gebhart/patrepeval huggingface dataset:
Hydroxylamine Contributes More to Abiotic N2O Production in Soils Than Nitrite (2019)

Nitrite (NO2-) and hydroxylamine (NH2OH) are important intermediates of the nitrogen (N) cycle in soils. They play a crucial role in the loss of nitrous oxide (N2O) and nitric oxide (NO) from soil due to their high reactivity. In this study, we collected soil samples from three ecosystems (grassland, arable land and forest with a riparian zone) and explored the contribution of NO2- and NH2OH to N2O formation in the different soils after exposure to oxic or anoxic pre-treatment. In addition, the importance of abiotic processes on the N2O formation from the two intermediates was studied by irradiating the soil samples with γ-irradiation. Our results demonstrate that NO2- addition induced the largest N2O production in the grassland soil, followed by the forest and arable soils. Only 9–39% of the produced N2O after NO2- addition came from abiotic processes. NH2OH addition increased N2O emissions the most from the arable soil, followed by the grassland and forest soils. The conversion of NH2OH to N2O was mostly (73–93%) abiotic. Anoxic pre-treatment decreased N2O production from NH2OH remarkably, especially for the grassland soil, while it increased N2O production from NO2- for most of the soils. Correlation analysis showed that NO2- effects on N2O production were strongly correlated with NH4+ content in soils with anoxic pre-treatment, while NH2OH effects on N2O production were strongly correlated to soil Mn and C content in soils with oxic pre-treatment. Our results indicate that NH2OH plays an important role for abiotic N2O formation in soils with low C and high Mn content, while the effect of NO2- was important mainly during biotic N2O production. Anoxic periods prior to N addition may increase the contribution of NO2-, but reduce the contribution of NH2OH, to soil N2O formation.
Data from Impaired SARS-CoV-2 Variant Neutralization and CD8<sup>+</sup> T-cell Responses Following 3 Doses of mRNA Vaccines in Myeloma: Correlation with Breakthrough Infections (2023)

&lt;div&gt;Abstract&lt;p&gt;Patients with multiple myeloma (MM) mount suboptimal neutralizing antibodies (nAb) following 2 doses of SARS-CoV-2 mRNA vaccines. Currently, circulating SARS-CoV-2 variants of concern (VOC) carry the risk of breakthrough infections. We evaluated immune recognition of current VOC including BA.1, BA.2, and BA.5 in 331 racially representative patients with MM following 2 or 3 doses of mRNA vaccines. The third dose increased nAbs against WA1 in 82%, but against BA variants in only 33% to 44% of patients. Vaccine-induced nAbs correlated with receptor-binding domain (RBD)–specific class-switched memory B cells. Vaccine-induced spike-specific T cells were detected in patients without seroconversion and cross-recognized variant-specific peptides but were predominantly CD4&lt;sup&gt;+&lt;/sup&gt; T cells. Detailed clinical/immunophenotypic analysis identified features correlating with nAb/B/T-cell responses. Patients who developed breakthrough infections following 3 vaccine doses had lower live-virus nAbs, including against VOC. Patients with MM remain susceptible to SARS-CoV-2 variants following 3 vaccine doses and should be prioritized for emerging approaches to elicit variant-nAb and CD8&lt;sup&gt;+&lt;/sup&gt; T cells.&lt;/p&gt;Significance:&lt;p&gt;Three doses of SARS-CoV-2 mRNA vaccines fail to yield detectable VOC nAbs in nearly 60% and spike-specific CD8&lt;sup&gt;+&lt;/sup&gt; T cells in &gt;80% of myeloma patients. Patients who develop breakthrough infections following vaccination have low levels of live-virus nAb.&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/bloodcancerdiscov/article/doi/10.1158/2643-3230.BCD-4-2-ITI" target="_blank"&gt;This article is highlighted in the In This Issue feature, p. 101&lt;/a&gt;&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
A simple probabilistic approach to classification and routing (2002)

The Language Exploitation Group in Management and Data Systems has developed classification and routing software which calculates the most likely category of a document and creates ranked lists of documents relevant to user-defined categories. The basic algorithm used is to represent categories as multinomial distributions based upon information gathered from training sets of relevant documents, and to use probability to classify and route new documents into these categories. The software has been proven by its entry in the international TREC5 competition, and the software is being extended with both contract and IR and D efforts.
Management and Outcome of Prosthetic Vascular Graft Infections: A Single Center Experience (2018)

Prosthetic vascular graft infection needs a multidisciplinary management with appropriate antibiotherapy, radical removal of the infected graft, and in situ reconstruction. This strategy gives satisfactory results in terms of mortality, morbidity, patency rates, and infection control.
Clinical significance of CD151 overexpression in subtypes of invasive breast cancer (2012)

CD151 overexpression may be a potential molecular therapeutic target for breast cancer, especially in QNBC subtype and more advanced stages of breast cancer.
Hydrogen-bond switching through a radical pair mechanism in a flavin-binding photoreceptor (2006)

BLUF (blue light sensing using FAD) domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae, where they control a range of physiological responses including photosynthesis gene expression, photophobia, and negative phototaxis. Other than in well known photoreceptors such as the rhodopsins and phytochromes, BLUF domains are sensitive to light through an oxidized flavin rather than an isomerizable cofactor. To understand the physicochemical basis of BLUF domain photoactivation, we have applied femtosecond transient absorption spectroscopy to the Slr1694 BLUF domain of Synechocystis PCC6803. We show that photoactivation of BLUF domains proceeds by means of a radical-pair mechanism, driven by electron and proton transfer from the protein to the flavin, resulting in the transient formation of anionic and neutral flavin radical species that finally result in the long-lived signaling state on a 100-ps timescale. A pronounced deuteration effect is observed on the lifetimes of the intermediate radical species, indicating that proton movements underlie their molecular transformations. We propose a photoactivation mechanism that involves a successive rupture of hydrogen bonds between a conserved tyrosine and glutamine by light-induced electron transfer from tyrosine to flavin and between the glutamine and flavin by subsequent protonation at flavin N5. These events allow a reorientation of the conserved glutamine, resulting in a switching of the hydrogen-bond network connecting the chromophore to the protein, followed by radical-pair recombination, which locks the glutamine in place. It is suggested that the redox potential of flavin generally defines the light sensitivity of flavin-binding photoreceptors.
Nucleation and motion of an isolated Abrikosov vortex (1991)

A new family of superconductor--normal-metal--insulator--superconductor (S/I/N/S) Josephson junctions have been developed in which a single Abrikosov vortex can be nucleated and systematically moved to selected positions. The location of the vortex within the junction is determined from the shape of the diffraction patterns. Methods have been developed to push the vortex to most any desired location within the junction by applying currents in either or both of the cross-strip legs of the junction. The elementary pinning force for a vortex in a pure Pb film was measured and found to be much smaller than for a Pb-Bi film. In addition, the vortex moves in much smaller steps for the Pb film than was found for the Pb-Bi films. For S/I/N/S junctions, the voltages and currents are in the microvolt and milliamp range; so very conventional detection can be used if a device is to be built based on the motion of a single Abrikosov vortex.
Urban Tomography (2010)

Abstract Urban Tomography is a novel application of mobile smartphone technology, designed to enable pervasive dense documentation of city life by many smartphone users at the same time and provide an automatically-archived historical record of places in time. Besides social-scientific inquiry and research, the system might enable community residents to document their own lives. We describe several pilot fieldwork applications in the use of Urban Tomography, providing insight into designing a system and protocols for conducting field documentation. We then discuss background, philosophy, and the technology of our system. Our website is: http://tomography.usc.edu. Acknowledgments Our research was supported in part by a grant from the University of Southern California-California State University at Long Beach METRANS Project, by the Annenberg Fellowship Program of the Office of the Provost at USC, by the financial support of the Office of the Provost at USC through an Advancing Scholarship in the Humanities and Social Sciences award, and by a grant from Google Research.
Role of a Proximal NF-Y Binding Promoter Element in S Phase-specific Expression of Mouse Ribonucleotide Reductase R2 Gene (1995)

Cell cycle-regulated transcription of the R2 gene of mouse ribonucleotide reductase was earlier shown to be controlled at the level of elongation by an S phase-specific release from a transcriptional block. However, the R2 promoter is activated very early when quiescent cells start to proliferate, and this activation is dependent on three upstream sequences located nucleotide -672 to nucleotide -527 from the transcription start. In this study, we use R2-luciferase reporter gene constructs and gel shift assays to demonstrate that, in addition to the upstream sequences, a proximal CCAAT element specifically binding the transcription factor NF-Y is required for continuous activity of the R2 promoter through the S phase. When the CCAAT element is deleted or mutated, promoter activity induced by the upstream elements decays before cells enter S phase, and the transcriptional block is released. This is a clear example of how changing of a proximal sequence element can alter not only the quantitative but also the qualitative response to upstream transcription activation domains.
Salmonella typhi resistant to Chloramphenicol, Ampicillin, and Other Antimicrobial Agents: Strains Isolated During an Extensive Typhoid Fever Epidemic in Mexico (1973)

During 1972 a large epidemic, in excess of 10,000 cases, of typhoid fever occurred in Mexico City, Pachuca, and other communities of Mexico. The main characteristic of the epidemic, in addition to the large number of persons affected, was the prevalence of a strain of Salmonella typhi which was highly resistant to chloramphenicol both in vivo and in vitro, and which belonged to a single phage type, Vi degraded approaching type A. Of 493 strains of S. typhi studied during the outbreak, 452 (91.7%) were resistant to chloramphenicol (CM), tetracycline (TC), streptomycin (SM), and sulfonamides (SU). The epidemic strain owes its resistance to an R factor which is easily transferable to Escherichia coli K-12 and which appears to be stable. In the third month of the outbreak, a strain of S. typhi resistant to CM, TC, SM, SU, ampicillin (AM), and kanamycin (KM) was isolated from a patient with severe typhoid fever. During the following 9 months, six additional strains of S. typhi resistant to AM, CM, TC, SM, and SU were also isolated. Transfer experiments to E. coli K-12 indicate that these strains are infected with two different R factors, one causing CM, TC, SM, and SU resistance and the other causing AM or AM and KM resistance. The frequency of transfer of the resistance in overnight crosses was in the order of 10(-4) for CM, TC, SM, and SU and 10(-6) for AM or AM, and KM. The appearance of these strains resistant both to chloramphenicol and ampicillin was a cause for concern for the clinicians; fortunately, they have remained an infrequent cause of disease.
Stoichiometric methylation of porcine adrenocorticotropin by protein carboxyl methyltransferase requires deamidation of asparagine 25. Evidence for methylation at the alpha-carboxyl group of atypical L-isoaspartyl residues. (1984)

The enzymatic methylation of porcine adrenocorticotropin (ACTH) in both its native form and a form which is deamidated at asparagine 25 has been compared using purified protein carboxyl methyltransferase from bovine brain. Incubation of deamidated ACTH with high concentrations of methyltransferase resulted in near stoichiometric levels of methyl incorporation (78 mol %), while the methylation of native ACTH was highly substoichiometric (3-12 mol %). The Km and Vmax for deamidated ACTH were 1.9 microM and 11,200 pmol/min/mg, respectively, making this peptide the most specific substrate known for the mammalian methyltransferase. Deamidation of asparagine 25 leads to the formation of an atypical isopeptide bond in which the resulting aspartyl residue is linked to the adjacent glycine 26 via its side-chain beta-carboxyl group rather than the usual alpha-carboxyl linkage (Gráf, L., Bajusz, S., Patthy A., Barát, E., and Cseh, G. (1971) Acta Biochim. Biophys. Acad. Sci. Hung. 6, 415-418; Bornstein, P., and Balian, G. (1977) Methods Enzymol. 47, 132-145). A synthetic isopeptide (beta-linked) analog of deamidated ACTH serves as a highly effective substrate for the methyltransferase, but the corresponding normal (alpha-linked) peptide does not, indicating that this enzyme selectively recognizes the alpha-carboxyl group of atypical beta-linked L-aspartyl residues (see also accompanying paper (Murray, E.D., Jr., and Clarke, S. (1984) J. Biol. Chem. 259, 10722-10732]. Methylation of atypical beta-linked L-aspartyl residues resulting from deamidation can account for previous observations that in vitro protein carboxyl methylation in mammalian systems almost always occurs with a low stoichiometry and that these protein methyl esters are considerably less stable than most chemically formed protein methyl esters.
Isolation and Characterization of a Novel Enzyme,Nα-Benzyloxycarbonyl Amino Acid Urethane Hydrolase, fromStreptococcus faecalisR ATCC 8043 (1985)

A novel enzyme, which was named Nα-benzyloxycarbonyl amino acid urethane hydrolase, was purified from a cell-free extract of Streptococcus faecalis R ATCC 8043, using Nα-benzyloxycarbonyl glycine as substrate. The enzyme was purified 1300-fold with an activity yield of 8%. The purified enzyme was homogeneous by disc electrophoresis. The molecular weight of the native enzyme is about 220,000 by gel filtration, and a molecular weight of 32,000 was determined for the reduced and denatured enzyme by gel electrophoresis in sodium dodecyl sulfate. The isoelectric point was 4.48. The enzyme was inhibited by p-chloromercuribenzoate. The presence of divalent cations (i.e., Co2+ or Zn2+) is essential for its activity.
Power Management Mechanism for routing in Ad-Hoc Wireless Networks (2006)

Power control techniques are used in wireless communications to reduce interference and save energy. This strategy has particularly interesting applications in a multihop MANET(mobile ad-hoc networks), because the transmission power required for the communication between two nodes is increased exponentially with their distance, and the total power required to transmit a packet via multihop may be less than the energy required to transmit it directly. In this paper, we propose a new power saving mechanism in a tree constructed by TDA (topology discovering algorithm) (Zabian and Bonuccelli, 2005). The idea is the reduction of power consumption in each node (when it is possible) by adjusting the transmission range that allows a significant power saving in all the network. Our results show that, the power consumption in a tree like that constructed by TDA is related to the height of the tree and tightly related to the packet size.
Catalytic Synthesis of Alkene–Carbon Monoxide Copolymers and Cooligomers. Edited by Ayusman Sen. (2004)

<em>Angewandte Chemie International Edition</em> is one of the prime chemistry journals in the world, publishing research articles, highlights, communications and reviews across all areas of chemistry.
A human case of ectopic fascioliasis in Korea (1982)

A case of ectopic fascioliasis involving cecum and ascending colon was reported. This case was a 19-year old Korean female who had a history of postprandial aggravation of intermittent abdominal pain of 3 weeks duration. She was presented with an abdominal mass in the right upper quadrant, for which an operation(right hemicolectomy) was performed. Whole cecum and ascending colon showed multifocal tunnel-like necrotizing granulmas with central cavitations. Numerous Charcot-Leyden crystals were seen along tracts of the worm. The lesion was distributed throughout the entire thickness of the wall. Parasitological examination confirmed the worm found in the intestinal wall to be juvenile form of Fasciola species. Possibilities were discussed on the localization of the fluke and the mode of infection of present case.
Luminescence characterization and room-temperature 1.6 &#x003BC;m electroluminescence in si/&#x003B2;-fesi<sub>2</sub>/si double heterostructures on si(001) by molecular beam epitaxy (2007)

We have fabricated Si/β-FeSi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Si double heterostructures light-emitting diodes on Si(001) by molecular beam epitaxy and 1.6 μm electroluminescence was realized at room temperature. The origin of luminescence was investigated using time-resolved photoluminescence measurements.
Enhanced P-Selectin Expression in Chronic and Dermographic Urticaria (1997)

In both chronic and dermographic urticaria, superficial perivascular leukocytic infiltrations are seen histologically in lesional skin. We have therefore investigated the role of endothelial adhesion molecule expression in these diseases. E-selectin, P-selectin, ICAM-1 and VCAM-1 expression was examined immunohistologically, and the serum levels of the soluble forms of these adhesion molecules were determined by EIA in patients with chronic urticaria, dermographic urticaria as well as in healthy controls (n = 8 in each group) and subjects with symptomatic allergic rhinitis (n = 7) for comparison. A significant increase (p<0.01) was observed for soluble P-selectin in dermographic urticaria (mean 487+/-44 ng/ml) and chronic urticaria (mean 464+/-74 ng/ml) compared to healthy controls (mean 149+/-15 ng/ml) and rhinitis subjects (mean 177+/-30 ng/ml). In contrast, the other adhesion molecules were not significantly elevated in both urticaria groups. Immunohistologically, a strong expression of P-selectin was found in superficial vessels of lesional and nonlesional skin in dermographic urticaria with only a mild increase of the other adhesion molecules studied, supporting the findings observed with the soluble forms in the patients' sera. Since an alteration of soluble P-selectin was not seen in symptomatic allergic rhinitis, an unspecific effect due to inflammation appears to be unlikely. These results therefore point to a potentially relevant role of the endothelial P-selectin expression in the evolution of urticarial whealing.
A role for Nrf2 in the prevention of salt‐induced vascular dysfunction (2013)

Consumption of a high salt (HS) diet results in vascular oxidant stress and impairs endothelium‐dependent relaxation in a variety of human and experimental models. Nuclear factor erythroid‐2‐related factor 2 (Nrf2) is a transcription factor that induces the expression of many critical antioxidant genes. We measured protein expression of Nrf2 and its cytosolic inhibitor, kelch‐like ECH‐associated protein 1 (Keap1), in mesenteric and cerebral arterial homogenates from Sprague‐Dawley (SD) rats fed HS (4% NaCl), low salt (LS), or HS with low dose angiotensin II (ANG II) infusion to restore normal plasma ANG II levels. While Nrf2 expression was similar between groups, Keap1 expression was significantly lower in ANG II‐infused rats (p &lt; 0.05). The Nrf2:Keap1 ratio normalized to LS was significantly increased in both mesenteric (LS = 100.00% ± 19.76; HS = 176.34% ± 29.98; HS + ANG II = 561.44% ± 210.39) and cerebral (LS = 100.00% ± 16.21; HS = 181.67% ± 69.31; HS + ANG II = 677.55% ± 172.38) arterial beds. The dietary supplement Protandim, shown to induce Nrf2 expression, improved endothelium‐dependent relaxation to acetylcholine in salt‐fed SD rats (HS = 0.50 μm ± 0.96; HS + Protandim = 6.67 μm ± 1.28; p = 0.008) and hamsters (HS = 1.33 μm ± 0.52; HS + Protandim = 5.60 μm ± 0.68; p &lt; 0.001 ). Together, these data suggest a functional role for the Nrf2 antioxidant defense system in preventing salt‐induced vascular dysfunction.
Equilibrium Phase Densities, Vapor Phase Compositions, and Interfacial Tensions for the Methane + Ethane + n-Pentane System at 294.15 K (2011)

The equilibrium phase densities, vapor phase compositions, and interfacial tensions of the ternary mixture (methane + ethane + n-pentane) have been measured simultaneously using the pendant drop technique at 294.15 K. The total mole compositions of the measured ternary mixtures are 50.61 % methane + 8.93 % ethane + 40.46 % n-pentane; 34.20 % methane + 6.04 % ethane + 59.76 % n-pentane; and 17.46 % methane + 3.08 % ethane + 79.40 % n-pentane, respectively. The measured phase densities and vapor phase compositions are compared with calculated equilibrium properties from the GERG2004 equation. No open interfacial tension data for these ternary systems have been reported at any isothermal conditions. The average experimental interfacial tension data can be described with the total deviations of about 3.2 %. The combined standard uncertainty at each experimental condition is calculated on the basis of ISO recommendations.
Procollagen segment-long-spacing crystallites: Their role in collagen fibrillogenesis* (macromolecular aggregates/exocytosis/cell culture/tissue homogenates/electron microscopy) (2016)

Naturally occurring segment-long-s acing crystallites of procollagen or collagen have been foun Tin the culture medium of fibroblasts from chick embryo tendon, human skin, and dermatosparaxic calf skin; in whole-mount preparations of cultured human skin fibroblasts; in homogenates of lathyritic chick embryo tendon, cartilage, and cornea; and in a partially purified preparation of procollagen. Bundles of similar aggregates occurred within secretory vacuoles of col- lagen-synthesizing fibroblasts and chondrocytes. These obser- vations suggest that fibroblasts and chondrocytes secrete pro- collagen assemblies that are stable in the extracellular envi- ronment. We propose that subsequent enzymatic processing is accompanied by direct incorporation of such structures into the assembling fibril, which then may be considered as an n X 67 nm staggered array of segment-long-spacing crystallites. Morphological and biochemical studies on collagen-secreting cells indicate that newly synthesized procollagen associates within cell vacuoles to form laterally arrayed aggregates that are released by exocytosis into the extracellular compartment. Peptide extensions at both ends of the molecule are enzymati- cally removed and the collagen is assembled as native fibrils (2-10). The state of aggregation of procollagen from the mo- ment of release to the appearance of fibrils remains unresolved. Two mechanisms are usually considered: (i) procollagen is se- creted and enzymatically processed, and the dispersed mono- mers self-assemble to form native fibrils (11, 12); and (ii) pro- collagen is secreted as small molecular aggregates that persist during and after processing and then assemble into fibrous arrays and undergo intermolecular rearrangement to form native fibrils (13, 14). This paper presents evidence for the existence of extracellular segment-long-spacing (SLS) aggregates that apparently were secreted as such and that appear to assemble in linear arrays.