gebhart/patrepeval huggingface dataset:
Inhibition of bacterial thioredoxin reductase: an antibiotic mechanism targeting bacteria lacking glutathione (2012)

Increasing antibiotic resistance makes the identification of new antibacterial principles an urgent task. The thioredoxin system including thioredoxin reductase (TrxR), thioredoxin (Trx), and NADPH plays critical roles in cellular DNA synthesis and defense against oxidative stress. Notably, TrxR is very different in structure and mechanism in mammals and bacteria. Ebselen [2-phenyl-1,2 benzisoselenazol-3(2H)-one], a well-known antioxidant and a substrate for mammalian TrxR and Trx, is rapidly bacteriocidal for methicillin-resistant Staphylococcus aureus by an unknown mechanism. We have discovered that ebselen is a competitive inhibitor of Escherichia coli TrxR with a Ki of 0.52 ± 0.13 μM, through reaction with the active site dithiol of the enzyme. Bacteria lacking glutathione (GSH) and glutaredoxin, in which TrxR and Trx are essential for DNA synthesis, were particularly sensitive to ebselen. In growth-inhibited E. coli strains, Trx1 and Trx2 were oxidized, demonstrating that electron transfer via thioredoxin was blocked. Ebselen and its sulfur analog ebsulfur were bactericidal for GSH-negative pathogens. Ebsulfur inhibited a clinically isolated Helicobacter pylori strain with a minimum inhibitory concentration value as low as 0.39 μg/ml. These results demonstrate that bacterial Trx and TrxR are viable antibacterial drug targets using benzisoselenazol and benzisothiazol derivates.
Abstract C30: Resistance to fluid shear stress is a conserved biophysical property of malignant cells (2013)

Abstract During metastasis, cancer cells enter the circulation in order to gain access to distant tissues, but how this fluid microenvironment influences cancer cell biology is poorly understood. A longstanding view is that circulating cancer cells derived from solid tissues may be susceptible to damage from hemodynamic shear forces, contributing to metastatic inefficiency. However, there have been few efforts to directly test this hypothesis. Here we report that compared to non-transformed epithelial cells, transformed cells are remarkably resistant to fluid shear stress (FSS) in a microfluidic protocol, exhibiting a biphasic decrease in viability when subjected to a series of millisecond pulses of high (750-6,300 dyn/cm2) FSS. We show that magnitude of FSS resistance is influenced by several oncogenes including myc, ras, and PI3K; is an adaptive and transient response triggered by reparable plasma membrane damage; and requires extracellular calcium and actin cytoskeletal dynamics, including the activity of Rho kinase. This novel property of malignant cancer cells may facilitate hematogenous metastasis and indicates, contrary to expectations, that cancer cells are quite resistant to destruction by hemodynamic shear forces. Citation Format: James Matthew Barnes, Jones T. Nauseef, Michael D. Henry. Resistance to fluid shear stress is a conserved biophysical property of malignant cells. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr C30.
Dynamic Focusing of Large Arrays for Wireless Power Transfer and Beyond (2020)

We present architectures, circuits, and algorithms for dynamic 3-D lensing and focusing of electromagnetic power in radiative near- and far-field regions by arrays that can be arbitrary and nonuniform. They can benefit applications such as wireless power transfer at a distance (WPT-AD), volumetric sensing and imaging, high-throughput communications, and optical phased arrays. Theoretical limits on system performance are calculated. An adaptive algorithm focuses the power at the receiver(s) without prior knowledge of its location(s). It uses orthogonal bases to change the phases of multiple elements simultaneously to enhance the dynamic range. One class of such 2-D orthogonal and pseudo-orthogonal masks is constructed using the Hadamard and pseudo-Hadamard matrices. Generation and recovery units (GU and RU) work collaboratively to focus energy quickly and reliably with no need for factory calibration. Orthogonality enables batch processing in high-latency and low-rate communication settings. Secondary vector-based calculations allow instantaneous refocusing at different locations using element-wise calculations. An emulator enables further evaluation of the system. We demonstrate modular WPT-AD GUs of up to 400 elements utilizing arrays of 65-nm CMOS ICs to focus power on RUs that convert the RF power to dc. Each RFIC synthesizes 16 independently phase-controlled RF outputs around 10 GHz from a common single low-frequency reference. Detailed measurements demonstrate the feasibility and effectiveness of RF lensing techniques presented in this article. More than 2 W of dc power can be recovered through a wireless transfer at distances greater than 1 m. The system can dynamically project power at various angles and at distances greater than 10 m. These developments are another step toward unified wireless power, sensing, and communication solutions in the future.
Highly sensitive surface plasmon resonance chemical sensor based on Goos-Hanchen effects (2006)

The resonance enhanced Goos-Hanchen shifts at attenuated total internal reflection enables the possibility for highly sensitive surface plasmon resonance sensor. The observed giant displacements result from the singular phase retardation at the resonance where the phase is continuous but changes dramatically. The phenomenon is proposed for chemical sensing and the superior sensitivity is demonstrated.
Biologically-informed deep neural networks provide quantitative assessment of intratumoral heterogeneity in post-treatment glioblastoma (2022)

Abstract Intratumoral heterogeneity poses a significant challenge to the diagnosis and treatment of glioblastoma (GBM). This heterogeneity is further exacerbated during GBM recurrence, as treatment-induced reactive changes produce additional intratumoral heterogeneity that is ambiguous to differentiate on clinical imaging. There is an urgent need to develop non-invasive approaches to map the heterogeneous landscape of histopathological alterations throughout the entire lesion for each patient. We propose to predictively fuse Magnetic Resonance Imaging (MRI) with the underlying intratumoral heterogeneity in recurrent GBM using machine learning (ML) by leveraging image-localized biopsies with their associated locoregional MRI features. To this end, we develop BioNet, a biologically-informed neural network model, to predict regional distributions of three tissue-specific gene modules: proliferating tumor, reactive/inflammatory cells, and infiltrated brain tissue. BioNet offers valuable insights into the integration of multiple implicit and qualitative biological domain knowledge, which are challenging to describe in mathematical formulations. BioNet performs significantly better than a range of existing methods on cross-validation and blind test datasets. Voxel-level prediction maps of the gene modules by BioNet help reveal intratumoral heterogeneity, which can improve surgical targeting of confirmatory biopsies and evaluation of neuro-oncological treatment effectiveness. The non-invasive nature of the approach can potentially facilitate regular monitoring of the gene modules over time, and making timely therapeutic adjustment. These results also highlight the emerging role of ML in precision medicine.
Potential usefulness of an artificial neural network for differential diagnosis of interstitial lung diseases: pilot study. (1990)

An artificial neural network approach was applied to the differential diagnosis of interstitial lung diseases. The neural network was designed to distinguish between nine types of interstitial lung diseases on the basis of 20 items of clinical and radiographic information. A data base for training and testing the neural network was created with 10 hypothetical cases for each of the nine diseases. The performance of the neural network was evaluated by means of receiver operating characteristic analysis. The decision performance of the neural network was high; it was comparable to that of chest radiologists and superior to that of senior radiology residents. The preliminary results strongly suggest that the neural network approach has potential utility in the computer-aided differential diagnosis of interstitial lung diseases.
Solid Composite Material Particularly with Ceramic Dispersates (1989)

Composites of materials in which the matrix material does not spontaneously or readily wet the disperse phase and in which the volume fraction of the disperse phase is less than that formed in a packed bed of dispersate particles can be made effectively by an indirect method of infiltrating a packed bed of dispersate particles, using pressure or other mechanical force as needed to overcome poor wetting and form an intermediate concentrated composite. The concentrated composite is then mixed with additional matrix-forming material to produce the finally desired composite. The technique is particularly valuable for composites with ceramic dispersates and metal or alloy matrixes.
Synthesis and Characterization of Ni<sup>III</sup>N3S2 Complexes as Active Site Models for the Oxidized Form of Nickel Superoxide Dismutase (2014)

Nickel complexes, [Ni(H2BA(R)TPP)](ClO4)2 (R = Ph for 1 or iPr for 2), supported by a pentadentate ligand H2BA(R)TPP were synthesized and oxidized to form Ni(III) species having a N3S2 coordination environment to mimic the active site of the oxidized form of nickel superoxide dismutase (NiSODox). The Ni(III) species 2(+) exhibited a rhombic signal with g values at 2.15, 2.12 and 2.02 similar to that of NiSODox. DFT calculations revealed that 2(+) has an unpaired electron primarily located in the dz2 orbital of the Ni(III) center, which strongly overlaps with the pz orbital of the axial pyridine nitrogen of H2BA(Pr)TPP.
Inhibition of <em>Aspergillus flavus</em> Growth and Aflatoxin Production in Transgenic Maize Expressing the &#945;-amylase Inhibitor from <em>Lablab purpureus</em> L. (2019)

Aflatoxin contamination in food and feed crops is a major challenge worldwide. Aflatoxins, produced by the fungus Aspergillus flavus (A. flavus) are potent carcinogens that substantially reduce crop value in maize and other oil rich crops like peanut besides posing serious threat to human and animal health. Different approaches, including traditional breeding, transgenic expression of resistance associated proteins, and RNA interference (RNAi)-based host-induced gene silencing of critical A. flavus gene targets, are being evaluated to increase aflatoxin resistance in susceptible crops. Past studies have shown an important role of α-amylase in A. flavus pathogenesis and aflatoxin production, suggesting this gene/enzyme is a potential target to reduce both A. flavus growth and aflatoxin production. In this regard, the current study was undertaken to evaluate heterologous expression (under control of the constitutive CaMV 35S promoter) of a Lablab purpureus L. α-amylase inhibitor-like protein (AILP) in maize against A. flavus. AILP is a 36-kDa protein, which is a competitive inhibitor of A. flavus α-amylase enzyme and belongs to the lectin–arcelin–α-amylase inhibitor protein family in common bean. In vitro studies prior to the current work had demonstrated the role of AILP in inhibition of A. flavus α-amylase activity and fungal growth. Fungal growth and aflatoxin production in mature kernels were monitored in real time using a GFP-expressing A. flavus strain. This kernel screening assay (KSA) is very simple to set up and provides reliable and reproducible data on infection and the extent of spread that could be quantified for evaluation of germplasm and transgenic lines. The fluorescence from the GFP strain is closely correlated to fungal growth and, by extension, it is well-correlated to aflatoxin values. The goal of the current work was to implement this previous knowledge in a commercially important crop like maize to increase aflatoxin resistance. Our results show a 35%–72% reduction in A. flavus growth in AILP-expressing transgenic maize kernels which, in turn, translated into a 62%–88% reduction in aflatoxin levels.
Detection and location of multicharacter sequences in lines of imaged text (1996)

A system for detecting and locating user-specified search strings, or phrases, in lines of imaged text is described. The phrases may be single words or multiple words, and may contain a partially specified word. The imaged text can be composed of a number of different fonts and graphics. Textlines in a deskewed image are hypothesized using multiresolution morphology. For each textline, the baseline, topline and x-height are identified by simple statistical methods and then used to normalize each textline bounding box. Columns of pixels in the resulting bounding box serve as feature vectors. One hidden Markov model is created for each userspecified phrase and another represents all text and graphics other than the user-specified phrases. Phrases are identified using Viterbi decoding on a spotting network created from the models. The operating point of the system can be varied to trade off the percentage of words correctly spotted and the percentage of false alarms. Results are given using a subset of the UW English Document Image Database I.
Technical Note: Production of Butter with Enhanced Conjugated Linoleic Acid for Use in Biomedical Studies with Animal Models (2000)

Cancer models utilize massive doses of carcinogen so that investigations of anticarcinogenic effects require equally large doses. Conjugated linoleic acids (CLA), predominately consumed in dairy products, are thought to be anticarcinogenic. Our objective was to naturally produce a CLA-enhanced butter for use in biomedical studies with animal models. To do this, we fed cows a low forage diet supplemented with sun-flower oil. This resulted in increases in content of CLA of milk fat, but the markedly elevated concentrations were transient and declined over a 3-wk period. By collecting milk fat over the first few days on the diet (d 7 to 10) and selecting cows with the greatest CLA concentrations, we were able to produce a butter in which CLA content was enhanced sevenfold over control butter (41 vs. 5 mg/g of fatty acids) and the cis-9, trans-11 isomer predominated (91%). Thus, butter produced by this method can be used to investigate the preventive role of CLA in natural foods with biomedical models of different types of cancer. Furthermore, the butter allows examination of the other beneficial health effects of CLA reported with animal models.
The Optical Effects of Capping Layers on the Performance of Transparent Organic Light-Emitting Diodes (2011)

In transparent organic light-emitting diodes (TOLEDs), the asymmetry in the optical paths causes difference between the bottom and top emitting lights, both in emissions and spectral distributions. Capping layers (CLs) can be used as an optical functional to enhance the emissions and adjust the spectral distributions. Here, we report on the optical effects of an organic CL, 1,1-bis[(di-4-tolylamino)phenyl]cyclohexane (TAPC), on the characteristics of TOLEDs Both simulated and experimental results are presented. We demonstrate the possibility of improving the total emission and achieving spectral matching of bottom and top emissions by varying the CL thickness. The optical effects of CLs have been interpreted from interference perspectives. Finally, we have presented a guideline that is practically useful in designing high-performance TOLEDs with CLs.
Suppression of Spurious SAW Signals (1986)

1.0 ABSTRACT Digital Radio applications of SAW require that individual spurious signals in the time domain be suppressed by about 60 dB. The first concept to be discussed involves a silicon thin film absorber with a tapered transition between the transducer and the free region. This arrangement suppresses end of IDT and end of substrate reflections by >80 dB. The second concept describes the metalization pattern between the transducers which eliminates reflections from the adjacent edges of the IDTs. Devices fabricated using these concepts have less than 0.1 dB amplitude ripple and less than 1.0 degree phase ripple in 30 percent relative bandwidth filters. Experimental verification of time domain and frequency domain results are shown.
Autoantibodies against a 43 KDa Muscle Protein in Inclusion Body Myositis (2011)

Circulating antibodies against a 43-kDa muscle autoantigen may lead to the discovery of a novel biomarker for IBM. Its high specificity for IBM among patients with autoimmune myopathies furthermore suggests a relationship to disease pathogenesis.
Wavelength beam combining of slab-coupled optical waveguide laser (SCOWL) arrays (2004)

A diffraction-limited output beam from a diode bar using slab-coupled optical waveguide laser (SCOWL) arrays is demonstrated. Even at 15-W peak power, the spatial brightness is at least 1 to 2 orders of magnitude higher than any commercially available diode power sources.
RhoC a new target for therapeutic vaccination against metastatic cancer (2008)

Most cancer deaths are due to the development of metastases. Increased expression of RhoC is linked to enhanced metastatic potential in multiple cancers. Consequently, the RhoC protein is an attractive target for drug design. The clinical application of immunotherapy against cancer is rapidly moving forward in multiple areas, including the adoptive transfer of anti-tumor-reactive T cells and the use of "therapeutic" vaccines. The over-expression of RhoC in cancer and the fact that immune escape by down regulation or loss of expression of this protein would reduce the morbidity and mortality of cancer makes RhoC a very attractive target for anti-cancer immunotherapy. Herein, we describe an HLA-A3 restricted epitope from RhoC, which is recognized by cytotoxic T cells. Moreover, RhoC-specific T cells show cytotoxic potential against HLA-matched cancer cells of different origin. Thus, RhoC may serve as an important and widely applicable target for anti-cancer immunotherapeutic strategies.
Small Molecules as Structural and Functional Mimics of Sialyl Lewis X Tetrasaccharide in Selectin Inhibition:  A Remarkable Enhancement of Inhibition by Additional Negative Charge and/or Hydrophobic Group (1997)

Several sialyl Lewis X (SLex) mimics that contain the essential functional groups for receptor interaction and a negative charge or a hydrophobic group have been developed as inhibitors of E-, P-, and L-selectins. Some of the mimics exhibit selectin inhibition activities 103−104-fold more potent than does the natural ligand tetrasaccharide, with IC50 in the low micromolar to high nanomolar range. The syntheses of these mimics are relatively simple, using TMSOTf-Ac2O mediated C-glycosylation with concurrent selective deprotection of the primary benzyl group and enzymatic aldol addition reactions as key steps.
Adaptive Thresholds for AMR Codec Mode Selection (2005)

The speech codecs from the adaptive multi-rate (AMR) codec family enable provisioning of excellent speech quality, at the same time providing a way forward towards state-of-the-art, spectrally efficient, high capacity cellular networks. One straightforward way to characterize the benefit of AMR speech codecs is that the robustness to interference and noise in radio networks is increased and that this advantage over other, nonadaptive, speech codecs can be capitalized on in several different ways, e.g., by enhancing speech quality or improving system capacity. In this paper, improved mode adaptation, where codec mode switching thresholds are adaptive to radio conditions, is discussed. Example simulations show that an adaptive thresholds algorithm applied to GSM can significantly improve objective speech quality. Corresponding improvements were also found in informal listening tests.
<title>Computer-aided diagnosis scheme for detecting pulmonary nodules using wavelet transform</title> (1995)

To aid radiologists in the detection of lung cancer, we are developing a computer-aided diagnosis (CAD) system that locates areas suspicious for nodules in digital chest radiographs. The system involves a difference-image approach and various feature-extraction techniques. To improve the sensitivity of the overall scheme, we investigated an approach based on the wavelet transform. We found that the wavelet transform is effective in detecting subtle nodules that were not detected by the difference-image technique. By combining the two schemes based on the difference-image and the wavelet transform, the sensitivity was increased from 81% to 86% while maintaining approximately the same level of specificity.
An approach for control of battery energy storage management systems considering multiple functions (2014)

This paper present a complete electrochemical energy storage management scheme to maximize potential value that can be brought forth to medium voltage feeders. In general, the potential performance benefits produced by possible energy storage applications include improved system reliability, dynamic stability, enhanced power quality, transmission capacity enhancement and area protection. Here we propose a unique control algorithm that enhances coordination of ancillary services applications mainly voltage support along with renewables capacity firming. Optimization of control parameters and set points are considered for management between the mentioned applications. The design is tested on an Electro Magnetic Transient Program (EMTP) simulation platform which shows that the method performs both the functions.
Micromachined Quartz Resonator Functionalized with Single Walled Carbon Nanotubes (2006)

Single walled carbon nanotubes (SWNTs) are reservoirs of gases as they can adsorb on their walls as well as retain gas molecules in their hollow cylindrical interior. This has important applications for example in fuel cell technology for hydrogen storage, as a gas sensor for realization of artificial nose, etc. Storage of gases by carbon nanotubes have been recently investigated by monitoring changes in their thermoelectric power and electrical resistivity due to their interaction with gas molecules. In this paper we present a gravimetric study of interaction of gas molecules with isolated SWNTs using a micromachined ultrasensitive quartz crystal microbalance (QCM). The adsorption and desorption of gas molecules with different molecular weights from carbon nanotubes revealed that changes in resonance frequency and quality factor of the resonating crystal scale as approximately M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.45</sup> , where M is the mass the of the gas molecule as compared to M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/3</sup> dependence observed in case of changes in thermoelectric power and electrical resistance for thin films of the carbon nanotubes. The use of QCM enables room temperature probing of gas interaction with isolated single walled carbon nanotubes. Specific interaction of gases with carbon nanotubes on QCM provides potential application of the device as a gas sensor
<title>Novel sol-gel fabrication of integrated optical waveguides</title> (1997)

The sol-gel method is employed to implement a new, simple and highly versatile fabrication process for integrated optical waveguides on silicon. Photosensitive glass films of several microns thickness are dip-coated and optical components of various configurations through suitable masks are directly inscribed in them by ultraviolet light. Undefined regions are removed by soaking the films in an organic solvent for a few minutes. The developed ridges are then treated and planarized with a cladding layer. Altogether, the procedure is reproducible, and leads to waveguides with low propagation losses, on the order of 0.13 dB/cm.