gebhart/patrepeval huggingface dataset:
HIV Controllers Have Low Inflammation Associated with a Strong HIV-Specific Immune Response in Blood (2019)

HIV controllers (HIC) maintain control of HIV replication without combined antiretroviral treatment (cART). The mechanisms leading to virus control are not fully known. We used gene expression and cellular analyses to compare HIC and HIV-1-infected individuals under cART. In the blood, HIC are characterized by a low inflammation, a downmodulation of natural killer inhibitory cell signaling, and an upregulation of T cell activation gene expression. This balance that persists after stimulation of cells with HIV antigens was consistent with functional analyses showing a bias toward a Th1 and cytotoxic T cell response and a lower production of inflammatory cytokines. Taking advantage of the characterization of HIC based upon their CD8<sup>+</sup> T lymphocyte capacity to suppress HIV-infection, we show here that unsupervised analysis of differentially expressed genes fits clearly with this cytotoxic activity, allowing the characterization of a specific signature of HIC. These results reveal significant features of HIC making the bridge between cellular function, gene signatures, and the regulation of inflammation and killing capacity of HIV-specific CD8<sup>+</sup> T cells. Moreover, these genetic profiles are consistent through analyses performed from blood to peripheral blood mononuclear cells and T cells. HIC maintain strong HIV-specific immune responses with low levels of inflammation. Our findings may pave the way for new immunotherapeutic approaches leading to strong HIV-1-specific immune responses while minimizing inflammation.<b>IMPORTANCE</b> A small minority of HIV-infected patients, called HIV controllers (HIC), maintains spontaneous control of HIV replication. It is therefore important to identify mechanisms that contribute to the control of HIV replication that may have implications for vaccine design. We observed a low inflammation, a downmodulation of natural killer inhibitory cell signaling, and an upregulation of T-cell activation gene expression in the blood of HIC compared to patients under combined antiretroviral treatment. This profile persists following <i>in vitro</i> stimulation of peripheral blood mononuclear cells with HIV antigens, and was consistent with functional analyses showing a Th1 and cytotoxic T cell response and a lower production of inflammatory cytokines. These results reveal significant features of HIC that maintain strong HIV-specific immune responses with low levels of inflammation. These findings define the immune status of HIC that is probably associated with the control of viral load.
Analysis of Allison Scanner Phase Portraits Using Action-Phase Coordinates (2019)

Allison scanners provide detailed information on the beam transverse phase space. An effective way for analyzing the beam distribution from these measurements is to use action-phase coordinates, where beam propagation in a linear lattice is reduced to advancing the phase. This report presents such analysis for measurements performed with a 2.1 MeV, 5 mA H⁻ beam in the MEBT of the PIP2IT test accelerator at Fermilab. In part, with the choice of calculating the Twiss parameters over the high intensity portion of the beam, the beam core is found to be phase-independent with intensity decreasing exponentially with action, while the beam tails exhibit a clear phase dependence that is stable over the beam line.
Memory-efficient hash joins (2014)

We present new hash tables for joins, and a hash join based on them, that consumes far less memory and is usually faster than recently published in-memory joins. Our hash join is not restricted to outer tables that fit wholly in memory. Key to this hash join is a new concise hash table (CHT), a linear probing hash table that has 100% fill factor, and uses a sparse bitmap with embedded population counts to almost entirely avoid collisions. This bitmap also serves as a Bloom filter for use in multi-table joins. We study the random access characteristics of hash joins, and renew the case for non-partitioned hash joins. We introduce a variant of partitioned joins in which only the build is partitioned, but the probe is not, as this is more efficient for large outer tables than traditional partitioned joins. This also avoids partitioning costs during the probe, while at the same time allowing parallel build without latching overheads. Additionally, we present a variant of CHT, called a concise array table (CAT), that can be used when the key domain is moderately dense. CAT is collision-free and avoids storing join keys in the hash table. We perform a detailed comparison of CHT and CAT against leading in-memory hash joins. Our experiments show that we can reduce the memory usage by one to three orders of magnitude, while also being competitive in performance.
Weak Electron–Phonon Coupling and Enhanced Thermoelectric Performance in n‐type PbTe–Cu2Se via Dynamic Phase Conversion (2022)

Abstract This study investigates Ga‐doped n‐type PbTe thermoelectric materials and the dynamic phase conversion process of the second phases via Cu 2 Se alloying. Introducing Cu 2 Se enhances its electrical transport properties while reducing its lattice thermal conductivity (κ lat ) via weak electron–phonon coupling. Cu 2 Te and CuGa(Te/Se) 2 (tetragonal phase) nanocrystals precipitate during the alloying process, resulting in Te vacancies and interstitial Cu in the PbTe matrix. At room temperature, Te vacancies and interstitial Cu atoms serve as n‐type dopants, increasing the carrier concentration and electrical conductivity from ≈1.18 × 10 19 cm −3 and ≈1870 S cm −1 to ≈2.26 × 10 19 cm −3 and ≈3029 S cm −1 , respectively. With increasing temperature, the sample exhibits a dynamic change in Cu 2 Te content and the generation of a new phase of CuGa(Te/Se) 2 (cubic phase), strengthening the phonon scattering and obtaining an ultralow κ lat . Pb 0.975 Ga 0.025 Te‐3%CuSe exhibits a maximum figure of merit of ≈1.63 at 823 K, making it promising for intermediate‐temperature device applications.
Optimization of interdigitated back contact silicon heterojunction solar cells: tailoring hetero‐interface band structures while maintaining surface passivation (2010)

Abstract Interdigitated back contact silicon heterojunction (IBC‐SHJ) solar cells have the potential for high open circuit voltage ( V OC ) due to the surface passivation and heterojunction contacts, and high short circuit current density ( J SC ) due to all back contact design. Intrinsic amorphous silicon (a‐Si:H) buffer layer at the rear surface improve the surface passivation hence V OC and J SC , but degrade fill factor (FF) from an “S” shape J – V curve. Two‐dimensional (2D) simulation using “Sentaurus device” demonstrates that the low FF is related to the valence band offset (energy barrier) at the hetero‐interface. Three approaches to the buffer layer are suggested to improve the FF: (1) reduced thickness, (2) increased conductivity, and/or (3) reduced band gap. Experimental IBC‐SHJ solar cells with reduced buffer thickness (&lt;5 nm) and increased conductivity with low boron doping significantly improves FF, consistent with simulation. However, this has only marginal effect on efficiency since J SC and V OC also decrease due to poor surface passivation. A narrow band gap a‐Si:H buffer layer improves cell efficiency to 13.5% with unoptimized passivation quality. These results demonstrate that tailoring the hetero‐interface band structure is critical for achieving high FF. Simulations predicts that efficiences &gt;23% are possible on planar devices with optimized pitch dimensions and achievable surface passivation, and 26% with light trapping. This work provides criterion to design IBC‐SHJ solar cell structures and optimize cell performance. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Abstract B82: Identification of tumor neoantigens for combination therapy in murine tumor models (2018)

Abstract The adoption of anti-CTLA-4 and anti-PD-1/PD-L1 blockade has dramatically changed the treatment approaches in multiple cancer types, and has demonstrated the power of the immune system to control the outgrowth of neoplastic lesions. Accumulating evidence suggests these successes are mediated by T cells targeting nonsynonymous mutations unique to the patient’s tumor. When used in combination with checkpoint inhibition, or other standard of care treatment modalities, vaccines targeting tumor neoantigens have the potential to greatly enhance patient survival. Recent advances in DNA/RNA sequencing and bioinformatic analysis have made it possible to rapidly identify nonsynonymous mutations being expressed in patient tumors. As the number of nonsynonymous mutations detected in patient samples can range from less than 10 to several thousand, it is necessary to develop strategies to identify and rank neoantigens with a greater probability of being immunogenic and mediating regression of established tumors. In the present study, we harvested tumors from mice bearing syngeneic tumors, and performed DNA/RNA sequencing to identify nonsynonymous mutations to use as tumor specific neoantigens. These potential neoantigens were ranked based upon their proposed in-silico MHC binding affinity, and the relative abundance of each transcript as determined by RNA-seq. Top ranking 9-mer neoantigens peptides were synthesized and evaluated. We assessed neoantigens for their ability to bind MHC in vitro, and expand antigen-specific T cells in vivo. To further augment the immunogenicity of our neoantigen 9-mer peptides, we used them in combination with an IL-15 super-agonist (ALT-803) and an anti-PD-L1 antibody. When used in combination with these immune-modulators, we observed a dramatic increase in the magnitude of the immune response generated against our neoantigens, which associated with increased tumor therapy. This study provides the rational for the combination of neoantigen vaccines with immune modulators to slow tumor growth and extend survival. Citation Format: Karin L. Lee, Andrew T. Nguyen, Steven C. Benz, Shahrooz Rabizadeh, James W. Hodge, Claudia Palena, Jeffrey Schlom, Duane H. Hamilton. Identification of tumor neoantigens for combination therapy in murine tumor models [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr B82.
The lysine-49 phospholipase A2 from the venom of Agkistrodon piscivorus piscivorus. Relation of structure and function to other phospholipases A2. (1986)

A new class of phospholipases A2 that have a lysine at position 49 differ from the more conventional Asp-49 enzymes with respect to the sequential binding of the essential cofactor, calcium, and the substrate, phospholipid, in the formation of the catalytic complex (Maraganore, J.M., Merutka, G., Cho, W., Welches, W., Kézdy, F.J., and Heinrikson, R.L. (1984) J. Biol. Chem. 259, 13839-13843). We report here the complete amino acid sequence of the Lys-49 enzyme from Agkistrodon piscivorus piscivorus. The sequence was determined by automated Edman degradation of the intact, S-carboxymethylcysteinyl protein and of peptides derived therefrom by cleavage with cyanogen bromide, chymotrypsin, trypsin, and endoproteinase Lys-C. Despite several changes at amino acid residues previously considered to be invariant, the Lys-49 enzymes are homologous to the Asp-49 phospholipases. Homology is especially apparent in the following: 1) the pattern of 14 half-cystine residues, 2) conservation of hydrophobic residues which have been shown to encircle the active site, and 3) conservation of Asp-99 and His-48 which have been implicated in the catalytic reaction itself. These observations together with kinetic and binding data imply that the Lys-49 phospholipases have a catalytic mechanism and a three-dimensional architecture similar to those of the Asp-49 enzymes. Modeling of the Lys-49 enzyme based upon the structure of bovine pancreatic phospholipase reveals that the epsilon-amino group of Lys-49 can fit easily in the calcium-binding site and, moreover, that this orientation of a cationic side chain at position 49 could account for the characteristic and novel feature of the Lys-49 phospholipases, i.e. that they are able to form complexes with phospholipid in the absence of calcium.
‘The right of the people to judge for themselves’ (2015)

Abstract This chapter first describes the insurrection that arose in Bulgaria the late nineteenth century, which led to the massacre of Bulgarian Christians by Turkish troops. That such outrages could be committed against their fellow Christians provoked furious anger among many Britons, including Nonconformists with their traditional sympathy for oppressed peoples. The discussions then turn to how the campaign against the Turkish atrocities in Bulgaria helped rebuild the alliance between Gladstone and the Dissenters; Dissenters' renewed support for the Liberal party; Nonconformists' objection to Irish Home Rule; and the growing mutual inter-dependence of the Liberal party and the Nonconformist chapels.
Effect of extensional viscosity on cocontinuity of immiscible polymer blends (2015)

Cocontinuous blends were prepared from polyethylene (PE) and polylactic acid (PLA). The extensional and shear rheological properties of PE and PLA were independently tuned by varying long chain branching architecture. Shear rheological properties of the blend components were characterized by capillary and oscillatory rheometry. Extensional rheological properties were characterized by orifice entrance pressure drop and sheet wind-up. It was found that branching significantly increased zero-shear viscosity and extensional viscosity, but did not alter the shear viscosity at the shear rates typically observed in mixing flows. Adding a branched polymer to the blend allowed the other blend component to percolate into a continuous network with less material. Blending with two branched materials significantly broadened the range of cocontinuous compositions from 39–59 vol. % with a linear/linear blend to 25–76 vol. % for a branched/branched blend. This was attributed to the ability of a strain hardening matrix to promote elongation, and hence percolation, of the minor phase. Domain size was minimized when a slight amount of strain hardening was introduced, as this allowed formation of narrow features while stabilizing them against fiber breakup. All blends showed a rate of morphological coarsening during annealing inversely proportional to zero-shear rate viscosity, suggesting that quiescent coarsening flows are dictated by low-rate shear flow properties and not extensional properties. We find that our results and coarsening rates in the literature show the same linear dependence on the ratio of interfacial tension to log volume average zero-shear viscosity with a coefficient of ∼0.03, indicating a simple universal relation.
Photo-inactivation of Neisseria gonorrhoeae: a paradigm changing approach for combating antibiotic-resistant gonococcal infections (2019)

Antimicrobial resistance in <i>Neisseria gonorrhoeae</i> is a major issue of public health, and there is a critical need for the development of new anti-gonococcal strategies. In this study, we investigated the effectiveness of antimicrobial blue light (aBL; 405 nm wavelength), an innovative non-pharmacological approach, for the inactivation of <i>N. gonorrhoeae</i>. Our findings indicated that aBL preferentially inactivated <i>N. gonorrhoeae</i>, including antibiotic-resistant strains, over human vaginal epithelial cells in vitro. Furthermore, no genotoxicity of aBL to the vaginal epithelial cells was observed at the radiant exposure for inactivating <i>N. gonorrhoeae</i>. aBL also effectively inactivated <i>N. gonorrhoeae</i> that had attached to and invaded into the vaginal epithelial cells in their co-cultures. No gonococcal resistance to aBL developed after 15 successive cycles of sub-therapeutic aBL inactivation. Taken together, aBL represents a potent potential treatment for antibiotic-resistant gonococcal infection.
Catalyst discovery through megalibraries of nanomaterials (2018)

The nanomaterial landscape is so vast that a high-throughput combinatorial approach is required to understand structure-function relationships. To address this challenge, an approach for the synthesis and screening of megalibraries of unique nanoscale features (>10,000,000) with tailorable location, size, and composition has been developed. Polymer pen lithography, a parallel lithographic technique, is combined with an ink spray-coating method to create pen arrays, where each pen has a different but deliberately chosen quantity and composition of ink. With this technique, gradients of Au-Cu bimetallic nanoparticles have been synthesized and then screened for activity by in situ Raman spectroscopy with respect to single-walled carbon nanotube (SWNT) growth. Au<sub>3</sub>Cu, a composition not previously known to catalyze SWNT growth, has been identified as the most active composition.
<title>Embedded cure monitor, strain gauge, and mechanical state estimator</title> (1999)

Pressed PZT Piezoelectric disks were embedded in a range of materials and their properties monitored under a wide range of conditions. The output depends on the temperature and pressure exerted on the PZT by the surrounding material and by the mechanical impedance mismatch between the embedded PZT and the surroundings. By monitoring the `Q' of the PZT (the ratio of energy stored to energy dissipated) it was found that the PZT discs could be used as cure monitors, strain gauges, and as embedded dynamic mechanical property estimators. This latter property is a means of gauging the `health of the material', and its degradation with time. These sensors were part of the MTS/US Navy embedded sensor program, so the sensors could be addressed and read remotely. The techniques, the data and the applications are discussed in this paper.
The Role of Aluminum in the Pathogenesis of Anemia in an Outpatient Hemodialysis Population (1989)

Anemia is a well-defined complication of aluminum overload in chronic dialysis patients which may be present before other manifestations of aluminum toxicity are obvious. Causes of anemia in chronic renal failure are multiple, and at the present time there is no marker for aluminum-induced anemia. Deferoxamine (DFO) treatment can correct aluminum-related anemia and microcytosis, but may be associated with side effects. Because of the possible role of aluminum in red blood cells in causing the anemia associated with aluminum overload, we attempted to test red blood cell (RBC) aluminum as a marker for aluminum-associated anemia and to assess the prevalence of aluminum-associated anemia in an outpatient dialysis population. Both random plasma aluminum and RBC aluminum correlated well with the increase in plasma aluminum seen following DFO challenge. However, RBC aluminum was affected less by changes in oral aluminum intake than plasma aluminum. There were strong correlations of RBC and plasma aluminum to corpuscular volume (MCV) in our patients. Moreover, patients within the highest quartile of RBC aluminum had a lower mean MCV (82.1 +/- 1.7 vs 89.6 +/- 1.7, p less than .01) and hematocrit (HCT) (24.3 +/- 4 vs 28.2 +/- 1.5, p less than .05) than those within the lowest quartile. These data suggest that aluminum toxicity is an important cause of microcytic anemia in outpatient hemodialysis patients. Prospective long-term studies are needed to further define the usefulness of RBC aluminum in diagnosing and following hemodialysis patients with aluminum-induced anemia.
O-Glycosylation Modulates Proprotein Convertase Activation of Angiopoietin-like Protein 3 (2010)

The angiopoietin-like protein 3 (ANGPTL3) is an important inhibitor of the endothelial and lipoprotein lipases and a promising drug target. ANGPTL3 undergoes proprotein convertase processing (RAPR(224)↓TT) for activation, and the processing site contains two potential GalNAc O-glycosylation sites immediately C-terminal (TT(226)). We developed an in vivo model system in CHO ldlD cells that was used to show that O-glycosylation in the processing site blocked processing of ANGPTL3. Genome-wide SNP association studies have identified the polypeptide GalNAc-transferase gene, GALNT2, as a candidate gene for low HDL and high triglyceride blood levels. We hypothesized that the GalNAc-T2 transferase performed critical O-glycosylation of proteins involved in lipid metabolism. Screening of a panel of proteins known to affect lipid metabolism for potential sites glycosylated by GalNAc-T2 led to identification of Thr(226) adjacent to the proprotein convertase processing site in ANGPTL3. We demonstrated that GalNAc-T2 glycosylation of Thr(226) in a peptide with the RAPR(224)↓TT processing site blocks in vitro furin cleavage. The study demonstrates that ANGPTL3 activation is modulated by O-glycosylation and that this step is probably controlled by GalNAc-T2.
Flow Boiling of R134a in Circular Microtubes—Part II: Study of Critical Heat Flux Condition (2011)

A detailed experimental study was carried out on the critical heat flux (CHF) condition for flow boiling of R134a in single circular microtubes. The test sections had inner diameters (ID) of 0.50 mm, 0.96 mm, and 1.60 mm. Experiments were conducted over a large range of mass flux, inlet subcooling, saturation pressure, and vapor quality. CHF occurred under saturated conditions at high qualities and increased with increasing mass fluxes, tube diameters, and inlet subcoolings. CHF generally, but not always, decreases with increasing saturation pressures and vapor qualities. The experimental data were mapped to the flow pattern maps developed by Hasan [2005, “Two-Phase Flow Regime Transitions in Microchannels: A Comparative Experimental Study,” Nanoscale Microscale Thermophys. Eng., 9, pp. 165–182] and Revellin and Thome [2007, “A New Type of Diabatic Flow Pattern Map for Boiling Heat Transfer in Microchannels,” J. Micromech. Microeng., 17, pp. 788–796]. Based on these maps, CHF mainly occurred in the annular flow regime in the larger tubes. The flow pattern for the 0.50 mm ID tube was not conclusively identified. Four correlations—the Bowring correlation, the Katto-Ohno correlation, the Thome correlation, and the Zhang correlation—were used to predict the experimental data. The correlations predicted the correct experimental trend, but the mean absolute error (MAE) was high (&gt;15%) A new correlation was developed to fit the experimental data with a MAE of 10%.
Time domain feedback equalizer for fast fading channel in OFDM with scattered pilot (2010)

In this paper, a new feedback equalization scheme to suppress inter-carrier interference (ICI) in an OFDM system using scattered pilot is investigated. On a fast fading channel severe ICI occurs due to a Doppler shift and it deteriorates a bit error rate (BER) seriously because of small subcarrier spacing. In an ISDB-T receiver the equalization is mainly processed in a frequency domain because the scattered pilot is transmitted over the subcarriers. However, the frequency domain equalization may not suppress severe ICI in the case of the fast fading channel with a large Doppler shift. The proposed equalization scheme uses the scattered pilot symbols transformed in a time domain as the reference signal for feedback taps. Numerical results through computer simulation show that the proposed scheme improves the BER performance especially with low carrier-to-noise ratio (CNR) conditions.