gebhart/patrepeval huggingface dataset:
ChemInform Abstract: 1,3‐Dioxolanylpurine Nucleosides (2R,4R), e.g. (II), and (2R,4S) with Selective Anti‐HIV‐1 Activity in Human Lymphocytes. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: The Raputindoles: Novel Cyclopentyl Bisindole Alkaloids from Raputia simulans. (2010)

Abstract Raputindoles A‐D (I)—(IV) are isolated and structurally characterized.
Determination of Stereochemistry of Acetoxy 1,3-Oxathiolane (1996)

Stereochemistries of acetoxy 1,3-oxathiolane 1 were determined by two methods. First, the structures of isomer 7 and isomer 9 were confirmed by the difference of their conversion rates to dihydrooxathiin 2 under acid catalysis. When the acetoxy leaving group is located in trans relationship to sulfur, a isomer in which carboxanilide is less hindered sterically against the 1,3-oxathiolane ring is isomer 7, and the other isomer of which the reaction rate is slower than 7 is isomer 9. Second, in the deuterium reactions of diastereomeric sulfoxides, the isomers of which methine hydrogen is substituted to deuterium were cis isomers 15 and 17, and another isomers of which methyl hydrogen is substituted to deuterium were trans isomers 16 and 18. Substitution of either methine or methyl hydrogen to deuterium resulted from stereospecific ring opening followed by recyclization by [2,3] sigmatropic rearrangement.
Creating 3D printed sensor systems with conductive composites (2020)

Abstract Fused filament fabrication (FFF), the printing of parts through the deposition of layers of melted thermoplastic, is one of the most widely used 3D printing processes due to its ease of use, low cost and accessibility. In this work, integration of 3D printed sensors and interconnect between embedded components into a printed part is demonstrated in an FFF process for the first time. The use of printed active materials for sensing allows interactivity with the end user through mechanisms like touch and temperature. Through dual extrusion in a low cost commercial printer, printing of both a conductive thermoplastic composite and a non-conducting filament are combined to create complex patterns. The piezoresistive and thermally responsive properties of the thermoplastic composite are used to create several different sensor modalities including a piezoresistive strain sensor, a contact switch and a resistive temperature sensor. A heated insertion technique is then developed for embedding of electrical components. The conductive thermoplastic is also used to incorporate a 3D printed circuit board in the same part, including in-line embedding within the body of the part during the printing process. The sensor performance and component embedding properties are characterized, and the process is used to print systems including relaxation oscillators and op-amp interface circuits for sensor monitoring.
Immune responses induced by a Leishmania (Leishmania) amazonensis recombinant antigen in mice and lymphocytes from vaccinated subjects (1997)

In the search for Leishmania recombinant antigens that can be used as a vaccine against American Cutaneous Leishmaniasis, we identified a Leishmania (Leishmania) amazonensis recombinant protein of 33 kD (Larp33) which is recognized by antibodies and peripheral blood leukocytes (PBL) from subjects vaccinated with Leishvacin, Larp33 was expressed in Escherichia coli after cloning of a 2.2 kb Sau3 digested genomic fragment of L. (L.) amazonensis into the pDS56-6 His vector. Immunoblotting analysis indicated that Larp33 corresponds to an approximately 40-kD native protein expressed in promastigotes of L. (L.) amazonensis and L. (Viannia) braziliensis. Northern blots of total RNA also demonstrated that the gene coding for this protein is expressed in promastigotes of the major lineages of Leishmania causing American Cutaneous Leishmaniasis. Larp33 induced partial protection in susceptible mouse strains (BALB/c and C57BL/10) against L. (L.) amazonensis after vaccination using Bacille Calmette-Guerin (BCG) as adjuvant. In vitro stimulation of splenocytes from BALB/c protected mice with Larp33 elicited the secretion of IL-2 and IFN-gamma, suggesting that a Th1 cell-mediated protective response is associated with the resistance observed in these mice. As revealed by its immunogenic and antigenic properties, this novel recombinant antigen is a suitable candidate to compose a vaccine against cutaneous leishmaniasis.
Mutation Analysis of 2009 Pandemic Influenza A(H1N1) Viruses Collected in Japan during the Peak Phase of the Pandemic (2011)

Our sequence analysis has revealed that both HA-S220T and NA-N248D are major non-synonymous mutations that clearly discriminate the 2009 pdm influenza viruses identified in the very early phase (May 2009) from those found in the peak phase (October 2009 to January 2010) in Japan. By phylogenetic analysis, we found 14 micro-clades within the viruses collected during the peak phase. Among them, 12 were new micro-clades, while two were previously reported. Oseltamivir resistance-related mutations, i.e., NA-H275Y and NA-N295S, were also detected in sporadic cases in Osaka and Tokyo.
Investigating the Degradation of Nb2O5 Thin Films Across 10,000 Lithiation/Delithiation Cycles (2021)

Nb2O5 is a Li+ intercalation transition metal oxide that is of current interest for lithium ion battery and capacitor electrodes. For orthorhombic (T) Nb2O5 films prepared by electrophoretic deposition (EPD) and subjected to lithiation/delithiation cycling, a remarkably reproducible degradation process is observed. It is characterized by the onset of irreversible capacity loss from a baseline specific capacity, Csp, of 400 (±50) F/g at 1000 (± 500) cycles. A gradual reduction of Csp occurs during the ensuing 9000 cycles after which the Csp stabilizes at 200 (±25) F/g. We investigate this degradation using six ex situ instrumental methods and more than 100 individual Nb2O5 films to characterize and understand the composition, atomic scale structure, chemical bonding, electrochemical, and electrical properties of these films during these 10,000 cycles. What emerges is a multidimensional picture of the degradation process in which the decline in Csp occurs concurrently with an increase in the charge transfer resistance, a loss of crystalline order, and the dissolution of niobium from the film.
Introducing Karl F. Warnick, Associate Editor for the Education Column [Education Column] (2012)

Karl F. Warnick received the BS and PhD degrees from Brigham Young University (BYU), Provo, UT, in 1994 and 1997, respectively. From 1998 to 2000, he was a Postdoctoral Research Associate and Visiting Assistant Professor in the Center for Computational Electromagnetics at the University of Illinois at Urbana-Champaign. Since 2000, he has been a faculty member in the Department of Electrical and Computer Engineering at BYU, where he is currently a Professor. In 2005 and 2007, he was a Visiting Professor at the Technische Universität München, Germany. Dr. Warnick has published many scientific articles and conference papers on electromagnetic theory, numerical methods, remote sensing, antenna applications, phased arrays, biomedical devices, and inverse scattering. He is the author of the books Problem Solving in Electromagnetics, Microwave Circuits, and Antenna Design for Communications Engineering (Artech House, 2006) with Peter Russer; Numerical Analysis for Electromagnetic Integral Equations (Artech House, 2008); and Numerical Methods for Engineering: An Introduction Using MATLAB and Computational Electromagnetics Examples (SciTech, 2010)
Exploring the Interrelationship Between Bioreactor Stability and Carbon Balance (2007)

Carbon balance is a common requirement in various mathematical modeling approaches which aim to model operation of a bioreactor. In this work, we study whether carbon balance is attained in a bioreactor which runs through various operational states. We conclude that carbon balance seems to be related to bioreactor stability. In the studied experimental data, carbon balance is closer during stable operational periods than during transient states.
Design and evaluation of alternative selection placement strategies in optimizing continuous queries (2003)

We design and evaluate alternative selection placement strategies for optimizing a very large number of continuous queries in an Internet environment. Two grouping strategies, PushDown and PullUp, in which selections are either pushed below, or pulled above, joins are proposed and investigated. While our earlier research has demonstrated that the incremental group optimization can significantly outperform an ungrouped approach, the results from the paper show that different incremental group optimization strategies can have significantly different performance characteristics. Surprisingly, in our studies, PullUp, in which selections are pulled above joins, is often better and achieves an average 10 fold performance improvement over PushDown (occasionally 100 times faster). Furthermore, a revised algorithm of PullUp, termed filtered PullUp is proposed that is able to further reduce the cost of PullUp by 75% when the union of the selection predicates is selective. Detailed cost models, which consider several special parameters, including (1) characteristics of queries to be grouped, and (2) characteristics of data changes, are presented. Preliminary experiments using an implementation of both strategies show that our models are fairly accurate in predicting the results obtained from the implementation of these techniques in the Niagara system.
Molecular-beam epitaxy of p-type m-plane GaN (2005)

We report on the plasma-assisted molecular-beam epitaxy of Mg-doped (101¯0) GaN on (101¯0) 6H–SiC. Secondary ion mass spectroscopy measurements show the incorporation of Mg into the GaN films with an enhanced Mg incorporation under N-rich conditions relative to Ga-rich growth. Transport measurements of Mg-doped layers grown under Ga-rich conditions show hole concentrations in the range of p=1×1018 to p=7×1018cm−3 and a dependence between hole concentration and Mg beam equivalent pressure. An anisotropy in in-plane hole mobilities was observed, with the hole mobility parallel to [112¯0] being higher than that parallel to [0001] for the same hole concentration. Mobilities parallel to [112¯0] were as high as ∼11.5cm2∕Vs (at p∼1.8×1018cm−3).
Asymptotic Performance of Timing with Dirty Templates for UWB Impulse Radios (2006)

Timing acquisition is one of the major challenges in ultra wideband (UWB) communications. Timing with dirty templates (TDT) is a recently proposed algorithm with attractive features such as low-complexity operation, and fast acquisition in the data-aided mode. This paper is devoted to TDT performance analysis. Specifically, upper bounds on the mean square error of the blind and data-aided TDT estimators are derived. It is shown that both estimators are consistent, while data-aided TDT has an edge over its blind counterpart. To ensure good asymptotic behavior, and for the upper bounds to be valid, the shape of the transmitted monocycle should satisfy certain constraints which are specified. Analytical results are corroborated by simulations.
Length-Dependent Plasmon Resonance in Single-Walled Carbon Nanotubes (2014)

The optical response of single-walled carbon nanotubes (SWCNTs) to far-infrared (FIR) radiation was systematically studied using various SWCNTs with different tube-length distributions. The observed peak position in the FIR spectra linearly scaled with the inverse of tube length irrespective of diameter, which is consistent with the dispersion relation predicted by the one-dimensional plasmon resonance model. The effects of chemical doping on the FIR spectra of the separated metallic and semiconducting SWCNTs clearly indicate that the motion of plasmons in the electronic band structures is primarily responsible for the optical response in these spectral regions. The observed absorption peaks are naturally sensitive to the presence of defects on the tube wall and correlated with the electric resistance, suggesting that the plasmons resonate with the current path length of the SWCNTs.
Effects of Cytokine Activation and Oxidative Stress on the Function of the Human Embryonic Stem Cell–Derived Retinal Pigment Epithelial Cells (2015)

Here, cytokines induced the MMP-1 and -2 gene and protein expression. Also, H2O2 induced MMP-3 and -9 gene expression, but not their protein secretion. These data propose that under oxidative stress and cytokine stimuli, mature hESC-RPE cells resemble their native counterpart in the human eye in regard to MMP secretion and expression and could be used to model retinal disorders involving alterations in MMP activity such as AMD, diabetic retinopathy, or proliferative vitreoretinopathy in vitro.
An Overview of the BlueGene/L Supercomputer (2002)

This paper gives an overview of the BlueGene/L Supercomputer. This is a jointly funded research partnership between IBM and the Lawrence Livermore National Laboratory as part of the United States Department of Energy ASCI Advanced Architecture Research Program. Application performance and scaling studies have recently been initiated with partners at a number of academic and government institutions,including the San Diego Supercomputer Center and the California Institute of Technology. This massively parallel system of 65,536 nodes is based on a new architecture that exploits system-on-a-chip technology to deliver target peak processing power of 360 teraFLOPS (trillion floating-point operations per second). The machine is scheduled to be operational in the 2004-2005 time frame, at price/performance and power consumption/performance targets unobtainable with conventional architectures.
Characterization of Kir1.1 Channels with the Use of a Radiolabeled Derivative of Tertiapin (2006)

Inward rectifier potassium channels (Kir) play critical roles in cell physiology. Despite representing the simplest tetrameric potassium channel structures, the pharmacology of this channel family remains largely undeveloped. In this respect, tertiapin (TPN), a 21 amino acid peptide isolated from bee venom, has been reported to inhibit Kir1.1 and Kir3.1/3.4 channels with high affinity by binding to the M1-M2 linker region of these channels. The features of the peptide-channel interaction have been explored electrophysiologically, and these studies have identified ways by which to alter the composition of the peptide without affecting its biological activity. In the present study, the TPN derivative, TPN-Y1/K12/Q13, has been synthesized and radiolabeled to high specific activity with (125)I. TPN-Y1/K12/Q13 and mono-iodo-TPN-Y1/K12/Q13 ([(127)I]TPN-Y1/K12/Q13) inhibit with high affinity rat but not human Kir1.1 channels stably expressed in HEK293 cells. [(125)I]TPN-Y1/K12/Q13 binds in a saturable, time-dependent, and reversible manner to HEK293 cells expressing rat Kir1.1, as well as to membranes derived from these cells, and the pharmacology of the binding reaction is consistent with peptide binding to Kir1.1 channels. Studies using chimeric channels indicate that the differences in TPN sensitivity between rat and human Kir1.1 channels are due to the presence of two nonconserved residues within the M1-M2 linker region. When these results are taken together, they demonstrate that [(125)I]TPN-Y1/K12/Q13 represents the first high specific activity radioligand for studying rat Kir1.1 channels and suggest its utility for identifying other Kir channel modulators.
Preparing to move: Assembly of the MSP amoeboid motility apparatus during spermiogenesis in Ascaris (2005)

We exploited the rapid, inducible conversion of non-motile Ascaris spermatids into crawling spermatozoa to examine the pattern of assembly of the MSP motility apparatus that powers sperm locomotion. In live sperm, the first detectable motile activity is the extension of spikes and, later, blebs from the cell surface. However, examination of cells by EM revealed that the formation of surface protrusions is preceded by assembly of MSP filament tails on the membranous organelles in the peripheral cytoplasm. These organelle-associated filament meshworks assemble within 30 sec after induction of spermiogenesis and persist until the membranous organelles are sequestered into the cell body when the lamellipod extends. The filopodia-like spikes, which are packed with bundles of filaments, extend and retract rapidly but last only a few seconds before giving way to, or converting into, blebs. Coalescence of these blebs, each supported by a dense mesh of filaments, often initiates lamellipod extension, which culminates in the formation of the robust, dynamic MSP fiber complexes that generate sperm motility. The same membrane phosphoprotein that orchestrates assembly of the fiber complexes at the leading edge of the lamellipod of mature sperm is also found at all sites of filament assembly during spermiogenesis. The orderly progression of steps that leads to construction of a functional motility apparatus illustrates the precise spatio-temporal control of MSP filament assembly in the developing cell and highlights the remarkable similarity in organization and plasticity shared by the MSP cytoskeleton and the actin filament arrays in conventional crawling cells.
Identification of Novel Autoantibodies in Type 1 Diabetic Patients Using a High-Density Protein Microarray (2014)

Autoantibodies can facilitate diagnostic and therapeutic means for type 1 diabetes (T1DM). We profiled autoantibodies from serum samples of 16 T1DM patients, 16 type 2 diabetic (T2DM) patients, and 27 healthy control subjects with normal glucose tolerance (NGT) by using protein microarrays containing 9,480 proteins. Two novel autoantibodies, anti-EEF1A1 and anti-UBE2L3, were selected from microarrays followed by immunofluorescence staining of pancreas. We then tested the validity of the candidates by ELISA in two independent test cohorts: 1) 95 adults with T1DM, 49 with T2DM, 11 with latent autoimmune diabetes in adults (LADA), 20 with Graves disease, and 66 with NGT and 2) 33 children with T1DM and 34 healthy children. Concentrations of these autoantibodies were significantly higher in T1DM patients than in NGT and T2DM subjects (P < 0.01), which was also confirmed in the test cohort of children (P < 0.05). Prevalence of anti-EEF1A1 and anti-UBE2L3 antibodies was 29.5% and 35.8% in T1DM, respectively. Of note, 40.9% of T1DM patients who lack anti-GAD antibodies (GADA) had anti-EEF1A1 and/or anti-UBE2L3 antibodies. These were also detected in patients with fulminant T1DM but not LADA. Our approach identified autoantibodies that can provide a new dimension of information indicative of T1DM independent of GADA and new insights into diagnosis and classification of T1DM.
Rip-off: playing the cooperative negotiation game (2011)

We propose Rip-off, a new multi-player bargaining game based on the well-studied weighted voting game (WVG) model from cooperative game theory. Many different solution concepts, such as the Core and the Shapley value have been proposed to analyze models such as WVGs. However, there is little work on analyzing how humans actually play in such settings. We conducted several experiments where we let humans play Rip-off. Our analysis reveals that although solutions of games played by humans do suffer from certain biases, a player's average payoff over several games is roughly reflected by the Shapley value.
Colon cancer in aged captive rhesus monkeys (Macaca mulatta) (1998)

The age-related incidence of malignant neoplasia was surveyed from a total of 301 necropsy cases of rhesus monkeys ranging in age from 13–37 years performed in the Pathology Service Unit of the Wisconsin Regional Primate Research Center during the past 15 years. All our aged monkeys lived in indoor cages and were fed with monkey chow and supplemental fruits during the past decades. In this survey, we found a total of 51 malignant neoplasms, and among them 25 cases were colon cancer. The incidence of colon cancer increased with advancing age: 3.2% at 13–19 years, 9.2% at 20–25 years, 13.5% at 26–29 years, and 20.7% at 30–37 years. Most cancers were located in the cecum and transverse regions with a unicentric origin. Two multicentric cases were associated with chronic hypertrophic colitis. Precancerous polypous lesions were not found in all cases. Histologically, all cases were mucinous adenocarcinoma and had local invasion to the muscular wall. Metastasis to the mesenteric lymph nodes was found in only two cases. As in humans, colon cancer is a common outcome of aging in nonhuman primates. Am. J. Primatol. 44:19–27, 1998. © 1998 Wiley-Liss, Inc.
Application of Quasiperiodic and Random Quasi-Phase-Matching to High-Harmonic-Generation (2009)

The utility of quasiperiodic and random quasi-phase matching is demonstrated theoretically for shaping the spectral emission of high harmonic generation. Demonstrated are simultaneous enhancement of arbitrary spectral regions and enhancement of an extremely wide bandwidth.
Resuscitation-Promoting Factors Are Required for β-Lactam Tolerance and the Permeability Barrier in Mycobacterium tuberculosis (2011)

Mycobacterial resuscitation-promoting factors (RPFs) have been of great interest since the discovery that they promote the growth of nonculturable Mycobacterium tuberculosis cells. Yet, their precise role in mycobacterial survival and infection has remained elusive. We performed a chemical screen to identify molecules that show preferential killing of a Mycobacterium tuberculosis mutant lacking RPFs over wild-type bacilli and found that the mutant has enhanced sensitivity to the β-lactam class of antibiotics. By monitoring β-lactam diffusion across the mycobacterial outer membrane, we found that the RPFs are required to maintain the outer membrane integrity, as their deletion results in an increase in outer membrane permeability.
Total Synthesis of the Hydroxyketone Kurasoin A Using Asymmetric Phase‐Transfer Alkylation. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Long-Term Exposure of Cells to Cdk4 Inhibitor Palbociclib Leads to Chromosomal Aberrations (2023)

Abstract Breast cancers are often driven by mutations, alterations and activation of cell cycle regulatory proteins, including the retinoblastoma tumor suppressor protein (Rb), cyclin E and cyclin-dependent kinases (Cdks), especially cyclin D:Cdk4/6 complexes. There are currently three FDA approved Cdk4/6 inhibitors (Cdk4i) for treating breast cancer. The standard treatment protocol is 21 days of continuous Cdk4i treatment, followed by a 7 day cessation period and then repeating the 28 day protocol. We asked the question of what happens to cells that reenter the cell cycle during the 7 day Cdk4i cessation period. Using RPE1 cells containing visual reporter endogenous histone 2B and p27 genes tagged with eGFP and mCherry, we treated the cells with a Cdk4i, Palbociclib for 1 to 42 days that spanned the clinical exposure, followed by drug release (washout) and video microscopic analysis. Surprisingly, we found that as little as 4 days of Cdk4i treatment and release resulted in a significant increase in micronuclei and multinucleated cells that had reentered the cell cycle. The peak chromosomal aberration occurred between 14 and 35 days, a timing that spans the clinical dosing regimen.These observations raise questions concerning the potential that cycling patients on and off of Cdk4 inhibitors may generate gross chromosomal changes to tumor cells that reenter the cell cycle during the 7 day clinical cessation (washout) period and thereby increase the potential to initiate secondary oncogenic events.