gebhart/patrepeval huggingface dataset:
Nanoallergens: A multivalent platform for studying and evaluating potency of allergen epitopes in cellular degranulation (2016)

Degranulation caused by type I hypersensitivity (allergies) is a complex biophysical process, and available experimental models for studying relevant immunoglobulin E binding epitopes on allergen proteins lack the ability to adequately evaluate, rank, and associate these epitopes individually and with each other. In this study, we propose a new allergy model system for studying potential allergen epitopes using nanoallergens, liposomes modified to effectively display IgE binding epitopes/haptens. By utilizing the covalently conjugated lipid tails on two hapten molecules (dinitrophenol and dansyl), hapten molecules were successfully incorporated into liposomes with high precision to form nanoallergens. Nanoallergens, with precisely controlled high-particle valency, can trigger degranulation with much greater sensitivity than commonly used bovine serum albumin conjugates. In rat basophil leukemia cell experiments, nanoallergens with only 2% hapten loading were able to trigger degranulation in vitro at concentrations as low as 10 pM. Additionally, unlike bovine serum albumin-hapten conjugates, nanoallergens allow exact control over particle size and valency. By varying the nanoallergen parameters such as size, valency, monovalent affinity of hapten, and specific IgE ratios, we exposed the importance of these variables on degranulation intensity while demonstrating nanoallergens' potential for evaluating both high- and low-affinity epitopes. The data presented in this article establish nanoallergen platform as a reliable and versatile allergy model to study and evaluate allergen epitopes in mast cell degranulation.
Anti-Helicobacter pylori Activity of Quinolone Alkaloids from Evodiae Fructus. (1999)

A biologically monitored fractionation of methanol extract of the fruit of Evodia rutaecarpa led to the isolation of six quinolone alkaloids, evocarpine (1), 1-methyl-2-[(4Z,7Z)-4,7-tridecadienyl]-4(1H)-quinolone (2), 1-methyl-2-[(6Z,9Z)-6,9-pentadecadienyl]-4(1H)-quinolo ne (3), 1-methyl-2-undecyl-4(1H)-quinolone (4), dihydroevocarpine (5), 1-methyl-2-pentadecyl-4(1H)-quinolone (6). They showed potent anti-Helicobacter pylori activity with the minimum inhibitory concentration (MIC) value of 10-20 microg/ml. However, they had no effect on Helicobacter pylori urease activity at the concentration of 300 microg/ml.
A Hidden Semi-Markov Model-Based Speech Synthesis System (2007)

A statistical speech synthesis system based on the hidden Markov model (HMM) was recently proposed. In this system, spectrum, excitation, and duration of speech are modeled simultaneously by context-dependent HMMs, and speech parameter vector sequences are generated from the HMMs themselves. This system defines a speech synthesis problem in a generative model framework and solves it based on the maximum likelihood (ML) criterion. However, there is an inconsistency: although state duration probability density functions (PDFs) are explicitly used in the synthesis part of the system, they have not been incorporated into its training part. This inconsistency can make the synthesized speech sound less natural. In this paper, we propose a statistical speech synthesis system based on a hidden semi-Markov model (HSMM), which can be viewed as an HMM with explicit state duration PDFs. The use of HSMMs can solve the above inconsistency because we can incorporate the state duration PDFs explicitly into both the synthesis and the training parts of the system. Subjective listening test results show that use of HSMMs improves the reported naturalness of synthesized speech.
Iterative Decoding of Low-Density Parity Check Codes (A Survey) (2006)

Much progress has been made on decoding algorithms for error-correcting codes in the last decade. In this article, we give an introduction to some fundamental results on iterative, message-passing algorithms for low-density parity check codes. For certain important stochastic channels, this line of work has enabled getting very close to Shannon capacity with algorithms that are extremely efficient (both in theory and practice).
A Remotely Powered Implantable Biomedical System With Location Detector (2014)

An universal remote powering and communication system is presented for the implantable medical devices. The system be interfaced with different sensors or actuators. A mobile external unit controls the operation of the implantable chip and reads the sensor's data. A locator system is proposed to align the mobile unit with the implant unit for the efficient magnetic power transfer. The location of the implant is detected with 6 mm resolution from the rectified voltage level at the implanted side. The rectified voltage level is fedback to the mobile unit to adjust the magnetic field strength and maximize the efficiency of the remote powering system. The sensor's data are transmitted by using a free running oscillator modulated with on-off key scheme. To tolerate large data carrier drifts, a custom designed receiver is implemented for the mobile unit. The circuits have been fabricated in 0.18 um CMOS technology. The remote powering link is optimized to deliver power at 13.56 MHz. On chip voltage regulator creates 1.8 V from a 0.9 V reference voltage to supply the sensor/actuator blocks. The implantable chip dissipates 595 μW and requires 1.48 V for start up.
A cycloaddition approach to 3-acyltetramic and 3-acyltetronic acids (1994)

1, 3-Dipolar cycloaddition of nitrite oxides to enamines formed from protected γ-amino- or γ-hydroxy-β-keto esters affords isoxazolecarboxylic esters that can be converted into 3-acyltetramic acids via dihydropyrroloisoxazol-4-ones, or into 3-acyltetronic acids.
Active Site and Electronic Structure Elucidation of Pt Nanoparticles Supported on Phase-Pure Molybdenum Carbide Nanotubes (2017)

We recently showed that phase-pure molybdenum carbide nanotubes can be durable supports for platinum (Pt) nanoparticles in hydrogen evolution reaction (HER). In this paper we further characterize surface properties of the same Pt/β-Mo<sub>2</sub>C catalyst platform using carbon monoxide (CO)-Pt and CO-Mo<sub>2</sub>C bond strength of different Pt particle sizes in the <3 nm range. Results from diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and temporal analysis of products (TAP) revealed the existence of different active sites as Pt particle size increases. Correlation between the resultant catalyst activity and deposited Pt particle size was further investigated using water-gas-shift (WGS) as a probe reaction, suggesting that precise control of particle diameter and thickness is needed for optimized catalytic activity.
Mouse Models of Multiple Sclerosis: Lost in Translation? (2015)

Multiple sclerosis (MS) is a chronic neurological disorder of the central nervous system (CNS) leading to progressive accumulation of neurological deficits arising from recurrent episodes of inflammation, demyelination and neuronal degeneration. While the aetiology of the disease is unknown MS is widely considered to be the result of aberrant T cell and antibody responses to CNS antigens giving rise to the common concept that MS is an autoimmune disease or that there is an autoimmune component in the pathogenesis. This idea has lead to the development of experimental autoimmune encephalomyelitis (EAE) mouse models of MS in which immunisation with CNS antigens induces neurological and pathological signs of disease in mice. In addition to EAE models, injection with neurotropic viruses has been used to examine how infections are implicated in the disease process and how they may generate autoimmune responses in the CNS. Viral models are also crucial to investigate the impact of blocking trafficking of immune responses into the CNS since an emerging side-effect of current immunotherapeutic approaches in MS is the reactivation of viruses within the CNS. To investigate myelin damage and repair in the absence of the adaptive immune response, toxin-induced demyelination using cuprizone, ethidium bromide and lysolecithin, which rapidly leads to remyelination when the toxins are withdrawn, is also reviewed. Mice also lend themselves to the vast array of transgenic technologies to probe specific pathways as well as the use of humanised transgenic mice to examine the impact of human molecules. Despite the vast array of mouse models EAE is the most frequently exploited paradigm used to develop therapeutic approaches. However, despite over one thousand compounds used in the treatment of EAE few have become licenced for treatment of MS so far. Thus, this review also debates the reasons for these failures in mouse models as well as discusses how mouse models can be better utilised to provide more powerful preclinical tools to develop rational therapies for multiple sclerosis.
Effects of Exogenous Growth Hormone on Milk Production and Nutrient Uptake by Muscle and Mammary Tissues of Dairy Cows in Mid-lactation (1987)

Responses to exogenous growth hormone were measured in lactating dairy cows surgically prepared to allow measurement of nutrient exchanges across mammary and hind-limb muscle tissues. Cows were injected daily with either saline or growth hormone, at a dose of 0.1 mg/kg liveweight, over periods of 6 days. During administration of growth hormone milk yield, milk fat content and yields of milk fat protein and lactose increased. Arterial plasma concentrations of glucose and non-esterified fatty acids were increased, uptake of glucose by leg muscle tissue decreased, lactate release from leg muscle tended to increase, mammary uptake of non-esterified fatty acids increased, blood flow to leg muscle tended to increase and blood flow to mammary tissue increased during injection of growth hormone. The results show that growth hormone affects supply to and utilization of key nutrients by tissues, resulting in the supply to the mammary gland of additional precursors for milk synthesis.
A straightforward closed-loop Wireless Power Transfer battery charger (2016)

Recent advances in Wireless Power Transfer (WPT) technology have allowed its application in numerous different fields. When employing loosely coupled coils to implement WPT systems, power transferred to the load tends to decrease as misalignment between antennas increases. In practical applications such as in electric vehicles (EV) wireless battery charging perfect coils positioning is hardly achieved without the use of position sensors. This paper presents a simple WPT system architecture with two closed-loops control algorithms that allow automatic power regulation up to a certain misalignment level. The proposed solution uses a small number of sensors and a simplex radio frequency communication channel to feed back voltage, current and power information from the secondary circuit to the primary side microcontroller.
Speculative Fictions and Curricular Futures (2021)

Situated within the local context of New Brunswick—a small, mostly rural, Canadian province with an aging population and a steady influx of new residents from other countries—this article speculates new curricular possibilities beyond the post-industrial and neoliberal structures of current curriculum and schooling. The authors approach their speculation creatively through a collectively-authored narrative meant to engage the idea of educational utopia within their shared place. In a subsequent discussion of the narrative, the authors reflect on the global phenomenon of neoliberal ideological intrusion into curriculum as manifest in New Brunswick, as well as the myriad forms that intrusion can take. Specifically, the authors discuss: the continued modeling of the school system on adult work, the rigid control of time and the dangers of flexibility in schooling, the desire to expand concepts of community involvement in education, and the urgent necessity of racial equity work in rural spaces. In concluding their discussion, the authors highlight the potential of dreaming new curricular possibilities to disrupt the status quo of education locally and globally.
Specificity and Polymorphism of the PlcR-PapR Quorum-Sensing System in the<i>Bacillus cereus</i>Group (2005)

The expression of extracellular virulence factors in various species of the Bacillus cereus group is controlled by the plcR and papR genes, which encode a transcriptional regulator and a cell-cell signaling peptide, respectively. A processed form of PapR, presumably a pentapeptide, specifically interacts with PlcR to facilitate its binding to its DNA targets. This activating mechanism is strain specific, with this specificity being determined by the first residue of the pentapeptide. We carried out in vivo complementation assays and compared the PlcR-PapR sequences of 29 strains from the B. cereus group. Our findings suggested that the fifth amino acid of the pentapeptide is also involved in the specificity of activation. We identified four classes of PlcR-PapR pairs, defining four distinct pherotypes in the B. cereus group. We used these findings to look at the evolution of the PlcR-PapR quorum-sensing system with regard to the phylogeny of the species forming the B. cereus group.
A fast MBAFF mode prediction strategy for H.264/AVC (2005)

As a new technique, MBAFF is added to H.264/AVC to achieve higher compression efficiency for interlaced video materials. However, at the same time the complexity increases largely because of the triple-pass nature of the algorithm. Therefore, reducing the coding complexity by detecting the encoding mode of each MB is necessary. A novel fast MBAFF mode prediction strategy is proposed in this paper, it gives out a promising estimation of the encoding mode for each MB and it requires only one pass of the data. Experiment results prove that the proposed algorithm significantly reduces the computation of coding, while preserving video quality to an acceptable level.
Formation of compounds by nitrogen ion implantation in iron (1983)

The phase composition of iron after implantation with doses form 1 × 1016 N+ cm−2 to 1 × × 1018 N+ cm−2 at room temperature is investigated by high-voltage electron microscopy and selected area diffraction. The formation of iron nitride and iron carbonitride phases are considered in dependence of implantation dose. In the dose range from 1 × 1016 up to 4 × 1016 N+ cm−2 γ-austenite solid solution is produced. In the dose range from 4 × 1016 up to 1 × 1018 N+ cm−2 α-martensite, α-Fe16N2 and ϵ-Fe2N1−x are observed in addition to the γ-austenite phase. The differrent crystal morphology of iron nitrides are imagined. It is found that ϵ-iron carbonitride can be proved above implantation doses of 7.5 × 1016 N+ cm−2. The implantation-induced phase formation of iron nitride phases are discussed. Die Phasenzusammensetzung von Eisen nach Implantation von 1 × 1016 N+ cm−2 bis 1 × × 1018 N+ cm−2 bei Raumtemperatur wird mit der Höchstspannungs-Elektronenmikroskopie und der Elektronen-Feinbereichsbeugung untersucht. Die Bildung von Eisennitrid- und Eisenkarbonnitrid-Phase wird in Abhängigkeit von der Implantationsdosis betrachtet. Im Dosisbereich von 1 × 1016 bis 1 × 1018 N+ cm−2 entsteht die γ-Austenit-Mischkristallphase. Im Dosisbereich von 4 × 1016 bis 1 × 1018 werden zusätzlich zur γ-Austenitphase, das α′-Martensit, Fe16N2 und ϵ-Fe2N1−x beobachtet. Die unterschiedlichen Kristallmorphologien der Eisennitride werden vorgestellt. Es wurde gefunden, daß ϵ-Eisenkarbonitride oberhalb einer Implantationsdosis von 7,5 × × 1016 N+ cm−2 nachgewiesen werden kann. Die Implantations-induzierte Phasenbildung von Eisennitriden wird diskutiert.
G<i>γ</i>1 + G<i>γ</i>2 = G<i>β</i>: Heterotrimeric G Protein G<i>γ</i>-Deficient Mutants Do Not Recapitulate All Phenotypes of G<i>β</i>-Deficient Mutants       (2008)

Heterotrimeric G proteins are signaling molecules ubiquitous among all eukaryotes. The Arabidopsis (Arabidopsis thaliana) genome contains one Galpha (GPA1), one Gbeta (AGB1), and two Ggamma subunit (AGG1 and AGG2) genes. The Gbeta requirement of a functional Ggamma subunit for active signaling predicts that a mutant lacking both AGG1 and AGG2 proteins should phenotypically resemble mutants lacking AGB1 in all respects. We previously reported that Gbeta- and Ggamma-deficient mutants coincide during plant pathogen interaction, lateral root development, gravitropic response, and some aspects of seed germination. Here, we report a number of phenotypic discrepancies between Gbeta- and Ggamma-deficient mutants, including the double mutant lacking both Ggamma subunits. While Gbeta-deficient mutants are hypersensitive to abscisic acid inhibition of seed germination and are hyposensitive to abscisic acid inhibition of stomatal opening and guard cell inward K+ currents, none of the available Ggamma-deficient mutants shows any deviation from the wild type in these responses, nor do they show the hypocotyl elongation and hook development defects that are characteristic of Gbeta-deficient mutants. In addition, striking discrepancies were observed in the aerial organs of Gbeta- versus Ggamma-deficient mutants. In fact, none of the distinctive traits observed in Gbeta-deficient mutants (such as reduced size of cotyledons, leaves, flowers, and siliques) is present in any of the Ggamma single and double mutants. Despite the considerable amount of phenotypic overlap between Gbeta- and Ggamma-deficient mutants, confirming the tight relationship between Gbeta and Ggamma subunits in plants, considering the significant differences reported here, we hypothesize the existence of new and as yet unknown elements in the heterotrimeric G protein signaling complex.
The proteasome inhibitors bortezomib and PR‐171 have antiproliferative and proapoptotic effects on primary human acute myeloid leukaemia cells (2007)

Proteasome inhibitors represent a new class of antineoplastic drugs that are considered in the treatment of haematological malignancies. We compared the effects of the reversible proteasome inhibitor bortezomib (Velcade) and the epoxomicin derivative PR-171, an irreversible inhibitor, on primary human acute myeloid leukaemia (AML) cells. Both drugs inhibited autocrine- and cytokine-dependent proliferation of primary AML blasts when tested at nanomolar levels (0.1-100 nmol/l). The antiproliferative effect was independent of basal chymotrypsin-like proteasome activity (showing a 20-fold variation between patients), genetic abnormalities, morphological differentiation and CD34 expression when testing a large group of consecutive patients (n = 54). The effect was retained in cocultures with bone marrow stromal cells. In addition, both drugs enhanced apoptosis. The effect of PR-171 could be detected at lower concentrations than for bortezomib, especially when testing the influence on clonogenic AML cell proliferation. Both drugs had divergent effects on AML cells' constitutive cytokine release. Furthermore, both drugs caused a decrease in proliferation and viability when tested in combination with idarubicin or cytarabine. An antiproliferative effect on primary human acute lymphoblastic leukaemia cells was also detected. We conclude that nanomolar levels of the proteasome inhibitors tested had dose-dependent antiproliferative and proapoptotic effects on primary AML cells in vitro.
Development and Genetic Characterization of A Novel Herbicide (Imazethapyr) Tolerant Mutant in Rice (Oryza sativa L.) (2017)

A novel mutant tolerant to the herbicide "Imazethapyr" was developed and characterized for genetic, sequence and protein level variations. This is a HTM in rice without any IPR (Intellectual Property Rights) infringements and hence can be used in rice breeding as a novel genetic stock by the public funded organizations in the country and elsewhere.
Differential Proximity Probing of Two DNA Binding Sites in the <i>Escherichia coli</i> RecA Protein Using Photo-Cross-Linking Methods (1996)

The DNA strand-exchange reaction catalyzed by the Escherichia coli RecA protein occurs between the two DNA binding sites that are functionally distinct. Site I is the site to which a DNA molecule (normally single-stranded DNA) binds first; this first binding makes site II available for additional DNA-binding (normally double- stranded DNA). Photo-cross linking was employed to identify the amino acid residues located close to the bound DNA molecule(s). A ssDNA oligo containing multiple 5-iodouracil residues (IdU) was cross-linked to RecA by irradiation with a XeC1 pulse laser (308 nm), and the cross-linked peptides were purified and sequenced. To differentiate the two DNA binding sites, we used two protocols for making RecA-ssDNA complexes: (1) IdU-containing oligo was mixed with a stoichiometric excess of RecA, a condition which favors the binding of the oligo to site I, and (2) RecA was first allowed to bind to a nonphotoreactive oligo and then chased with the IdU-containing oligo, a condition which favors the binding of the IdU-oligo to site II. We observed that when RecA was in excess (site I probing), cross-linking occurred to Met-164 which is located in the disordered loop 1 of the RecA crystal structure [Story, R.M., Weber, I.T., & Steitz, T.A. (1992) Nature 355, 318-325]. When site II was probed, the majority of cross-linking occurred to Met-202 or Phe-203, located in loop 2. These results support the idea that, as predicted by Story and co-workers (1992), the disordered loops are involved in DNA binding. The results also suggest that the two sites are not only functionally but also physically distinct.
Acclimation to Very Low CO<sub>2</sub>: Contribution of Limiting CO<sub>2</sub> Inducible Proteins, LCIB and LCIA, to Inorganic Carbon Uptake in <i>Chlamydomonas reinhardtii</i> (2014)

The limiting-CO2 inducible CO2-concentrating mechanism (CCM) of microalgae represents an effective strategy to capture CO2 when its availability is limited. At least two limiting-CO2 acclimation states, termed low CO2 and very low CO2, have been demonstrated in the model microalga Chlamydomonas reinhardtii, and many questions still remain unanswered regarding both the regulation of these acclimation states and the molecular mechanism underlying operation of the CCM in these two states. This study examines the role of two proteins, Limiting CO2 Inducible A (LCIA; also named NAR1.2) and LCIB, in the CCM of C. reinhardtii. The identification of an LCIA-LCIB double mutant based on its inability to survive in very low CO2 suggests that both LCIA and LCIB are critical for survival in very low CO2. The contrasting effects of individual mutations in LCIB and LCIA compared with the effects of LCIB-LCIA double mutations on growth and inorganic carbon-dependent photosynthetic O2 evolution reveal distinct roles of LCIA and LCIB in the CCM. Although both LCIA and LCIB are essential for very low CO2 acclimation, LCIB appears to function in a CO2 uptake system, whereas LCIA appears to be associated with a HCO3(-) transport system. The contrasting and complementary roles of LCIA and LCIB in acclimation to low CO2 and very low CO2 suggest a possible mechanism of differential regulation of the CCM based on the inhibition of HCO3(-) transporters by moderate to high levels of CO2.