gebhart/patrepeval huggingface dataset:
Biased probe for plasma diagnostics in spherical electrostatic inertial plasma confinement (1990)

The biased probe, as a unique extension of the Langmuir probe, offers several advantages in measuring the charged-particle flux versus position in a beam-dominated plasma such as encountered in the spherical electrostatic inertial confinement (SEIC) device. The probe operates in a non-Maxwellian and locally non-neutral plasma, where the Debye length is large compared to the probe itself. Its conical particle acceptance extension minimizes the measurement error caused by the distortion of the SEIC potential structures. Either the ion or electron flux can be measured using the proper bias on its inner collecting element.
Blue Myoglobin Reconstituted with an Iron Porphycene Shows Extremely High Oxygen Affinity (2002)

Myoglobin will be a good scaffold for engineering a function into proteins. To modulate the physiological function of myoglobin, almost all approaches have been demonstrated by site-directed mutagenesis, however, there are few studies which show a significant improvement in the function. In contrast, we focused on the replacement of heme in the protein with an artificial prosthetic group. Recently, we prepared a novel myoglobin reconstituted with an iron porphycene as a structural isomer of mesoheme. The bluish colored reconstituted myoglobin is relatively stable and the deoxymyoglobin reversibly binds ligands. Interestingly, the O2 affinity of the reconstituted myoglobin, 1.1 x 109 M-1, is a significant 1,400-fold higher than that of the native myoglobin. Furthermore, the unfavorable autoxidation kinetics show 7-fold decrease in rate for the reconstituted myoglobin relative to the native myoglobin, indicating the stable oxy-form against autoxidation. The net results come from the slow dissociation of the O2 ligand in the reconstituted myoglobin, koff = 0.11 s-1, because of the formation of strong hydrogen bond between His64 and negatively charged dioxygen. The present study indicates that the replacement of native heme with an artificially created prosthetic group will give us a unique function into a hemoprotein.
EXIT-constrained BICM-ID design using extended mapping (2012)

This article proposes a novel design framework, EXIT-constrained binary switching algorithm (EBSA), for achieving near Shannon limit performance with single parity check and irregular repetition coded bit interleaved coded modulation and iterative detection with extended mapping (SI-BICM-ID-EM). EBSA is composed of node degree allocation optimization using linear programming (LP) and labeling optimization based on adaptive binary switching algorithm jointly. This technique achieves exact matching between the Demapper (Dem) and decoder's extrinsic information transfer (EXIT) curves while the convergence tunnel opens until the desired mutual information (MI) point. Moreover, this article proposes a combined use of SI-BICM-ID-EM with Doped-ACCumulator (D-ACC) and modulation doping (MD) to further improve the performance. In fact, the use of D-ACC and SI-BICM-ID (noted as DSI-BICM-ID-EM) enables the right-most point of the EXIT curve of the combined demapper and D-ACC decoder (D dacc ), denoted as DemD dacc , to reach a point very close to the (1.0, 1.0) MI point. Furthermore, MD provides us with additional degree-of-freedom in "bending" the shape of the demapper EXIT curve by choosing the mixing ratio of modulation formats, and hence the left most point of the demapper EXIT curve can flexibly be lifted up/pushed down with MD aided DSI-BICM-ID-EM (referred to as MDSI-BICM-ID-EM). Results of the simulations show that near-Shannon limit performance can be achieved with the proposed technique; with a parameter set obtained by EBSA for MDSI-BICM-ID-EM, the threshold signal-to-noise power ratio (SNR) is only roughly 0.5 dB away from the Shannon limit, for which the required computational complexity per iteration is at the same order as a Turbo code with only memory-2 convolutional constituent codes.
Artificial intelligence in neurodegenerative disease research: use of IBM Watson to identify additional RNA-binding proteins altered in amyotrophic lateral sclerosis (2017)

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease with no effective treatments. Numerous RNA-binding proteins (RBPs) have been shown to be altered in ALS, with mutations in 11 RBPs causing familial forms of the disease, and 6 more RBPs showing abnormal expression/distribution in ALS albeit without any known mutations. RBP dysregulation is widely accepted as a contributing factor in ALS pathobiology. There are at least 1542 RBPs in the human genome; therefore, other unidentified RBPs may also be linked to the pathogenesis of ALS. We used IBM Watson<sup>®</sup> to sieve through all RBPs in the genome and identify new RBPs linked to ALS (ALS-RBPs). IBM Watson extracted features from published literature to create semantic similarities and identify new connections between entities of interest. IBM Watson analyzed all published abstracts of previously known ALS-RBPs, and applied that text-based knowledge to all RBPs in the genome, ranking them by semantic similarity to the known set. We then validated the Watson top-ten-ranked RBPs at the protein and RNA levels in tissues from ALS and non-neurological disease controls, as well as in patient-derived induced pluripotent stem cells. 5 RBPs previously unlinked to ALS, hnRNPU, Syncrip, RBMS3, Caprin-1 and NUPL2, showed significant alterations in ALS compared to controls. Overall, we successfully used IBM Watson to help identify additional RBPs altered in ALS, highlighting the use of artificial intelligence tools to accelerate scientific discovery in ALS and possibly other complex neurological disorders.
Urine and Plasma Osmolality in Patients with Autosomal Dominant Polycystic Kidney Disease: Reliable Indicators of Vasopressin Activity and Disease Prognosis? (2015)

These data suggest that neither urine nor plasma osmolality are valid measures to identify ADPKD patients that may benefit from increasing water intake. Copeptin appears a better alternative for this purpose.
Elimination of line-shape distortion in laser absorption spectroscopy in atomic beams (1983)

Line shapes observed when direct laser absorption is used in an atomic beam of sodium show asymmetries not present in fluorescence detection. Such line-shape distortion, which can be explained by resonant light diffraction by the atoms in the atomic beam, may be eliminated by imaging the fields in the interaction region at the surface of a detector located outside the beam apparatus.
A B-Box 2 Surface Patch Important for TRIM5α Self-Association, Capsid Binding Avidity, and Retrovirus Restriction (2009)

TRIM5alpha is a tripartite motif (TRIM) protein that consists of RING, B-box 2, coiled-coil, and B30.2(SPRY) domains. The TRIM5alpha(rh) protein from rhesus monkeys recognizes the human immunodeficiency virus type 1 (HIV-1) capsid as it enters the host cell and blocks virus infection prior to reverse transcription. HIV-1-restricting ability can be eliminated by disruption of the B-box 2 domain. Changes in the TRIM5alpha(rh) B-box 2 domain have been associated with alterations in TRIM5alpha(rh) turnover, the formation of cytoplasmic bodies and higher-order oligomerization. We present here the nuclear magnetic resonance structure of the TRIM5 B-box 2 domain and identify an unusual hydrophobic patch (cluster 1) on the domain surface. Alteration of cluster 1 or the flanking arginine 121 resulted in various degrees of inactivation of HIV-1 restriction, in some cases depending on compensatory changes in other nearby charged residues. For this panel of TRIM5alpha(rh) B-box 2 mutants, inhibition of HIV-1 infection was strongly correlated with higher-order self-association and binding affinity for capsid complexes but not with TRIM5alpha(rh) half-life or the formation of cytoplasmic bodies. Thus, promoting cooperative TRIM5alpha(rh) interactions with the HIV-1 capsid represents a major mechanism whereby the B-box 2 domain potentiates HIV-1 restriction.
Serological response of sheep to plasmid-encoded proteins of Yersinia species following natural infection with Y. enterocolitica and Y. pseudotuberculosis (1993)

A prospective study of the serological response to natural infection with Yersinia enterocolitica and Y. pseudotuberculosis was performed in an experimental flock of sheep. A preliminary investigation with immunoblotting techniques showed that lambs infected with virulent Yersinia spp. produced antibodies to several yersinia outer-membrane proteins (yops) encoded by a virulence plasmid (pYV) of Y. enterocolitica or Y. pseudotuberculosis. Thereafter, an enzyme immunoassay (EIA) was developed to measure antibodies to yops. Criteria for interpreting the EIA were established by examining sera from a negative control population of lambs which had not been infected with Yersinia spp. since birth. Test samples comprised 25 pairs of pre- and post-infection sera from animals with bacteriologically proven infections with Yersinia spp. The results showed that infection of lambs with pYV-bearing strains of Y. enterocolitica or Y. pseudotuberculosis invariably evoked a significant antibody response to yops, even though all the infections were subclinical. No animal infected with so-called "environmental", pYV-negative Yersinia spp. seroconverted to yops. EIA with yops as antigen provided a sensitive and specific means to diagnose subclinical infection of lambs with virulent Yersinia spp.
Parameter estimation of cardiac geometry by ECG-gated PET imaging: validation using magnetic resonance imaging and echocardiography. (1995)

This model-based analysis offers accurate estimates of regional recovery coefficients directly from gated cardiac PET images and may also prove useful for the assessment of myocardial contractile function. These recovery coefficients are essential for the correction of partial volume effects when quantitative PET studies are performed.
Performance optimization of PM-16QAM transmission system enabled by real-time self-adaptive coding (2017)

We experimentally demonstrate self-adaptive coded 5×100 Gb/s WDM polarization multiplexed 16 quadrature amplitude modulation transmission over a 100 km fiber link, which is enabled by a real-time control plane. The real-time optical signal-to-noise ratio (OSNR) is measured using an optical performance monitoring device. The OSNR measurement is processed and fed back using control plane logic and messaging to the transmitter side for code adaptation, where the binary data are adaptively encoded with three types of low-density parity-check (LDPC) codes with code rates of 0.8, 0.75, and 0.7 of large girth. The total code-adaptation latency is measured to be 2273 ms. Compared with transmission without adaptation, average net capacity improvements of 102%, 36%, and 7.5% are obtained, respectively, by adaptive LDPC coding.
Risk-Adjusted Employer-Paid Benefits in Wrongful Death Cases (1989)

Abstract No abstract available.
Performance and field tests of a handheld Compton camera using 3-D position-sensitive scintillators coupled to multi-pixel photon counter arrays (2014)

After the nuclear disaster in Fukushima, radiation decontamination has become particularly urgent. To help identify radiation hotspots and ensure effective decontamination operation, we have developed a novel Compton camera based on Ce-doped Gd3Al2Ga3O12 scintillators and multi-pixel photon counter (MPPC) arrays. Even though its sensitivity is several times better than that of other cameras being tested in Fukushima, we introduce a depth-of-interaction (DOI) method to further improve the angular resolution. For gamma rays, the DOI information, in addition to 2-D position, is obtained by measuring the pulse-height ratio of the MPPC arrays coupled to ends of the scintillator. We present the detailed performance and results of various field tests conducted in Fukushima with the prototype 2-D and DOI Compton cameras. Moreover, we demonstrate stereo measurement of gamma rays that enables measurement of not only direction but also approximate distance to radioactive hotspots.
Modelling mercury sorption of a polysulfide coating made from sulfur and limonene (2022)

A polymer made from sulfur and limonene was used to coat silica gel and then evaluated as a mercury sorbent. A kinetic model of mercury uptake was established for a range of pH values and concentrations of sodium chloride. Mercury uptake was generally rapid from pH = 3 to pH = 11. At neutral pH, the sorbent (500 mg with a 10:1 ratio of silica to polymer) could remove 90% of mercury within one minute from a 100 mL solution 5 ppm in HgCl2 and 99% over 5 minutes. It was found that sodium chloride, at concentrations comparable to seawater, dramatically reduced mercury uptake rates and capacity. It was also found that the spent sorbent was stable in acidic and neutral media, but degraded at pH 11 which led to mercury leaching. These results help define the conditions under which the sorbent could be used, which is an important advance for using this material in remediation processes.
FP512ASSOCIATION OF INTRADIALYTIC RELATIVE BLOOD VOLUME AND CENTRAL-VENOUS OXYGEN SATURATION WITH MORTALITY AMONG HEMODIALYSIS PATIENTS (2018)

INTRODUCTION AND AIMS: Dialysis patients have an increased ischemic stroke risk. Stroke risk scores, including the CHADS2, ATRIA and CHA2DS2VASC, have been developed to identify patients with an increased stroke risk in patients with atrial fibrillation allowing for personalization of vitamin K antagonist prescription. In the original articles, CHADS2 (C-statistic 0.82), ATRIA (C-statistic 0.73) and CHA2DS2VASC (C-statistic 0.67) had reasonable predictive abilities. However, the predictive performances of these stroke risk scores have not been validated in dialysis patients. Therefore, the aim of this study was to validate existing stroke risk scores in dialysis patients. METHODS: A total of 755 incident dialysis patients from the NECOSAD study were prospectively followed for validated ischemic stroke within five years of dialysis. Hazard ratios with 95% confidence intervals (CIs) were calculated using Cox proportional hazards analyses for high and intermediate risk scores as compared with low risk scores for the CHADS2 (low risk 0, intermediate risk1-2 and high risk !3) and ATRIA (low risk 0-5, intermediate risk6 and high risk !7) and high as compared with intermediate risk score (no events in low risk score) for the CHA2DS2VASC (low risk 0, intermediate risk1 and high risk !2). Furthermore, we evaluated the discriminative performance of these bleeding risk groups by calculating Harrell's Cstatistics. RESULTS: During a median follow-up of 2.0 years (interquartile range 0.9-3.7), 58 (7.7% of all patients) first ischemic stroke events occurred. Of the 755 patients, 14% were classified as high risk by the CHADS2, 28% by the ATRIA and 72% by the CHA2DS2VASC (Table A high risk score as compared with a low risk score was associated with a 8.2-fold (95% CI 1.1-63.1) increased ischemic stroke risk for the CHADS2 and a 2.2-fold (95% CI 1.3-3.9) increased ischemic stroke risk for the ATRIA. A high CHA2DS2VASC risk score as compared with an intermediate risk score was associated with a 8.7-fold (2.1-35.7) increased ischemic stroke. The C-statistics were 0.59 for the CHADS2, 0.61 for the ATRIA and 0.62 for the CHA2DS2VASC. CONCLUSIONS: In this prospective cohort with validated data on ischemic stroke, we showed that high stroke risk scores were associated with an increased ischemic stroke risk. However, there were large differences between the different stroke risk scores in the identification of high risk patients. Furthermore, we showed that the CHADS2, ATRIA and CHA2DS2VASC had poor predictive abilities. Therefore, these stroke risk scores may not be useful for guiding individual decision-making in dialysis patients.
Pyridine nucleotide synthesis in 3T3 cells (1979)

Abstract The biosynthesis of NAD has been examined in 3T3 cells. The net synthesis of pyridine nucleotides does not occur when cells are cultured in the absence of performed pyridine ring compounds; however, growth continues normally for up to four cell doublings resulting in cells with a total pyridine nucleotide content that is reduced by as much as 12‐fold. The mechanism that adjust the relative amounts of NADP and NAD are also altered such that the amount of NADP relative to NAD increases 5‐fold. Both nicotinate and nicotinamide can be used as a precursor for NAD biosynthesis, however nicotinate is utilized less efficiently than nicotinamide. The presence of functional pathways for the biosynthesis of NAD from nicotinate via nicotinate mononucleotide and nicotinate adenine dinucleotide and from nicotinamide via nicotinamide mononucleotide has been demonstrated by identification of biosynthetic intermediates following short term exposure of cells to radiolabelled precursors. When cells are grown in Dulbecco's modified Eagle's medium which contains 33 μM nicotinamide the biosynthesis of NAD proceeds by a single pathway with nicotinamide mononucleotide as the only intermediate. Nicotinamide ribonucleoside which previously has been postulated to be an intermediate in the conversion of nicotinamide to NAD is not an intermediate in NAD biosynthesis.
A layered DCT coder for Internet video (2002)

Several compression schemes for Internet video utilize block-based conditional replenishment (CR) where block updates are coded independently of the past. In the current Internet video tools, blocks are compressed with a single-layer representation. We propose a new approach that compresses image blocks using a layered representation. Our layered-DCT (LDCT) compression algorithm, derived from progressive JPEG, has been combined with CR and optimized for efficient software implementation to provide an improved solution for Internet packet video. Although LDCT is constrained to a layered representation, its compression performance is as good or better than the single layer Intra-H.261 and baseline JPEG coding schemes.
Direct Absorption and Photoacoustic Spectroscopy for Gas Sensing and Analysis: A Critical Review (2022)

Abstract Optical spectroscopy has a broad scientific basis in chemistry, physics, and material science, with diverse applications in medicine, pharmaceuticals, agriculture, and environmental monitoring. Fourier transform infrared (FTIR) spectrometers and tunable laser spectrometers (TLS) are key devices for measuring optical spectra. Superior performance in terms of sensitivity, selectivity, accuracy, and resolution is required for applications in gas sensing. This review deals with gas measurement based on either direct optical absorption spectroscopy or photoacoustic spectroscopy. Both approaches are applicable to FTIR spectroscopy or TLS. In photoacoustic spectroscopy, cantilever‐based photoacoustic spectroscopy is focused due its high performance. A literature survey is conducted revealing the recent technological advances. Theoretical fundamental detection limits are derived for TLS and FTIR, considering both direct absorption and photoacoustic spectroscopies. A theoretical comparison reveals which technology performs better. The minimum normalized absorption coefficient and normalized noise equivalent absorption coefficient appear as key parameters for this comparison. For TLS‐based systems, direct absorption spectroscopy is found to be the best for lower laser power and longer path length. For FTIR‐based systems, direct absorption is found to be the best for low temperature sources, higher spectrometer throughput, faster mirror velocity, and longer gas cells.
Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells (2022)

Reactivation of fetal hemoglobin expression by the downregulation of BCL11A is a promising treatment for β-hemoglobinopathies. A detailed understanding of BCL11A-mediated repression of γ-globin gene (HBG1/2) transcription is lacking, as studies to date used perturbations by shRNA or CRISPR-Cas9 gene editing. We leveraged the dTAG PROTAC degradation platform to acutely deplete BCL11A protein in erythroid cells and examined consequences by nascent transcriptomics, proteomics, chromatin accessibility, and histone profiling. Among 31 genes repressed by BCL11A, HBG1/2 and HBZ show the most abundant and progressive changes in transcription and chromatin accessibility upon BCL11A loss. Transcriptional changes at HBG1/2 were detected in <2 h. Robust HBG1/2 reactivation upon acute BCL11A depletion occurred without the loss of promoter 5-methylcytosine (5mC). Using targeted protein degradation, we establish a hierarchy of gene reactivation at BCL11A targets, in which nascent transcription is followed by increased chromatin accessibility, and both are uncoupled from promoter DNA methylation at the HBG1/2 loci.
TRPM7 kinase-mediated immunomodulation in macrophage plays a central role in magnesium ion-induced bone regeneration (2021)

Despite the widespread observations on the osteogenic effects of magnesium ion (Mg<sup>2+</sup>), the diverse roles of Mg<sup>2+</sup> during bone healing have not been systematically dissected. Here, we reveal a previously unknown, biphasic mode of action of Mg<sup>2+</sup> in bone repair. During the early inflammation phase, Mg<sup>2+</sup> contributes to an upregulated expression of transient receptor potential cation channel member 7 (TRPM7), and a TRPM7-dependent influx of Mg<sup>2+</sup> in the monocyte-macrophage lineage, resulting in the cleavage and nuclear accumulation of TRPM7-cleaved kinase fragments (M7CKs). This then triggers the phosphorylation of Histone H3 at serine 10, in a TRPM7-dependent manner at the promoters of inflammatory cytokines, leading to the formation of a pro-osteogenic immune microenvironment. In the later remodeling phase, however, the continued exposure of Mg<sup>2+</sup> not only lead to the over-activation of NF-κB signaling in macrophages and increased number of osteoclastic-like cells but also decelerates bone maturation through the suppression of hydroxyapatite precipitation. Thus, the negative effects of Mg<sup>2+</sup> on osteogenesis can override the initial pro-osteogenic benefits of Mg<sup>2+</sup>. Taken together, this study establishes a paradigm shift in the understanding of the diverse and multifaceted roles of Mg<sup>2+</sup> in bone healing.
Deletion mapping of chr. 16q in breast cancer using dual color FISH with highly efficient cosmid contig probes (1993)

Breast cancer is known to have frequent allelic loss on the long arm of chr.16. To facilitate identification of genes from 16q involved in breast cancer progression, the authors performed dual color FISH with chr. 16 centromeric reference probe (detected in red) and locus-specific cosmid contigs (in green) distributed along chr.16q in order to define the region of common deletion. Six breast cancer cell lines and 23 primary breast cancers were examined. Cells were scored as carrying a deletion when the fraction of cells showing fewer locus specific signals than centromeric signals plus the fraction of cells showing less than two locus specific signals was greater than 0.5. Five of 6 breast cancer cell lines showed deletion on chr.16q. The region around 16q24 was deleted in 4 of 5 cell lines. Breast cancer cases were preselected on the basis of p53 deletion by FISH because of the high correlation between p53 deletion and 17q deletion. Chr.16q deletions were found in 13 cases (56%); 10 cases (43%) with the break point between the centromere and 17q12, and 3 cases (13%) with the break point between 16q13 and 16q21. Intriguingly, the common region of deletion in clinical breast cancer, 16q22 to q24,more » appears to include the locus (16q22.1) for E-cadherin gene encoding cell adhesion protein which might be associated with progression of breast cancer.« less