gebhart/patrepeval huggingface dataset:
Monoclonal antibody to a major surface glycoprotein immunogen differentiates isolates and subpopulations of Trichomonas vaginalis (1986)

To produce monoclonal antibodies (MAbs) to highly immunogenic membrane proteins of Trichomonas vaginalis NYH286, the sera of subcutaneously infected BALB/c mice were first monitored for antibody to trichomonad surface proteins. The sera possessed antibody to one major surface protein by 7 days and antibody to numerous other trichomonad membrane proteins by 4 weeks postinfection. A hybridoma was then generated that synthesized an MAb, designated C20A3, which reacted to a parasite-derived glycoprotein possessing a molecular weight of 267,000 (267K glycoprotein). The immunogen corresponded to the single high-molecular-weight immunogenic surface protein recognized by 7-day mouse antisera. The MAb differentiated T. vaginalis isolates by a whole-cell enzyme-linked immunosorbent assay and by indirect immunofluorescence, using either fixed or live organisms. All isolates, however, possessed C20A3-reactive material when tested by enzyme-linked immunosorbent assay, using detergent extracts of the isolates incubated with MAb-coated microtiter well plates. The epitope was accessible to antibody binding on live T. vaginalis organisms expressing the major immunogen, and the 267K glycoprotein was readily removed from the parasite membranes by trypsinizing the intact trichomonads. The antigen incorporated radiolabeled glucose, mannose, and acetate. Also, an unlabeled 267K glycoprotein on nitrocellulose blots was detected by 125I-concanavalin A and 125I-wheat germ agglutinin, confirming the glycoprotein nature of the immunogen. Finally, of seven isolates used in this study, one possessed a cross-reactive 170K, rather than 267K, antigen. The data reinforce the idea that antigenic heterogeneity among T. vaginalis isolates may be a function of the presence or absence of high-molecular-weight glycoprotein immunogens from trichomonal membranes.
ColotypeR: A tool to classify colon cancers by consensus molecular subtype and subtype-specific risk of recurrence. (2018)

632 Background: Colon cancer is highly heterogeneous in prognosis and response to treatment. The consensus molecular subtypes (CMS1-4, and mixed) partition colon cancers into distinct groups. CMS4 tumors, a mesenchymal subtype, have the worst prognosis and poor response to standard chemotherapies. There is a critical need for accurate molecular subtyping, and subtype-specific management. Methods: Affymetrix microarrays colon cancer datasets (N = 813; GSE39582, GSE14333) were partitioned into training (AT; N = 370) and validation sets (AV; N = 443) balanced for clinical traits. A novel multistate gene methodology was used to predict CMS, and prognosticate subtype-specific relapse-free survival (RFS) in the training set. Accuracy of CMS prediction and prognostic significance was validated in the AV and TCGA colon cancer (COAD; N = 458) sets. Results: In the training set, a 20-gene panel (ColotypeR-CMS) predicts CMS subtype. Mean accuracy for CMS1-4 prediction was 0.87 in AV and 0.81 in COAD. In AV, 5-year RFS is 0.52 (95%CI 0.43 – 0.63) in the predicted CMS4, and 0.70 (95%CI 0.65 – 0.77) in the non-CMS4 samples. The risk of relapse for non-CMS4 samples was refined by a genomic score (ColotypeR-Risk) computed using expression of 25 genes in the training set. ColotypeR-Risk was prognostic of RFS (p = 0.0004) among the AV non-CMS4 samples, and also prognostic (p = 0.0001) among the stage II non-CMS4 AV samples not treated with chemotherapy. The prognostic significance of ColotypeR-Risk among non-CMS4 samples is independent of tumor location (right or left) and CMS subtype (CMS1-3 or mixed). ColotypeR-Risk was also prognostic of RFS in non-CMS4 samples in COAD (p = 0.005). Conclusions: ColotypeR identifies the consensus molecular subtypes (CMS1, CMS2, CMS3, CMS4, or mixed), and assesses subtype-specific risk of recurrence of colon cancer. ColotypeR identifies prognostic risk and molecular features that could help guide the management of colon cancer patients.
Daidzin inhibits mitochondrial aldehyde dehydrogenase and suppresses ethanol intake of Syrian golden hamsters (1997)

Daidzin is the major active principle in extracts of radix puerariae , a traditional Chinese medication that suppresses the ethanol intake of Syrian golden hamsters. It is the first isoflavone recognized to have this effect. Daidzin is also a potent and selective inhibitor of human mitochondrial aldehyde dehydrogenase (ALDH-2). To establish a link between these two activities, we have tested a series of synthetic structural analogs of daidzin. The results demonstrate a direct correlation between ALDH-2 inhibition and ethanol intake suppression and raise the possibility that daidzin may, in fact, suppress ethanol intake of golden hamsters by inhibiting ALDH-2. Hamster liver contains not only mitochondrial ALDH-2 but also high concentrations of a cytosolic form, ALDH-1, which is a very efficient catalyst of acetaldehyde oxidation. Further, the cytosolic isozyme is completely resistant to daidzin inhibition. This unusual property of the hamster ALDH-1 isozyme accounts for the fact we previously observed that daidzin can suppress ethanol intake of this species without blocking acetaldehyde metabolism. Thus, the mechanism by which daidzin suppresses ethanol intake in golden hamsters clearly differs from that proposed for the classic ALDH inhibitor disulfiram. We postulate that a physiological pathway catalyzed by ALDH-2, so far undefined, controls ethanol intake of golden hamsters and mediates the antidipsotropic effect of daidzin.
Extremely High Mobility of Two-Dimensional Electron Gas in Selectively Doped GaAs/N-AlGaAs Heterojunction Structures Grown by MBE (1981)

Selectively Si-doped GaAs/ N -AlGaAs heterojunction structures have been grown by MBE. Two-dimensional electron gas accumulating at the interface of the heterojunction showed mobilities as high as 69,000 cm 2 /Vs at 77 K and 100,000 cm 2 /Vs at 4.2 K, with a sheet electron concentration of 5.5×10 11 cm -2 , which are higher than any reported so far. An enhancementmode high electron mobility transistor (E-HEMT), which was first fabricated from the heterojunction material, showed a field effect mobility of 49,300 cm 2 /Vs at 77 K, suggesting that this heterojunction material has potential for application to low-power, high-speed integrated circuits.
Magnetically Shielded Miniature Hall Thruster: Development and Initial Testing (2013)

The scaling of magnetically shielded Hall thrusters to low-power is investigated through the development and fabrication of a 4 cm Hall thruster. During initial testing, the magnetically shielded miniature Hall thruster was operated at 275 V discharge voltage and 325 W discharge power. Inspection of the channel walls after testing suggests that the outer discharge channel wall was successfully shielded from high-energy ion erosion while the inner channel wall showed evidence of weaker shielding, likely due to magnetic circuit saturation. Scanning planar probe measurements taken at 4.4 cm and 10.8 cm downstream of the thruster face provided ion current density profiles. The ion current calculated by integrating these data was 1.04 A with a plume divergence half-angle of 30°. Swept retarding potential analyzer measurements taken at 80 cm axially downstream of the thruster measured the most probable ion voltage to be 252 V. The total thruster efficiency was calculated from probe measurements to be 43% (anode efficiency of 59%) corresponding to a thrust of 19 mN at a specific impulse of 1870 s. Discharge channel erosion rates were found to be approximately three orders of magnitude less than unshielded Hall thrusters, suggesting a significant increase in projected operational life.
Recent Developments in Phyroshock Simulation Using Fixtures With Tunable Resonant Frequencies (1994)

Pyroshock is a potentially severe environment produced by the detonation of explosively actuated components and stage separation hardware. Electronic components exposed to pyroshock events during flight or deployment can be damaged by this high frequency, high G shock. Flight qualification of these components may be accomplished using one of many existing techniques to simulate the pyroshock environment in the laboratory. Two new techniques developed at Sandia National Laboratories allow larger components to be tested to a wide variety of pyroshock environments. The frequency content and amplitude of the simulated pyroshock can be easily controlled in a predictable manner. The pyroshock environment is produced by the resonant response of a test fixture that has been excited by a mechanical impact. The resonant fixture has a dominant frequency that can be continuously adjusted over a frequency range that is typically found in most pyroshock environments. The test apparatus and techniques utilized by each method will be described in this paper. Experimental results will be presented which illustrate the capabilities of each method.
Trustworthiness Assessment of Wireless Sensor Data for Business Applications (2009)

Nowadays, wireless sensor networks appear to be mature enough to be used by business applications. These applications rely on trustworthy sensor data to control business processes. In this paper, we propose an approach to assess the trustworthiness of sensor data during their lifecycle, from acquisition at the nodes, through processing, to delivery to business applications. We rely on the subjective logic framework to compute the probability that sensor data are trustworthy enough to be used by applications. With the definition of new operators for subjective logic, we develop a trust model, that allows to detect erroneous sensor data which are originated either unintentionally due to defective sensor nodes or intentionally by attackers.
Temporal–spatial, spectral, and source level distributions of fin whale vocalizations in the Norwegian Sea observed with a coherent hydrophone array (2018)

Abstract To better understand fin whale vocalization behaviour in the Norwegian and Barents Seas, a large-aperture densely sampled coherent hydrophone array was deployed in late winter 2014 to monitor their vocalizations instantaneously over wide areas via passive ocean acoustic waveguide remote sensing (POAWRS). Here, we (i) provide a time-frequency characterization for different call types observed (20 Hz pulses, 130 Hz upsweeps, 30–100 Hz downsweep chirps, and 18–19 Hz backbeats); (ii) compare their relative abundances in three different coastal regions off Alesund, Lofoten, and Northern Finnmark; (iii) estimate the temporal and spatial distributions; (iv) source level distributions; and (v) probability of detection (PoD) regions for the more abundant 20 Hz pulse and 130 Hz upsweep call types. The fin whale vocalizations received over the diel cycle (24 h) were significantly more abundant by a factor of roughly seven off Northern Finnmark than the other two regions, associated with fish feeding activities. The source levels are estimated to be 190.5±7.4 dB for the fin whale 20 Hz pulses and 170.3 ± 5.2 dB for the 130 Hz upsweeps. We find that fin whales are capable of producing each vocalization type either independently or simultaneously with other types, and the 20 Hz sound production in the fin whales involves a mechanism that generates a significantly less-intense second-order harmonic of the fundamental.
A Resampling Method Based on Filter Designed by Window Function Considering Frequency Aliasing (2020)

Resampling technology is becoming increasingly critical, as different frequency components are required to be measured in one device. In this paper, a resampling method based on filter designed by window function is proposed to satisfy the requirements of different sampling rates. The frequency responses of the filter in the resampling model based on the Farrow structure are investigated, and the design criterion of the filter in the resampling model is proposed. A fractional delay filter design model based on window function method is established. A fractional delay filter coefficient matrix, which is expressed by a polynomial form, is constructed. Then, the expression related to the subfilter coefficients is obtained and subfilter coefficients are solved by the least-square method. The simulation results show that the filter designed by the proposed method has better performance when used for resampling as compared those designed by existing methods, and can efficiently prevent the occurrence of frequency aliasing and mirroring components in the process of sampling rate conversion. Therefore, the proposed method meets the conditions for application to existing measurement devices.
A Novel Model System to Examine Agents Used in Breast Cancer Therapy. (1995)

Abstract : We have isolated a multiprotein complex for DNA synthesis, designated the DNA synthesome. from human breast cancer (MDA MB-468) cells, biopsied human breast tumor tissue and xenografts from nude mice injected with the human breast cancer cell line MCF-7. The breast cell DNA synthesome was shown to fully support the in vitro replication of simian virus 40 (SV40) origin-containing DNA in the presence of the viral large T-antigen. The proteins and enzymes found to copurify with the breast cell DNA synthesome include: DNA polymerases alpha, delta, and epsilon, DNA primase, proliferating cell nuclear antigen (PCNA), replication factor C (RF-C), replication protein A (RP-A), DNA ligase, DNA topoisomerases I and II and poly(ADP-ribose) polymerase. To begin to determine the organization of these DNA synthetic proteins within the breast cell DNA synthesome, we performed co-immunoprecipitation experiments with antibodies directed against DNA polymerases alpha, epsilon and PCNA. We found that DNA polymerases alpha, epsilon, DNA primase, RF-C and PCNA tightly associate with each other in the complex, whereas DNA polymerase epsilon, PARP and several other components interact with the synthesome via an association with only PCNA or DNA polymerase alpha. Furthermore we employed the breast cell DNA synthesome as a model to study the mechanisms of action of two anti-breast cancer agents that target the DNA synthetic process, irinotecan (CPT-11/SN-38) and etoposide (VP-16). We obtained novel data suggesting that both SN-38 and VP-16 stabilized cleavable complexes represent blocks to replication fork progression, as each agent caused an accumulation of short DNA products during synthesome mediated in vitro replication. Overall, our results indicate that breast cancer cells utilize an asymmetric multiprotein complex to mediate DNA synthesis and that utilization of the DNA synthesome as a drug model may provide important new insights into the mechanisms of action of SN-38 and VP-16.c
Identification and characterization of <i>Bph14</i> , a gene conferring resistance to brown planthopper in rice (2009)

Planthoppers are highly destructive pests in crop production worldwide. Brown planthopper (BPH) causes the most serious damage of the rice crop globally among all rice pests. Growing resistant varieties is the most effective and environment-friendly strategy for protecting the crop from BPH. More than 19 BPH-resistance genes have been reported and used to various extents in rice breeding and production. In this study, we cloned Bph14, a gene conferring resistance to BPH at seedling and maturity stages of the rice plant, using a map-base cloning approach. We show that Bph14 encodes a coiled-coil, nucleotide-binding, and leucine-rich repeat (CC-NB-LRR) protein. Sequence comparison indicates that Bph14 carries a unique LRR domain that might function in recognition of the BPH insect invasion and activating the defense response. Bph14 is predominantly expressed in vascular bundles, the site of BPH feeding. Expression of Bph14 activates the salicylic acid signaling pathway and induces callose deposition in phloem cells and trypsin inhibitor production after planthopper infestation, thus reducing the feeding, growth rate, and longevity of the BPH insects. Our work provides insights into the molecular mechanisms of rice defense against insects and facilitates the development of resistant varieties to control this devastating insect.
Modeling and dynamic control of compliant framed wheeled modular mobile robots (2004)

Dynamic models and controllers for compliant framed wheeled modular mobile robots are studied in this paper. This is a new type of wheeled mobile robot using axle and frame modules that can provide both full suspension and enhanced steering capability without additional hardware. In this research modular kinematic and dynamic models of the modules are developed and assembled into a scalable dynamic system model such that a wide variety of configurations could be described. Dynamic control is then achieved by coordinated control of the individual wheel torques as specified by a backstepping controller scaled to the dimension of the system configuration. These results are applied to a two-axle scout case study in order to demonstrate their implementation and performance. Simulation and experimental results illustrate dynamic control of trajectory tracking while path following.
Surfing the High Energy Output Branch of Nonlinear Energy Harvesters (2016)

Hysteresis and multistability are fundamental phenomena of driven nonlinear oscillators, which, however, restrict many applications such as mechanical energy harvesting. We introduce an electrical control mechanism to switch from the low to the high energy output branch of a nonlinear energy harvester by exploiting the strong interplay between its electrical and mechanical degrees of freedom. This method improves the energy conversion efficiency over a wide bandwidth in a frequency-amplitude-varying environment using only a small energy budget. The underlying effect is independent of the device scale and the transduction method and is explained using a modified Duffing oscillator model.
Mechanism of Self‐Regulation and In Vivo Performance of the Cleveland Clinic Continuous‐Flow Total Artificial Heart (2016)

Cleveland Clinic's continuous-flow total artificial heart (CFTAH) provides systemic and pulmonary circulations using one assembly (one motor, two impellers). The right pump hydraulic output to the pulmonary circulation is self-regulated by the rotating assembly's passive axial movement in response to atrial differential pressure to balance itself to the left pump output. This combination of features integrates a biocompatible, pressure-balancing regulator with a double-ended pump. The CFTAH requires no flow or pressure sensors. The only control parameter is pump speed, modulated at programmable rates (60-120 beats/min) and amplitudes (0 to ±25%) to provide flow pulses. In bench studies, passive self-regulation (range: -5 mm Hg ≤ [left atrial pressure - right atrial pressure] ≤ 10 mm Hg) was demonstrated over a systemic/vascular resistance ratio range of 2.0-20 and a flow range of 3-9 L/min. Performance of the most recent pump configuration was demonstrated in chronic studies, including three consecutive long-term experiments (30, 90, and 90 days). These experiments were performed at a constant postoperative mean speed with a ±15% speed modulation, demonstrating a totally self-regulating mode of operation, from 3 days after implant to explant, despite a weight gain of up to 40%. The mechanism of self-regulation functioned properly, continuously throughout the chronic in vivo experiments, demonstrating the performance goals.
Expression Profiling Identifies Genes Expressed Early During Lint Fibre Initiation in Cotton (2005)

Cotton fibres are a subset of single epidermal cells that elongate from the seed coat to produce the long cellulose strands or lint used for spinning into yarn. To identify genes that might regulate lint fibre initiation, expression profiles of 0 days post-anthesis (dpa) whole ovules from six reduced fibre or fibreless mutants were compared with wild-type linted cotton using cDNA microarrays. Numerous clones were differentially expressed, but when only those genes that are normally expressed in the ovule outer integument (where fibres develop) were considered, just 13 different cDNA clones were down-regulated in some or all of the mutants. These included: a Myb transcription factor (GhMyb25) similar to the Antirrhinum Myb AmMIXTA, a putative homeodomain protein (related to Arabidopsis ATML1), a cyclin D gene, some previously identified fibre-expressed structural and metabolic genes, such as lipid transfer protein, alpha-expansin and sucrose synthase, as well as some unknown genes. Laser capture microdissection and reverse transcription-PCR were used to show that both the GhMyb25 and the homeodomain gene were predominantly ovule specific and were up-regulated on the day of anthesis in fibre initials relative to adjacent non-fibre ovule epidermal cells. Their spatial and temporal expression pattern therefore coincided with the time and location of fibre initiation. Constitutive overexpression of GhMyb25 in transgenic tobacco resulted in an increase in branched long-stalked leaf trichomes. The involvement of cell cycle genes prompted DNA content measurements that indicated that fibre initials, like leaf trichomes, undergo DNA endoreduplication. Cotton fibre initiation therefore has some parallels with leaf trichome development, although the detailed molecular mechanisms are clearly different.
Strained Silacycles in Organic Synthesis: A New Reagent for the Enantioselective Allylation of Aldehydes. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Transformation of Pseudomonas fluorescens with genes for biosynthesis of phenazine-1-carboxylic acid improves biocontrol of rhizoctonia root rot and in situ antibiotic production (2004)

A seven-gene operon for the synthesis of phenazine-1-carboxylic acid was introduced into Pseudomonas fluorescens Q8r1-96, an aggressive root colonizer that produces 2,4-diacetylphloroglucinol and consistently suppresses take-all of wheat. The recombinant strains produced both antifungal metabolites and maintained population sizes comparable to those of Q8r1-96 over a seven-week period in the rhizosphere of wheat. The strains were no more suppressive of take-all or Pythium root rot than was Q8r1-96, but suppressed Rhizoctonia root rot at a dose of only 10(2) CFU per seed, one to two orders of magnitude lower than the dose of Q8r1-96 required for comparable disease control.
CNN Inference: Dynamic and Predictive Quantization (2018)

Deep Learning techniques like Convolutional Neural Networks (CNN) are the de-facto method for image classification with broad usage spanning across automotive, industrial, medicine, robotics etc. Efficient implementation of CNN inference on embedded device requires a quantization method, which minimizes the accuracy loss, ability to generalize across deployment scenarios as well as real-time processing. Existing literature doesn't address all these three requirements simultaneously. In this paper, we propose a novel quantization algorithm to overcome above mentioned challenges. The proposed solution dynamically selects the scale for quantizing activations and uses Kalman filter to predict quantization scale to reduce accuracy loss. The proposed solution exploits the range statistics from previous inference processes to estimate quantization scale, enabling real-time solution. The proposed solution is implemented on TI's TDA family of embedded automotive processors. The proposed solution is running real time semantic segmentation on TDA2x processor within 0.1% accuracy loss compared floating point algorithm. The solution performs well across multiple deployment scenarios (e.g. rain, snow, night etc) demonstrating generalization capability of the solution.