gebhart/patrepeval huggingface dataset:
Identification of Bacterial Species That Can Utilize Fructose-Asparagine (2017)

<i>Salmonella enterica</i> serovar Typhimurium is the only organism demonstrated to utilize fructose-asparagine (F-Asn) as a source of carbon and nitrogen. In this report, we first used a bioinformatics approach to identify other microorganisms that encode homologs of the <i>Salmonella</i> F-Asn utilization enzymes FraB (deglycase), FraD (kinase), and FraE (asparaginase). These candidate organisms were then tested with up to four different methods to confirm their ability to utilize F-Asn. The easiest and most broadly applicable method utilized a biological toxicity assay, which is based on the observation that F-Asn is toxic to a <i>Salmonella fraB</i> mutant. Candidate organisms were grown in a rich medium containing F-Asn, and depletion of F-Asn from the medium was inferred by the growth of a <i>Salmonella fraB</i> mutant in that same medium. For select organisms, the toxicity assay was cross-validated by direct mass spectrometry-aided measurement of F-Asn in the spent-culture media and through demonstration of FraB and FraD enzyme activity in cellular extracts. For prototrophs, F-Asn utilization was additionally confirmed by growth in a minimal medium containing F-Asn as the sole carbon source. Collectively, these studies established that <i>Clostridium</i><i>bolteae</i>, <i>Clostridium acetobutylicum</i>, and <i>Clostridium clostridioforme</i> can utilize F-Asn, but <i>Clostridium difficile</i> cannot; <i>Klebsiella oxytoca</i> and some <i>Klebsiella pneumoniae</i> subspecies can utilize F-Asn; and some <i>Citrobacter rodentium</i> and <i>Citrobacter freundii</i> strains can also utilize F-Asn. Within <i>Salmonella enterica</i>, the host-adapted serovars Typhi and Paratyphi A have lost the ability to utilize F-Asn.<b>IMPORTANCE</b> Fructose-asparagine (F-Asn) is a precursor to acrylamide that is found in human foods, and it is also a nutrient source for <i>Salmonella enterica</i>, a foodborne pathogen. Here, we determined that among the normal intestinal microbiota, there are species of <i>Clostridium</i> that encode the enzymes required for F-Asn utilization. Using complementary experimental approaches, we have confirmed that three members of <i>Clostridium</i>, two members of <i>Klebsiella</i>, and two members of <i>Citrobacter</i> can indeed utilize F-Asn. The <i>Clostridium</i> spp. likely compete with <i>Salmonella</i> for F-Asn in the gut and contribute to competitive exclusion. FraB, one of the enzymes in the F-Asn utilization pathway, is a potential drug target because inhibition of this enzyme leads to the accumulation of a toxic metabolite that inhibits the growth of <i>Salmonella</i> species. This study identifies the potential off-target organisms that need to be considered when developing therapeutics directed at FraB.
Microrectenna: A Terahertz Antenna and Rectifier on a Chip (2007)

A microrectenna that would operate at a frequency of 2.5 THz has been designed and partially fabricated. The circuit is intended to be a prototype of an extremely compact device that could be used to convert radio-beamed power to DC to drive microdevices (see Figure 1). The microrectenna (see Figure 2) circuit consists of an antenna, a diode rectifier and a DC output port. The antenna consists of a twin slot array in a conducting ground plane (denoted the antenna ground plane) over an enclosed quarter-wavelength-thick resonant cavity (denoted the reflecting ground plane). The circuit also contains a planar high-frequency low-parasitic Schottky-barrier diode, a low-impedance microstrip transmission line, capacitors, and contact beam leads. The entire 3-D circuit is fabricated monolithically from a single GaAs wafer. The resonant cavity renders the slot radiation pattern unidirectional with a half-power beam width of about 65. A unique metal mesh on the rear of the wafer forms the backplate for the cavity but allows the GaAs to be wet etched from the rear surface of the twin slot antennas and ground plane. The beam leads protrude past the edge of the chip and are used both to mount the microrectenna and to make the DC electrical connection with external circuitry. The antenna ground plane and the components on top of it are formed on a 2- m thick GaAs membrane that is grown in the initial wafer MBE (molecular beam epitaxy) process. The side walls of the antenna cavity are not metal coated and, hence, would cause some loss of power; however, the relatively high permittivity (epsilon=13) of the GaAs keeps the cavity modes well confined, without the usual surface-wave losses associated with thick dielectric substrates. The Schottky-barrier diode has the usual submicron dimensions associated with THz operation and is formed in a mesa process above the antenna ground plane. The diode is connected at the midpoint of a microstrip transmission line, which is formed on 1- m-thick SiO (permittivity of 5) laid down on top of the GaAs membrane. The twin slots are fed in phase by this structure. To prevent radio-frequency (RF) leakage past the slot antennas, low-loss capacitors are integrated into the microstrip transmission line at the edges of the slots. The DC current- carrying lines extend from the outer edges of the capacitors, widen approaching the edges of the chip, and continue past the edges of the chip to become the beam leads used in tacking down the devices. The structure provides a self-contained RF to DC converter that works in the THz range.
<sup>13</sup>C NMR measurements of human gluconeogenic fluxes after ingestion of [U-<sup>13</sup>C]propionate, phenylacetate, and acetaminophen (1998)

Anaplerotic, pyruvate recycling, and gluconeogenic fluxes were measured by 13C isotopomer analysis of plasma glucose, urinary phenylacetylglutamine, and urinary glucuronide in normal, 24-h-fasted individuals after ingestion of [U-13C]propionate, phenylacetate, and acetaminophen. Plasma glucose isotopomer analysis reported a total anaplerotic flux of 5.92 +/- 1.03 (SD) relative to citrate synthase. This was not significantly different from glucuronide and phenylacetylglutamine analyses (6.08 +/- 1.16 and 7. 14 +/- 1.94, respectively). Estimates of pyruvate recycling from glucose and glucuronide isotopomer distributions were almost identical (3.55 +/- 0.99 and 3.66 +/- 1.11, respectively), whereas phenylacetylglutamine reported a significantly higher estimate (5.74 +/- 2.13). As a consequence, net gluconeogenic flux reported by phenylacetylglutamine (1.41 +/- 0.28) was significantly less than that reported by glucose (2.37 +/- 0.64) and glucuronide (2.42 +/- 0. 76). This difference in fluxes detected by analysis of phenylacetylglutamine vs. hexose is likely due to compartmentation of hepatic metabolism of propionate. Net gluconeogenic flux estimates made by use of this stable isotope method are in good agreement with recent measurements in humans with [14C]propionate.
<title>Dielectrophoretic trapping without embedded electrodes</title> (2000)

We observe dielectrophoretic effects in mixed electrokinetic and dielectrophoretic flows in uniform arrays of posts. Above a threshold applied electric field, flowing filaments of concentrated and rarefied particles appear in the flow. Above a higher-threshold applied field, zones of highly concentrated, immobilized particles appear. At the lower and higher thresholds, dielectrophoresis apparently begins to dominate diffusion and advection/electrokinesis, respectively. The patterns of filaments and trapped zones depend dramatically on the angle of the array with respect to the mean applied electric field and the shape of the posts in the array.
VirtualScan: a new compressed scan technology for test cost reduction (2005)

This work describes the VirtualScan technology for scan test cost reduction. Scan chains in a VirtualScan circuit are split into shorter ones and the gap between external scan ports and internal scan chains are bridged with a broadcaster and a compactor. Test patterns for a VirtualScan circuit are generated directly by one-pass VirtualScan ATPG, in which multi-capture clocking and maximum test compaction are supported. In addition, VirtualScan ATPG avoids unknown-value and aliasing effects algorithmically without adding any additional circuitry. The VirtualScan technology has achieved successful tape-outs of industrial chips and has been proven to be an efficient and easy-to-implement solution for scan test cost reduction.
A Steroid Receptor Coactivator Stimulator MCB-613 Attenuates Adverse Remodeling After Myocardial Infarction (2021)

Abstract Previous work from ours and other laboratories have shown that steroid receptor coactivators (SRCs) are involved in heart development and in mitigating cardiac dysfunction in cardiac injury models. Members of the p160 SRC family, SRC-1 (NCOA1), SRC-2 (NCOA2/TIF2/GRIP1) and SRC-3 (NCOA3/AIB1/ACTR/pCIP), interact with nuclear receptors and other transcription factors to drive target gene expression by assembling transcriptional coactivator complexes to increase transcription. This indicates a potential for SRC targeting drugs pertinent to cell migration, proliferation and survival-promoting paracrine interactions in cardiac tissue injury responses. We have identified a small molecule activator of SRCs (MCB-613) that selectively and reversibly binds to SRCs as shown by surface plasmon resonance and is a potent SRC stimulator that acts to greatly enhance SRC transcriptional activity with no apparent toxicity in mice. We postulated that MCB-613 could enable wound repair and preservation of cardiac function after an acute MI by reducing the extent of injury-related fibrosis and the subsequent chronic loss of cardiac function associated with non-contracting scar tissue. We thus tested the effect of MCB-613 on the cardiac injury response by administering MCB-613 two hours after ischemic injury in a mouse model of MI. Along with measurements of functional cardiac output and damage, we sought to identify the cell-type specific responses responsible for MCB-613’s cardio-protective effects by utilizing single cell transcriptomics of cardiac interstitial cells to characterize the effects of SRC stimulation on cardiac function post-MI. We show that MCB-613, a potent small molecule stimulator of steroid receptor coactivators (SRCs) attenuates pathological remodeling post-MI. MCB-613 decreases infarct size, apoptosis, hypertrophy, and fibrosis while maintaining significant cardiac function. MCB-613, when given within hours post-MI, induces lasting protection from adverse remodeling concomitant with: (i) inhibition of macrophage inflammatory signaling and IL-1 signaling which attenuates the acute inflammatory response, (ii) attenuation of fibroblast differentiation, and (iii) promotion of Tsc22d3 expressing macrophages - all of which may limit inflammatory damage. Our results indicate MCB-613 controls the cellular interstitial cardiac repair response to ischemia. Distinct molecular and cellular mechanisms related to stimulation of SRC-3 have been identified that pave the way for the further exploration of SRCs as drug targets that can be engaged to improve the management of myocardial injury response outcomes. SRC stimulation with MCB-613 (and derivatives) is a potential novel therapeutic approach for inhibiting cardiac dysfunction after MI.
Organic‐Free Synthesis of Silicoaluminophosphate Molecular Sieves (2018)

Silicoaluminophosphate (SAPO) molecular sieves are an important class of microporous materials and are useful for industrial catalysis and separations. They have been synthesized exclusively by the use of expensive and environmentally unfriendly organic structure-directing agents. Now the synthesis of SAPO molecular sieves is reported with MER, EDI, GIS, and ANA topologies under wholly inorganic conditions. Multinuclear MAS NMR analyses demonstrate the presence of Si, Al, and P atoms in their frameworks. These SAPO materials all have unusually high framework charge densities (0.25-0.46), owing to the small size of alkali metal cations used as an inorganic structure-directing agent. A continuous Si increase in the synthesis gel for MER-type SAPO molecular sieves led to the formation of framework Si(0Al) units, decreasing the number of extra-framework cations per unit cell and thus making the resulting solid useful for CO<sub>2</sub> adsorption.
5-Lipoxygenase Reaction Products Modulate Alveolar Macrophage Phagocytosis of<i>Klebsiella pneumoniae</i> (1998)

The leukotrienes are potent lipid mediators of inflammation formed by the 5-lipoxygenase-catalyzed oxidation of arachidonic acid. Although the effects of leukotrienes on neutrophil chemotaxis and activation have been established, their role in modulating innate host defense mechanisms is poorly understood. In a previous study (M. Bailie, T. Standiford, L. Laichalk, M. Coffey, R. Strieter, and M. Peters-Golden, J. Immunol. 157:5221-5224, 1996), we used 5-lipoxygenase knockout mice to establish a critical role for endogenous leukotrienes in pulmonary clearance and alveolar macrophage phagocytosis of Klebsiella pneumoniae. In the present study, we investigated the role of specific endogenous leukotrienes in phagocytosis of K. pneumoniae and explored the possibility that exogenous leukotrienes could restore phagocytosis in alveolar macrophages with endogenous leukotriene synthesis inhibition and enhance this process in leukotriene-competent cells. Rat alveolar macrophages produced leukotriene B4 (LTB4), LTC4, and 5-hydoxyeicosatetraenoic acid (5-HETE) during the process of phagocytosis, and the inhibition of endogenous leukotriene synthesis with zileuton and MK-886 dramatically attenuated phagocytosis. We also observed a reduction in phagocytosis when we treated alveolar macrophages with antagonists to the plasma membrane receptors for either LTB4, cysteinyl-leukotrienes, or both. In leukotriene-competent cells, LTC4 augmented phagocytosis to the greatest extent, followed by 5-HETE and LTB4. These 5-lipoxygenase reaction products demonstrated similar relative abilities to reconstitute phagocytosis in zileuton-treated rat alveolar macrophages and in alveolar macrophages from 5-lipoxygenase knockout mice. We conclude that endogenous synthesis of all major 5-lipoxygenase reaction products plays an essential role in phagocytosis. The restorative and pharmacologic effects of LTC4, LTB4, and 5-HETE may provide a basis for their exogenous administration as an adjunctive treatment for patients with gram-negative bacterial pneumonia.
Imaging and localizing fish and marine mammals with acoustics. (2011)

During the 2006 ocean acoustic waveguide remote sensing (OAWRS) experiment in the Gulf of Maine, large shoals of Atlantic herring were instantaneously imaged in the frequency range from 300 to 1200 Hz. Simultaneously, several thousand instances of marine mammal vocalizations were passively recorded on a high resolution towed horizontal receiving array. A vast majority of the vocalizations were from humback whales in the 300–600 Hz frequency range. Vocalizations from other marine mammals species ranging from 40 Hz to over 3 kHz were also recorded. Various approaches are employed to localize and track the whales both passively and actively. The bearing of calling whales can be found by beamforming their vocalizations measured on the receiving array. An efficient and robust matched filter is designed to enhance the signal-to-noise ratio of the whale vocalizations. The array invariant method [Lee and Makris, J. Acoust. Soc. Am. (2006)] is then applied for instantaneous whale range estimation. The array invariant approach has been verified theoretically with modeled complex nonlinear whale vocalizations propagated long ranges exceeding 50 km in a range-dependent ocean waveguide. The whale range estimates obtained with the array invariance technique are verified by hyperbolic localization of the vocalization signals measured by the moving receiver array along a given track.
Investigation on Arc Behavior During Arc Motion in Air DC Circuit Breaker (2013)

In this paper, the complicated arc phenomena in air dc circuit breakers that are widely used in rail transit and vessels are investigated with both experimental and numerical approaches. Initially, the basic arc motion characteristics in the switch are presented by the recorded waveforms and images in the carefully designed breaking experiments. Phenomena of arc stagnation and back commutation are revealed and the influence of arc chamber width on the arc stagnation is preliminarily discussed according to the experimental results. Then, to make the nature of arc motion clear and to determine the influence details of the arc chamber width on arc motion characteristics, a simplified model based on magnetohydrodynamics theory is built and four cases with the arc chambers of different widths are calculated. The simulated arc behavior is presented by the temperature distribution sequences. In addition, the formation process of back commutation is described in detail by the variation of arc column. The influence mechanism of arc chamber width on arc motion is analyzed according to the differences of pressure propagation and temperature distribution in the arc chamber. Furthermore, the calculated arc displacement curves show that the arc stagnation time could be shortened and the risk of back commutation could be reduced by decreasing the arc chamber width within the reasonable extent.
Recognition of hand drawn chemical diagrams (2007)

Chemists often use hand-drawn structural diagrams to capture and communicate ideas about organic compounds. However, the software available today for specifying these structures to a computer relies on a traditional mouse and keyboard interface, and as a result lacks the ease of use, naturalness, and speed of drawing on paper. In response, we have developed a novel sketch-based system capable of interpreting handdrawn organic chemistry diagrams, allowing users to draw molecules with a pen-based input device in much the same way that they would on paper. The system’s ability to interpret a sketch is based on knowledge about both chemistry and chemical drawing conventions. The system employs a trainable symbol recognizer incorporating both feature-based and image-based methods to locate and identify symbols in the sketch. Analysis of the spatial context around each symbol allows the system to choose among competing interpretations and determine an initial structure for the molecule. Finally, knowledge of chemistry (in particular chemical valence) enables the system to check the validity of its interpretation and, when necessary, refine it to recover from inconsistencies. We demonstrate that the system is capable of recognizing diagrams of common organic molecules and show that using domain knowledge produces a noticeable improvement in recognition accuracy.
Reconstructing Orientation Field From Fingerprint Minutiae to Improve Minutiae-Matching Accuracy (2009)

Minutiae are very important features for fingerprint representation, and most practical fingerprint recognition systems only store the minutiae template in the database for further usage. The conventional methods to utilize minutiae information are treating it as a point set and finding the matched points from different minutiae sets. In this paper, we propose a novel algorithm to use minutiae for fingerprint recognition, in which the fingerprint's orientation field is reconstructed from minutiae and further utilized in the matching stage to enhance the system's performance. First, we produce "virtual" minutiae by using interpolation in the sparse area, and then use an orientation model to reconstruct the orientation field from all "real" and "virtual" minutiae. A decision fusion scheme is used to combine the reconstructed orientation field matching with conventional minutiae-based matching. Since orientation field is an important global feature of fingerprints, the proposed method can obtain better results than conventional methods. Experimental results illustrate its effectiveness.
Abstract 320: New metastatic murine prostate cancer cell lines and preclinical model of human prostate cancer. (2013)

Abstract Defining oncogene-specific molecular pathways required for the induction and maintenance of prostate cancer is essential for the rational design of new therapies. Identifying molecular predictors of prostate cancer patient survival is important for patient therapeutic substratification. We generated murine prostate cancer cell lines via selective transduction with a single oncogene (c-Myc, Ha-Ras, NeuT, and v-Src). These cell lines demonstrate contact-independent growth characteristics in soft agar, and have the substantial growth advantage over primary prostate epithelial cells. Each of the prostate lines grew tumor in immune competent mice after subcutaneous injection, and develop lung metastasis in c-Myc, Ha-Ras, and v-Src cell line groups. RNA samples were prepared from the these cell lines, Microarray analysis identified a total of 2635 out of 22115 genes that were significantly altered in expression (at least two-fold change) in oncogene over-expressing cell lines when compared with prostate epithelial cell control samples. The distinct oncogene expression signature was compared to gene signatures obtained from other published databases to identify similarities to human prostate cancer phenotypes. Comparisons were performed against gene signatures representative of differential expression in advanced state vs. early stage prostate cancer, high grade vs low grade prostate cancer, recurrent vs. nonrecurrent, the results indicate a significant degree of similarity between the prostate oncogene expression signature and high-grade disease; between the oncogene expression signature and the advanced stage disease phenotype. Interrogation of two distinct cohorts of Prostate cancer patient samples using the oncogene signature demonstrated an ability to distinguish tumor from normal prostate with a predictive value for prostate cancer of 98 - 99%. The signature provided in blinded study independent substratification of reduced recurrence free survival by Kaplan-Meier analysis. The generation of new oncogene-specific prostate cancer cell lines that recapitulate human prostate cancer gene expression, that metastasize in immune-competent mice, are a valuable new resource for testing targeted therapy. The molecular signatures identified herein provide further value over current markers of prediction and outcome. Citation Format: Xiaoming Ju, Richard G. Pestell. New metastatic murine prostate cancer cell lines and preclinical model of human prostate cancer. [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 320. doi:10.1158/1538-7445.AM2013-320