gebhart/patrepeval huggingface dataset:
Neuronal Acetylcholine Receptors with α7 Subunits Are Concentrated on Somatic Spines for Synaptic Signaling in Embryonic Chick Ciliary Ganglia (1999)

Nicotinic acetylcholine receptors containing alpha7 subunits are widely distributed in the vertebrate nervous system. In the chick ciliary ganglion such receptors generate large synaptic currents but appear to be excluded from postsynaptic densities on the cells. We show here that alpha7-containing receptors are concentrated on somatic spines in close proximity to putative sites of presynaptic transmitter release. Intermediate voltage electron microscopy on thick sections, together with tomographic reconstruction, permitted three-dimensional analysis of finger-like projections emanating from cell bodies. The projections were identified as spines based on their morphology, cytoskeletal content, and proximity to presynaptic elements. Both in situ and after ganglionic dissociation, the spines were grouped on the cell surface and tightly folded into mats. Immunogold labeling of receptors containing alpha7 subunits showed them to be preferentially concentrated on the somatic spines. Postsynaptic densities were present in vivo both on the soma near spines and occasionally on the spines themselves. Synaptic vesicle-filled projections from the presynaptic calyx were interdigitated among the spines. Moreover, the synaptic vesicles often abutted the membrane and sometimes included Omega profiles as if caught in an exocytotic event, even when no postsynaptic densities were juxtaposed on the spine. The results suggest several mechanisms for delivering transmitter to alpha7-containing receptors, and they support new ideas about synaptic signaling via spines. They also indicate that neurons must have specific mechanisms for targeting alpha7-containing receptors to desired locations.
The Performance of Modular Precast Concrete Frames, That Are Not Part of the Primary Lateral Force Resisting System, under Simulated Seismic Loading (1995)

Two research projects investigated the performance of full-sized precast concrete beam and column sub-assemblies tested under simulated seismic attack. The assemblies are suitable for rapid-erection, modular frames. The principal role of the modular frames is to support gravity loads. The frames are not part of the 'primary' lateral force resisting system. The 'secondary' frames rely on the 'primary' system for lateral stability. However, additional flexure, shear and axial forces can be induced in the 'secondary' frames because of lateral deformations that arise from the flexibility of the 'primary' systems during seismic activity. The aim of the projects was to establish the deformational capacities and the adequacy of detailing of various beam-to-column connections of two types of 'secondary' frames, during seismic events.
FLU-v, a Broad-Spectrum Influenza Vaccine, Induces Cross-Reactive Cellular Immune Responses in Humans Measured by Dual IFN-γ and Granzyme B ELISpot Assay (2022)

Previous reports demonstrated that FLU-v, a peptide-based broad-spectrum influenza vaccine candidate, induced antibody and cellular immune responses in humans. Here, we evaluate cellular effector functions and cross-reactivity. PBMC sampled pre- (day 0) and post-vaccination (days 42 and 180) from vaccine (n = 58) and placebo (n = 27) recipients were tested in vitro for responses to FLU-v and inactivated influenza strains (A/H3N2, A/H1N1, A/H5N1, A/H7N9, B/Yamagata) using IFN-γ and granzyme B ELISpot. FLU-v induced a significant increase in the number of IFN-γ- and granzyme-B-secreting cells responding to the vaccine antigens from pre-vaccination (medians: 5 SFU/106 cells for both markers) to day 42 (125 and 40 SFU/106 cells, p &lt; 0.0001 for both) and day 180 (75 and 20 SFU/106 cells, p &lt; 0.0001 and p = 0.0047). The fold increase from pre-vaccination to day 42 for IFN-γ-, granzyme-B-, and double-positive-secreting cells responding to FLU-v was significantly elevated compared to placebo (medians: 16.3-fold vs. 1.0-fold, p &lt; 0.0001; 3.5-fold vs. 1.0-fold, p &lt; 0.0001; 3.0-fold vs. 1.0-fold, p = 0.0012, respectively). Stimulation of PBMC with inactivated influenza strains showed significantly higher fold increases from pre-vaccination to day 42 in the vaccine group compared to placebo for IFN-γ-secreting cells reacting to H1N1 (medians: 2.3-fold vs. 0.8-fold, p = 0.0083), H3N2 (1.7-fold vs. 0.8-fold, p = 0.0178), and H5N1 (1.7-fold vs. 1.0-fold, p = 0.0441); for granzyme B secreting cells reacting to H1N1 (3.5-fold vs. 1.0-fold, p = 0.0075); and for double positive cells reacting to H1N1 (2.9-fold vs. 1.0-fold, p = 0.0219), H3N2 (1.7-fold vs. 0.9-fold, p = 0.0136), and the B strain (2.0-fold vs. 0.8-fold, p = 0.0227). The correlation observed between number of cells secreting IFN-γ or granzyme B in response to FLU-v and to the influenza strains supported vaccine-induced cross-reactivity. In conclusion, adjuvanted FLU-v vaccination induced cross-reactive cellular responses with cytotoxic capacity, further supporting the development of FLU-v as a broad-spectrum influenza vaccine.
P1‐499: Correction of bias in estimating rate of cognitive decline using auxiliary telephone cognitive evaluation data (2011)

In longitudinal studies of cognitive decline, missing data may arise due to drop out, lost to follow-up, death or missed visits. Most analyses assume that the data are missing at random (MAR). There is evidence that loss to follow-up may be occur at higher rates in persons with more rapid cognitive decline suggesting that the MAR assumption may result in biased estimation of rates of cognitive decline. In the Einstein Aging Study, participants receive cognitive assessments on the telephone and in-person. Participants with missing in-person assessments often have a telephone assessment. The telephone assessment provides an opportunity to test the MAR assumption under the assumption of auxiliary variable MAR (A-MAR), and correct the bias if it is violated. We used two methods to jointly model the in-house Free and Cued Selective Reminding (FCSRT) and the telephone Memory Impairment Screen (MIS): (1) A linear mixed model in which the FCSRT and MIS had separate, correlated random effects, and (2) A linear mixed model in which the FCSRT and MIS share a common random effect. The second model more tightly links the auxiliary variable (MIS) to the variable of primary interest (FCSRT). We compared results from these models to that in which the missingness was ignored. A sample of 1818 EAS participants with a baseline age of 79.0±5.4 years (Mean±SE), 13.1±3.6 years of education, an average of 3.0 waves of in-house assessments (maximum 19) and a total of 4222 person-years of follow-up. Participants with lower MIS score were more likely to have missing FCSRT. The estimated rate of decline in FCSRT ignoring the missingness was 0.333 (SE = 0.020) points per year. In the correlated random effects model, the estimate was 0.363 (SE = 0.0198) points per year. In the shared random effects model, the estimate was 0.368 (SE = 0.0198) points per year. The naïve estimate of cognitive decline that ignored potentially informative missing data was underestimated by approximately 10%. Joint modeling with auxiliary telephone data has the potential to correct some of the bias associated with informative missingness. This or similar strategies could improve estimates of age and dementia related cognitive decline.
High-Throughput Sequencing-Based Immune Repertoire Study during Infectious Disease (2016)

The selectivity of the adaptive immune response is based on the enormous diversity of T and B cell antigen-specific receptors. The immune repertoire, the collection of T and B cells with functional diversity in the circulatory system at any given time, is dynamic and reflects the essence of immune selectivity. In this article, we review the recent advances in immune repertoire study of infectious diseases, which were achieved by traditional techniques and high-throughput sequencing (HTS) techniques. HTS techniques enable the determination of complementary regions of lymphocyte receptors with unprecedented efficiency and scale. This progress in methodology enhances the understanding of immunologic changes during pathogen challenge and also provides a basis for further development of novel diagnostic markers, immunotherapies, and vaccines.
ChemInform Abstract: ENAMINES AND IMINIUM SALTS FROM AMIDO ACIDS (1984)

Abstract Bei der Destillation der Carbonsäuren (I), (III), (VI) und (IX) (Synthesen im experimentellen Teil beschrieben) unter der gegebenen Reaktionsbedingung bilden sich bicyclische Enamine, die in Form der Salze (II), (IV), (VII) und (X) isoliert werden.
Effect of preplant seed conditioning treatment on the germination of switchgrass (Panicum virgatum L.). (2000)

Switchgrass (Panicum virgatum. L.) is being developed and evaluated as summer forage and for biomass production in eastern Canada. Uneven germination and slow seedling growth in spring are some of the factors limiting its cultivation. A study was conducted to reduce seed dormancy and to improve germination at suboptimal temperatures in switchgrass cultivars Cave-in-Rock (CIR), Dakota (DK) and New Jersey 50 (NJ). Seeds of these cultivars were conditioned either with 0.2% potassium nitrate (KNO 3 ) or 1mM gibberellic acid or osmo-conditioned with polyethylene glycol 8000 (PEG) solution with or without 0.2% KNO 3 or 1 mM gibberellic acid (GA 3 ); or matriconditioned with Micro-Cel E (MC) with either water, 0.2% KNO 3 or 1 mM GA 3 . The seeds were conditioned at 8 or 16°C for 4 days and then germinated at 8, 16 or 24°C. Conditioning treatment and temperature influenced germination. For CIR seeds germinated at 8°C, conditioning with PEG at 8°C increased germination from 0 (control) to 22%. All the conditioning treatments germinated earlier and the proportion of seeds that eventually germinated was higher than for the unconditioned control. In the cultivar NJ conditioning at 16°C with water or 1 mM GA 3 increased germination to 12 and 17% respectively (0 for the control) when seeds were germinated at 8°C. When germinated at 16°C treatments containing 1 mM GA 3 germinated earlier. Osmoconditioning in PEG with 1 mM GA 3 had the highest final germination at 56% (37% for control). Cultivar DK did not significantly respond to the various conditioning treatments. Overall, both osmoconditioning and matriconditioning hastened germination and total germination in switchgrass cultivars CIR and NJ.
Mechanical property measurement of nano-scale metal films on the novel paddle cantilever beams using four step phase-shifting method (2008)

A test structure with nano-scale metal films, which is deposited on the novel paddle-like cantilever beam, was successfully fabricated and calibrated using standard C-MOS processes. Compared to the traditional cantilevered beam, the 40 mum thickness paddle-like structure provides the uniform stress distribution along the whole beam to decrease the measurement variation. The deflections of argentums, gold, and copper films (50-250 nm) driven by the electrostatic force were measured using four step phase-shifting method. The results present that the test structure and the optical (FSPS) method work properly. Furthermore, argentums presents that the deflection decreases after deposition to demonstrate that the tensile residual stress in the film. Oppositely, gold and copper films show compressive residual stress in them.
Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov., halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in Bacillus rRNA group 1 (2005)

Eleven novel strains of marine-inhabiting lactic acid bacteria that were isolated from living and decaying marine organisms collected from a temperate area of Japan are described. The isolates were motile with peritrichous flagella and non-sporulating. They lacked catalase, quinones and cytochromes. Fermentation products from glucose were lactate, formate, acetate and ethanol. Lactate yield as percentage conversion from glucose was affected by the pH of the fermentation medium: approximately 55 % at the optimal growth pH of 8.0, greater than approximately 70 % at pH 7.0 and less than approximately 30 % at pH 9.0. The molar ratio of the other three products was the same at each cultivation pH, approximately 2 : 1 : 1. Carbohydrates and related compounds were aerobically metabolized to acetate and pyruvate as well as lactate. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth was 2.0-3.0 % (w/v), with a range of 0-25.5 %. The optimum pH for growth was 8.0-9.5, with a range of 6.0-10.0. The G+C content of the DNA was 38.5-40.7 mol%. The isolates constituted two genomic species (DNA-DNA relatedness of less than 41 %) each characterized by sugar fermentation profiles. The cell-wall peptidoglycan of both phenotypes contained meso-diaminopimelic acid. The major cellular fatty acids were C(16 : 0) and a-C(13 : 0). Comparative sequence analysis of the 16S rRNA genes revealed that these isolates represent novel species constituting a phylogenetic unit outside the radiation of typical lactic acid bacteria and an independent line of descent within the group composed of the halophilic/halotolerant/alkaliphilic and/or alkalitolerant species in Bacillus rRNA group 1, with 94.8-95.1 % similarity to the genus Paraliobacillus, 93.7-94.1 % to the genus Gracilibacillus and 93.8-94.2 % to Virgibacillus marismortui. On the basis of possession of physiological and biochemical characteristics common to typical lactic acid bacteria within Bacillus rRNA group 1, chemotaxonomic characteristics and phylogenetic independence, a new genus and two species, Halolactibacillus halophilus gen. nov., sp. nov. and Halolatibacillus miurensis sp. nov., are proposed. The type strains are Halolactibacillus halophilus M2-2T (=DSM 17073T=IAM 15242T=NBRC 100868T=NRIC 0628T) (G+C content 40.2 mol%) and Halolactibacillus miurensis M23-1T (=DSM 17074T=IAM 15247T=NBRC 100873T=NRIC 0633T) (G+C content 38.5 mol%).
An intranasal vaccine durably protects against SARS-CoV-2 variants in mice (2021)

ABSTRACT SARS-CoV-2 variants that attenuate antibody neutralization could jeopardize vaccine efficacy and the end of the COVID-19 pandemic. We recently reported the protective activity of a single-dose intranasally-administered spike protein-based chimpanzee adenovirus-vectored vaccine (ChAd-SARS-CoV-2-S) in animals, which has advanced to human trials. Here, we assessed its durability, dose-response, and cross-protective activity in mice. A single intranasal dose of ChAd-SARS-CoV-2-S induced durably high neutralizing and Fc effector antibody responses in serum and S-specific IgG and IgA secreting long-lived plasma cells in the bone marrow. Protection against a historical SARS-CoV-2 strain was observed across a 100-fold vaccine dose range and over a 200-day period. At 6 weeks or 9 months after vaccination, serum antibodies neutralized SARS-CoV-2 strains with B.1.351 and B.1.1.28 spike proteins and conferred almost complete protection in the upper and lower respiratory tracts after challenge. Thus, in mice, intranasal immunization with ChAd-SARS-CoV-2-S provides durable protection against historical and emerging SARS-CoV-2 strains.
Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes (2023)

Complex mechanisms regulate the cellular distribution of cholesterol, a critical component of eukaryote membranes involved in regulation of membrane protein functions directly and through the physiochemical properties of membranes. StarD4, a member of the steroidogenic acute regulator-related lipid-transfer (StART) domain (StARD)-containing protein family, is a highly efficient sterol-specific transfer protein involved in cholesterol homeostasis. Its mechanism of cargo loading and release remains unknown despite recent insights into the key role of phosphatidylinositol phosphates in modulating its interactions with target membranes. We have used large-scale atomistic Molecular dynamics (MD) simulations to study how the dynamics of cholesterol bound to the StarD4 protein can affect interaction with target membranes, and cargo delivery. We identify the two major cholesterol (CHL) binding modes in the hydrophobic pocket of StarD4, one near S136&S147 (the Ser-mode), and another closer to the putative release gate located near W171, R92&Y117 (the Trp-mode). We show that conformational changes of StarD4 associated directly with the transition between these binding modes facilitate the opening of the gate. To understand the dynamics of this connection we apply a machine-learning algorithm for the detection of rare events in MD trajectories (RED), which reveals the structural motifs involved in the opening of a front gate and a back corridor in the StarD4 structure occurring together with the spontaneous transition of CHL from the Ser-mode of binding to the Trp-mode. Further analysis of MD trajectory data with the information-theory based NbIT method reveals the allosteric network connecting the CHL binding site to the functionally important structural components of the gate and corridor. Mutations of residues in the allosteric network are shown to affect the performance of the allosteric connection. These findings outline an allosteric mechanism which prepares the CHL-bound StarD4 to release and deliver the cargo when it is bound to the target membrane.
Thermal Properties of 1.3 µm AlGaInAs Multi Quantum Well Ridge Waveguide Lasers (2000)

We have fabricated 1.3 µm AlGaInAs/InP multi-quantum-well (MQW) ridge waveguide lasers with both junction-up and junction-down mounting, and compared the thermal resistance ( R th ) and other laser characteristics such as the maximum CW operating temperature ( T max ), characteristic temperature of threshold current ( T 0 ), and the maximum CW output power ( P max ). The thermal resistance was found to be 73.6 K/W and 43.5 K/W for junction-up and -down mounting, respectively. T 0 , T max and P max were also improved by 7 K, 20°C and 20% in the junction-down configuration, respectively, which is due to a reduction of the thermal resistance. A CW T max as high as 185°C has also been achieved with 350-µm-long high-reflective-coated lasers, which is one of the highest CW operation temperature reported to date for InP-based long wavelength lasers.
Material Design for Transparent Ferromagnets with ZnO-Based Magnetic Semiconductors (2000)

Ferromagnetism of ZnO-based magnetic semiconductors was investigated by ab initio calculations based on the local density approximation. In a system of Mn atom doped ZnO, the ferromagnetic ordering of Mn magnetic moments was induced by hole doping. It was also found that 3 d transition metal atoms of V, Cr, Fe, Co and Ni showed the ferromagnetic ordering of their magnetic moments in ZnO without any additional carrier doping treatments. Appearance of the ferromagnetism in these systems suggests possibility for a fabrication of a transparent ferromagnet which will have great impact on industrial applications in magneto optical devices.
Preparación de micro-supercondensadores mediante electrosprayado de materiales carbonosos nanoestructurados (2015)

Los materiales carbonosos nanoestructurados presentan excelentes propiedades eléctricas, texturales y estructurales, que pueden ser aprovechadas para la fabricación de microcondensadores de elevada potencia y energía, fundamentales en el desarrollo de dispositivos electrónicos portátiles. Sin embargo, el reducido tamaño de sus partículas dificulta su procesado en láminas delgadas, impidiendo un control adecuado de la forma y el espesor de capas finas de estos materiales. Los procedimientos basados en la preparación directa de materiales carbonosos sobre el colector de corriente condicionan la composición y estructura del electrodo, lo que provoca un aumento de los costes de producción. Por ello, es necesario el desarrollo de nuevos procedimientos de fabricación de capas finas que permitan la completa implementación de estos dispositivos. En este sentido, destaca la técnica de electrosprayado. Esta técnica está basada en las fuerzas electrohidrodinámicas. Cuando un líquido fluye a través de un capilar y se aplica un campo eléctrico (este campo eléctrico se suele establecer entre el capilar y un colector de corriente plano), el correspondiente menisco se deforma en un cono, conocido como cono de Taylor. Cuando el voltaje del campo eléctrico alcanza un determinado valor límite, las fuerzas electrohidrodinámicas superan la tensión superficial del líquido, produciendo la salida de un chorro de pequeño diámetro. Generalmente, ese chorro rompe formando un espray, formado por gotas de tamaño nanométrico altamente cargadas. En este trabajo se propone el uso de la técnica de electrosprayado para el depósito controlado de una lámina delgada y continua de un material carbonoso nanoestructurado, directamente sobre el colector de corriente. Las láminas delgadas resultantes fueron caracterizadas como electrodos en supercondensadores con un electrolito acuoso.
Dynamic mixing deposition of niobium nitride films by cathodic arc plasma in ambient nitrogen (2001)

Two cathodic arc plasma deposition processes have been used to deposit niobium nitride films in ambient nitrogen: (a) cathodic arc plasma deposition without dynamic mixing and (b) cathodic arc plasma deposition with energetic ion dynamic mixing. Smooth and continuous niobium nitride films were fabricated at low temperature in process (b) but at higher temperature (500 °C) in process (a). The effects of the substrate temperature on the film composition and preferred orientation were investigated. In process (a), films deposited at room temperature and 300 °C exhibited a preferred orientation of (220) whereas those deposited at 500 °C showed a preferred orientation of (200). The nitrogen content in the film synthesized in process (b) is higher than that in the films deposited in process (a). Our results show that with energetic ion dynamic mixing, niobium nitride films with excellent properties can be fabricated at low substrate temperature using a niobium metal arc plasma source in a nitrogen plasma immersion configuration.
Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2 (2022)

The work was funded by Institut Pasteur, Fondation pour la Recherche Médicale, Urgence COVID-19 Fundraising Campaign of Institut Pasteur, ANRS, the Vaccine Research Institute, Labex IBEID, ANR/FRM Flash Covid PROTEO-SARS-CoV-2 and IDISCOVR.
Synthesis, Crystallographic Studies, and Characterization of K2Bi8Se13‐xSx Solid Solutions. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Field transmission test of 2.5 Gb/s Y-00 cipher in 160-km (40 km × 4 spans) installed optical fiber for secure optical fiber communications (2014)

Field transmission test of 2.5-Gb/s Y-00 cipher in 160-km (40 km × 4 spans) is demonstrated in the installed optical fiber for secure optical fiber communications. A long term investigation of an intensity modulated Y-00 transmitter and receiver with signal intensity levels of 4096 is conducted and the bit error rate of < 10−9 for a month is successfully achieved.