L<sub>1</sub> regularization. The graph representation was found to out-perform the FEM method for low-resolution meshes, and the FEM method was found to be more accurate for high-resolution meshes.
[Expression and significance of INSM1 and SOX11 in pancreatic neuroendocrine tumor and solid pseudopapillary neoplasm]. (2023)

The positive expression patterns of INSM1 and SOX11 in PNET and SPN respectively are conductive to distinguish the both tumors. The combination of both take precedence over some corresponding conventional immunohistochemical markers in terms of sensitivity and specificity.
A voltage ratio-based efficiency control method for 3 kW wireless power transmission (2014)

This paper presents a novel control method for wireless power transmission (WPT). The proposed method can maximize the power efficiency only by controlling the voltage ratio between the primary and the secondary side. Experimental measurement results of the prototype system with 3 kW power transmission show the efficiency difference between the proposed control method and the available maximum value is less than 0.3 % even with a large variation of coil-to-coil distance and load voltage. The automatic controller for the proposed method provides the load-following operation, maintaining both constant power and high efficiency, using a WLAN connection.
A Comparison of Machine Learning Techniques for Fiber Non-Linearity Compensation: Multilayer Perceptron vs. Learned Digital BackPropagation (2023)

In this paper, we analyze the performances of a Multilayer Perceptron (MLP) and the physics-based model called Learned Digital Backpropagation (LDBP) for compensating for fiber non-linear impairments in coherent transmission systems. We applied both methods numerically to a single-channel single polarization 200Gb/s 16QAM system along 5x100km and 10x100km of standard single-mode fiber. We evaluated both techniques in terms of bit error rate (BER) and computational complexity (CC). Furthermore, we identified three study cases for the MLP depending on its position in the receiver. In our setup, the results showed that the LDBP improves BER much better than the MLP, even at 1 step/span. We also showed that the CC of the LDBP is lower than the MLP one concerning real multiplications per symbol. However, in the real life, the LDBP, being a sequential technique, might take more processing time than the MLP which is easily parallelizable.
Spatial Multiplexing in Fiber Optics: The 10X Scaling of Metro/Core Capacities (2014)

Optical networks have economically enabled an unabated exponential traffic growth over the past decades, with commercial wavelength-division multiplexed (WDM) systems carrying over 20 Tb/s of traffic per fiber, closely approaching the nonlinear Shannon limit. Looking at all physical dimensions available for further capacity scaling, it becomes clear that tapping into the spatial dimension is the only long-term scalable solution to overcome the looming optical network capacity crunch. As such, space-division multiplexing (SDM) is bound to become an important optical networking technology over the next decade. Integration of SDM components will be key in reducing cost, footprint, and energy consumption, while integration-induced crosstalk may be compensated through the use of digital signal processing similar to that of vectoring used in digital subscriber lines (DSL) or multiple-input-multiple-output (MIMO) techniques used in long-term evolution (LTE) wireless systems.