gebhart/patrepeval huggingface dataset:
Identification of Urinary microRNA Profiles in Rats That May Diagnose Hepatotoxicity (2011)

Circulating microRNAs (miRNAs) have emerged as novel noninvasive biomarkers for several diseases and other types of tissue injury. This study tested the hypothesis that changes in the levels of urinary miRNAs correlate with liver injury induced by hepatotoxicants. Sprague-Dawley rats were administered acetaminophen (APAP) or carbon tetrachloride (CCl(4)) and one nonhepatotoxicant (penicillin/PCN). Urine samples were collected over a 24 h period after a single oral dose of APAP (1250 mg/kg), CCl(4) (2000 mg/kg), or PCN (2400 mg/kg). APAP and CCl(4) induced liver injury based upon increased serum alanine and aspartate aminotransferase levels and histopathological findings, including liver necrosis. APAP and CCl(4) both significantly increased the urinary levels of 44 and 28 miRNAs, respectively. In addition, 10 of the increased miRNAs were in common between APAP and CCl(4). In contrast, PCN caused a slight decrease of a different nonoverlapping set of urinary miRNAs. Cluster analysis revealed a distinct urinary miRNA pattern from the hepatotoxicant-treated groups when compared with vehicle controls and PCN. Analysis of hepatic miRNA levels suggested that the liver was the source of the increased urinary miRNAs after APAP exposure; however, the results from CCl(4) were equivocal. Computational analysis was used to predict target genes of the 10 shared hepatotoxicant-induced miRNAs. Liver gene expression profiling using whole genome microarrays identified eight putative miRNA target genes that were significantly altered in the liver of APAP- and CCl(4)-treated animals. In conclusion, the patterns of urinary miRNA may hold promise as biomarkers of hepatotoxicant-induced liver injury.
Prion protein is expressed on long-term repopulating hematopoietic stem cells and is important for their self-renewal (2006)

Although the wild-type prion protein (PrP) is abundant and widely expressed in various types of tissues and cells, its physiological function(s) remain unknown, and PrP knockout mice do not exhibit overt and undisputed phenotypes. Here we showed that PrP is expressed on the surface of several bone marrow cell populations successively enriched in long-term (LT) hematopoietic stem cells (HSCs) using flow cytometry analysis. Affinity purification of the PrP-positive and -negative fractions from these populations, followed by competitive bone marrow reconstitution assays, shows that all LT HSCs express PrP. HSCs from PrP-null bone marrow exhibited impaired self-renewal in serial transplantation of lethally irradiated mouse recipients both in the presence and absence of competitors. When treated with a cell cycle-specific myelotoxic agent, the animals reconstituted with PrP-null HSCs exhibit increased sensitivity to hematopoietic cell depletion. Ectopic expression of PrP in PrP-null bone marrow cells by retroviral infection rescued the defective hematopoietic engraftment during serial transplantation. Therefore, PrP is a marker for HSCs and supports their self-renewal.
Large intestine–targeted, nanoparticle-releasing oral vaccine to control genitorectal viral infection (2020)

Both rectal and vaginal mucosal surfaces serve as transmission routes for pathogenic microorganisms. Vaccination through large intestinal mucosa, previously proven protective for both mucosal sites in animal studies, can be achieved successfully by direct intra-colorectal (i.c.r.) administration, which is, however, clinically impractical. Oral delivery seems preferable, but risks vaccine destruction in the upper gastrointestinal tract. Therefore, we designed a large intestine-targeted oral delivery with pH-dependent microparticles containing vaccine nanoparticles, which induced colorectal immunity in mice comparably to colorectal vaccination and protected against rectal or vaginal viral challenge. Conversely, vaccine targeted to the small intestine induced only small intestinal immunity and provided no rectal or vaginal protection, demonstrating functional compartmentalization within the gut mucosal immune system. Therefore, using this oral vaccine delivery system to target the large intestine, but not the small intestine, may represent a feasible novel strategy for immune protection of rectal and vaginal mucosa.
Smart Technical Textiles for Structural Health Monitoring (2013)

First Name is required invalid characters Last Name is required invalid characters Email Address is required Invalid Email Address Invalid Email Address
A T-Coil-Enhanced 8.5 Gb/s High-Swing SST Transmitter in 65 nm Bulk CMOS With $≪ -$16 dB Return Loss Over 10 GHz Bandwidth (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A source-series-terminated (SST) transmitter in a 65 nm bulk CMOS technology is presented. The circuit exhibits an eye height greater than 1.0 V for data rates of up to 8.5 Gb/s. A thin-oxide pre-driver stage running at 1.0 V drives 22 parallel connected thick-oxide SST output stages operated at 1.5 V that feature a 5-bit 2-tap FIR filter whose adaptation is independent of the impedance tuning. To achieve a return loss of <formula formulatype="inline"><tex Notation="TeX">$≪-$</tex> </formula>16 dB up to 10 GHz a 40 <formula formulatype="inline"><tex Notation="TeX">$\mu$</tex> </formula>m<formula formulatype="inline"><tex Notation="TeX">$\,\times\,$</tex> </formula>40 <formula formulatype="inline"><tex Notation="TeX">$\mu$</tex> </formula>m T-coil complements the transmitter output. This half-bit-rate clock SST transmitter has a duty-cycle restoration capability of 5x, and the common-mode voltage noise is below 10 mV rms for high-, mid- and low-level terminations. The chip consumes 96 mW at 8.5 Gb/s and occupies 180 <formula formulatype="inline"><tex Notation="TeX">$\mu$</tex></formula>m <formula formulatype="inline"> <tex Notation="TeX">$\times\, \hbox{360}\ \mu$</tex></formula>m. In addition to the transmitter design, guidelines for the T-coil design are presented. </para>
Modeling large-area influence in digital halftoning for electrophotographic printers (2011)

Digital halftoning provides a mechanism for rendering continuous-tone images on devices such as printers. With electrophotography, the deposition of toner within the area of a given printer addressable pixel is strongly influenced by the halftone values of the immediately neighboring pixels. To account for these effects, it is necessary to embed a printer model in the halftoning algorithm. In our previous work, we used an efficient strategy to account for the impact of a 5x5 neighborhood of pixels on the central pixel absorptance. Now we examine the potential influence of a much larger neighborhood (45x45) of the digital halftone image on the measured value of a printed pixel at the center of that neighborhood. The experiment shows that the extended model yields a significant improvement in the accuracy of the prediction of the pixel values of the printed and measured halftone image.
An Efficient One-Pot SyntheticMethod for 2,4-Disubstituted 7-Arylpyrido[4,3-d]pyrimidines from 2,4-Disubstituted6-(Arylethynyl)pyrimidine-5-carbaldehydes and tert-Butylamine (2008)

Unexpected thermal cyclization of 2,4-disubstituted 6-(aryl-ethynyl)pyrimidine-5-carbaldehydes with tert-butylamine proceeded to give 2,4-disubstituted 7-arylpyrido[4,3-d]pyrimidines in good yields in the absence of any catalysts. The intermediate compounds were isolated and possible mechanism of the reactions is discussed.
Abstract B008: Activation of the bile acid pathway promotes tumorigenesis in clear cell renal cell carcinoma (2023)

Abstract Clear cell renal cell carcinoma (ccRCC) incidence has risen steadily over the last decade. We and others have demonstrated that elevated lipid uptake and storage is required for ccRCC cell viability; however, the role of stored cholesterol, the most abundant component in ccRCC intracellular lipid droplets, remains unclear. We recently demonstrated that ccRCC cells acquire exogenous cholesterol through the HDL receptor SCARB1, inhibition or suppression of which induces apoptosis. Here, we show that elevated expression of 3 beta-hydroxy steroid dehydrogenase type 7 (HSD3B7), which metabolizes cholesterol-derived oxysterols in the bile acid biosynthetic pathway, is essential for ccRCC cell survival. Repressing HSD3B7 expression genetically, or treating ccRCC cells with a newly identified HSD3B7 inhibitor, resulted in toxic oxysterol accumulation, impaired proliferation, and increased apoptosis in vitro and in vivo. These data demonstrate that bile acid synthesis regulates cholesterol homeostasis in ccRCC and identifies HSD3B7 as a plausible therapeutic target. Citation Format: Romain Riscal, Sarah Gardner, Madeleine Carens, Clementina Mesaros, Jimmy Xu, Nate Coffey, Leah Davis, Austin Vogt, Adam Olia, Jennifer Finan, Jason Godfrey, Ian Blair, Brian Keith, Ronen Marmorstein, Nicolas Skuli, Celeste Simon. Activation of the bile acid pathway promotes tumorigenesis in clear cell renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B008.
In-Situ Gas-Phase Luminescence and Time-of-Flight Mass Spectroscopic Detection of Photofragments during Photochemical Synthesis of Copper Particles from Bis(tert-butylacetoacetato)copper (2000)

During the 308 nm laser-driven photochemical synthesis of Cu particles from bis(tert-butylacetoacetato)copper, gas-phase photogenerated intermediates are identified by luminescence and time-of-flight mass spectroscopies. Pure Cu deposits are obtained as homogeneous, granular 200 nm particles. In the gas phase, luminescent photoproducts are observed and atomic Cu, Cu2, and dissociated ligand are identified spectroscopically. In addition, mass spectroscopy identifies Cu atoms, the dissociated ligand, a monoligated complex, and fragments of the ligands. The implications of the photofragmentation that produces copper atoms and dimers for the laser-assisted production of the Cu deposits are discussed.
Insights into the bile acid transportation system: The human ileal lipid‐binding protein‐cholyltaurine complex and its comparison with homologous structures (2002)

Bile acids are generated in vivo from cholesterol in the liver, and they undergo an enterohepatic circulation involving the small intestine, liver, and kidney. To understand the molecular mechanism of this transportation, it is essential to gain insight into the three-dimensional (3D) structures of proteins involved in the bile acid recycling in free and complexed form and to compare them with homologous members of this protein family. Here we report the solution structure of the human ileal lipid-binding protein (ILBP) in free form and in complex with cholyltaurine. Both structures are compared with a previously published structure of the porcine ILBP-cholylglycine complex and with related lipid-binding proteins. Protein structures were determined in solution by using two-dimensional (2D)- and 3D-homo and heteronuclear NMR techniques, leading to an almost complete resonance assignment and a significant number of distance constraints for distance geometry and restrained molecular dynamics simulations. The identification of several intermolecular distance constraints unambiguously determines the cholyltaurine-binding site. The bile acid is deeply buried within ILBP with its flexible side-chain situated close to the fatty acid portal as entry region into the inner ILBP core. This binding mode differs significantly from the orientation of cholylglycine in porcine ILBP. A detailed analysis using the GRID/CPCA strategy reveals differences in favorable interactions between protein-binding sites and potential ligands. This characterization will allow for the rational design of potential inhibitors for this relevant system.
Layer 1 virtual private networks: driving forces and realization by GMPLS (2005)

This article describes an emerging service for next-generation networks, layer 1 virtual private networks. L1VPNs allow customers desiring to connect multiple sites to be supported over a single shared layer 1 network. In the article we first describe the transport network's evolution and the shift in expectations of both service providers and customers. We provide an overview of the motivation for L1VPNs and examples of network usage. We follow by reviewing existing GMPLS mechanisms (addressing, discovery, and signaling) for realizing L1VPN functionality and identifying other work areas.
Development of reverse phase protein microarrays for clinical applications and patient-tailored therapy. (2007)

While genomics provide important information about the somatic genetic changes, and RNA transcript profiling can reveal important expression changes that correlate with outcome and response to therapy, it is the proteins that do the work in the cell. At a functional level, derangements within the proteome, driven by post-translational and epigenetic modifications, such as phosphorylation, is the cause of a vast majority of human diseases. Cancer, for instance, is a manifestation of deranged cellular protein molecular networks and cell signaling pathways that are based on genetic changes at the DNA level. Importantly, the protein pathways contain the drug targets in signaling networks that govern overall cellular survival, proliferation, invasion and cell death. Consequently, the promise of proteomics resides in the ability to extend analysis beyond correlation to causality. A critical gap in the information knowledge base of molecular profiling is an understanding of the ongoing activity of protein signaling in human tissue: what is activated and "in use" within the human body at any given point in time. To address this gap, we have invented a new technology, called reverse phase protein microarrays, that can generate a functional read-out of cell signaling networks or pathways for an individual patient obtained directly from a biopsy specimen. This "wiring diagram" can serve as the basis for both, selection of a therapy and patient stratification.
Reconstitution of Bovine A1 Adenosine Receptors and G Proteins in Phospholipid Vesicles:  βγ-Subunit Composition Influences Guanine Nucleotide Exchange and Agonist Binding (1997)

We have studied the interactions of purified A1 adenosine receptors and G proteins reconstituted into phospholipid vesicles to investigate how the betagamma composition of G protein heterotrimers influences coupling. Recombinant hexahistidine-tagged bovine A1 adenosine receptors were expressed in Sf9 cells and purified to homogeneity by sequential chromatography over heparin-sepharose, xanthine amino congener-agarose, and nickel-nitrilotriacetic acid columns. These receptors were reconstituted with pure recombinant G proteins of defined subunit composition. Receptor-G protein complexes containing alphai2 and beta1gamma2 or beta1gamma3 and stimulated with the agonist, (R)-phenylisopropyladenosine, exchange guanine nucleotide 2-3 times more rapidly than do complexes containing beta1gamma1. This difference is not overcome by increasing the concentration of betagamma subunits. Receptor-G protein complexes containing beta1gamma1 also bind less of the agonist, [125I]-iodoaminobenzyladenosine (125I-ABA), than do complexes containing beta1gamma3. Kinetic experiments show that 125I-ABA dissociates 2-fold more rapidly from receptor-G protein complexes containing beta1gamma1 than from complexes containing the other betagamma subunits. The affinity of the interaction between immobilized Galphai2 subunits and beta1gamma1 or beta1gamma2 measured with an optical biosensor in the absence of receptor is similar. Taken together, these data implicate the gamma-subunit in influencing the interaction between the A1 adenosine receptor and G proteins.
Quantum Cascade Infrared Laser Spectroscopy for Real-Time Cigarette Smoke Analysis (2003)

A compact, fast-response, infrared spectrometer using pulsed quantum cascade (QC) lasers has been applied to the analysis of gases in mainstream and sidestream cigarette smoke. QC lasers have many advantages over the traditional lead salt tunable diode lasers, including near-room-temperature operation with thermoelectric cooling and single mode operation with improved long-term stability. The instrument uses a 36-m, 0.3-L multiple pass absorption gas cell to obtain a time response of 0.1 s for the mainstream system and 0.4 s for the sidestream system. A precision of 10-4 absorbance units in 1 s is achieved using pulse normalization to reduce pulse-to-pulse intensity variations. Laser line widths (hwhm) of 0.006 cm-1 at 967 and 0.010 cm-1 at 1900 cm-1 are obtained in pulsed operation. With this instrument, we have measured the concentrations of ammonia and ethylene using a QC laser at 967 cm-1 and nitric oxide using a laser at 1900 cm-1 in both mainstream and sidestream smoke from two types of cigarettes. A data rate of 20 Hz provides sufficient temporal resolution to reveal the concentration profiles for these gas components during each 2-s puff in the mainstream smoke. In addition, the concentration profiles before, during, and after the puffs are observed in the sidestream smoke. Simultaneous measurements of CO2 are obtained using a nondispersive infrared analyzer, and the emission ratios of the analyte gases relative to the amount of CO2 produced during combustion are calculated using two types of reference cigarettes.
RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways (2023)

SARS-CoV-2 has the capacity to evolve mutations to escape vaccine-and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool. Here, we challenged rhesus macaques with SARS-CoV-2 Delta and simultaneously treated them with aerosolized RBD-62, a protein developed through multiple rounds of <i>in vitro</i> evolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment gave equivalent protection in upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 did not block the development of memory responses to Delta and did not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.
Ultra low field magnetic resonance imaging for the investigation of hyperpolarized contrast agents (2016)

In NMR/MRI experiments at ultra low magnetic fields hyperpolarization techniques based on parahydrogen (pH2) could offer a simple way to circumvent the lack of the low equilibrium polarization of the sample. A chemical exchange reaction, taking place at B0 fields in the mT range, transfers polarized spins from pH2 via a transfer catalyst to the sample. This transfer reaction can enhance the sample polarization in B0 fields in the mT range by a factor of 105, offering sample polarizations comparable to polarization fields of 103-104 T. To investigate these newly developed techniques a SQUID based NMR/MRI system operating at a static magnetic field in the mT range is being developed. By using a SQUID for detecting the NMR Signal, the system can benefit from its very low intrinsic noise level. Additionally, SQUIDs are wide band detectors and can detect the signal of multiple kernels simultaneously. A design of an ultra low field MRI system and first results will be presented.
<title>Measurements of ultrashort optical waveforms using frequency-resolved optical gating</title> (1995)

The intensity and phase of the approximately 10 femtosecond pulse from a self-modelocked Ti:sapphire laser was reconstructed using frequency-resolved optical gating (FROG). Our results verify recent models which show that uncompensated higher-order dispersion in the laser cavity is the main limitation on pulse duration.
A new AGV scheduling algorithm based on harmony search for material transfer in a real-world manufacturing system (2018)

With the development of advanced manufacturing technology, more and more enterprises utilize automated guided vehicles to transfer materials for computer numerical control machines in the workshop. Because automated guided vehicle scheduling problem is non-deterministic polynomial–hard, highly efficient automated guided vehicle scheduling algorithms are necessary to improve productivity of the workshop. In order to solve this problem, a mathematical model with a new objective function is established firstly, which incorporates two indicators, that is, the standard deviation of the waiting time of computer numerical control material buffers and the total travel distance of automated guided vehicle, reflecting the overall capacity of computer numerical control machines and the energy efficiency of automated guided vehicles during the actual production, respectively. Then, an improved harmony search algorithm is proposed, which includes an effective discrete encoding scheme of harmony, a new initialization method for harmony memory based on opposition-based learning strategy, a dynamic harmony memory considering rate parameter and a local search strategy. The property of the proposed algorithm is evaluated through three cases from the real-world manufacturing system for producing back cover of smart phone. Compared with the competing algorithms, the results demonstrate the superiority of proposed algorithm for solving automated guided vehicle scheduling problem obviously.
A Differential 3.3V BICMOS Buffer with Current Consumption and Linearity Control for RF Mixer (2007)

A design of a 3.3 Volts BiCMOS buffer with current consumption and linearity control is presented. This buffer with a low output impedance is fully differential and designed to be used with RF (radio frequency) mixer in low IF (intermediate frequency) architecture. The proposed buffer is directly connected to the output of the RF mixer and designed to drive off- chip low impedance load as SAW (surface acoustic wave) or discrete differential filters. A good flexibility is obtained about the control of the linearity performance with the possibility to adjust the power consumption. The linearity and current consumption are independently adjustable and an optimum of the 3rd order linearity performance is achieved for each current consumption value. A schematic of the differential Bi-CMOS 3.3 volts buffer is proposed and some linearity simulation results are presented and discussed in terms of output IM3 level and current consumption. The results show a saving of half power in comparison with a buffer with no linearity control for the same output IM3 level.
Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth (2018)

The results illustrated that the acetogenic bacteria reallocate protein synthesis, focusing more on the translation of genes for the generation of reduced electron carriers via electron bifurcation, rather than on those for carbon metabolism under autotrophic growth.