gebhart/patrepeval huggingface dataset:
Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov (1989)

Crude cell extracts of 26 isolates of Salmonella serotype typhi (S. typhi) and 48 other Salmonella isolates representing 28 serotypes and seven DNA hybridization subgroups were analyzed for electrophoretic variants of 24 metabolic enzymes by starch gel electrophoresis. All strains of S. typhi had identical isoenzyme patterns, indicating that they were a single clone. All of the enzymes detected in the remaining strains were polymorphic, and the degree of genetic variation was quite high. The average number of alleles per enzyme locus was 4.7, and the mean genetic diversity per locus was 0.556. Thirty-two distinct allele profiles, or electrophoretic types (ETs), were found in these 48 strains of Salmonella serotypes other than S. typhi. Analysis of the genetic relationships of the ETs to each other showed that, with one exception, the ETs formed subgroups that were consistent with the subgroupings based on DNA hybridization studies. ET profiles were not always linked to specific serologic patterns. These data show that multilocus enzyme electrophoresis has a potential application in epidemiologic and taxonomic studies of salmonellae, although it is not differential for S. typhi. We also propose a new species, Salmonella bongori comb. nov., a new combination base on the elevation of Salmonella choleraesuis subsp. bongori to the level of species.
Augmented Switching Linear Dynamical System Model for Gas Concentration Estimation with MOX Sensors in an Open Sampling System (2014)

In this paper, we introduce a Bayesian time series model approach for gas concentration estimation using Metal Oxide (MOX) sensors in Open Sampling System (OSS). Our approach focuses on the compensation of the slow response of MOX sensors, while concurrently solving the problem of estimating the gas concentration in OSS. The proposed Augmented Switching Linear System model allows to include all the sources of uncertainty arising at each step of the problem in a single coherent probabilistic formulation. In particular, the problem of detecting on-line the current sensor dynamical regime and estimating the underlying gas concentration under environmental disturbances and noisy measurements is formulated and solved as a statistical inference problem. Our model improves, with respect to the state of the art, where system modeling approaches have been already introduced, but only provided an indirect relative measures proportional to the gas concentration and the problem of modeling uncertainty was ignored. Our approach is validated experimentally and the performances in terms of speed of and quality of the gas concentration estimation are compared with the ones obtained using a photo-ionization detector.
Biological functions of human Fc gamma RIIa/Fc gamma RIIc in B cells. (1994)

The human immunoglobulin receptor IIa (FcRIIa) was transfected into the FcR- mouse B cell line IIA1.6 to study its role in mediating endocytosis of human IgG complexes as well as its possible function in inhibiting the attenuated increased calcium level in B cells after antigen receptor cross-linking. Using FcRIIa mutants with truncated cytoplasmic domains we show that the region within the cytoplasmic region necessary for endocytosis differs from that necessary for the abrogation of the elevated calcium level in B cells induced after antigen receptor cross-linking. Deletion of 14 amino acids at the carboxy terminus led to a slow internalization of FcRIIa bound human IgG, whereas the mutant lacking 30 amino acids completely failed to mediate IgG uptake. The mutant lacking 14 amino acids at the carboxy terminus is not tyrosine phosphorylated in the course of receptor-mediated IgG uptake. This suggests that phosphorylation of FcRIIa is not necessary to mediate this function. FcRIIa cross-linking leads to a rapid transient rise in the intracellular calcium concentration due to calcium release from intracellular stores. Using the FcRIIa mutants we could further show that the signal delivered by FcRIIa is strongly dependent on the last 14 amino acids of the cytoplasmic tail. Analyses of the tyrosine phosphorylation of FcRIIa revealed that the calcium release mediated by FcRIIa cross-linking is dependent on tyrosine phosphorylation. In contrast, inhibition of the antigen receptor (sIgG) induced rise in intracellular calcium concentration by FcRIIa-sIgG co-cross-linking was not impaired when 30 amino acids were deleted at the carboxy terminus. FcRIIa wild type was rapidly phosphorylated when co-cross-linked with sIgG, but phosphorylation is not a prerequisite to inhibit calcium influx induced by sIgG cross-linking. These results show that distinct regions within the cytoplasmic tail of FcRIIa are necessary for the various signals transmitted to the cell.
A new parameterization for surface and groundwater interactions and its impact on water budgets with the variable infiltration capacity (VIC) land surface model (2003)

This paper describes a new parameterization to represent surface and groundwater interaction dynamics for land surface models. With the new parameterization, effects of surface and groundwater interactions on soil moisture, evapotranspiration, runoff, and recharge can be dynamically taken into account. The new parameterization is implemented into the three‐layer variable infiltration capacity (VIC‐3L) model, which is a hydrologically based land surface scheme. The new version of VIC (called VIC‐ground) is applied to two watersheds in Pennsylvania over multiple years. Results show that VIC‐ground can properly simulate the movement of the daily groundwater table over multiple years at the study sites. Preliminary comparisons of VIC simulations with and without consideration of the dynamics of surface and groundwater interactions show an important impact of such interactions on the partitioning of water budget components. In particular, soil moisture of the lower layer from the VIC‐ground simulations is generally wetter than that from VIC‐3L. For the top thin soil layer and the upper layer of VIC‐3L, soil moisture is generally drier in VIC‐ground than that in VIC‐3L. Such characteristics of VIC‐ground result in lower surface runoff peaks and higher base flow, as well as generally less evapotranspiration compared to VIC‐3L at the two study sites. Results at both sites show that it takes 3–4 years to have the effects of the initializations of groundwater tables disappear when the groundwater table is initialized to be deeper than the observed level, while it takes much less time (e.g., about 1.5 years) if the groundwater table is initialized to be shallower than the observed level. In addition, the preliminary sensitivity studies at both sites show that there is a more significant persistent signature of the impact of the precipitation when its amount is halved (i.e., 0.5 ppt) than that when its amount is doubled (i.e., 2 ppt).
Wideband Localization of the Dominant Leaky Wave Poles in Dielectric Covered Antennas (2006)

This letter discusses the properties of printed antennas whose radiation patterns (their directivity or their shape) are enhanced by means of dielectric superlayers which support leaky waves. In particular the characterizing complex leaky wave poles of the spectral Green's function are approximated analytically, for the first time over large frequency bandwidths. The localization of the poles is a simple mathematical "trick," however, the results provide further physical insights into wave phenomena that before had to be investigated numerically
Biochemical and Domain Analyses of FSUAxe6B, a Modular Acetyl Xylan Esterase, Identify a Unique Carbohydrate Binding Module in <i>Fibrobacter succinogenes</i> S85 (2009)

Acetyl xylan esterase (EC 3.1.1.72) is a member of a set of enzymes required to depolymerize hemicellulose, especially xylan that is composed of a main chain of beta-1,4-linked xylopyranoside residues decorated with acetyl side groups. Fibrobacter succinogenes S85 Axe6B (FSUAxe6B) is an acetyl xylan esterase encoded in the genome of this rumen bacterium. The enzyme is a modular protein comprised of an esterase domain, a carbohydrate-binding module, and a region of unknown function. Sequences that are homologous to the region of unknown function are paralogously distributed, thus far, only in F. succinogenes. Therefore, the sequences were designated Fibrobacter succinogenes-specific paralogous module 1 (FPm-1). The FPm-1s are associated with at least 24 polypeptides in the genome of F. succinogenes S85. A bioinformatics search showed that most of the FPm-1-appended polypeptides are putative carbohydrate-active enzymes, suggesting a potential role in carbohydrate metabolism. Truncational analysis of FSUAxe6B, together with catalytic and substrate binding studies, has allowed us to delineate the functional modules in the polypeptide. The N-terminal half of FSUAxe6B harbors the activity that cleaves side chain acetyl groups from xylan-like substrates, and the binding of insoluble xylan was determined to originate from FPm-1. Site-directed mutagenesis studies of highly conserved active-site residues in the esterase domain suggested that the esterase activity is derived from a tetrad composed of Ser(44), His(273), Glu(194), and Asp(270), with both Glu(194) and Asp(270) functioning as helper acids, instead of a single carboxylate residue proposed to initiate catalysis.
Restoring Native Plant and Pollinator Communities on New York City Green Roofs (2010)

Urban development has dramatically decreased habitat for native plants and other wildlife. One of the native insect groups affected by this change are the bees and wasps (Order: Hymenoptera), which provide valuable ecosystem services like pollination of crops and ornamental plants. These insects are experiencing rapid population declines in urbanizing areas. A major obstacle to restoring pollinator populations in cities is the scarcity of space available that can be managed as habitat. A potential solution to this is to create patches of native vegetation on green roofs. Green roofs consist of live plants, growing media, and a drainage layer on top of a waterproof membrane. Most green roofs are planted with a mixture of non-native succulent plants (mostly from the genus Sedum), which are favored for their high survivorship and low maintenance requirements. On roofs with somewhat deeper media, a greater diversity of plants, including native plants typical of local grasslands, can persist. Here, we report on the differences in abundance and diversity of Hymenoptera attracted to native green roofs, Sedum green roofs, non-vegetated roofs, and ground-level green spaces. Preliminary data indicate extensive insect use of green roofs, with higher abundances on roofs planted with native species. The next phase of this research will involve comparing how the landscape context provided by different neighborhoods affects the development of the green roof biological communities.
Tumor necrosis factor regulates intestinal epithelial cell migration by receptor-dependent mechanisms (2003)

Altered mucosal integrity and increased cytokine production, including tumor necrosis factor (TNF), are the hallmarks of inflammatory bowel disease (IBD). In this study, we addressed the role of TNF receptors (TNFR) on intestinal epithelial cell migration in an in vitro wound closure model. With mouse TNFR1 or TNFR2 knockout intestinal epithelial cells, gene transfection, and pharmacological inhibitors, we show a concentration-dependent receptor-mediated regulation of intestinal cell migration by TNF. A physiological TNF level (1 ng/ml) enhances migration through TNFR2, whereas a pathological level (100 ng/ml) inhibits wound closure through TNFR1. Increased rate of wound closure by TNFR2 or inhibition by TNFR1 cannot be explained by either increased proliferation or apoptosis, respectively. Furthermore, inhibiting Src tyrosine kinase decreases TNF-induced focal adhesion kinase (FAK) tyrosine phosphorylation and cellular migration. We therefore conclude that TNFR2 activates a novel Src-regulated pathway involving FAK tyrosine phosphorylation that enhances migration of intestinal epithelial cells.
The Polymerization Pocket “a” within the Carboxyl-terminal Region of the γ Chain of Human Fibrinogen Is Adjacent to but Independent from the Calcium-binding Site (1997)

The carboxyl-terminal region of the gamma chain of fibrinogen is involved in calcium binding, fibrin polymerization, factor XIIIa-mediated cross-linking, and binding to the platelet fibrin(ogen) receptor. Protein fragments encoding amino acids Val143 to Val411 (rFbggammaC30) or Val143 to Leu427 (gamma'C30) from the carboxyl end of the gamma or gamma' chains, respectively, of human fibrinogen were expressed in yeast (Pichia pastoris) and characterized as to their cross-linking by factor XIIIa, polymerization pocket, and calcium-binding site. rFbggammaC30 and gamma'C30 were both readily cross-linked by factor XIIIa, but only rFbggammaC30 was capable of inhibiting thrombin-induced platelet aggregation. Two mutants, gammaC30-Q329R and gammaC30-D364A, which were based on the three-dimensional structure of the polymerization pocket within rFbggammaC30 and on information derived from naturally occurring mutant fibrinogens, were also expressed and characterized. rFbggammaC30 inhibited (desAA)fibrin polymerization in a dose-dependent manner, while the two mutant forms did not. Similarly, rFbggammaC30 and gamma'C30 were protected from plasmin degradation by the presence of Ca2+ or the peptide Gly-Pro-Arg-Pro, indicating that a functional Ca2+-binding site and polymerization pocket are contained within each of these fragments. The mutant fragments, however, were protected from plasmin only by metal ions, while no protective effect was conferred by GPRP or by any other peptide tested. These results indicate that the polymerization pocket "a", which binds the peptide GPRP, functions independently from the nearby calcium-binding site and that amino acids Gln329 and Asp364 play a crucial role in fibrin polymerization.
Study of Ag-In solder as low temperature wafer bonding intermediate layer (2008)

Indium-silver as solder materials for low temperature bonding had been introduced earlier. In theory the final bonding interface composition is determined by the overall materials composition. Wafer bonding based multiple intermediate layers facilitates precise control of the formed alloy composition and the joint thickness. Thus the bonding temperature and post-bonding re-melting temperature could be easily designed by controlling the multilayer materials. In this paper, a more fundamental study of In-Ag solder materials is carried out in chip-to-chip level by using flip-chip based thermocompression bonding. Bonding at 180°C for various time duration under various bonding pressure is studied. Approaches of forming Ag<sub>2</sub>In with re-melting temperature higher than 400°C at the bonding interface are proposed and discussed. Knowledge learned in this process technology can support us to develop sophisticated wafer level packaging process based wafer bonding for applications of MEMS and IC packages.
RPA facilitates rejoining of DNA double-strand breaks in an in vitro assay utilizing genomic DNA as substrate (2001)

The results suggest that in addition to its role in homologous recombination, RPA may also have a supportive role in some forms of non-homologous end-joining.
Deep Convolutional Neural Network with Structured Prediction for Weakly Supervised Audio Event Detection (2019)

Audio event detection (AED) is a task of recognizing the types of audio events in an audio stream and estimating their temporal positions. AED is typically based on fully supervised approaches, requiring strong labels including both the presence and temporal position of each audio event. However, fully supervised datasets are not easily available due to the heavy cost of human annotation. Recently, weakly supervised approaches for AED have been proposed, utilizing large scale datasets with weak labels including only the occurrence of events in recordings. In this work, we introduce a deep convolutional neural network (CNN) model called DSNet based on densely connected convolution networks (DenseNets) and squeeze-and-excitation networks (SENets) for weakly supervised training of AED. DSNet alleviates the vanishing-gradient problem and strengthens feature propagation and models interdependencies between channels. We also propose a structured prediction method for weakly supervised AED. We apply a recurrent neural network (RNN) based framework and a prediction smoothness cost function to consider long-term contextual information with reduced error propagation. In post-processing, conditional random fields (CRFs) are applied to take into account the dependency between segments and delineate the borders of audio events precisely. We evaluated our proposed models on the DCASE 2017 task 4 dataset and obtained state-of-the-art results on both audio tagging and event detection tasks.
Short‐range high‐resolution radar utilizing standing wave for measuring of distance and velocity of a moving target (2006)

Abstract For automobile safety, supplemental equipment such as seat belts and air bags is used. These devices are activated after an accident. In contrast, from the point of view of accident prevention, automotive radar has been developed for collision avoidance. Presently, typical radars are the frequency‐modulated type and the pulse‐modulated type. It is known that measurement of an object over short range is difficult with these types of radar. Here, we propose a method of realization for radar using a standing wave that can measure a moving target within 2 m at a speed of 0 km/h to 100 km/h in simulations, within the specification of low‐power radio equipment to detect moving objects at 24 GHz with a narrow bandwidth of 76 MHz. This radar is not subject to the problems of FMCW radar such as leakage of the transmitted signal and false targets due to nonlinearity of the mixer. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 89(5): 52–60, 2006; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecja.20165
Carbapenem-Resistant <b> <i>Klebsiella pneumoniae</i> in Singapore Producing IMP-1 β-Lactamase and Lacking an Outer Membrane Protein </b> (2001)

IMP metallo-β-lactamases hydrolyze virtually all β-lactams and are insensitive to clinically available inhibitors. IMP-1 has been reported repeatedly since 1991 in Japan (8), where it is now scattered in Pseudomonas aeruginosa and Serratia marcescens and has been found in Klebsiella pneumoniae (H. Kurkawa, Y. Tetsuya, N. Shibata, K. Shibayama, and Y. Arakawa, Letter, Lancet 354:955, 1999). Carriage ofblaIMP-1 has not been confirmed outside Japan, but related enzymes—IMP-2 and -4—have been found in acinetobacters in Italy (9) and Hong Kong (1); IMP-4 was also found in Citrobacter youngae in Guangzhou, China (2).
Structure of the Vesicular Stomatitis Virus Nucleoprotein-RNA Complex (2006)

Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.
Self-Assembled Tetrahedral DNA Nanostructures Promote Adipose-Derived Stem Cell Migration via lncRNA XLOC 010623 and RHOA/ROCK2 Signal Pathway (2016)

Self-assembled tetrahedral DNA nanostructures (TDNs) with precise sizes have been extensively applied in various fields owing to their exceptional mechanical rigidity, structural stability, and modification versatility. In addition, TDNs can be internalized by mammalian cells and remain mainly intact within the cytoplasm by escaping degradation by nucleases. Here, we studied the effects of TDNs on cell migration and the underlying molecular mechanisms. TDNs remarkably enhanced the migration of rat adipose-derived stem cells and down-regulated the long noncoding RNA (lncRNA) XLOC 010623 to activate the mRNA expression of Tiam1 and Rac1. Furthermore, TDNs highly up-regulated the mRNA and protein expression of RHOA, ROCK2, and VCL. These results indicate that TDNs suppressed the transcription of lncRNA XLOC 010623 and activated the TIAM1/RAC1 and RHOA/ROCK2 signaling pathways to promote cell migration. On the basis of these findings, TDNs show a high potential for application in tissue repair and regenerative medicine as a functional three-dimensional DNA nanomaterial.
<i>S</i> -Adenosylhomocysteine toxicity in normal and adenosine kinase-deficient lymphoblasts of human origin (1979)

The human lymphoblast line WI-L2 is subject to growth inhibition by a combination of the adenosine deaminase (ADA; adenosine aminohydrolase, EC 3.5.4.4.) inhibitor erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA) and adenosine. Although adenosine-induced pyrimidine starvation appears to contribute to this effect, uridine only partially reverses adenosine toxicity in WI-L2 and not at all in strain 107, an adenosine kinase-(ATP:adenosine 5'-phosphotransferase, EC 2.7.1.20) deficient derivative of WI-L2. Treatment of both cell lines with EHNA and adenosine leads to striking elevations in intracellular S-adenosyl-L-homocysteine (AdoHcy), a potent inhibitor of S-adenosyl-L-methionine (AdoMet)-dependent methylation reactions. The methylation in vivo of both DNA and RNA is inhibited by concentrations of EHNA and adenosine that elevate intracellular AdoHcy. Addition of 100 muM L-homocysteine thiolactone to cells treated with EHNA and adenosine enhances adenosine toxicity and further elevates AdoHcy to levels approximately 60-fold higher than those obtained in the absence of this amino acid, presumably by combining with adenosine to form AdoHcy in a reaction catalyzed by S-adenosylhomocysteine hydrolase (EC 3.3.1.1). In the adenosine kinase-deficient strain 107, a combination of ADA inhibition and L-homocysteine thiolactone markedly increases intracellular AdoHcy and inhibits growth even in the absence of exogenous adenosine. These results demonstrate a form of toxicity from endogenously produced adenosine and support the view that AdoHcy, by inhibiting methylation, is a mediator of uridine-resistant adenosine toxicity in these human lymphoblast lines. Furthermore, they suggest that AdoHcy may play a role in the pathogenesis of the severe combined immunodeficiency disease found in most children with heritable ADA deficiency.