gebhart/patrepeval huggingface dataset:
Energetically Informed Niche Models of Hydrogenotrophs Detected in Sediments of Serpentinized Fluids of the Samail Ophiolite of Oman (2022)

Abstract A geochemical gradient established by mixing between reduced, hyperalkaline (pH &gt; 11), H 2 ‐rich fluids generated through the process of serpentinization and surrounding surface water (pH ∼ 8) in the Samail Ophiolite of Oman provides an opportunity to characterize the geochemical and biological factors that influence the distribution of H 2 oxidizing chemotrophs, hydrogenotrophs. In this study, 16S rRNA gene amplicon sequencing was implemented to characterize hydrogenotrophs in sediments underlying surface expressed serpentinized fluids in Oman. Hydrogenotroph phylotype distribution was evaluated as functions of chemical energy supplies for their given metabolic redox reactions. Through this approach, it was discovered that hydrogenotrophic taxa are likely constrained to sediments with overlying fluids that have &lt;∼60 μ m O 2 , including microorganisms of the genus, Hydrogenophaga . Sulfate reducers of the family, Thermodesulfovibrionaceae , likely require &gt;∼10 μ m SO 4 −2 for survival. In sediments with fluids having &gt;∼10 μ m SO 4 −2 , sulfate reducers likely outcompete microorganisms of the methanogen genus, Methanobacterium , for H 2 . Additionally, differences in distribution between Thermodesulfovibrionaceae and Methanobacterium may be driven by the availability of electron acceptors and the redox reaction that is most energy yielding in the fluid. Taken together, observations from the Oman geochemical gradient result in a hydrogenotroph niche model that can be used to evaluate global distribution patterns of hydrogenotrophs in continental serpentinized fluids. On a global scale, based on previous studies, Methanobacterium is constrained to fluids that have &lt;∼10 μ m SO 4 −2 .
Does the Route of Feeding Modify the Inflammatory Response? (1994)

The responses to endotoxin in human subjects who received parenteral nutrition were similar compared with subjects who received enteral nutrition, although platelet count and plasma interleukin-6 concentration were diminished.
New Resiliency in Truly Combinatorial Auctions (and Implementation in Surviving Strategies) (2008)

Following Micali and Valiant [MV07.a], a mechanism is resilient if it achieves its objective without any problem of (1) equilibrium selection and (2) player collusion. To advance resilient mechanism design,We put forward a new meaningful benchmark for the COMBINED social welfare-revenue performance of any mechanism in truly combinatorial auctions.We put forward a NEW notion of implementation, much more general than the ones used so far, which we believe to be of independent interest.We put forward a new RESILIENT mechanism that, by leveraging the knowledge that the players have about each other, guarantees at least one half of our benchmark under a very general collusion model.
Local On-Chip Temperature Tuning of InGaAs Quantum Dots (2007)

Quantum network based on InGaAs quantum dots (QDs) rely on QDs being in resonance with each other. We developed a new technique based on temperature tuning to spectrally align QDs located on the same chip.
Synthesis and properties of polyurethane coatings: the effect of different types of soft segments and their ratios (2013)

Polyurethane (PU) coatings were prepared using siloxane polyol [poly(dimethyl siloxane), PDMS], polyether polyol [poly(propylene oxide glycol), PPG], and polyester polyol [poly(tetramethylene adipate glycol), PTAd]. The PTAd/PPG ratio was altered, whereas the PDMS content was fixed during PU synthesis. The structural elucidation of the synthesized PU was performed by Fourier transform infrared (FT-IR), 1H NMR, 13C NMR, and 29Si NMR spectroscopic techniques. The PU-film surface was characterized by X-ray Photoelectron Spectrometer and atomic force microscopy techniques and it was found that the surface smoothness depended on the PPG/PTAd ratio. The PU melting temperature, crystallinity, mechanical properties (tensile strength and Young’s modulus), and adhesive strength were also depended on the PPG/PTAd ratio. The adhesive strength to poly(vinyl chloride) of the coating with the proper polyol ratio (PTAd 12.50 mol% and PPG 16.67 mol%) was almost unaffected after immersion (three months) in artificial salt.
Performance (2009)

This chapter contains sections titled: Introduction Layer 1 Peak Bit Rates Terminal Categories Link Level Performance Link Budgets Spectral Efficiency Latency LTE Refarming to GSM Spectrum Dimensioning Capacity Management Examples from HSPA Networks Summary References
Characterization of Changes in Serum Anti-Glycan Antibodies in Crohn's Disease – a Longitudinal Analysis (2011)

While the levels of anti-glycan antibodies fluctuate in a subgroup of CD patients the antibody status is widely stable over time.
Spin-parity analysis of the centrally produced KK system at 800 GeV (1997)

Results are presented of the spin-parity analysis on a sample of centrally produced mesons in the reaction pp → pslow(KsKs)pfast with 800 GeV protons on liquid hydrogen. The spin-parity analysis in the mass region between threshold and 1.58 GeV/c2 shows that the KsKs system is produced mainly in S wave. The ƒo(1500) is clearly observed in this region. Above 1.58 GeV/c2 two solution are possible, one with mainly S wave and another with mainly D wave. This ambiguity prevents a unique determination of the spin of the ƒj(1710) meson.
Calculation of vibrational lifetimes in amorphous silicon using molecular dynamics simulations (1998)

The decay of normal-mode excitations is calculated for amorphous silicon through molecular-dynamics simulations within periodic supercells consisting of 216 and 4096 atoms. Phenomenological structural and interatomic potential models are employed. At moderate temperatures, lifetimes are found to be on the order of 10 ps and lifetimes of localized and extended nonpropagating modes are comparable. These features are in agreement with related perturbation theory calculations, and in strong disagreement with the frustrated anharmonic decay predicted by the fracton model and apparently with the results of anti-Stokes Raman experiments performed at $T=10$ K.
Interaction of C1 inhibitor with thrombin on the endothelial surface (2011)

Thrombin, the central bioregulatory enzyme of haemostasis, also has a potent vasopermeability effect on the surface of endothelial cells, and has therefore been considered a major link between the activation of the coagulation pathway and inflammation. C1 inhibitor inhibits thrombin with a low second-order rate constant that can be increased by heparin. The aim of this study was to investigate whether the C1 inhibitor-induced inhibition of thrombin is potentiated on the endothelial surface. The interaction of C1 inhibitor and thrombin was evaluated in an in-vitro system of human umbilical vein endothelial cells (HUVECs) to which purified C1 inhibitor and thrombin have been added. The role of heparins and selectins has been tested by adding heparinase and Mab to selectins. Kinetic analysis under pseudo-first-order conditions showed that the inhibitory effect of C1 inhibitor on thrombin is greater on the surface of endothelial cells. After incubating nanomolar concentrations of thrombin and micromolar concentrations of C1 inhibitor in a purified system, thrombin activity remained significant, but was almost totally suppressed in the presence of HUVECs. The abolition of such suppression by heparinase and Mab to selectins supports the involvement of heparin and selectins in C1 inhibitor-thrombin interaction. Furthermore, the second-order rate constant was 25 ± 3 /s per mol/l in our purified system, but increased to 100 ± 9 /s per mol/l in the presence of HUVECs. Our results indicate that C1 inhibitor can inhibit thrombin activity on vascular endothelium via binding to selectins and potentiation by heparins. This may contribute to the modulation of thrombin activity on vasopermeability and on coagulation especially when the major natural anticoagulant pathways are impaired.
Ordered Overlayers of C60 on GaAs(11O) Studied with Scanning Tunneling Microscopy (2005)

Studies of C60 overlayer growth on GaAs(110) with scanning tunneling microscopy show large first monolayer islands that are locally well ordered, structurally stable, and commensurate with the GaAs surface owing to molecule-substrate interactions. Within the distorted close-packed structure, two distinct adsorption sites were identified, one ofthem being elevated because of stress in the C60 monolayer.
[Type 1 cardiorenal syndrome and its possible pathophysiological mechanisms]. (2013)

Cardiorenal syndrome (CRS) type 1, consisting of acute cardiac events leading to acute kidney injury (AKI), is characterized by multiple factors and its pathophysiology is very complex. Given the circulating nature of many inflammatory mediators, it is tempting to examine the immune-mediated mechanism as a mediator of organ crosstalk. In this pilot study, we examined the possible role of immune-mediated mechanisms in the pathogenesis of this syndrome. We enrolled 12 patients with acute heart failure (AHF), 7 patients with type 1 CRS, and 5 healthy volunteers. EDTA plasma samples from the 3 groups were incubated with a monocyte cell line (U937) and cell apoptosis was subsequently evaluated by different methods. In addition, quantitative determination of TNF-alpha, IL-6 and IL-18 production in the supernatants was performed by ELISA. In U937 cells treated with type 1 CRS plasma, the results showed DNA ladder formation with different molecular weight fractions, suggesting the presence of apoptotic events. In fact, quantitative analysis of apoptosis and caspase-3 levels showed significantly higher apoptosis rates in cells incubated with plasma from patients with type 1 CRS (p<0.05). TNF-alpha levels in the supernatants were significantly elevated in both the AHF and type 1 CRS groups compared with control subjects (p<0.05). Furthermore, in patients with type 1 CRS the levels of the proinflammatory cytokines IL-6 and IL-18 were significantly higher than in AHF patients and the control group (p<0.05). This pilot study explores the premise of an immune-mediated process in the pathophysiology of type 1 CRS. These preliminary findings suggest the presence of defective regulation of apoptosis in patients with this syndrome and the involvement of an immune-mediated mechanism in its pathogenesis. Furthermore, inflammatory pathways seem to play a central role in organ crosstalk and may be fundamental to distant organ damage.
Multiobjective Optimization-Aided Metamaterials-by-Design With Application to Highly Directive Nanodevices (2017)

A formal inverse design procedure which combines the advantageous aspects of both multiobjective optimization and system-by-design is proposed. The solution technique provides a systematic method to discover the various tradeoffs inherent in engineering design. To showcase the robustness and flexibility of the proposed approach, two unique highly directive nanodevices are explored. First, the problem of achieving highly directive scattering from core-shell nanoparticles is investigated. Then, a Yagi-Uda nanoloop array is designed with the goal of producing highly directive radiation patterns. The results of these studies reveal the underlying physics of these devices while also providing the engineer with a wide variety of candidate designs to choose from, showcasing the utility of the proposed metamaterials-by-design approach based on multiobjective optimization.
Large-mode-area Er-doped fiber chirped-pulse amplification system for high-energy sub-picosecond pulses at 1.55 μm (2008)

We demonstrate a chirped-pulse amplification system generating 25 &mu;J compressed pulses at a center wavelength of 1552.5 nm. The seed module and the amplifier chain are all in-fiber (with a few small fiber-pigtailed free-space components), followed by a free-space diffraction grating pulse compressor. The amplifier chain contains a pre-amplifier and a booster whose gain fibers are 45/125 &mu;m core/cladding-diameter, core-pumped Er-doped fibers. The pump lasers for both amplifiers are single-mode 1480 nm Raman lasers capable of up to 8 W output. The seed module generates up to 2 ns chirped pulses that are amplified and subsequently compressed to <800 fs duration. At a repetition rate of 50 kHz, the 2 ns pulses from the seed module were amplified to 72 &mu;J, resulting in 25 &mu;J after pulse compression. The corresponding peak power levels after the amplifier chain and compressor were 36 kW and 31 MW, respectively.
Supplementary Movie 1 from Molecular Imaging of CXCR4 Receptor Expression in Human Cancer Xenografts with [<sup>64</sup>Cu]AMD3100 Positron Emission Tomography (2023)

Supplementary Movie 1 from Molecular Imaging of CXCR4 Receptor Expression in Human Cancer Xenografts with [&lt;sup&gt;64&lt;/sup&gt;Cu]AMD3100 Positron Emission Tomography
Representative traces for processor models with infinite cache (2002)

Performance evaluation of processor designs using dynamic instruction traces is a critical part of the iterative design process. The widening gap between the billions of instructions in such traces for benchmark programs and the throughput of timers performing the analysis in the tens of thousands of instructions per second has led to the use of reduced traces during design. This opens up the issue of whether these traces are truly representative of the actual workload in these benchmark programs. The first key result in this paper is the introduction of a new metric, called the R-metric, to evaluate the representativeness of these reduced traces when applied to a wide class of processor designs. The second key result, is the development of a novel graph-based heuristic to generate reduced traces based on the notions incorporated in the metric. These ideas have been implemented in a prototype system (SMART) for generating representative and reduced traces. Extensive experimental results are presented on various benchmarks to demonstrate the quality of the synthetic traces and the uses of the R-metric.
2,4-Dichlorophenol Degradation Using Streptomyces viridosporus T7A Lignin Peroxidase (1997)

The Streptomyces viridosporus T7A bacterium produces the extracellular lignin peroxidase ALiP-P3. The ALiP-P3-catalyzed oxidation of 2,4-dichlorophenol (DCP) was examined to understand its kinetic behavior. Initial rate data of the oxidation of DCP were obtained by a spectrophotometric peroxidase assay, and the kinetics were best modeled with a random-binding bireactant system, which differs from the ping-pong bireactant system that is typically used for horseradish peroxidase and lignin peroxidase from the fungus Phanerochaete chrysosporium, and suggests that either DCP or H2O2 may bind first to ALiP-P3. Chloride ion measurements indicate that 16% of the reacted DCP was fully dechlorinated by ALiP-P3. Chemical ionization mass spectrometry was also utilized to identify the DCP degradation product as a hydrophobic chlorinated dimer of mass 322.
Supplementary Figure 1 from A Highly Potent and Specific MET Therapeutic Protein Antagonist with Both Ligand-Dependent and Ligand-Independent Activity (2023)

&lt;p&gt;PDF - 31KB, Characterisation of cell line panel for MET and HGF expression&lt;/p&gt;
<title>Lidar measurements of atmospheric mercury</title> (1990)

Mercury is the only atmospheric pollutant that is present in the atmosphere in atomic form. Range-resolved Hg mapping can be performed using the differential absorption lidar (dial) technique employing the 254 nm Hg resonance line. We have used the lidar technique both for mapping of industrial plumes and for background concentration measurements. Our studies also include mercury of geophysical origin. A field test has been performed in Icelandic geothermal fields. We have also attempted studies of Hg emission from lake surfaces.
The Usefulness of an Oral-Health Promotion Program on Japanese Working-Age Population: A Pilot Study. (2021)

Yukihide Aoyama, Terumitsu Murakami, Chiyoko Uchiyama, Yoshihiro Tamura, Toshiaki Oyama, Itoyo Tokuda, Keiji Wada, Yukio Yamamoto, Wataru Kobayashi, Kazushige Ihara, Koichi Murashita, Shigeyuki Nakaji. IJCPD 2021;17:183. https://doi.org/10.15236/ijcpd.2021.17.3.183
10-Gb/s upgrade of bidirectional CWDM systems using electronic equalization and FEC (2005)

We discuss options for upgrading coarse wavelength-division multiplexed (CWDM) optical access links over standard single-mode fiber (SSMF) by increasing per-channel data rates from 2.5 to 10 Gb/s. We identify electronic equalization and forward error correction (FEC) as the enabling technologies to overcome the dispersion limit of SSMF. In addition, we show how FEC enhances the tolerance to in-band crosstalk, and paves the way toward fully bidirectional CWDM transmission. Due to the lack of CWDM sources rated for 10-Gb/s operation, we demonstrate full-spectrum (1310 to 1610 nm) 10-Gb/s CWDM transmission over standard-dispersion fiber using uncooled, directly modulated lasers specified for 2.5 Gb/s. All 16 CWDM channels could be transmitted over more than 40 km, yielding a capacity-times-distance product of 6.4 Tb/s/km. The longest transmission distance (80 km) was achieved at 1610 nm, equivalent to 1600 ps/nm of chromatic dispersion.
Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds (2010)

Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be "signature" of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1-2 angstroms (mean 1.61A) C(alpha) RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the 'twilight' and 'midnight' zones wherein <30% and <10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plague-causative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools.
Dendritic Cells Are Less Susceptible to Human Immunodeficiency Virus Type 2 (HIV-2) Infection than to HIV-1 Infection (2007)

Human immunodeficiency virus type 1 (HIV-1) infection of dendritic cells (DCs) has been documented in vivo and may be an important contributor to HIV-1 transmission and pathogenesis. HIV-1-specific CD4(+) T cells respond to HIV antigens presented by HIV-1-infected DCs and in this process become infected, thereby providing a mechanism through which HIV-1-specific CD4(+) T cells could become preferentially infected in vivo. HIV-2 disease is attenuated with respect to HIV-1 disease, and host immune responses are thought to be contributory. Here we investigated the susceptibility of primary myeloid DCs (mDCs) and plasmacytoid DCs (pDCs) to infection by HIV-2. We found that neither CCR5-tropic primary HIV-2 isolates nor a lab-adapted CXCR4-tropic HIV-2 strain could efficiently infect mDCs or pDCs, though these viruses could infect primary CD4(+) T cells in vitro. HIV-2-exposed mDCs were also incapable of transferring virus to autologous CD4(+) T cells. Despite this, we found that HIV-2-specific CD4(+) T cells contained more viral DNA than memory CD4(+) T cells of other specificities in vivo. These data suggest that either infection of DCs is not an important contributor to infection of HIV-2-specific CD4(+) T cells in vivo or that infection of DCs by HIV-2 occurs at a level that is undetectable in vitro. The frequent carriage of HIV-2 DNA within HIV-2-specific CD4(+) T cells, however, does not appear to be incompatible with preserved numbers and functionality of HIV-2-specific CD4(+) T cells in vivo, suggesting that additional mechanisms contribute to maintenance of HIV-2-specific CD4(+) T-cell help in vivo.
Recent advances in SRI'S IraqComm&#x2122; Iraqi Arabic-English speech-to-speech translation system (2009)

We summarize recent progress on SRI's IraqCommtrade Iraqi Arabic-English two-way speech-to-speech translation system. In the past year we made substantial developments in our speech recognition and machine translation technology, leading to significant improvements in both accuracy and speed of the IraqComm system. On the 2008 NIST-evaluation dataset our twoway speech-to-text (S2T) system achieved 6% to 8% absolute improvement in BLEU in both directions, compared to our previous year system.
A temporally scalable video codec and its applications to a video conferencing system with dynamic network adaption for mobiles (2011)

In this paper we present a multipoint video conferencing system that adapts to heterogeneous members including mobiles. The system is built upon a low complexity scalable extension of our H.264 codec DAVC, and a congestion-aware dynamic adaptation layer. We show that our temporally scaled video codec DSVC has the same RD performance as the non-scaled version with comparable configuration. We achieve this by QP cascading, i.e., assigning gradually refining quantization parameters to the declining temporal layers. The different quantization of frames does not lead to visually distinguishable quality fluctuations. We also present and analyze a mobile-compliant version of DSVC at reduced complexity that still admits comparable performance. Finally, we report on early work of dynamic layer tuning. Derived of delay variation measures, senders exploit scalable video layering to adapt the video transmission to varying network conditions. Initial results indicate that video performance remains close to optimal.
Supplementary Fig 1D from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression (2023)

Supplementary Fig 1D from Single Nucleotide Polymorphism–Based Genome-Wide Chromosome Copy Change, Loss of Heterozygosity, and Aneuploidy in Barrett's Esophagus Neoplastic Progression