gebhart/patrepeval huggingface dataset:
The PDZ-binding Chloride Channel ClC-3B Localizes to the Golgi and Associates with Cystic Fibrosis Transmembrane Conductance Regulator-interacting PDZ Proteins (2003)

ClC chloride channels are widely distributed in organisms across the evolutionary spectrum, and members of the mammalian family play crucial roles in cellular function and are mutated in several human diseases (Jentsch, T. J., Stein, V., Weinreich, F., and Zdebik, A. A. (2002) Physiol. Rev. 82, 503-568). Within the ClC-3, -4, -5 branch of the family that are intracellular channels, two alternatively spliced ClC-3 isoforms were recognized recently (Ogura, T., Furukawa, T., Toyozaki, T., Yamada, K., Zheng, Y. J., Katayama, Y., Nakaya, H., and Inagaki, N. (2002) FASEB J. 16, 863-865). ClC-3A resides in late endosomes where it serves as an anion shunt during acidification. We show here that the ClC-3B PDZ-binding isoform resides in the Golgi where it co-localizes with a small amount of the other known PDZ-binding chloride channel, CFTR (cystic fibrosis transmembrane conductance regulator). Both channel proteins bind the Golgi PDZ protein, GOPC (Golgi-associated PDZ and coiled-coil motif-containing protein). Interestingly, however, when overexpressed, GOPC, which is thought to influence traffic in the endocytic/secretory pathway, causes a large reduction in the amounts of both channels, probably by leading them to the degradative end of this pathway. ClC-3B as well as CFTR also binds EBP50 (ERM-binding phosphoprotein 50) and PDZK1, which are concentrated at the plasma membrane. However, only PDZK1 was found to promote interaction between the two channels, perhaps because they were able to bind to two different PDZ domains in PDZK1. Thus while small portions of the populations of ClC-3B and CFTR may associate and co-localize, the bulk of the two populations reside in different organelles of cells where they are expressed heterologously or endogenously, and therefore their cellular functions are likely to be distinct and not primarily related.
Single Realization Stochastic FDTD for Weak Scattering Waves in Biological Random Media (2012)

This paper introduces an iterative scheme to overcome the unresolved issues presented in S-FDTD (stochastic finite-difference time-domain) for obtaining ensemble average field values recently reported by Smith and Furse in an attempt to replace the brute force multiple-realization also known as Monte-Carlo approach with a single-realization scheme. Our formulation is particularly useful for studying light interactions with biological cells and tissues having sub-wavelength scale features. Numerical results demonstrate that such a small scale variation can be effectively modeled with a random medium problem which when simulated with the proposed S-FDTD indeed produces a very accurate result.
Gas Flow Characteristics in a Plasma Process Chamber and Proposal of New Pulse-Controlled Gas Injection Method Using Interference Matrix Operation for Rapid Stabilization of Gas Pressure (2011)

To realize precise and high-throughput multiprocesses in a single plasma process chamber with a rapid alternative of multiple gases, gas flow characteristics in a plasma process chamber are investigated and a pulse-controlled gas injection method is developed. It is found that gas replacement characteristics greatly depend on the gas supply method used. An upper shower plate has a great advantage in realizing a rapid gas replacement over the case without using the upper shower plate, resulting from the realization of the down flow pattern of feed gas in the chamber. The pulse-controlled gas injection method employs the intentional overshoot pulse at the beginning of gas supply to rapidly stabilize gas pressure. Interference matrix operation is newly introduced to determine the pulse size for the arbitrary gas flow pattern in the chamber. The optimum pulse size can be successfully obtained in the case of HBr addition to a pure Ar plasma.
Superoxide dismutase participates in the enzymatic formation of the tyrosine radical of ribonucleotide reductase from Escherichia coli. (1986)

One of the two nonidentical subunits of Escherichia coli ribonucleotide reductase, protein B2, contains in its active form two antiferromagnetically coupled Fe(III) ions and an organic free radical that arises by the one-electron oxidation of tyrosine-122 of the polypeptide chain. Protein B2 lacking the tyrosine radical but with the iron center intact (called protein B2/HU because it is produced by treatment with hydroxyurea) is enzymatically inactive. Previously, it was found that a crude extract from E. coli transforms B2/HU into B2 in the presence of dithiothreitol, Mg2+, and oxygen. On purification of the enzyme system, we now find that radical introduction requires three separate proteins as well as NADPH and FMN. One of the proteins is superoxide dismutase. We hypothesize that the overall reaction involves a reduction of the iron center followed by the oxidation of iron and tyrosine-122. Superoxide dismutase may then be involved in the second step to protect an oxidation-sensitive intermediate. Alternatively, the enzyme might be directly involved in the oxidation step.
Interaction of differentiated human adipocytes with macrophages leads to trogocytosis and selective IL-6 secretion (2015)

Obesity leads to adipose tissue inflammation that is characterized by increased release of proinflammatory molecules and the recruitment of activated immune cells. Although macrophages are present in the highest number among the immune cells in obese adipose tissue, not much is known about their direct interaction with adipocytes. We have introduced an ex vivo experimental system to characterize the cellular interactions and the profile of secreted cytokines in cocultures of macrophages and human adipocytes differentiated from either mesenchymal stem cells or a preadipocyte cell line. As observed by time-lapse microscopy, flow, and laser-scanning cytometry, macrophages phagocytosed bites of adipocytes (trogocytosis), which led to their de novo, phagocytosis and NF-κB-dependent synthesis, then release of interleukin (IL)-6 and monocyte chemoattractant protein (MCP)-1. IL-6 secretion was not accompanied by secretion of other proinflammatory cytokines, such as tumor necrosis factor (TNF)-α and IL-8, except MCP-1. LPS-induced release of TNF-α, IL-8 and MCP-1 was decreased in the presence of the differentiated adipocytes but the IL-6 level did not subside suggesting that phagocytosis-dependent IL-6 secretion may have significant regulatory function in the inflamed adipose tissue.
Desulfurization of Model Diesel Fuel on Activated Carbon Modified with Iron Oxyhydroxide Nanoparticles: Effect of <i>tert</i>-Butylbenzene and Naphthalene Concentrations (2013)

Commercially activated carbon Filtrasorb 400 (F400) was modified with iron oxyhydroxide nanoparticles and tested, in a continuous process, as a diesel fuel desulfurization medium. Model diesel fuel (MDF) was prepared as a mixture of decane and hexadecane, with 20 ppm of sulfur from dibenzothiophenes (dibenzothiophene (DBT) and 4,6-dimethyldibenzothiophene (DMDBT)), and different concentrations of tert-butylbenzene and naphthalene. The calculated selectivities and adsorption capacities for DBT and DMDBT were analyzed at different concentration of aromatics. The results indicate that, while the concentration of naphthalene greatly affects the adsorption capacity of both DBT and DMDBT, the concentration of tert-butylbenzene only affects DMDBT uptake. At low concentration of aromatics, iron-containing carbon performs better than unmodified carbon and further oxidized species were identified on the surface of the iron-modified activated carbon. This indicates that iron is acting as an acidic center, attracting basic DBT and DMDBT, and is acting as an oxidant for the adsorbed species. With an increase in the content of aromatics in MDF, the difference in the desulfurization performance between the studied materials diminishes. After thermal regeneration of the iron-containing sample, 95% of the pore volume is recovered and only a 10% loss in the DBT and DMDBT adsorption capacity is observed.
Mechanical characteristics and applications of diamondlike-carbon cantilevers fabricated by focused-ion-beam chemical vapor deposition (2006)

Diamondlike-carbon (DLC) cantilevers were fabricated with a commercially available focused-ion-beam chemical-vapor-deposition (FIB-CVD) system using a beam of 30keV Ga+ ions, and the mechanical characteristics of the cantilevers were measured. Vibration frequency of the cantilevers was passively measured using scanning electron microscopy. Resonant frequency of DLC cantilevers fabricated at 0.1–0.5pA beam current was found to be constant. The equivalent spring constant of the cantilevers was identified by squeezing the tip of a Si3N4 cantilever and a DLC cantilever together. Using the measured displacement, the spring constant of the DLC cantilever was calculated as (1.1±0.2)×10−2N∕m. Furthermore, Young’s modulus and the density of the DLC cantilevers were measured to be 187±32GPa and (3.8±0.7)×103kg∕m3, respectively. The DLC cantilevers were used as mass sensors in an ultrasensitive sensing application. A small amount of DLC was deposited on the tip of a DLC cantilever as a mass adhesion by FIB-CVD at 0.5pA beam current. As a result, the authors were able to measure a small amount of mass shift in the femtogram range using a DLC cantilever.
Surveying of Pure and Hybrid Plasmonic Structures Based on Graphene for Terahertz Antenna (2016)

Graphene is a unique material for the implementation of terahertz antennas due to extraordinary properties of the resulting devices, such as tunability and compactness. Existing graphene antennas are based on pure plasmonic structures, which are compact but show moderate to high losses. To achieve higher efficiency with low cost, one can apply the theory behind dielectric resonator antennas widely used in millimeter-wave systems. This paper presents the concept of hybridization of surface plasmon and dielectric wave modes. Radiation efficiency, reconfigurability, and miniaturization of antennas built upon this principle are qualitatively discussed and compared with those of pure plasmonic antennas. To this end, a quantitative study of pure and hybrid plasmonic one-dimensional guided-wave structures is performed. The results show that hybrid structures can be employed to design terahertz antennas with high radiation efficiency and gain, moderate miniaturization, and tunability, while terahertz antennas based on pure plasmonic structures can provide high miniaturization and tunability yet with low radiation efficiency and gain.
Efficient Massively Parallel Join Optimization for Large Queries (2022)

Modern data analytical workloads often need to run queries over a large number of tables. An optimal query plan for such queries is crucial for being able to run these queries within acceptable time bounds. However, with queries involving many tables, finding the optimal join order becomes a bottleneck in query optimization. Due to the exponential nature of join order optimization, optimizers resort to heuristic solutions after a threshold number of tables. Our objective is two fold: (a) reduce the optimization time for generating optimal plans; and (b) improve the quality of the heuristic solution.
Associations between Maternal Circulating DNA Methylation during Pregnancy and Exposures to Environmental Metals in the National Childrens Study (2014)

Associations between Maternal Circulating DNA Methylation during Pregnancy and Exposures to Environmental Metals in the National Children's StudyAbstract Number:2816 Kelly Bakulski*, Jason Feinberg, Shannon Brown, Laura Caulfield, Lynn Goldman, Andrew Feinberg, and Dani Fallin Kelly Bakulski* Johns Hopkins University, United States, E-mail Address: [email protected] , Jason Feinberg Johns Hopkins University, United States, E-mail Address: [email protected] , Shannon Brown Johns Hopkins University, United States, E-mail Address: [email protected] , Laura Caulfield Johns Hopkins University, United States, E-mail Address: [email protected] , Lynn Goldman George Washington University, United States, E-mail Address: [email protected] , Andrew Feinberg Johns Hopkins University, United States, E-mail Address: [email protected] , and Dani Fallin Johns Hopkins University, United States, E-mail Address: [email protected] AbstractBackground: Early life environments can influence later life health outcomes and DNA methylation may represent a persistent mark of these conditions. The relationships between maternal metals exposures in early pregnancy and subsequent DNA methylation measurements in moms and babies are poorly understood.Methods: Blood and urine metals exposures were measured in 138 pregnant women enrolled in the National Children's Study Vanguard sites during trimester one. Repeated measures of buffy coat genome-wide DNA methylation were assessed on the Illumina 450K array during trimesters one and three as well as from the cord blood in a subset of babies (n=81). We tested for region and site specific associations between DNA methylation and metal exposures, adjusting for cell type composition and other potential confounding factors.Results: In our study population, mean blood cadmium exposure was 0.27 µg/L (95% CI: 0.11-0.62), mean blood manganese was 11.7 µg/L (95% CI: 7.2-19.7), mean blood lead was 0.52 µg/dL (95% CI: 0.18-1.14), mean blood selenium was 178.7 µg/L (95% CI: 143.1-210.3), and mean total blood mercury was 0.99 µg/L (95% CI: 0.11-3.3). Fifteen CpG sites were associated with cadmium exposure in trimester one at a genome-wide significance level of p-value<10-7 and ten of those sites replicated in terms of magnitude and direction in trimester three. Similarly, fifteen sites reached genome-wide significance in trimester one for mercury and fourteen of those replicated in trimester three.Conclusions: We observed maternal DNA methylation differences with trimester one cadmium and mercury exposure levels that persisted to trimester three DNA methylation in a cohort of normal births. The identified regions may act as biomarkers of exposure in cohorts lacking prenatal exposure information. Cord blood methylation and urinary metals exposures will be discussed.
Population-based serology reveals risk factors for RSV infection in children younger than 5 years (2021)

Respiratory syncytial virus (RSV) infection is a leading cause of hospitalization in infants. Underlying risk factors for RSV infection in the general population are not well understood, as previous work has focused on severe outcomes of infection in a clinical setting. Here we use RSV-specific IgG and IgA antibody measurements from two population-based cross-sectional serosurveys carried out in the Netherlands (n = 682) to classify children up to 5 years as seronegative or seropositive. We employ a generalized additive model to estimate the probability of prior RSV infection as function of age, date of birth within the year, and other risk factors. The analyses show that the majority of children have experienced a RSV infection before the age of 2 years. Age and birthdate are strong predictors of RSV infection in the first years of life, and children born in summer have higher estimated probability of infection than those born in winter [e.g., 0.56 (95% CI 0.45-0.66) vs. 0.32 (0.21-0.45) at age 1 year]. Our analyses reveal that the mean age at infection depends on date of birth, which has implications for the design of vaccination programmes and prioritisation schemes for the prophylactic use of monoclonal antibodies.
Nonlinear Generation of Ultra-flat broadened Spectrum Based on Adaptive Pulse Shaping (2011)

We report a technique to nonlinearly generate precise spectral shapes in an adaptable and power-efficient fashion. The generation of a spectrum with a 7-nm 0.5-dB bandwidth is demonstrated to prove the validity of the approach.
Evaluation of uncertainty in the adjustment of fundamental constants (2016)

Combining multiple measurement results for the same quantity is an important task in metrology and in many other areas. Examples include the determination of fundamental constants, the calculation of reference values in interlaboratory comparisons, or the meta-analysis of clinical studies. However, neither the GUM nor its supplements give any guidance for this task. Various approaches are applied such as weighted least-squares in conjunction with the Birge ratio or random effects models. While the former approach, which is based on a location-scale model, is particularly popular in metrology, the latter represents a standard tool used in statistics for meta-analysis. We investigate the reliability and robustness of the location-scale model and the random effects model with particular focus on resulting coverage or credible intervals. The interval estimates are obtained by adopting a Bayesian point of view in conjunction with a non-informative prior that is determined by a currently favored principle for selecting non-informative priors. Both approaches are compared by applying them to simulated data as well as to data for the Planck constant and the Newtonian constant of gravitation. Our results suggest that the proposed Bayesian inference based on the random effects model is more reliable and less sensitive to model misspecifications than the approach based on the location-scale model.
Method for predicting RNA secondary structure. (1975)

We report a method for predicting the most stable secondary structure of RNA from its primary sequence of nucleotides. The technique consists of a series of three computer programs interfaced to take the nucleotide sequence of any RNA and (a) list all possible helical regions, using modified Watson-Crick base-pairing rules; (b) create all possible secondary structures by forming permutations of compatible helical regions; and (c)evaluate each structure for total free energy of formation from a completely extended chain. A free energy distribution and the base-by-base bonding interactions of each possible structure are catalogued by the system and are readily available for examination. The method has been applied to 62 tRNA sequences. The total free-energy of the predicted most stable structures ranged from -19 to -41 kcal/mole (-22 to -49 kJ/mole). The number of structures created was also highly sequence-dependent and ranged from 200 to 13,000. In nearly all cases the cloverleaf is predicted to be the structure with the lowest free energy of formation.
Cell-Type-Specific Recruitment of Amygdala Interneurons to Hippocampal Theta Rhythm and Noxious Stimuli In Vivo (2012)

Neuronal synchrony in the basolateral amygdala (BLA) is critical for emotional behavior. Coordinated theta-frequency oscillations between the BLA and the hippocampus and precisely timed integration of salient sensory stimuli in the BLA are involved in fear conditioning. We characterized GABAergic interneuron types of the BLA and determined their contribution to shaping these network activities. Using in vivo recordings in rats combined with the anatomical identification of neurons, we found that the firing of BLA interneurons associated with network activities was cell type specific. The firing of calbindin-positive interneurons targeting dendrites was precisely theta-modulated, but other cell types were heterogeneously modulated, including parvalbumin-positive basket cells. Salient sensory stimuli selectively triggered axo-axonic cells firing and inhibited firing of a disctinct projecting interneuron type. Thus, GABA is released onto BLA principal neurons in a time-, domain-, and sensory-specific manner. These specific synaptic actions likely cooperate to promote amygdalo-hippocampal synchrony involved in emotional memory formation.
Coûts comparés d’une rachi-anesthésie et d’une anesthésie générale dans la chirurgie du col du fémur (1998)

Le but de cette etude prospective est d’evaluer et de comparer les couts d’une rachi-anesthesie et d’une anesthesie generale chez les patients operes pour une fracture du col du femur. Un questionnaire a ete elabore pour collecter des informations sur les dispositifs medicaux, les medicaments et les fluides medicaux utilises lors de chaque anesthesie durant les periodes d’induction operatoire, et de sejour en salle de reveil. Du 10 mars 1997 au 24 avril 1997, 32 malades ont ete operes : 15 ont beneficie d’une anesthesie generale (6 hommes et 9 femmes, âge moyen 81 ans, extremes 67 a 93 ans, avec des durees moyennes d’intervention et de sejour en salle de reveil respectivement de 103 et 130 min), 17 ont beneficie d’une rachi-anesthesie (6 hommes et 11 femmes, âge moyen 83 ans, extremes 65 a 93 ans, avec des durees moyennes d’intervention et de sejour en salle de reveil respectivement de 100 et 101 min). Les resultats montrent une elevation de cout en consommables significative pour l’anesthesie generale (+ 164 F par patient) et confirment les donnees de la litterature : les anesthesies locoregionales coutent beaucoup moins cher que les anesthesies generales. En effet, la difference de cout entre AG et RA est minime concernant les DM (17,15 F en moyenne par patient) alors qu’elle est consequente au niveau des produits employes dont essentiellement le protoxyde d’azote (32,55 F en moyenne par patient), et le Diprivan ® (31,62 F par patient). En outre, la difference significative de la duree de sejour en salle de reveil revele un benefice direct pour le patient ayant beneficie d’une rachi-anesthesie et un gain de temps pour l’equipe soignante que l’on pourrait chiffrer en economie de depenses ou diminution de la charge de travail. En tenant compte de leurs avantages associes (une surveillance « peri-anesthesique » allegee, une duree de sejour en salle de reveil ecourtee, une conduite simplifiee de l’analgesie), favoriser le developpement des anesthesies locoregionales et de l’analgesie locoregionale s’affiche en evidence pour les partenaires hospitaliers dans le respect des contre-indications et avec le consentement du patient.
Monocúspide de homoenxerto decelularizado no tratamento do truncus arteriosus com a técnica de Barbero Marcial (2008)

The use decellularized homograft monocuspid in the treatment of truncus arterious by Barbero Marcial techniqueMonocúspide de homoenxerto decelularizado no tratamento do truncus arteriosus com
Homologous Subunits of 1,3-Beta-Glucan Synthase Are Important for Spore Wall Assembly in <i>Saccharomyces cerevisiae</i> (2006)

During sporulation in Saccharomyces cerevisiae, the four haploid nuclei are encapsulated within multilayered spore walls. Glucan, the major constituent of the spore wall, is synthesized by 1,3-beta-glucan synthase, which is composed of a putative catalytic subunit encoded by FKS1 and FKS2. Although another homolog, encoded by FKS3, was identified by homology searching, its function is unknown. In this report, we show that FKS2 and FKS3 are required for spore wall assembly. The ascospores of fks2 and fks3 mutants were enveloped by an abnormal spore wall with reduced resistance to diethyl ether, elevated temperatures, and ethanol. However, deletion of the FKS1 gene did not result in a defective spore wall. The construction of fusion genes that expressed Fks1p and Fks2p under the control of the FKS2 promoter revealed that asci transformed with FKS2p-driven Fks1p and Fks2p were resistant to elevated temperatures, which suggests that the expression of FKS2 plays an important role in spore wall assembly. The expression of FKS1p-driven Fks3p during vegetative growth did not affect 1,3-beta-glucan synthase activity in vitro but effectively suppressed the growth defect of the temperature-sensitive fks1 mutant by stabilizing Rho1p, which is a regulatory subunit of glucan synthase. Based on these results, we propose that FKS2 encodes the primary 1,3-beta-glucan synthase in sporulation and that FKS3 is required for normal spore wall formation because it affects the upstream regulation of 1,3-beta-glucan synthase.