gebhart/patrepeval huggingface dataset:
Astrovirus Induces Diarrhea in the Absence of Inflammation and Cell Death (2003)

Astroviruses are a leading cause of infantile viral gastroenteritis worldwide. Very little is known about the mechanisms of astrovirus-induced diarrhea. One reason for this is the lack of a small-animal model. Recently, we isolated a novel strain of astrovirus (TAstV-2) from turkeys with the emerging infectious disease poult enteritis mortality syndrome. In the present studies, we demonstrate that TAstV-2 causes growth depression, decreased thymus size, and enteric infection in infected turkeys. Infectious TAstV-2 can be recovered from multiple tissues, including the blood, suggesting that there is a viremic stage during infection. In spite of the severe diarrhea, histopathologic changes in the intestine were mild and there was a surprising lack of inflammation. This may be due to the increased activation of the potent immunosuppressive cytokine transforming growth factor beta during astrovirus infection. These studies suggest that the turkey will be a useful small-animal model with which to study astrovirus pathogenesis and immunity.
Principles of using Cold Atmospheric Plasma Stimulated Media for Cancer Treatment (2015)

To date, the significant anti-cancer capacity of cold atmospheric plasma (CAP) on dozens of cancer cell lines has been demonstrated in vitro and in mice models. Conventionally, CAP was directly applied to irradiate cancer cells or tumor tissue. Over past three years, the CAP irradiated media was also found to kill cancer cells as effectively as the direct CAP treatment. As a novel strategy, using the CAP stimulated (CAPs) media has become a promising anti-cancer tool. In this study, we demonstrated several principles to optimize the anti-cancer capacity of the CAPs media on glioblastoma cells and breast cancer cells. Specifically, using larger wells on a multi-well plate, smaller gaps between the plasma source and the media, and smaller media volume enabled us to obtain a stronger anti-cancer CAPs media composition without increasing the treatment time. Furthermore, cysteine was the main target of effective reactive species in the CAPs media. Glioblastoma cells were more resistant to the CAPs media than breast cancer cells. Glioblastoma cells consumed the effective reactive species faster than breast cancer cells did. In contrast to nitric oxide, hydrogen peroxide was more likely to be the effective reactive species.
A Complex Family of Highly Heterogeneous and Internally Repetitive Hyperactive Antifreeze Proteins from the Beetle <i>Tenebrio</i> <i>molitor</i><sup>,</sup> (1999)

We have previously identified a Thr- and Cys-rich thermal hysteresis (antifreeze) protein (THP) in the beetle Tenebrio molitor that has 10-100 times the freezing point depression activity of fish antifreeze proteins. Because this 8.4 kDa protein is significantly different in its properties from THP preparations previously reported from this insect, a thorough search was undertaken for other antifreeze types. Many active proteins were observed, but all appeared to be isoforms of the THP that differed in their number of 12-amino acid repeats (consensus sequence CTxSxxCxxAxT), amino acid substitutions, and N-linked glycosylation. Mass spectral analysis has matched most of these isoforms with cDNA sequences of 17 different clones from a larval fat body library that encode eight different mature THPs containing 84, 96, or 120 amino acids. Genomic Southern blots suggest there may be 30-50 tightly linked copies of the gene, which is a signature consistently seen with unrelated fish antifreeze protein genes, and one that has been associated with the need to rapidly increase gene product in response to climate change. A three-dimensional model is proposed for the fully disulfide-bonded structure of T. molitor THP, which can accommodate addition or deletion of 12-amino acid repeats. The structure is a beta-helix that places most of the Thr in a regular array on one side of the protein to form a putative ice-binding surface.
A Novel STT-MRAM Design With Electric-Field-Assisted Synthetic Anti-Ferromagnetic Free Layer (2018)

Spin-transfer torque magnetic random-access memory (STT-MRAM) is one of the next-generation nonvolatile memories, which has the most promising industrial prospect and has generated lots of new ideas. One of the continuous challenges in STT-MRAM development is to reduce the critical write current. Recently, one published paper reported that under a small electric bias voltage, the synthetic anti-ferromagnetic (SAF) multilayer system could be switched between an anti-ferromagnetic coupling state and a ferromagnetic coupling state. Based on this phenomenon, we propose a new type of STT-MRAM of which the critical write current can be reduced by an assisting electric-field (E-field). Micromagnetic simulation has been performed to study the dynamic switching behavior of the magnetization of the SAF free layer with tunable Ruderman-Kittel-Kasuya-Yosida interaction under the impact of an E-field.
Increased x-ray power from a transition-radiation source (1991)

Soft x rays were produced by a stack of 12 aluminum foils, each 1.0 μm thick, which were bombarded by a relativistic electron beam whose maximum power was ∼10 kW. The maximum total soft x-ray flux was measured to be 8 mW, a factor of 10 over the previous value. The maximum average power per unit area was ∼0.3 mW/cm2 over 8.5 cm2 area at 3 m from the transition radiator. Using an Intel mask, we obtained lithographs with features of 0.5 μm. Exposure times of the bare resist were as short as 150 s for 4.3 cm2 of wafer area (the resist had a 230 mJ/cm2 energy dose per unit area). The shortest time for mask/wafer exposure was 300 s for 8.5 cm2. We reduced the exposure time of the photoresist by a factor of 9 from the previous value.
Iha: a Novel <i>Escherichia coli</i> O157:H7 Adherence-Conferring Molecule Encoded on a Recently Acquired Chromosomal Island of Conserved Structure (2000)

The mechanisms used by Shiga toxin (Stx)-producing Escherichia coli to adhere to epithelial cells are incompletely understood. Two cosmids from an E. coli O157:H7 DNA library contain an adherence-conferring chromosomal gene encoding a protein similar to iron-regulated gene A (IrgA) of Vibrio cholerae (M. B. Goldberg, S. A. Boyko, J. R. Butterton, J. A. Stoebner, S. M. Payne, and S. B. Calderwood, Mol. Microbiol. 6:2407-2418, 1992). We have termed the product of this gene the IrgA homologue adhesin (Iha), which is encoded by iha. Iha is 67 kDa in E. coli O157:H7 and 78 kDa in laboratory E. coli and is structurally unlike other known adhesins. DNA adjacent to iha contains tellurite resistance loci and is conserved in structure in distantly related pathogenic E. coli, but it is absent from nontoxigenic E. coli O55:H7, sorbitol-fermenting Stx-producing E. coli O157:H-, and laboratory E. coli. We have termed this region the tellurite resistance- and adherence-conferring island. We conclude that Iha is a novel bacterial adherence-conferring protein and is contained within an E. coli chromosomal island of conserved structure. Pathogenic E. coli O157:H7 has only recently acquired this island.
Technical Development of a New Meningococcal Conjugate Vaccine (2015)

Although many years of application of meningococcal polysaccharide vaccines have had minimal success in preventing meningococcal epidemics in the meningitis belt of Africa, our collaborative efforts to develop a MenA conjugate vaccine yielded a safe and highly effective vaccine.
A Time Amplifier Assisted Frequency-to-Digital Converter Based Digital Fractional-<i>N</i> PLL (2021)

This article presents a wide input-range delay chain based time amplifier (TA) and its application to a 6.5-GHz digital fractional- N phase-locked loop (PLL). The TA includes a delay-averaging linearity enhancement technique and the PLL is based on an improved dual-mode ring oscillator (DMRO) delta-sigma (ΔΣ) frequency-to-digital converter (FDC). The TA mitigates contributions to the PLL's phase noise from DMRO flicker noise, which would otherwise degrade the PLL's in-band phase noise, and from ΔΣ FDC quantization error, which would otherwise degrade the PLL's phase noise at high bandwidth settings. This paper also presents a delay-free asynchronous DMRO phase sampling scheme, and the first experimental demonstration of a recently-proposed ΔΣ FDC digital gain calibration technique. The TA-assisted PLL achieves a random jitter of 145 fs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</sub> , a total jitter that ranges from 151 to 270 fs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</sub> as a result of fractional spurs, and a worst-case fractional spur of -49 dBc without requiring nonlinearity calibration.
T-cell redirected killing and cure of pancreatic and gastric cancer xenografts by targeting Trop-2. (2015)

262 Background: Trop-2 [also called tumor-associated calcium signal transducer 2 (TACSTD2), EGP-1 (epithelial glycoprotein-1), GA733-1, or M1S1]is a 35 kDa transmembrane glycoprotein that is overexpressed relative to normal tissues in a variety of human cancers, including pancreatic and gastric carcinomas, where increased expression correlates with poor prognosis. Trop-2 appears to be more tumor-specific than the related molecule, EpCAM (Trop-1). MT110, the EpCAM antibody x CD3 bispecific T-cell engager (BiTE), is currently undergoing a Phase I study in various solid tumors, including lung, gastric, colorectal, breast, prostate, and ovarian cancers. We produced a similar T-cell redirecting bispecific tandem scFv, E1-3, using the variable domains of hRS7 (humanized anti-Trop-2 mAb) and Okt-3 (anti-CD3 mAb). Methods: T-cell activation, cytokine induction and cytotoxicity were evaluated ex vivo using PBMCs or purified T cells with human pancreatic (Capan-1 and BxPC3) and gastric (NCI-N87) cancer cell lines as target cells. In vivo activity was assayed with NCI-N87 xenografts that were inoculated s.c. in a mixture with twice the number of human PBMCs and matrigel. Results: In the presence of target cells and PBMCs, E1-3 potently induced T-cell activation, proliferation, and dose-dependent cytokine production of IL-2 (>2 ng/mL), IL-6 (>1 ng/mL), IL-10 (>7 ng/mL), TNF-α (>1 ng/mL) and IFN-γ (>50 ng/mL). In vitro, E1-3 mediated a highly potent T-cell lysis of BxPC3 [IC 50 =0.09(±0.04) pM], Capan-1 [IC 50 =1.2(±1.1) pM] and NCI-N87 [IC 50 =1.2(±1.2) pM] target cells. In vivo, two 50-µg doses of E1-3 given three days apart cured all of the mice (N=8) bearing NCI-N87 xenografts (P=0.0005; Log-Rank). Tumors in the control group (PBMCs only) reached the endpoint (TV>1 cm 3 ) with a median of 39.5 days. All mice remained tumor-free in the E1-3 group at 78 days. Conclusions: Trop-2 is an attractive target for T-cell-mediated killing of pancreatic, gastric and other epithelial cancers.
Implementation Aspects of Antenna Selection for MIMO Systems (2006)

Antenna selection is a promising technique for reducing complexity of multiple-antenna (MIMO) systems. In antenna selection, more antenna elements than RF transceiver chains are available for up-conversion and down-conversion. A subset of the available antenna elements is selected and connected to the RF chains. The reduction in the number of RF chains helps to reduce the implementation cost of multi-antenna systems. This paper considers a number of "practical" issues in the implementation of such systems. We discuss schemes for the channel estimation for all all antenna elements, and show that antenna selection is robust to channel estimation errors. RF preprocessing can be used to enhance the array gain of antenna selection schemes; the performance is robust to errors in the RF elements used for the preprocessing Finally, we analyze both bulk selection and per-tone selection in MIMO-OFDM systems, and show that the former is usually preferable. Results from simulations with 802.11n-compliant systems, and capacity results in measured channels show that SNR and capacity gains can be achieved with antenna selection in practical situations.
Effects of Hydrophobicity on Antimicrobial Activity, Selectivity, and Functional Mechanism of Guanidinium‐Functionalized Polymers (2021)

Abstract In this study, a series of guanidinium‐functionalized polycarbonate random co‐polymers is prepared from organocatalytic ring‐opening polymerization to investigate the effect of the hydrophobic side chain (ethyl, propyl, isopropyl, benzyl, and hexyl) on their antimicrobial activity and selectivity. Although the polymers exhibit similar minimum inhibitory concentrations, the more hydrophobic polymers exhibit a faster rate of bacteria elimination. At higher percentage content (20 mol%), polymers with more hydrophobic side chains suffer from poor selectivity due to their high hemolytic activity. The highly hydrophobic co‐polymer, containing the hydrophobic hexyl‐functionalized cyclic carbonate, kills bacteria via a membrane‐disruptive mechanism. Micelle formation leads to a lower extent of membrane disruption. This study unravels the effects of hydrophobic side chains on the activities of the polymers and their killing mechanism, providing insights into the design of new antimicrobial polymers.
Software fault tolerance using dynamically reconfigurable FPGAs (2002)

An emerging class of Field-Programmable Gate Arrays (FPGAs) permits partial reconfiguration of the device without disturbing the rest of the array-even while the device is operating. Dynamic device reconfiguration allows novel approaches to the migration of algorithms from software to hardware. New simulation tools are required in order to fully exploit the FPGA's versatility. We demonstrate how FPGA cells can be programmed and reprogrammed to provide a virtual FPGA that is much larger than the physical FPGA. In the context of dependable computing, our FPGA-based approach shows promise of significant performance gains over traditional software-intensive approaches. We apply this capability to the enhancement of software fault tolerance.
Maximum likelihood parameter estimation for image ringing artifact removal (2002)

At low bit rates, image compression codecs based on overlapping transforms introduce spurious oscillation known as ringing artifacts in the vicinity of major edges. The image quality can be enhanced considerably by removing the artifacts. We present a maximum likelihood approach to the ringing artifact removal problem. Our approach employs a parameter estimation method based on the k-means algorithm with the number of clusters determined by a cluster separation measure. The proposed algorithm and its simplified approximation are applied to JPEG2000 compressed images to demonstrate their effectiveness.
Adaptive distributed transforms for irregularly sampled Wireless Sensor Networks (2009)

We develop energy-efficient, adaptive distributed transforms for data gathering in wireless sensor networks. In particular, we consider a class of unidirectional transforms that are computed as data is forwarded to the sink along a given routing tree and develop a tree-based Karhunen-Loeve Transform (KLT) that is optimal in that it achieves maximum data de-correlation among this class of transforms. As an alternative to this KLT (which incurs communication overhead in order to learn second order data statistics), we propose a backward adaptive filter optimization algorithm for distributed wavelet transforms that i) achieves near optimal performance and ii) has no communication overhead in learning statistics.
First Synthesis of Free Cholesterol−BODIPY Conjugates (2006)

Analogues of cholesterol (compounds 1 and 2) and coprostanol (compound 3) containing the BODIPY fluorophore in the aliphatic tail of the free sterol have been synthesized starting with bisnorcholenic acid, cholenic acid 3beta-acetate, and lithocholic acid, respectively. An ester linkage joining the fluorophore to the sterol nucleus interfered with the ability of the fluorescent sterol to pack with phospholipids in monolayers. However, an analogue in which the linker was devoid of polar atoms exhibited a substantially similar physical behavior to cholesterol in model membranes with respect to localization in raft domains.
Analysis of a Two-Scale Cahn–Hilliard Model for Binary Image Inpainting (2007)

Image inpainting is the process of filling in missing parts of damaged images based on information gleaned from surrounding areas. We consider a model for inpainting binary images using a modified Cahn–Hilliard equation. We prove for the steady state problem that the isophote directions are matched at the boundary of inpainting regions. Our model has two scales, the diffuse interface scale, $\varepsilon$, on which it can accomplish topological transitions, and the feature scale of the image. We show via simulations that a dynamic two-step method involving the diffuse interface scale allows us to connect regions across larger inpainting domains. For the model problem of stripe inpainting, we show that this issue is related to a bifurcation structure with respect to the scale $\varepsilon$.
A new laser-processed polysilicon TFT architecture (2001)

A new top gate polysilicon thin-film transistor (TFT) architecture is introduced which requires only a single laser process step to simultaneously crystallize the channel and activate the source-drain. The dummy-gate TFT (DGTFT) uses a light blocking layer patterned with the gate mask combined with two backside expose steps to allow a self-aligned device structure. N-channel TFTs fabricated using the new process have field effect mobilities greater than 100 cm/sup 2//Vs. By controlling the backside exposures it is also possible to form offset or graded doping structures to reduce field enhanced leakage currents.
Characterization of the Chromosomal Binding Sites andDimerization Partners of the Viral Oncoprotein Meq in Marek'sDisease Virus-Transformed TCells (2003)

Marek's disease virus (MDV) is an acute transforming alphaherpesvirus that causes T-cell lymphomas in chickens. We previously reported the identification of a putative oncogene, meq, that is encoded only by the oncogenic serotype of MDV. The gene product, Meq, is a latent protein that is consistently expressed in MDV-transformed lymphoblastoid cells and tumor cells. Meq has a bZIP (basic leucine zipper) structure resembling the family of Jun/Fos. The mechanism whereby Meq transforms T cells remains poorly understood. In this study, we explored the properties of Meq as a transcriptional factor. We analyzed Meq's dimerization partners and its target genes in MSB-1, an MDV-transformed T-cell line. By using in vitro assays, we first demonstrated Meq's potential to dimerize with a variety of bZIP proteins. We then identified c-Jun as the primary dimerization partner of Meq. Both are found to be colocalized in the nucleus and corecruited to promoters with AP-1 sequences. By using chromatin immunoprecipitation (ChIP), we scanned the entire MDV genome for Meq binding sites and found three regions that were enriched with Meq binding: the MDV lytic replication origin, the promoter for Meq, and the promoter for ICP4. Transactivation assays using the above promoters showed that Meq/Meq homodimers exhibited repression activity, whereas Meq/Jun heterodimers showed activation. Finally, we were able to show by ChIP that Meq is recruited to the interleukin-2 promoter in a region encompassing an AP-1 site. Thus, in addition to providing general knowledge about the transcriptional properties of Meq, our studies revealed for the first time the ability of Meq to interact with the latent MDV and host genomes. Our data suggest, therefore, a role for Meq in viral genome regulation during latency, in addition to its putative causal role in T-cell transformation.
Two Major Recessive Soybean Genes Conferring Soybean Rust Resistance (2008)

Soybean rust (SBR) caused by Phakopsora pachyrhizi Syd. is currently the most threatening fungal disease of soybean [ Glycine max (L.) Merr.] in the Americas. Development of resistant or tolerant cultivars is a major goal in several soybean breeding programs. Four loci, all carrying dominant alleles that confer a resistant phenotype, have been described. We investigated the genetic basis of the resistance in PI 200456 and PI 224270 by crossing each of them with a susceptible cultivar (CD 208). Phenotypic segregation ratios for F 2 plants and F 2:3 lines showed that the resistance in each resistant parent was controlled by a single recessive gene. A test for allelism demonstrated that these genes are non‐allelic. This is the first report of recessive genes controlling SBR resistance in soybean and may represent a different type of resistance for breeding programs aimed at development of more durable resistance.
A three-dimensional scanning apparatus based on structured illumination method and its application in dental scanning (2017)

We demonstrated a three-dimensional (3D) dental scanning apparatus based on structured illumination. A liquid lens was used for tuning focus and a piezomotor stage was used for shift of structured light. A simple algorithm, which detects intensity modulation, was used to perform optical sectioning with structured illumination. We reconstructed 3D point cloud, which represents the 3D coordinates of the digitized surface, of a dental gypsum cast by piling up sectioned images. We performed 3D registration of individual 3D point cloud, which includes alignment and merging the 3D point clouds, to exhibit a 3D model of the dental cast.
Pulse Compression And Raman Amplification In Optical Fibres (1988)

Experimental and theoretical investigations on Raman amplification in fibres have been carried out and simultaneous amplification and pulse compression observed. With a fibre design optimised for amplification high gain may be obtained at practical pump power levels.
Battery monitoring current sensors: The fluxgate concept (2009)

One of the difficulties concerning battery monitoring applications is the current measurement. Typically the measurement range (DC) can vary from 10 mA up to 1000 A. Today's available current transducers are not well adapted to work with good accuracy in this very large domain. In this paper a new measurement principle based on a technology of type ldquofluxgaterdquo [1] is presented, which allows reaching a wide measurement range while guaranteeing an excellent accuracy. The key idea is to use the magnetic field created by the primary (battery) current acting on a saturable inductor. By measuring the intervals to reach inductor saturation and the load current and making use of a suitable microcontroller it is possible to accurately evaluate the value of the primary current for both high and low current levels.
Live-Attenuated Respiratory Syncytial Virus Vaccine Candidate With Deletion of RNA Synthesis Regulatory Protein M2-2 is Highly Immunogenic in Children (2018)

NCT02237209, NCT02040831.
Low-complexity MAP based channel support estimation for Impulse Radio Ultra-Wideband (IR-UWB) communications (2011)

The paper addresses the problem of channel estimation in Impulse-Radio Ultra-Wideband (IR-UWB) communication system. The IEEE 802.15.4a channel model is used where the channel is assumed to be Linear Time Invariant (LTI) and thus the problem of channel estimation becomes the estimation of the sparse channel taps and their delays. Since, the bandwidth of the signal is very large, Nyquist rate sampling is impractical, therefore, we propose to estimate the channel taps from the sub-sampled versions of the received signal profile. We adopt the Bayesian framework to estimate the channel support by incorporating the a priori multipath arrival time statistics. In the first approach, we adopt a two-step method by employing Compressive Sensing to obtain coarse estimates and then refine them by applying Maximum A Posteriori (MAP) criterion. In the second approach, we develop a Low-Complexity MAP (LC-MAP) estimator. The computational complexity is reduced by identifying nearly orthogonal clusters in the received profile and by leveraging the structure of the sensing matrix.