gebhart/patrepeval huggingface dataset:
Gastrointestinal Delivery of Baculovirus Displaying Influenza Virus Hemagglutinin Protects Mice against Heterologous H5N1 Infection (2010)

The recent outbreaks of influenza A H5N1 virus in birds and humans have necessitated the development of potent H5N1 vaccines. In this study, we evaluated the protective potential of an immediate-early promoter-based baculovirus displaying hemagglutinin (BacHA) against highly pathogenic avian influenza (HPAI) H5N1 virus infection in a mouse model. Gastrointestinal delivery of BacHA significantly enhanced the systemic immune response in terms of HA-specific serum IgG and hemagglutination inhibition (HI) titers. In addition, BacHA vaccine was able to significantly enhance the mucosal IgA level. The inclusion of recombinant cholera toxin B subunit as a mucosal adjuvant along with BacHA vaccine did not influence either the systemic or mucosal immunity. Interestingly, an inactivated form of BacHA was able to induce only a negligible level of immune responses compared to its live counterpart. Microneutralization assay also indicated that live BacHA vaccine was able to induce strong cross-clade neutralization against heterologous H5N1 strains (clade 1.0, clade 2.1, and clade 8.0) compared to the inactivated BacHA. Viral challenge studies showed that live BacHA was able to provide 100% protection against 5 50% mouse lethal doses (MLD(50)) of homologous (clade 2.1) and heterologous (clade 1) H5N1. Moreover, histopathological examinations revealed that mice vaccinated with live BacHA had only minimal bronchitis in lungs and regained their body weight more rapidly postchallenge. Furthermore, immunohistochemistry results demonstrated that the live BacHA was able to transduce and express HA in the intestinal epithelial cells in vitro and in vivo. We have demonstrated that recombinant baculovirus with a white spot syndrome virus (WSSV) immediate-early promoter 1 (ie1) acted as a vector as well as a protein vaccine and will enable the rapid production of prepandemic and pandemic vaccines without any biosafety concerns.
Effect of Irrigation Method on Essential Oil Yield and Rate of Oil Evaporation in Mint Grown under Controlled Condition1 (1977)

Abstract Peppermint ( Mentha piperita L. cv. Black Mitcham) grown in a controlled environment under simulated sprinkler irrigation produced essential oil in 23% lower yield than did identical plants grown under simulated furrow irrigation. With spearmint ( M. spicata L.) sprinkler irrigation produced oil yields 34% lower than furrow irrigation. When the sprinkler system was on, the rate of essential oil evaporation increased 4 to 5-fold over the rate increase observed in furrow irrigated controls, and an elevated rate of evaporation persisted for several hours after cessation of sprinkling. Physical damage to the oil glands by falling water droplets did not appear to be the major cause of increased evaporation, as studies in water-saturated chambers showed that high humidity alone could cause rapid rates of oil evaporation. Apparently, wetting of the foliage under sprinkler irrigation results in hydration and swelling of the cuticle enclosing the oil glands. Consequently, the permeability of the cuticular membrane may be altered, allowing more rapid evaporation of the volatile oil. The increased rate of oil evaporation in sprinkler irrigated mint may be one of the factors responsible for lowered yields with this irrigation method.
Ciguatoxins Evoke Potent CGRP Release by Activation of Voltage-Gated Sodium Channel Subtypes NaV1.9, NaV1.7 and NaV1.1 (2017)

Ciguatoxins (CTXs) are marine toxins that cause ciguatera fish poisoning, a debilitating disease dominated by sensory and neurological disturbances that include cold allodynia and various painful symptoms as well as long-lasting pruritus. Although CTXs are known as the most potent mammalian sodium channel activator toxins, the etiology of many of its neurosensory symptoms remains unresolved. We recently described that local application of 1 nM Pacific Ciguatoxin-1 (P-CTX-1) into the skin of human subjects induces a long-lasting, painful axon reflex flare and that CTXs are particularly effective in releasing calcitonin-gene related peptide (CGRP) from nerve terminals. In this study, we used mouse and rat skin preparations and enzyme-linked immunosorbent assays (ELISA) to study the molecular mechanism by which P-CTX-1 induces CGRP release. We show that P-CTX-1 induces CGRP release more effectively in mouse as compared to rat skin, exhibiting EC50 concentrations in the low nanomolar range. P-CTX-1-induced CGRP release from skin is dependent on extracellular calcium and sodium, but independent from the activation of various thermosensory transient receptor potential (TRP) ion channels. In contrast, lidocaine and tetrodotoxin (TTX) reduce CGRP release by 53–75%, with the remaining fraction involving L-type and T-type voltage-gated calcium channels (VGCC). Using transgenic mice, we revealed that the TTX-resistant voltage-gated sodium channel (VGSC) NaV1.9, but not NaV1.8 or NaV1.7 alone and the combined activation of the TTX-sensitive VGSC subtypes NaV1.7 and NaV1.1 carry the largest part of the P-CTX-1-caused CGRP release of 42% and 34%, respectively. Given the contribution of CGRP to nociceptive and itch sensing pathways, our findings contribute to a better understanding of sensory symptoms of acute and chronic ciguatera that may help in the identification of potential therapeutics.
An in situ estimation of anisotropic elastic moduli for a submarine shale (1994)

Direct arrival times and slownesses from wide‐aperture walkaway vertical seismic profile data acquired in a layered anisotropic medium can be processed to give a direct estimate of the phase slowness surface associated with the medium at the depth of the receivers. This slowness surface can, in turn, be fit by an estimated transversely isotropic medium with a vertical symmetry axis (a “TIV” medium). While the method requires that the medium between the receivers and the surface be horizontally stratified, no further measurement or knowledge of that medium is required. When applied to data acquired in a compacting shale sequence (here termed the “Petronas shale”) encountered by a well in the South China Sea, the method yields an estimated TIV medium that fits the data extremely well over 180° of propagation angles sampled by 201 source positions. The medium is strongly anisotropic. The anisotropy is significantly anelliptic and implies that the quasi‐shear mode should be triplicated for off‐axis propagation. Estimated density‐normalized moduli (in units of km 2 /s 2 ) for the Petronas shale are A 11 = 6.99 ± 0.21, A 33 = 5.53 ± 0.17, A 55 = 0.91 ± 0.05, and A 13 = 2.64 ± 0.26. Densities in the logged zone just below the survey lie in the range between 2200 and 2400 kg/m 3 with an average value close to 2300 kg/m 3 .
Physical evolution of nanograting inscription on the surface of fused silica (2012)

The nanograting inscription on the surface of a fused silica substrate is systematically investigated on a shot-to-shot basis. Three different evolutionary processes are observed with pulse fluence ranging from slightly below to well above the single shot ablation threshold. This dependence is explained by the interplay between local intensity distribution and incubation effect.
Scintillator selection for MR-compatible gamma detectors (2003)

We investigated the magnetic susceptibility of several scintillators to select the best material for MR-compatible gamma detectors. NaI(Tl) in an Al container, NaI(Tl) in a Cu container and CsI(Tl) are candidates for MR-compatible gamma probes, imaging probes or SPECT, while BGO, LSO, LGSO, and GSO are the candidates for MR-compatible PET. In addition, we investigated image artifacts and distortion by scanning these scintillators with an MR-scanner. Results show that the magnetic susceptibility of NaI(Tl), CsI(Tl), BGO, and LSO showed similarities to that of human tissue. Of these scintillators, NaI(Tl) in a Cu container showed the closest to that of susceptibility to human tissue and fewest artifacts on the MRI image. It is a good material for an MR-compatible gamma probe or imaging probe as well as SPECT. For MR-compatible PET, BGO, and LSO showed similar susceptibility to that of human tissue and small artifacts on the MRI images. However, LGSO and GSO showed much greater susceptibility than human tissue, and produced significant artifacts and distortion in the MRI images due to the presence of gadolinium (Gd) in these scintillators.
Double Double Descent: On Generalization Errors in Transfer Learning between Linear Regression Tasks (2020)

We study the transfer learning process between two linear regression problems. An important and timely special case is when the regressors are overparameterized and perfectly interpolate their training data. We examine a parameter transfer mechanism whereby a subset of the parameters of the target task solution are constrained to the values learned for a related source task. We analytically characterize the generalization error of the target task in terms of the salient factors in the transfer learning architecture, i.e., the number of examples available, the number of (free) parameters in each of the tasks, the number of parameters transferred from the source to target task, and the relation between the two tasks. Our non-asymptotic analysis shows that the generalization error of the target task follows a two-dimensional double descent trend (with respect to the number of free parameters in each of the tasks) that is controlled by the transfer learning factors. Our analysis points to specific cases where the transfer of parameters is beneficial as a substitute for extra overparameterization (i.e., additional free parameters in the target task). Specifically, we show that the usefulness of a transfer learning setting is fragile and depends on a delicate interplay among the set of transferred parameters, the relation between the tasks, and the true solution. We also demonstrate that overparameterized transfer learning is not necessarily more beneficial when the source task is closer or identical to the target task.
Epstein‐Barr Virus Vectors Provide Prolonged Robust Factor IX Expression in Mice (2003)

We demonstrate that vectors incorporating components from Epstein-Barr virus (EBV) for retention and from human genomic DNA for replication greatly enhance the level and duration of marker gene expression in dividing cultured cells. The same types of vectors were tested in vivo by high-pressure tail vein injection of naked DNA in mice, resulting in liver delivery and expression. The therapeutic gene was a human factor IX (hFIX) minigene comprising genomically derived 5', 3', and intronic sequences that provided relatively good gene expression in vivo. We demonstrated that addition of the EBV EBNA1 gene and its family of repeats binding sites provided a 10- to 100-fold increase in prolonged hFIX expression in mouse liver. A single 25-microg dose of vector DNA generated normal (>5 microg/mL) levels of hFIX throughout the 8 month duration of the experiment. Vector DNA with or without the EBV sequences was retained in liver cells, and vector replication was not a factor in these nondividing liver cells. Instead, it appears that enhancement of stable hFIX expression by the EBV components was responsible for the increased level and duration of therapeutic gene expression. The EBV sequences also significantly enhanced stable expression of a vector carrying the full genomic hFIX gene delivered to mouse liver. These results underline the crucial importance of appropriate gene expression signals on gene therapy vectors and the utility of EBV sequences in particular for increasing stable gene expression.
Vesicular hydrogen silsesquioxane-mediated synthesis of nanocrystalline silicon dispersed in a mesoporous silica/suboxide matrix, with potential for electrochemical applications (2014)

Silicon nanoparticles embedded in a mesoporous SiO<sub>2</sub>/SiO<sub>x</sub>matrix have been prepared by pyrolysis of condensed hydrogen silsesquioxane vesicles.
Info about speakers and lectures (2011)

These plenary lectures discuss the following: component-based architectures for the synthesis of intelligent networked systems; and Cyber systems coordination: structured environment and intelligent robot.
Small-molecule Modulators of KEAP1-Nrf2 (2016)

Medicinal Chemistry Reviews is an outstanding 600 page volume providing timely and critical reviews of important topics in medicinal chemistry. It is provided free of charge to MEDI members in electronic format. Members can also order a print copy, for the cost of printing, shipping and handling
2-(3-Fluoro-4-methylsulfonylaminophenyl)propanamides as Potent Transient Receptor Potential Vanilloid 1 (TRPV1) Antagonists: Structure–Activity Relationships of 2-Amino Derivatives in theN-(6-Trifluoromethylpyridin-3-ylmethyl) C-Region (2012)

A series of N-(2-amino-6-trifluoromethylpyridin-3-ylmethyl)-2-(3-fluoro-4-methylsulfonylaminophenyl)propanamides were designed combining previously identified pharmacophoric elements and evaluated as hTRPV1 antagonists. The SAR analysis indicated that specific hydrophobic interactions of the 2-amino substituents in the C-region of the ligand were critical for high hTRPV1 binding potency. In particular, compound 49S was an excellent TRPV1 antagonist (K(i(CAP)) = 0.2 nM; IC(50(pH)) = 6.3 nM) and was thus approximately 100- and 20-fold more potent, respectively, than the parent compounds 2 and 3 for capsaicin antagonism. Furthermore, it demonstrated strong analgesic activity in the rat neuropathic model superior to 2 with almost no side effects. Compound 49S antagonized capsaicin induced hypothermia in mice but showed TRPV1-related hyperthermia. The basis for the high potency of 49S compared to 2 is suggested by docking analysis with our hTRPV1 homology model in which the 4-methylpiperidinyl group in the C-region of 49S made additional hydrophobic interactions with the hydrophobic region.
Compact mid-infrared graphene thermopile enabled by a nanopatterning technique of electrolyte gates (2018)

A central challenge in making two-dimensional (2D) material-based devices faster, smaller, and more efficient is to control their charge carrier density at the nanometer scale. Traditional gating techniques based on capacitive coupling through a gate dielectric cannot generate strong and uniform electric fields at this scale due to divergence of the fields in dielectrics. This field divergence limits the gating strength, boundary sharpness, and minimum feature size of local gates, precluding certain device concepts (such as plasmonics and metamaterials based on spatial charge density variation) and resulting in large device footprints. Here we present a nanopatterned electrolyte gating concept that allows locally creating excess charges by combining electrolyte gating with an ion-impenetrable e-beam-defined resist mask. Electrostatic simulations indicate high carrier density variations of Δn ∼ 1014 cm-2 across a length of only 15 nm at the mask boundaries on the surface of a 2D conductor. We implement this technique using cross-linked poly(methyl methacrylate), experimentally prove its ion-impenetrability and demonstrate e-beam patterning of the resist mask down to 30 nm half-pitch resolution. The spatial versatility enables us to demonstrate a compact mid-infrared graphene thermopile with a geometry optimized for Gaussian incident radiation. The thermopile has a small footprint despite the number of thermocouples in the device, paving the way for more compact high-speed thermal detectors and cameras.
Novel perspectives for the application of total internal reflection microscopy (2009)

Total Internal Reflection Microscopy (TIRM) is a sensitive non-invasive technique to measure the interaction potentials between a colloidal particle and a wall with femtonewton resolution. The equilibrium distribution of the particle-wall separation distance z is sampled monitoring the intensity I scattered by the Brownian particle under evanescent illumination. Central to the data analysis is the knowledge of the relation between I and the corresponding z, which typically must be known a priori. This poses considerable constraints to the experimental conditions where TIRM can be applied (short penetration depth of the evanescent wave, transparent surfaces). Here, we introduce a method to experimentally determine I(z) by relying only on the distance-dependent particle-wall hydrodynamic interactions. We demonstrate that this method largely extends the range of conditions accessible with TIRM, and even allows measurements on highly reflecting gold surfaces where multiple reflections lead to a complex (z).
Defining changes in physical limitation from the patient perspective: insights from the VITALITY‐HFpEF randomized trial (2022)

In the VITALITY-HFpEF trial, a change in KCCQ-PLS of ≥8.33 points (corresponding to an improvement in ≥2 response categories of KCCQ-PLS) may represent the minimal clinically important difference for improvement and a change of ≤ -4.17 points (corresponding to a worsening in ≥1 response category of KCCQ-PLS) may suggest deterioration in patients with HFpEF.
Diffuse Back-Illumination Extinction Imaging Of Soot Formation From A Liquid Fuel Film (2022)

The transient combustion of a liquid iso-octane film, isolated from the often co-existing combustion of liquid sprays, was investigated within the nominally quiescent ambient of a constant volume chamber using a custom-made liquid fuel film generation system. Soot formation throughout the combustion process, from ignition to extinction, was visualized using high-speed diffuse back-illumination extinction imaging technique, providing temporally resolved spatial distribution of soot optical thickness (KL) in the chamber. The impact of ambient pressure and ambient oxygen content on soot formation was examined over a range of 2 – 5 bar (absolute) and 16 – 30% (in terms of molar fraction of oxygen), respectively. Regardless of the test conditions, the fuel film combustion entailed three stages, namely flame initiation, steady burning and flame extinction. While the ambient oxygen content was kept constant, the flame gradually became turbulent-like and the flame flickering less distinct as ambient pressure was increased. The total amount of soot generated within the chamber was found to first increase then decrease with the ambient pressure, due to the competing impacts of increasing pressure on promoting soot-formation reaction rate and enhancing mixing of fuel vapour with the entrained air. Increasing ambient oxygen content, on the other hand, consistently enhanced soot formation, which may be associated with its impact on boosting flame temperature and consequently liquid fuel evaporation rate. In addition, flame flickering remained distinct for ambient oxygen content above atmospheric level, while becoming substantially less observable for that below atmospheric level. Flickering frequency, for all test conditions with distinct flame flickering, had a value of approximately 10 Hz and gradually increased with time during the steady burning stage, suggesting the shrinkage of the fuel film diameter. Flickering of the flame resulted in fluctuations in the total amount of soot presented in the combustion chamber. The power of this fluctuation varied with time, and this temporal variation of fluctuation power also depended on experimental conditions, due to its dependency on the combined effects of soot concentration and volume of the flame.
Antibody to Cryptococcus neoformans capsular glucuronoxylomannan promotes expression of interleukin‐12Rβ2 subunit on human T cells in vitro through effects mediated by antigen‐presenting cells (2002)

The results reported herein show that T cells responding to encapsulated Cryptococcus neoformans cells had reduced expression of interleukin-12 receptor beta2 (IL-12Rbeta2) in comparison to those responding to non-encapsulated cells. This suggested that encapsulation with glucuronoxylomannan (GXM), the principal constituent of the C. neoformans polysaccharide antiphagocytic capsule, inhibited expression of the IL-12Rbeta2 subunit on T cells responding to cryptococcal antigens. Addition of GXM-binding monoclonal antibody (mAb) overcame this effect by promoting IL-12Rbeta2 expression and by decreasing IL-1R expression on T cells. This effect may be a consequence of mAb-induced changes on antigen-presenting cells (APC) that are closely related to increased phagocytosis. Blocking of phagocytosis with monoiodacetic acid (MIA) precluded up-regulation of B7 expression on APC and was associated with diminished IL-12Rbeta2 expression on T cells. The observed effects on T cells were interpreted as a consequence of increased APC function due to enhanced phagocytosis. These findings suggest a mechanism by which specific antibody can promote the polarization of the cellular immune response towards a Th1-like response and thus contribute to an enhanced cellular immune response against C. neoformans.
Efficient DFA grouping for traffic identification (2012)

Traffic Identification is a key function performed by Internet Service Providers' (ISP) administrators to evaluate and improve network services. However, traffic identification needs to be done in real-time and at wire speed to be useful for network tuning. Deep Packet Inspection (DPI) is widely used for identifying normal applications and attacks in the network by looking for well-known patterns within the packets. Such patterns are mostly expressed by Regular Expressions (RE), which are then evaluated by abstract machines known as Deterministic Finite Automata (DFA). Some previous studies grouped DFAs together to evaluate multiple patterns on a single DFA match's run. Efficient grouping algorithms would combine several DFAs without exceeding the available machine's memory. This work proposes and evaluates a new method to combine several DFAs into a single one. Additionally we compared this algorithm to state-of-the-art approaches using a compressed DFA model. Experimental results show that our algorithm generates less groups and transitions than existent algorithms.
2017 HRS/EHRA/ECAS/APHRS/SOLAECE expert consensus statement on catheter and surgical ablation of atrial fibrillation: executive summary (2017)

During the past three decades, catheter and surgical ablation of atrial fibrillation (AF) have evolved from investigational procedures to their current role as effective treatment options for patients with AF. Surgical ablation of AF, using either standard, minimally invasive, or hybrid techniques, is available in most major hospitals throughout the world. Catheter ablation of AF is even more widely available, and is now the most commonly performed catheter ablation procedure.
Oral Antimicrobial Rinse to Reduce Mycobacterial Culture Contamination among Tuberculosis Suspects in Uganda: A Prospective Study (2012)

Oral rinse prior to sputum expectoration is a promising strategy to reduce mycobacterial culture contamination in areas with high HIV prevalence, if strategies can be devised to reduce the adverse impact of oral rinse on smear- and culture-positivity.