gebhart/patrepeval huggingface dataset:
Peripheral co-immunization with CCL27 drives robust mucosal responses to SARS-CoV-2 synDNA antigens and provides heterologous protection against Delta variant challenge (2022)

Abstract SARS-CoV-2, which causes COVID-19 has caused a global pandemic which has claimed over 5 million lives to date. Emerging variants of concern and waning vaccine-induced immunity continually challenge viral control measures. We previously reported on the immunogenicity of a DNA vaccine encoding the spike glycoprotein of SARS-CoV-2, however directing vaccine-induced humoral and cell-mediated responses to mucosal surfaces such as the respiratory mucosa remains a challenge. We immunized mice with synthetic DNA (synDNA) plasmids expressing the wild-type SARS-CoV-2 spike protein (pS) alone, or with the DNA-encoded molecular adjuvant cutaneous T cell-attracting chemokine (pCTACK) Mice co-immunized with pS and pCTACK had increased spike-specific IFNy T cell responses compared to those receiving pS alone. While groups had similar levels of spike receptor binding domain (RBD)-specific IgG in their serum, in the mucosa, co-immunization with pCTACK enhanced RBD-specific IgA and only the cecal extract from pCTACK co-immunized animals neutralized pseudotyped viruses. When ACE2 transgenic mice were immunized, rested, and challenged with the heterologous SARS-CoV-2 Delta variant, co-immunization with pCTACK supported 100% survival while immunization with wild-type spike DNA antigens supported 60% survival. Importantly 100% of pCTACK co-immunized animals were protected from infection-induced weight loss. These studies demonstrate that chemokine adjuvants can direct vaccine-induced responses to specific immunological sites and that such responses can have significant impact on heterologous challenge outcomes and support the continued study of molecular chemokine adjuvants in the context of SARS-CoV-2 vaccines. We would like to thank the Animal Facility staff at the Wistar Institute and the Public Health agency of Canada for providing care to the animals used in these studies and for additional financial support. We would also like to thank the flow cytometry core facility at the Wistar Institute. This work was supported by NIH NCI award T32 CA09171 (ENG) and NIH NIAID award T32-AI-055400 (EMP) with additional support from CEPI/Inovio Pharmaceuticals.
Supplementary Table 3 from Adjuvant Sirolimus Does Not Improve Outcome in Pet Dogs Receiving Standard-of-Care Therapy for Appendicular Osteosarcoma: A Prospective, Randomized Trial of 324 Dogs (2023)

&lt;p&gt;Supplementary Table 3 contains a summary of the outcomes, with statistical comparisons, of the dogs enrolled in the SOC clinical trial arm. This includes the DFI and outcomes of the groups of dogs stratified by tumor location and ALP status.&lt;/p&gt;
Multiuser code acquisition in multipath channels (2005)

An adaptive algorithm for code acquisition in a direct sequence CDMA system is proposed. The algorithm is based on simultaneous channel estimation for multiple users. Its operation is demonstrated with up to four users transmitting over a 2 km shallow water channel within a 24 kHz acoustic bandwidth. Experimental results demonstrate the possibility of successful acquisition in the presence of strong multipath, with acquisition times on the order of a few hundred chip intervals.
Sugar rearrangements mediated by Lewis acidic molecular sieves in liquid media (2013)

Monosaccharide and disaccharide isomerization and epimerization reactions are catalyzed by Lewis acidic sites&#13;\n(M = Sn, Ti, Zr) isolated in silica-based heterogeneous solids, with selectivity and stereochem. specificity that are&#13;\ninaccessible to sugar rearrangements involving enolate intermediates catalyzed by bases. Such selectivity and&#13;\nspecificity reflect the ability of electrophilic Lewis acid centers to coordinate with oxygenated sugar functional&#13;\ngroups and to subsequently mediate intramol. rearrangements of specific H and C atoms, the mechanistic&#13;\ndetails of which are probed using D and ^(13)C isotopically-labeled reactants. Here, we discuss recent progress in&#13;\nunderstanding the influence of: (i) heteroatom and solvent identity on active site structures and reaction&#13;\nmechanisms and (ii) the surrounding silicate environments on the turnover rates of sugar reactions. For&#13;\nexample, glucose isomerization to fructose is mediated by Lewis acidic Ti sites isolated within hydrophobic&#13;\nand hydrophilic environments provided by cryst. mol. sieves with the Beta topol. and by amorphous silica.&#13;\nMeasured first-order rate consts. (per total Ti atom; 373 K), detd. from batch reactor studies under conditions of&#13;\nstrict kinetic control, are an order of magnitude higher in liq. water for hydrophobic than for hydrophilic solids.&#13;\nMechanistic interpretation of these rate consts. indicates that the environments surrounding Ti centers influence&#13;\nfree energy differences between isomerization transition states and two bound solvent mols. that adsorb&#13;\ncompetitively at Lewis sites and are most abundant surface intermediates during catalysis. Similar roles of&#13;\nhydrophobic pockets confining Lewis centers are found in heterogeneous, homogeneous and enzymic active&#13;\nsites that mediate sugar reactions. These findings help clarify the mechanistic details and site requirements for&#13;\nsugar conversion on heterogeneous Lewis acid solids, and also provide guidance for active site structural&#13;\nmodification to promote desired reaction pathways and thus to develop new heterogeneous catalysts for&#13;\nselective sugar conversion in liq. media.
Effect of solvent additives on bulk heterojunction morphology of organic photovoltaics and their impact on device performance (2015)

ABSTRACT Morphology of the active layer in an organic photovoltaic (OPV) device is known to have a significant impact on the device performance. It is, however, difficult to characterize nanoscale morphologies in detail, especially at the ensemble level. Herein, we report the utilization of small angle neutron scattering (SANS) to investigate variations in the nanoscale morphologies of the active layer of poly(3‐hexylthiophene‐2,5‐diyl):[6,6]‐phenyl‐C 61 ‐butyric acid methyl ester (P3HT:PCBM) bulk heterojunction OPV depending on the composition of casting solvent. Both the power law and the poly hard sphere model were utilized to characterize the state of the donor and acceptor components, respectively, from the obtained SANS data. Furthermore, the relationship between the nanoscale morphology and device performance is outlined. It was found that the use of 2‐chlorophenol, a poor solvent for P3HT and, at the same time, a very good solvent for PCBM, leads to nanomorphology featuring ordered, highly crystalline P3HT and small (15.2 nm) PCBM domains. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 128–134
Density functional theory study of the oxygen reduction reaction mechanism in a BN co-doped graphene electrocatalyst (2014)

Density functional theory calculations were performed to explore the stability and chemistry of active sites, and the mechanism of the ORR in a metal free BN co-doped graphene electrocatalyst. The results show that formation of graphitic G-BCxNy defects is energetically favorable than vacancy induced V-BCxNy defects in graphene. We find O2 physisorption on G-BC3, G-BC2N and G-BCN2 defects. Thus these defects are unlikely sites that initiate the ORR. In contrast, the chemisorption of ORR species O2, OOH and O, and the downhill energy landscape of the ORR on G-BN3 sites show that G-BN3 sites are active for the complete 4e− reduction of O2 to 2H2O. We furthermore explore the catalytic activity of vacancy induced V-BCxNy defects for the ORR. Much stronger adsorption of O2 and OH on V-BCxNy sites compared to G-BN3 sites indicates that V-BCxNy sites would likely be blocked by OH and the catalytic activity is limited to G-BN3 sites. Thus, an enhancement in catalytic activity and selectivity of BN co-doped graphene for a net 4e− complete O2 reduction can be achieved by increasing the concentration of G-BN3 defects.
Data-Driven Healthcare: Challenges and Opportunities for Interactive Visualization (2016)

The healthcare industry's widespread digitization efforts are reshaping one of the largest sectors of the world's economy. This transformation is enabling systems that promise to use ever-improving data-driven evidence to help doctors make more precise diagnoses, institutions identify at risk patients for intervention, clinicians develop more personalized treatment plans, and researchers better understand medical outcomes within complex patient populations. Given the scale and complexity of the data required to achieve these goals, advanced data visualization tools have the potential to play a critical role. This article reviews a number of visualization challenges unique to the healthcare discipline.
A Sub-Band Approach to Modification of Musical Transients (2012)

Abstract The transient modifier is a type of audio effect that changes the level of the transient parts in a musical signal while leaving the steady-state parts unchanged. This article presents a high-performance algorithm for transient detection and modification, one that is capable of modifying transients in polyphonic or multi-voiced signals, and capable of modifying both hard (percussive) and soft (non-percussive) transients. The detection and modification of transients are performed in the frequency-domain using a sub-band approach. Detection is based on both phase and energy information using an adaptive threshold, and modification is carried out independently at each sub-band. The performance of the proposed sub-band approach was compared with other transient-modification algorithms using subjective listening tests. We show that the sub-band approach with adaptive threshold mostly outperforms other approaches.
Synthesis and Characterization of Diaminodithio- and Aminotrithiophosphoric Acid Esters (2007)

The synthesis and characterization of a series of five new diaminodithiophosphoric acid esters (R1R2N)2P(S)SR and five new aminotrithiophosphoric acid esters (R1R2N)P(S)(SR)2 are described. The structure of two of these compounds, the diaminodithio derivative (iPr2N)2P(S)SCH2Ph and the aminotrithio derivative (iPr2N)P(S)(SCH2Ph)2, has been determined by single crystal X-ray diffraction. These series of compounds are potentially usable as agents for reversible addition-fragmentation chain transfer polymerization.
Supplementary Figure 1 from Transporter-Mediated Protection against Thiopurine-Induced Hematopoietic Toxicity (2023)

Supplementary Figure 1 from Transporter-Mediated Protection against Thiopurine-Induced Hematopoietic Toxicity
General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM (2019)

Abstract Despite their great potential to facilitate rapid preparation of quite impure samples, affinity grids have not yet been widely employed in single particle cryo-EM. Here, we chemically functionalize graphene oxide coated grids and use a highly specific covalent affinity tag system. Importantly, our polyethylene glycol spacer keeps particles away from the air-water interface and graphene oxide surface, protecting them from denaturation or aggregation and permits high-resolution reconstructions of small particles.
Satellitism of Platelets to Monocytes in a Patient with Hypogammaglobulinaemia (1978)

The first case of platelet satellitism to monocytes in a patient with hypogammaglobulinaemia is described. Platelet adherence was observed with heparinized blood and was dependent on the patient's plasma. The ultrastructural findings observed with the transmission (TEM) and scanning electron microscope (SEM) are reported.
Characterization Of A UV Resist for 248 nm Lithography (1989)

A study is presented of the performance of a Novolak-resin naphtoquinone-diazide sensitized resist exposed in the deep-UV. The material under study is PR-1024MB-600, designed for exposure in the UV (280-340 nm) range, including the i-line and h-line as well as deep UV (248 nm). The A, B, C exposure parameters of the photoresist have been measured at 248 nm. Classical bleaching characteristics are observed at low energy; the photoresist transmittance increases with dose. At higher doses the photoresist transmittance decreases, suggesting UV radiation effects on the resin. A model for the behavior and the associated parameter-extraction method for the UV transmittance versus dose in the presence of a variable resin absorbence are proposed. The development characteristics of the photoresist exposed at 248 nm are meas-ured and the results for exposure with less than 5 mJ/cm<sup>2</sup>/pulse and total dose less than 1 f/cm<sup>2</sup> show normal positive pho-toresist characteristics. Higher total dose, with low energy per pulse yields a negative tone mode. This tone reversal behavior suggests UV-induced cross-linking. Exposure using high pulse energies (&gt; 25 mlicm<sup>2</sup> per pulse) also yields a negative tone response. Thermal calculations suggest a heating effect. The image reversal performance of the PR-1024MB resist with addition of low-volatility amines is also demonstrated. Under similar conditions the image reversal process is 10-20 times more sensitive than in positive tone operation. In image reversal the deep-UV photoresist contrast exceeds 2, larger than the value observed in the normal mode.
Polypeptide Folding-Mediated Tuning of the Optical and Structural Properties of Gold Nanoparticle Assemblies (2011)

Responsive hybrid nanomaterials with well-defined properties are of significant interest for the development of biosensors with additional applications in tissue engineering and drug delivery. Here, we present a detailed characterization using UV-vis spectroscopy and small angle X-ray scattering of a hybrid material comprised of polypeptide-decorated gold nanoparticles with highly controllable assembly properties. The assembly is triggered by a folding-dependent bridging of the particles mediated by the heteroassociation of immobilized helix-loop-helix polypeptides and a complementary nonlinear polypeptide present in solution. The polypeptides are de novo designed to associate and fold into a heterotrimeric complex comprised of two disulfide-linked four-helix bundles. The particles form structured assemblies with a highly defined interparticle gap (4.8±0.4 nm) that correlates to the size of the folded polypeptides. Transitions in particle aggregation dynamics, mass-fractal dimensions and ordering, as a function of particle size and the concentration of the bridging polypeptide, are observed; these have significant effects on the optical properties of the assemblies. The assembly and ordering of the particles are highly complex processes that are affected by a large number of variables including the number of polypeptides bridging the particles and the particle mobility within the aggregates. A fundamental understanding of these processes is of paramount interest for the development of novel hybrid nanomaterials with tunable structural and optical properties and for the optimization of nanoparticle-based colorimetric biodetection strategies.
Continuous theta burst TMS of area MT impairs attentive motion tracking (2018)

Multiple object tracking (MOT) is impaired in amblyopia. This deficit has been associated with reduced MT activity during MOT task performance, suggesting that MT plays an important role in attentive tracking. To test this possibility, we assessed whether modulation of MT activity using inhibitory continuous theta burst stimulation (cTBS) would influence MOT performance in participants with normal vision. The MOT stimulus consisted of 4 targets and 4 distractors and was presented at 10° eccentricity (right and left hemifields). Functional MRI-guided cTBS was applied to left MT at 100% of active motor threshold intensity. Participants (n=15, age: 27±3) attended separate active and sham cTBS sessions. During cTBS, the MOT task was presented at each participant's speed threshold. Percent correct (based on partial report) for 40 trials was measured at baseline (before cTBS) and 5min and 30min after cTBS stimulation. Baseline accuracy did not vary between the right and left hemifields. There was a significant interaction between cTBS type (active/sham) and measurement time (baseline/post cTBS 5min or 30min) (F2,18=5.71, p=0.01). For active cTBS, there was a significant reduction in accuracy from baseline for the right hemifield after 5min (10 ± 2% reduction; t14 = 1.95, p = 0.03) and after 30min (15±3% reduction; t14=2.96, p=0.01). The left hemifield exhibited improved accuracy 30min after active cTBS (6±1.5% improvement, t14=-2.24, p=0.02). For sham cTBS, accuracy improved in both hemifields equally (right: 9 ± 2% improvement; t14=-2.94, p=0.02 and left: 9±1.5% improvement; t14=1.95, p=0.04). Our results demonstrate that cTBS of MT impaired MOT accuracy. There were improvements in MOT accuracy in the control hemifield and in the sham condition suggesting a task learning effect. These results highlight the importance of lower-level motion processing for MOT and support previous findings indicating that impaired MT function is responsible for MOT deficits in patients with amblyopia. Meeting abstract presented at VSS 2018
Real-Time Determination of Filtrate Contamination During Openhole WirelineSampling by Optical Spectroscopy (2000)

The key objectives of openhole wireline sampling are to identify desired fluids and to collect representative formation samples. Optical methods such as visible – near-infrared spectroscopy (NIR) are used to identify and quantify mixed oil, water, and gas flows in-situ during wireline logging. In wells drilled with oil based muds (OBM) or synthetic based muds (SBM), differentiating crude oil from the filtrate base fluid is critical. The widely used current practice is to measure the increase in fluid coloration (by NIR) vs. time to qualitatively assess the increasing fraction of crude oil with pumping time. Here, we describe new methods of utilizing NIR log data to provide quantitatively during sampling the %-OBM contamination in the extracted fluid. In addition, these methods allow prediction of contamination at future times during the sampling job, thereby determining the effectiveness of further pumping. The significant improvement in sampling efficiency is demonstrated with several log examples. Finally, using our methods, mud performance in the downhole environment can be monitored and optimized in subsequent jobs.
Surface atomic structures, surface energies, and equilibrium crystal shape of molybdenum (1998)

Using first-principles calculations, we calculated the atomic structures and surface energies of molybdenum surfaces in the (100), (110), (111), and (211) orientations. The equilibrium crystal shape of molybdenum is then found using the Wulff construction. We find that all four orientations appear on the Wulff plot and hence they are stable.
InGaAsP avalanche photodetectors for non-gated 1.06 micron photon-counting receivers (2007)

For the detection of single photons at 1.06 &#956;m, silicon-based single photon avalanche diodes (SPADs) used at shorter wavelengths have very low single photon detection efficiency (~1 - 2%), while InP/InGaAs SPADs designed for telecommunications wavelengths near 1.5 &#956;m exhibit dark count rates that generally inhibit non-gated (free-running) operation. To bridge this "single photon detection gap" for wavelengths just beyond 1 &#956;m, we have developed high performance, large area (80 - 200 &#956;m diameter) InP-based InGaAsP quaternary absorber SPADs optimized for operation at 1.06 &#956;m. We demonstrate dark count rates that are sufficiently low to allow for non-gated operation while achieving detection efficiencies far surpassing those found for Si SPADs. At a detection efficiency of 10%, 80 &#956;m diameter devices exhibit dark count rates below 1000 Hz and photon counting rates exceeding 1 MHz when operated at -40 °C.
Fast frequency synthesizer concept based on digital tuning and I/Q signal processing (2003)

The design of frequency synthesizers is especially challenging for wireless applications due to the requirements for high spectral purity, high frequency range, and fast tuning together with reasonable power consumption. The idea of combining digital and analog synthesis techniques for achieving these goals is discussed and analyzed. The proposed architecture uses I/Q modulation to translate a digitally synthesized tuneable low frequency tone to the final frequency range. In practical implementations, however, unavoidable mismatches between the amplitudes and phases of the I and Q branches result in imperfect sideband rejection degrading the spectral purity of the synthesized signal. A compensation structure based on digital pre-distortion of the low frequency tone is presented to enhance the signal quality. Furthermore, practical algorithms for updating the compensator parameters are proposed based on minimizing the envelope variation of the synthesizer output signal. Simulation results are also presented to illustrate the efficiency of the proposed synthesizer concept.
Antigens in Bovine Estrual and Cystic Follicles (1984)

The antigenic spectra of estrual or cystic follicular fluid (FF) consisted of 11 blood serum antigens while that of estrual or cystic ovary consisted of 9 identical antigens of which 2 were ovarian specific. The two ovarian-specific antigens were detected with antisera to estrual or cystic ovary but not with antisera to nonestrual ovaries. They were in higher concentration in estrual ovary than cystic ovary, were localized in bovine oocyte zona pellucida by immunofluorescence and light scattering, and cross-reacted with prostate tissue. Cystic FF contained a higher concentration (P less than 0.05) of IgG than at any stage of the cycle except estrus, and a lower concentration (P less than 0.05) of estradiol-17 beta than at estrus. It was hypothesized that increased levels of estradiol during estrus alter the permeability of the follicle wall unmasking a zona pellucida antigen in the preovulatory follicle. The appearance of this previously unexposed antigen at estrus could lead to an inflammatory-like response triggering ovulation.