gebhart/patrepeval huggingface dataset:
Virulence Studies of Different Sequence Types and Geographical Origins of Streptococcus suis Serotype 2 in a Mouse Model of Infection (2016)

Multilocus sequence typing previously identified three predominant sequence types (STs) of Streptococcus suis serotype 2: ST1 strains predominate in Eurasia while North American (NA) strains are generally ST25 and ST28. However, ST25/ST28 and ST1 strains have also been isolated in Asia and NA, respectively. Using a well-standardized mouse model of infection, the virulence of strains belonging to different STs and different geographical origins was evaluated. Results demonstrated that although a certain tendency may be observed, S. suis serotype 2 virulence is difficult to predict based on ST and geographical origin alone; strains belonging to the same ST presented important differences of virulence and did not always correlate with origin. The only exception appears to be NA ST28 strains, which were generally less virulent in both systemic and central nervous system (CNS) infection models. Persistent and high levels of bacteremia accompanied by elevated CNS inflammation are required to cause meningitis. Although widely used, in vitro tests such as phagocytosis and killing assays require further standardization in order to be used as predictive tests for evaluating virulence of strains. The use of strains other than archetypal strains has increased our knowledge and understanding of the S. suis serotype 2 population dynamics.
5d time-light transport matrix: What can we reason about scene properties? (2008)

Can time-of-flight cameras be used for performing multi-path analysis of global light transport?Traditional cameras estimate intensity per pixel, I(x,y,).In this position paper, we argue that emerging technologies will soon support cameras with a temporal-profile at each pixel at picosecond resolution, allowing us an ultra-high speed capture of the time-image, I(x,y,t).This time-image contains the time profile of irradiance at a pixel.Importantly, the speed of light is relevant, and the transient properties of light transport come into play.We propose that measurements of the transient properties of light will enable new methods for reasoning about scene content, and we show a few example scenarios in which transient reasoning exposes scene properties that are beyond the reach of traditional machine vision.
When the human brain goes diving: using near-infrared spectroscopy to measure cerebral and systemic cardiovascular responses to deep, breath-hold diving in elite freedivers (2021)

Continuous measurements of haemodynamic and oxygenation changes in free living animals remain elusive. However, developments in biomedical technologies may help to fill this knowledge gap. One such technology is continuous-wave near-infrared spectroscopy (CW-NIRS)-a wearable and non-invasive optical technology. Here, we develop a marinized CW-NIRS system and deploy it on elite competition freedivers to test its capacity to function during deep freediving to 107 m depth. We use the oxyhaemoglobin and deoxyhaemoglobin concentration changes measured with CW-NIRS to monitor cerebral haemodynamic changes and oxygenation, arterial saturation and heart rate. Furthermore, using concentration changes in oxyhaemoglobin engendered by cardiac pulsation, we demonstrate the ability to conduct additional feature exploration of cardiac-dependent haemodynamic changes. Freedivers showed cerebral haemodynamic changes characteristic of apnoeic diving, while some divers also showed considerable elevations in venous blood volumes close to the end of diving. Some freedivers also showed pronounced arterial deoxygenation, the most extreme of which resulted in an arterial saturation of 25%. Freedivers also displayed heart rate changes that were comparable to diving mammals both in magnitude and patterns of change. Finally, changes in cardiac waveform associated with heart rates less than 40 bpm were associated with changes indicative of a reduction in vascular compliance. The success here of CW-NIRS to non-invasively measure a suite of physiological phenomenon in a deep-diving mammal highlights its efficacy as a future physiological monitoring tool for human freedivers as well as free living animals. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.
Saturable absorber modelocked polarization maintaining Erbium-doped fiber laser (1992)

We passively modelock an erbium-doped fiber laser (EDFL) that generates 40pJ pulses 320fs wide and that operates in a single state of polarization (polarization extinction ratio better than 18dB). The self-starting of the laser is controlled by a semiconductor saturable absorber, and the fiber acts as the gain medium with some soliton pulse shaping. We squash the fiber preform to make the fiber polarization maintaining, and we design the core size and core-cladding index difference so the fiber is single mode and near the zero dispersion wavelength in the erbium-gain band.
Origin of the High Carrier Mobilities of Nonperipheral Octahexyl Substituted Phthalocyanine (2015)

The carrier transport properties of nonperipheral octahexyl substituted phthalocyanine H2Pc(C6H13)8np in its crystal and columnar (Col) liquid crystal (LC) phase were investigated using density functional theory (DFT) calculations in combination with molecular dynamics (MD) and kinetic Monte Carlo (KMC) simulations. In the crystal phase, we found that the nonperipherally substituted chains of H2Pc(C6H13)8np, that interpenetrate adjacent phthalocyanines (Pcs), significantly alter the Pc-core stacking such that higher hole mobilities are observed for this system than for the nonsubstituted H2Pc. This chain interpenetration was found to be inherited by the column stacking in the Col phase and hindered the Pc-core in-plane rotations between adjacent Pcs. This rotational hindrance further caused a nonuniform distribution of the adjacent dimer Pc-core in-plane orientation configurations. The relatively high carrier mobility in the Col phase in this system can be rationalized by the nonuniform distribution of the dimer configurations that give relatively high electronic coupling between the adjacent dimers. Our results show the remarkable effects of nonperipheral substitutions on the carrier transport properties in both the crystal and Col LC phases.
Feasibility study of lego-inspired construction with bendable concrete (2020)

Current construction of engineering structures faces a variety of challenges, such as shortage of skilled labor, low adaptation to new technologies, and increasing concerns for negative impacts on the environment. These challenges have significantly compromised the productivity and economic benefits of the construction industry. Further, construction activities have been linked to significant emissions, particularly CO2 associated with global warming. This study proposes a new paradigm of construction – Lego-inspired construction, and investigates the feasibility. Inspired by Lego blocks that can be assembled via dry joints and disassembled for different objects, this study presents blocks made using a bendable concrete, aiming to assemble various structures with dry joints. The blocks are used to assemble a prototype footbridge to demonstrate the assembling process, which is compatible with robotic systems for construction automation. The footbridge demonstrated reasonable load-carrying capability in mechanical testing. After the testing, the footbridge was disassembled, and the blocks were reused to assemble a frame for buildings. The proposed Lego-inspired construction is promising to greatly improve the construction efficiency and reduce the adverse impacts on the natural environment caused by conventional construction approaches.
Characterization of γδ T cell subsets in organ transplantation (2010)

γδ T cells are innate-type lymphocytes that preferentially act as regulators of local effector immune responses. Recent reports found an altered distribution of the two main subpopulations of blood γδ T cells (Vδ1 and Vδ2) in operationally tolerant liver transplant recipients. Based on this, γδ T cells subset quantification was proposed as a biomarker of immunologic risk in liver transplantation. The specific characteristics of γδ T cell subsets in transplantation remain however unknown. We have investigated here the phenotype, repertoire and functional properties of γδ T cell subsets in a large population of allograft recipients. Our results indicate that alterations in the γδ T cell compartment are not restricted to tolerant liver recipients. In fact, most immunosuppressed liver and kidney recipients also display an enlarged peripheral blood γδ T cell pool mainly resulting from an expansion of Vδ1 T cells exhibiting an oligoclonal repertoire and different phenotypic and cytokine production traits than Vδ2 T cells. We propose that persistent viral infections are likely to contribute to these alterations. Our data provide novel insight in the biology of γδ T cells and a rationale for exploring these lymphocytes in more depth into the pathogenesis of viral infections in transplantation.
Supplementary Methods and Materials from <i>In Vivo</i> Persistence, Tumor Localization, and Antitumor Activity of CAR-Engineered T Cells Is Enhanced by Costimulatory Signaling through CD137 (4-1BB) (2023)

Supplementary Methods and Materials from &lt;i&gt;In Vivo&lt;/i&gt; Persistence, Tumor Localization, and Antitumor Activity of CAR-Engineered T Cells Is Enhanced by Costimulatory Signaling through CD137 (4-1BB)
General framework for the reconfiguration of satellite constellations (2009)

From remote sensing to navigation and communication, satellite constellations have become an indispensible component of our society’s infrastructure. Recent events, including China’s intercept of their Feng Yun-1C weather satellite and the United States’ intercept of a non-functioning satellite, have dramatically increased the amount of space debris, which poses an increased risk for on-orbit collisions. When the loss or degradation of a satellite in a constellation is experienced—be it from a collision with space debris, on-orbit malfunctions, or natural causes—the constellation may no longer be capable of fulfilling its mission requirements. Instead of simply accepting the degraded performance, stakeholders may consider reconfiguration of the remaining spacecraft. In this research, a general framework for the reconfiguration of satellite constellations is developed. 
The key characteristic that separates this research from others that have come before it is that the future state of the reconfigured constellation is not assumed a priori; rather, it is this state that is found. In other words, the reconfigured geometry can occupy any feasible region (this is mission dependent) of the design space in an attempt to provide optimal performance with respect to multiple-criterion. These include the propellant expended, time of transfer, reduction in mission life, coverage performance, and risk due to maneuvering. When modeled as mathematical functions, some of these concerns exhibit continuous behavior; however, most have nonlinear, discrete, discontinuous, and/or multimodal characteristics. 
The framework adapts a best-in-class parallel Multi-Objective Evolutionary Algorithm to approximate the optimal hypervolumes for this complex tradeoff-space. Several loss scenarios for the Global Positioning System constellation are presented to demonstrate the framework. An a posteriori procedure for decision support is introduced that enables down-selection to a final design from thousands of non-dominated reconfiguration alternatives. 
Among the significant results to emerge from this research are the lessons learned as a result of the application of stochastic optimization to the constellation design problem domain. One such lesson indicates that objective functions related to coverage have the greatest influence on the multi-modality of the design space. Other results demonstrate that increasing the number of design variables and/or the application of operational constraints (such as fuel budgets) do not necessarily make the reconfiguration problem more difficult to solve; in some cases it becomes easier. The method itself is successful in providing a global context to decision makers that allows for defendable design selection in what was previously a computationally intractable optimization problem.
Preoperative Hydronephrosis, Ureteroscopic Biopsy Grade and Urinary Cytology Can Improve Prediction of Advanced Upper Tract Urothelial Carcinoma (2010)

Preoperative evaluation for hydronephrosis, ureteroscopic grade and cytology can identify patients at risk for advanced upper tract urothelial carcinoma. Such knowledge may impact surgery choice and extent as well as the need for perioperative chemotherapy regimens.
Pertussis toxin B-oligomer dissociates T cell activation and HIV replication in CD4 T cells released from infected lymphoid tissue (2005)

PTX-B and PT-9K/129G inhibit both R5 and X4 HIV-1 replication in human lymphoid tissue ex vivo. In contrast to PHA and IL-2, they promote the proliferation of CD4 T lymphocytes emigrated from tissue, including HIV-infected cells, without triggering virus replication. Therefore, these emigrated CD4 T cells represent a novel model of a latent inducible HIV reservoir. Thus, PTX-B and the clinically approved PT-9K/129G are potential antiretroviral agents endowed with immunostimulatory capacity.
Evaluation of properties of YAG (Ce) ceramic scintillators (2005)

We measured basic properties of three ceramic Y/sub 3/Al/sub 5/O/sub 12/ (YAG) scintillators doped with Ce to a concentration of 0.5, 0.05, and 0.005 mol%, in comparison with a monocrystalline YAG scintillator with unknown amount of Ce doping. First, optical transparency and emission spectra were investigated. We confirmed that the transparency of the ceramics is comparable to that of the monocrystalline one (/spl sim/80%) in wavelengths longer than /spl sim/500 nm. The ceramics did not show an indication of lattice defects which is present in the monocrystalline YAG. Then the response to /spl gamma/-rays was studied using a phototube as a scintillation light detector. The 0.5 mol% sample exhibited the highest light yield (/spl sim/40% of CsI), with an energy resolution of about 7.2% at /sup 137/Cs 662 keV photoabsorption peak. The optimum Ce concentration for a /spl sim/2 mm thick ceramic YAG was determined to be /spl sim/0.1 mol%. Using the delayed coincidence method, the principal time constant of the ceramic YAGs was measured as /spl sim/80 ns. By irradiating 5.49 MeV /spl alpha/-particles, the /spl alpha/-ray to /spl gamma/-ray light yield ratio of the ceramic YAGs was found to depend negatively on the amount of Ce; namely, 0.28, 0.20, and 0.13 in the increasing order of the Ce concentration. The 200-1000 keV intrinsic background of the 0.5 mol% ceramic was /spl sim/10/sup -5/ counts/s/cm/sup 3/, indicating that it is not significantly contaminated by radioactive impurities.
COVID-19 convalescent plasma and randomized clinical trials: explaining conflicting outcomes and finding signals of efficacy (2021)

Abstract Convalescent plasma (CP) recurs as a frontline treatment in epidemics because it is available as soon as there are survivors. The COVID-19 pandemic represented the first large-scale opportunity to shed light into mechanisms of action, safety and efficacy of CP using modern evidence-based medicine approaches. Studies ranging from observational case series to randomized controlled trials (RCT) have reported highly variable efficacy results for COVID-19 CP (CCP), resulting in uncertainty. Reasons for CCP success and failure may be hidden in study details, which are usually difficult to explain to physicians and the public but provide fertile ground for designing next-generation studies. We analyzed variables associated with efficacy such as clinical settings, disease severity, CCP SARS-CoV-2 antibody levels and function, dose, timing of administration (variously defined as time from onset of symptoms, molecular diagnosis, diagnosis of pneumonia, or hospitalization, or by serostatus), outcomes (defined as hospitalization, requirement for ventilation, clinical improvement or mortality), CCP provenance and time for collection, and criteria for efficacy. Focusing only on the results from the 30 available RCTs we noted that these were more likely to show signals of efficacy, including reductions in mortality, if the plasma neutralizing titer was ≥ 160 and the time to randomization was ≤ 9 days, consistent with passive antibody therapy efficacy requiring dosing with sufficient antibody. The fact that most studies revealed signals of efficacy despite variability in CCP and its use suggest likely therapeutic effects that become apparent despite the data noise. Despite the recent WHO guidelines discouraging CCP usage, the Omicron variant of concern is reminding us the superiority of polyclonal antibody therapies over monoclonal antibodies, and CCP from vaccinated convalescents is likely to be evaluated soon
New technetium 99m-labeled brain perfusion imaging agents (1990)

In developing new brain perfusion imaging agents, three types of neutral and lipid-soluble technetium 99m complexes have been reported: 99mTc-ethylene cysteinate dimer, 99mTc-hexamethyl propylene amine oxime, and 99mTc-boric acid adduct of technetium oxime. Structure-activity relationships of these complexes on brain uptake and retention have been investigated. The new 99mTc-brain perfusion imaging agents are useful in detecting various cerebral vascular abnormalities. The exact trapping mechanisms and their relationship with potential clinical applications still remain to be elucidated. However, initial clinical studies with 99mTc agents do show parallel clinical efficacy as those reported for the iodine 123-labeled brain perfusion agents, isopropyliodoamphetamine and N,N,N'-trimethyl-N'-[2-hydroxy-3-methyl-5-iodobenzyl]-1,3-propanediamine .
Dopamine Release at Individual Presynaptic Terminals Visualized with FFNs (2009)

The nervous system transmits signals between neurons via neurotransmitter release during synaptic vesicle fusion. To observe neurotransmitter uptake and release from individual presynaptic terminals directly, we designed fluorescent false neurotransmitters as substrates for the synaptic vesicle monoamine transporter. Using these probes to image dopamine release in the striatum, we made several observations pertinent to synaptic plasticity. We found that the fraction of synaptic vesicles releasing neurotransmitter per stimulus was dependent on the stimulus frequency. A kinetically distinct "reserve" synaptic vesicle population was not observed under these experimental conditions. A frequency-dependent heterogeneity of presynaptic terminals was revealed that was dependent in part on D2 dopamine receptors, indicating a mechanism for frequency-dependent coding of presynaptic selection. Hui Zhang and Niko G. Gubernator contributed equally to this work.
Experimental Study of Fouling Resistance in Twisted Tube Heat Exchanger (2012)

This paper discusses fouling of a twisted tube heat exchanger under different conditions of fluid velocity and heat input. The fluid velocity was varied from 0.5 to 2.0 m/s, whereas the heat input to the heat exchanger was varied from 200 to 800 W. The experimental results show that for low fluid velocity of 0.5 m/s, the fouling resistance showed noticeable variation with respect to heat input, whereas for high velocity ranges, that is, 1.0–2 m/s, the variation in fouling resistance is less. The fouling in twisted tube steadily increases with time for different values of heat input from 1000 min onward for fluid velocity in the range from 1.0 to 2.0 m/s. It is also observed that fouling resistance curves overlap for various values of heat input. During the initial 1000 min of the test duration, the maximum fouling in a twisted tube heat exchanger decreases with increase in fluid velocity from 1.0 to 2.0 m/s. This behavior of the fouling rate can be attributed to the fact that at higher fluid velocity, flow becomes turbulent, and this in turn flushes the fouling particles. The time-series correlations for the fouling resistance are found to be logarithmic in nature.
Targeted nanoparticles towards increased L cell stimulation as a strategy to improve oral peptide delivery in incretin-based diabetes treatment (2020)

The delivery of therapeutic peptides via the oral route remains one of biggest challenges in the pharmaceutical industry. Recently, we have described an alternative improved drug delivery system for peptide delivery via the oral route, consisting of a lipidic nanocapsule. Despite the striking effects observed, it is still essential to develop strategies to strengthen the nanocarriers' glucagon-like peptide-1 (GLP-1) secretory effect of the nanocarrier and/or prolong its antidiabetic effect in vivo to facilitate its translation into the clinic. For this purpose, we developed and compared different fatty acid-targeted lipid and polymeric nanoparticles and evaluated the L cell stimulation induced by the nanocarriers in murine L cells in vitro and in normal healthy mice in vivo. We further examined the antidiabetic effect in vivo in an obese/diabetic mouse model induced by high-fat diet feeding and examined the effect of the oral administration frequency. Among the tested nanocarriers, only lipid-based nanocarriers that were surface-modified with DSPE-PEG<sub>2000</sub> on the surface were able to significantly strengthen the biological effect of the nanocarriers. They increased endogenous GLP-1 levels up to 8-fold in vivo in normoglycemic mice. Moreover, they effectively prolonged the in vivo antidiabetic effect by normalizing the plasma glucose levels in obese/diabetic mice following long-term treatment (one month). Ultimately, the targeted nanocarriers were as effective when the administration frequency was reduced from once daily to once every other day.
Predictive value of quantitative HER2, HER3 and p95HER2 levels in HER2-positive advanced breast cancer patients treated with lapatinib following progression on trastuzumab (2017)

Lapatinib is a HER1 and HER2 tyrosine kinase inhibitor (TKI) approved in second line treatment of advanced or metastatic breast cancer following progression on trastuzumab-containing therapy. Biomarkers for activity of lapatinib and other TKIs are lacking. Formalin-fixed, paraffin-embedded primary tumor samples were obtained from 189 HER2-positive patients treated with lapatinib plus capecitabine following progression on trastuzumab. The HERmark<sup>®</sup> Breast Cancer Assay was used to quantify HER2 protein expression. HER3 and p95HER2 protein expression was quantified using the VeraTag<sup>®</sup> technology. Overall survival (OS) was inversely correlated with HER2 (HR = 1.9/log; P = 0.009) for patients with tumors above the cut-off positivity level by the HERmark assay. OS was significantly shorter for those with above median HER2 levels (HR = 1.7; P = 0.015) and trended shorter for those below the cut-off level of positivity by the HERmark assay (HR = 1.7; P = 0.057) compared to cases with moderate HER2 overexpression. The relationship between HER2 protein expression and OS was best captured with a U-shaped parabolic function (P = 0.004), with the best prognosis at moderate levels of HER2 protein overexpression. In a multivariate model including HER2, increasing p95HER2 expression was associated with longer OS (HR = 0.35/log; P = 0.027). Continuous HER3 did not significantly correlate with OS. Patients with moderately overexpressed HER2 levels and high p95HER2 expression may have best outcomes while receiving lapatinib following progression on trastuzumab. Further study is warranted to explore the predictive utility of quantitative HER2 and p95HER2 in guiding HER2-directed therapies.
All-optical quasi-phase matching and quantum path control by counter propagating pulse trains (2007)

We enhance high-order harmonic generation at 70eV in argon and 145eV in helium by orders of magnitude using counterpropagating pulsetrains. We also demonstrate coherent control on attosecond timescales by selective enhancement of different quantum trajectories.