gebhart/patrepeval huggingface dataset:
Regulation-defective mutants of type I cAMP-dependent protein kinase. Consequences of replacing arginine 94 and arginine 95 (1993)

The type I alpha regulatory subunits of cAMP-dependent protein kinase contain an autoinhibitor site, Arg94-Arg-Gly-Ala-Ile, which serves as a pseudosubstrate. To evaluate their contribution to subunit association, Arg94 and Arg95, key determinants for peptide recognition, were replaced singly and in tandem with Ala, Glu, and His. Unlike substrate peptides in which replacement of either arginine leads to an increase in Km of approximately 3 orders of magnitude, replacement of either arginine causes only a maximal 20-fold decrease in subunit association. Replacement of both arginine residues with alanine, however, generates a regulatory subunit that can no longer recombine with the catalytic subunit under physiological conditions when the regulatory subunit is saturated with cAMP. To evaluate more fully the specific consequences of replacing these 2 arginine residues, a rapid gel filtration chromatographic method was developed so that subunit affinity could be measured independently of assaying for catalytic activity. The R94,95A mutant shows a Kd(app) = 677 nM, representing an increase of greater than 3 orders of magnitude compared with the native subunits in the presence of MgATP. In the absence of MgATP, the Kd(app) for native regulatory subunit was 125 nM, whereas the Kd(app) for the R94,R95A mutant regulatory subunit was determined to 2.87 microM. When this mutant holoenzyme is assayed at microM concentrations, no activity is observed, whereas below microM, activity is observed because of cAMP-independent subunit dissociation.
A comparison of mathematical methods for the analysis of DNA histograms obtained by flow cytometry (1982)

Twelve methods for analysing FCM-histograms were compared using the same set of data. Some of the histograms that were analysed were simulated by computer and some were taken from experiments. Simulated data were generated assuming synchronously growing cell populations and (i) measurement coefficients of variation (CV) from 2 to 16%; (ii) constant measurement CV or VC's increasing from G1 to G2 phase, and (iii) varying fractions of cells in each phase. Simulated data were also generated assuming synchronous cell populations in which a block in early S phase was applied and released. DNA histograms were measured for L-929 cells at various times after mitotic selection. Labelling indices were also measured for these cells at the same time. The fractions of cells in the G1, S, and (G2 + M) phases were calculated by each analytical method and compared with the actual fractions used for simulation, or in case of experimental data, with autoradiographic results. Generally, all methods yielded reasonably accurate fractions of cells in each phase with relative errors in the range of 10-20%. However, most methods tended to overestimate G1 fractions and underestimate S fractions. In addition, variations in the shape of the S phase distribution often caused considerable errors. Phase fractions were also calculated for histograms of kinetically perturbed populations, simulated as well as experimental. The errors were only slightly larger than for histograms from asynchronously growing cell populations.
HIV Testing and Treatment with the Use of a Community Health Approach in Rural Africa (2019)

Universal HIV treatment did not result in a significantly lower incidence of HIV infection than standard care, probably owing to the availability of comprehensive baseline HIV testing and the rapid expansion of ART eligibility in the control group. (Funded by the National Institutes of Health and others; SEARCH ClinicalTrials.gov number, NCT01864603.).
Intruder tracking using wireless sensor network (2010)

Nowadays, almost all the countries are facing threats from terrorists and intruders from their border areas, challenging the internal security of the country in those areas. So many civilian and military applications require locating an intruder in a secured area. Target tracking, data processing and analysis play a major role in this type of applications. The proposed system is to develop a centralized computer application that needs to identify moving objects in a specific area using sensors. The system will be basically designed to detect human intruders. The objective is to design and implement an object tracking system using a wireless sensor network. This application is able to detect and track objects, and report direction and speed of the intruder to a central base station. The human intruder is detected using a passive infrared (PIR) sensor. The sensor is connected to a MICAz sensor node. The PIR sensor is able to detect the humans and provide information about the direction of the movement. The gathered information from the sensor network is to be given to the base station for processing. The proposed system provides an environment for easy deployment and which does not require any existing infrastructure or constant monitoring by humans.
Secondary Cosmic Positrons in an Anisotropic Diffusion Model (2016)

One aim of cosmic ray measurements is the search for possible signatures of annihilating or decaying dark matter. The so-called positron excess has attracted a lot of attention in this context. On the other hand it has been proposed that the data might challenge the established diffusion model for cosmic ray propagation. We investigate an anisotropic diffusion model by solving the corresponding equations analytically. Depending on the propagation parameters we find that the spectral features of the positron spectrum are affected significantly. We also discuss the influence of the anisotropy on hadronic spectra.
Superconductivity in a PbFCl-type pnictide: NbSiAs (2012)

We report a new superconductor, NbSiAs, with a PbFCl-type structure, which exhibits bulk superconductivity with a superconducting transition temperature (Tc) of 8.2 K and a shielding volume fraction of 40 vol%. Isothermal magnetization and heat capacity measurements indicate NbSiAs is a BCS-like type II superconductor with a normalized specific heat jump value (Cel/γTc) of ∼1.95. Strongly hybridized bonds between Nb 4d and Si 3p orbitals enhance the Debye temperature, which is favorable for the emergence of superconductivity.
Intrabone transplantation of CD34+ cells with optimized delivery does not enhance engraftment in a rhesus macaque model (2020)

Intrabone (IB) injection of umbilical cord blood has been proposed as a potential mechanism to improve transplant engraftment and prevent graft failure. However, conventional IB techniques produce low retention of transplanted cells in the marrow. To overcome this barrier, we developed an optimized IB (OIB) injection method using low-volume, computer-controlled slow infusion that promotes cellular retention in the marrow. Here, we compare engraftment of CD34+ cells transplanted in a myeloablative rhesus macaque (RM) model using the OIB method compared with IV delivery. RM CD34+ cells obtained by apheresis were split equally for transduction with lentiviral vectors encoding either green fluorescent protein or yellow fluorescent protein reporters. Following conditioning, one marked autologous population of CD34+ cells was injected directly IB using the OIB method and the other was injected via slow IV push into the same animal (n = 3). Daily flow cytometry of blood quantified the proportion of engrafting cells deriving from each source. Marrow retention was examined using positron emission tomography/computed tomography imaging of 89Zirconium (89Zr)-oxine-labeled CD34+ cells. CD34+ cells injected via the OIB method were retained in the marrow and engrafted in all 3 animals. However, OIB-transplanted progenitor cells did not engraft any faster than those delivered IV and contributed significantly less to hematopoiesis than IV-delivered cells at all time points. Rigorous testing of our OIB delivery system in a competitive RM myeloablative transplant model showed no engraftment advantage over conventional IV infusion. Given the increased complexity and potential risks of IB vs IV approaches, our data do not support IB transplantation as a strategy to improve hematopoietic engraftment.
Conversion of cellulose rich municipal solid waste blends using ionic liquids: feedstock convertibility and process scale-up (2017)

Process development and scale-up of an ionic liquid based process that converts actual household waste (cellulose rich fraction) to fermentable sugars.
Smartphone Fluorescence Spectroscopy (2014)

We demonstrate the first use of smartphone spectrophotometry for readout of fluorescence-based biological assays. We evaluated the smartphone fluorimeter in the context of a fluorescent molecular beacon (MB) assay for detection of specific nucleic acid sequences in a liquid test sample and compared performance against a conventional laboratory fluorimeter. The capability of distinguishing a one-point mismatch is also demonstrated by detecting single-base mutation in target nucleic acids. Our approach offers a route toward portable biomolecular assays for viral/bacterial pathogens, disease biomarkers, and toxins.
The Effect of Cardiac Compression on Defibrillation Efficacy and the Upper Limit of Vulnerability (1995)

Shock delivery during cardiac compression improves defibrillation efficacy. Additionally, cardiac compression decreases both DFT and ULV, which supports the ULV hypothesis of defibrillation. Finally, maintaining the heart's geometric and volumetric state during ULV testing in paced rhythm and DFT testing in ventricular fibrillation moves the ULV higher than the DFT-the position predicted by the ULV hypothesis for defibrillation.
Structural and Kinetic Analysis of Prolyl-isomerization/Phosphorylation Cross-Talk in the CTD Code (2012)

The C-terminal domain (CTD) of eukaryotic RNA polymerase II is an essential regulator for RNA polymerase II-mediated transcription. It is composed of multiple repeats of a consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4)Ser(5)Pro(6)Ser(7). CTD regulation of transcription is mediated by both phosphorylation of the serines and prolyl isomerization of the two prolines. Interestingly, the phosphorylation sites are typically close to prolines, and thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Experimental evidence of cross-talk between these two regulatory mechanisms has been elusive. Pin1 is a highly conserved phosphorylation-specific peptidyl-prolyl isomerase (PPIase) that recognizes the phospho-Ser/Thr (pSer/Thr)-Pro motif with CTD as one of its primary substrates in vivo. In the present study, we provide structural snapshots and kinetic evidence that support the concept of cross-talk between prolyl isomerization and phosphorylation. We determined the structures of Pin1 bound with two substrate isosteres that mimic peptides containing pSer/Thr-Pro motifs in cis or trans conformations. The results unequivocally demonstrate the utility of both cis- and trans-locked alkene isosteres as close geometric mimics of peptides bound to a protein target. Building on this result, we identified a specific case in which Pin1 differentially affects the rate of dephosphorylation catalyzed by two phosphatases (Scp1 and Ssu72) that target the same serine residue in the CTD heptad repeat but have different preferences for the isomerization state of the adjacent proline residue. These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation.
Feasibility Study of Economics and Performance of Solar Photovoltaics in Nitro, West Virginia (2010)

The study described in this report assessed brownfield sites designated by the City of Nitro, West Virginia for solar photovoltaic (PV) installations. The study analyzed three different types of PV systems for eight sites. The report estimates the cost, performance, and site impacts of thin film technology and crystalline silicon panels (both fixed-axis tracking and single-axis tracking systems).Potential job creation and electrical rate increases were also considered, and the report recommends financing options that could assist in the implementation of a system.
Novel Targeting Strategies for Leukemia-Initiating Cells in Myeloid Neoplasms (2013)

Abstract In this session we will present results from our chemo-genomic screens designed to categorize more accurately human acute myeloid leukemia (AML) subsets based on both their genetic make-up (RNA and exon Next Generation Sequencing) and their response to clinically-approved chemicals. The success of this project relies on our recent development of newly defined culture conditions that support the majority of leukemia stem cells in short-term cultures (Pabst et. al., submitted) and availability of a large collection of clinically annotated specimens (J.H., BCLQ). Integration of chemical and genetic data is possible through our novel bioinformatics tools developed for this purpose (Lemieux et. al., submitted). In addition to the generation of more accurate prognostic tools, these studies set the stage for drug repositioning and personalized medicine for human AML. Disclosures: No relevant conflicts of interest to declare.
Total synthesis, from D-xylose, of chiral, ring-contracted 1D-myo-inositol 1,4,5-trisphosphate and 1,3,4,5-tetrakisphosphate analogues with C-2 excised (1998)

A route to chiral, cyclopentane-based congeners of the second messenger 1D-myo-inositol 1,4,5-trisphosphate and its enigmatic metabolite 1D-myo-inositol 1,3,4,5-tetrakisphosphate, starting from D-xylose, is described. Reaction of allyl α-D-xylopyranoside 7 with 2,2,3,3-tetramethoxybutane gave a 1∶1 mixture of the 2,3- and 3,4-butanediacetal-protected derivatives 8 and 9. The latter was converted in four steps into 2-O-benzyl-3,4-bis-O-(p-methoxybenzyl)-D-xylopyranose 15, which on reduction with sodium borohydride gave 2-O-benzyl-3,4-bis-O-(p-methoxybenzyl)-D-xylitol 16. Swern oxidation followed by samarium(II) iodide-mediated pinacol coupling gave a 1∶3 mixture of 1L-1,2,3,4/5-1-benzyloxy-2,3-dihydroxy-4,5-bis-(p-methoxybenzyloxy)cyclopentane 18 and 1L-1,2,4/3,5-3-benzyloxy-1,2-dihydroxy-4,5-bis-(p-methoxybenzyloxy)cyclopentane 19. The identity of the latter was confirmed by conversion into known compounds, and further elaboration gave the target compounds, 1D-1,2,4/3,5-cyclopentanepentaol 1,3,4-trisphosphate 5 and 1D-1,2,4/3,5-cyclopentanepentaol-1,2,3,4-tetrakisphosphate 6.
Scintillators and detectors for MeV X-ray and neutron imaging (2020)

High energy X-rays and neutrons can provide 3-D volumetric views of large objects made of multiple materials. Lenscoupled computed tomography using a scintillator imaged on a CCD camera obtains high spatial resolution, while a surface-mounted segmented scintillator on an amorphous silicon (A-Si) array can provide high throughput. For MeV Xray CT, a new polycrystalline transparent ceramic scintillator referred to as “GLO” offers excellent stopping power and light yield for improved contrast in sizes up to a 12” field-of-view. For MeV neutron CT, we have fabricated both contiguous and segmented plates of “Hi-LY” plastic scintillator, offering light yields 3x higher than standard plastic.
Demonstrating spectrum sensing in colored noise for signals with partial spectral overlap (2017)

Wideband spectrum sensing aims to identify the occupied frequency bands. Conventional methods for single antenna spectrum sensors threshold the received power spectra to detect discrete frequency bins that are occupied. However, such methods neither group bins that are occupied by the same signal nor aggregate occupied bins over time to learn distinct frequency bands occupied by intermittently transmitting signals. This paper demonstrates a method to learn the frequency bands occupied by intermittently transmitting incumbent radios that occupy adjacent frequency bands without a guard band, such as by LTE-Advanced, or are spectrally overlapping, such as by IEEE 802.11. It formulates the wideband sensing problem as the factorization of a matrix consisting of multiple power spectrum measurements. A novel extreme ray based non-negative matrix factorization algorithm estimates the noise power spectrum and also determines the received power spectrum of the incumbent radios. Energy detection and a combinatorial algorithm is used to determine the unique supports of the received signals. Using a USRP N210 software defined radio as a receiver, we demonstrate that this algorithm can determine the frequency bands occupied by nearby transmitters in the 2.4GHz ISM band. Furthermore, we demonstrate that the algorithm learns the power spectrum of the colored noise experienced by the USRP.
Evaluation of Gelation Systems for Conformance Control (2000)

Abstract This paper presents the results of laboratory tests measuring typical gel system effectiveness in conformance control. The evaluated gel systems are a metal-complexed polymer system, an organic crosslinked-polymer system, and an in-situ polymerized system. All the systems are typical, commercially available systems used for water control in sandstone formations. The effects of temperature, differential pressure vs. permeability, and adsorption are investigated and quantified. The first set of core-flood experiments was performed with 1-ft long, 2-in. diameter Brown sandstone cores. The test temperatures were 140° and 240°F. The second set of experiments was run in a composite system with two 6-in. long, 1-in. diameter parallel coreholders. One coreholder contained a Brown sandstone core and the other coreholder held a Berea sandstone core. The permeability of the Brown sandstone core was 5 to 10 times greater than that of the Berea sandstone. The parametric studies carried out with these gels show the effect of differential pressure vs. permeability behavior of the water-control systems during placement adsorption characteristics the effect of the gel systems on nontargeted intervals when placed without zonal isolation The organic crosslinked-polymer system provided the highest gel-threshold pressure. The test results indicate an improved injectivity profile after an in-situ gelation treatment. The permeability of the untargeted intervals was also affected during nonselective treatments. A larger slug had a larger impact on nontargeted zones proportional to the zones’ permeabilities. Therefore, zonal isolation is strongly recommended. Polymer adsorption on rock surfaces and sensitivity of the metal-based crosslinker to the chemical environment can reduce gel-system effectiveness.
Varifocal Metalens for Optical Sectioning Fluorescence Microscopy (2021)

Fluorescence microscopy with optical sectioning capabilities is extensively utilized in biological research to obtain three-dimensional structural images of volumetric samples. Tunable lenses have been applied in microscopy for axial scanning to acquire multiplane images. However, images acquired by conventional tunable lenses suffer from spherical aberration and distortions. Here, we design, fabricate, and implement a dielectric Moiré metalens for fluorescence imaging. The Moiré metalens consists of two complementary phase metasurfaces, with variable focal length, ranging from ∼10 to ∼125 mm at 532 nm by tuning mutual angles. In addition, a telecentric configuration using the Moiré metalens is designed for high-contrast multiplane fluorescence imaging. The performance of our system is evaluated by optically sectioned images obtained from HiLo illumination of fluorescently labeled beads, as well as ex vivo mice intestine tissue samples. The compact design of the varifocal metalens may find important applications in fluorescence microscopy and endoscopy for clinical purposes.
ChemInform Abstract: An Efficient Approach to 1,1‐Diarylethylenes (III): Aluminum(III) Chloride Catalyzed Reaction of 1,1,1‐Trichloroethane (II) with Aromatic Compounds (I). (1992)

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.
Extended Release of Native Drug Conjugated in Polyketal Microparticles (2016)

Polyketals, which can be biodegradable, have good biocompatibility, and are pH-sensitive, could have broad applicability in drug delivery and other biomedical applications. However, facile synthesis of high molecular weight polyketals is challenging, and short durations of drug release from polyketal particulate formulations limit their application in drug delivery. Here we report the synthesis of a di-isopropenyl ether monomer and its use to synthesize high molecular weight estradiol-polyketal conjugates by addition polymerization. Microparticles were prepared from the estradiol-polyketal conjugate, where estradiol was incorporated into the polymer backbone. The particles had high drug loading and significantly prolonged drug release. Release of estradiol from the drug-polyketal conjugate microparticles was acid-responsive, as evidenced by faster drug release at low pH and with co-incorporation of PLGA. Tissue reaction to the microparticles was benign in vivo. Polyketal drug conjugates are promising candidates for long-acting drug delivery systems to treat chronic diseases.
Optimization of the surface code design for Majorana-based qubits (2020)

The surface code is a prominent topological error-correcting code exhibiting high fault-tolerance accuracy thresholds. Conventional schemes for error correction with the surface code place qubits on a planar grid and assume native CNOT gates between the data qubits with nearest-neighbor ancilla qubits.Here, we present surface code error-correction schemes using <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow class="MJX-TeXAtom-ORD"><mml:mtext class="MJX-tex-mathit" mathvariant="italic">only</mml:mtext></mml:mrow></mml:math> Pauli measurements on single qubits and on pairs of nearest-neighbor qubits. In particular, we provide several qubit layouts that offer favorable trade-offs between qubit overhead, circuit depth and connectivity degree. We also develop minimized measurement sequences for syndrome extraction, enabling reduced logical error rates and improved fault-tolerance thresholds.Our work applies to topologically protected qubits realized with Majorana zero modes and to similar systems in which multi-qubit Pauli measurements rather than CNOT gates are the native operations.
The molecular fingerprint of lung inflammation after blunt chest trauma (2015)

Taken together, the provided global perspective of the inflammatory response following blunt chest trauma could provide a molecular framework for future research in trauma pathophysiology.
The spirituality of young Australians (2007)

A research project conducted in 2003–2006, the Spirit of Generation Y, using both extended interviews and a nationwide survey, revealed three main strands in the spirituality of young Australians: traditional, alternative and humanist. Their involvement in traditional religions was declining, like that of their parents, and although some adopted alternative spiritualities, the stronger trends were toward indifference or humanism. Eclecticism in worldviews and cautiously relativistic values seem to be responses to an uncertain world, in which isolated individuals have only fragile support structures for their identity.