gebhart/patrepeval huggingface dataset:
Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation (2020)

SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and <b>Δ</b>H69/<b>Δ</b>V70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. <i>In vitro</i>, the Spike escape double mutant bearing <b>Δ</b>H69/<b>Δ</b>V70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. The <b>Δ</b>H69/<b>Δ</b>V70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against <b>Δ</b>H69/<b>Δ</b>V70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.
Evaluation of Outcome in Elderly Critically Ill Patients with Nosocomial Klebsiella Pneumoniae Bacteremia (2005)

Background: Gram-negative bacteremia is considered to have little impact on mortality in ICU patients. However, this may not be true in elderly patients. Objective: To determine outcome and attributable mortality in elderly critically ill patients with nosocomial bacteremia involving Klebsiella pneumoniae. Design: A retrospective matched cohort study. Setting: Thirty-bed medical ICU at Taipei Veterans General Hospital. Patients: Thirty-one medical ICU patients aged more than 65 years old with K. pneumoniae bacteremia and 62 matched control patients. Methods: The matching of the control patients (1:2 ratio) was done on the basis of the APACHE II score and age. Without the impact of K. pneumoniae bacteremia, this matching procedure was expected to result in a similar mortality rate for the 2 groups. Results: Elderly patients with K. pneumoniae bacteremia had a significantly higher mortality rate (61.3% vs 26.1%, p=0.003) and more thrombocytopenia (51.6% vs 26.1%, p=0.034) than the control group. Attributable mortality was 35.2%. There was no significant difference in length of ICU stay (33.48 days vs. 32.69 days, p=0.858) and number of ventilator days (31.90 days vs. 29.01 days, p=0.434) between the two groups. Conclusions: After adjusting for severity of disease, Klebsiella pneumoniae bacteremia had significantly increased mortality among the elderly patients.
A Large Gene Cluster for the <i>Clostridium cellulovorans</i> Cellulosome (2000)

A large gene cluster for the Clostridium cellulovorans cellulosome has been cloned and sequenced upstream and downstream of the cbpA and exgS genes (C.-C. Liu and R. H. Doi, Gene 211:39-47, 1998). Gene walking revealed that the engL gene cluster (Y. Tamaru and R. H. Doi, J. Bacteriol. 182:244-247, 2000) was located downstream of the cbpA-exgS genes. Further DNA sequencing revealed that this cluster contains the genes for the scaffolding protein CbpA, the exoglucanase ExgS, several endoglucanases of family 9, the mannanase ManA, and the hydrophobic protein HbpA containing a surface layer homology domain and a hydrophobic (or cohesin) domain. The sequence of the clustered genes is cbpA-exgS-engH-engK-hbpA-engL-man A-engM-engN and is about 22 kb in length. The engN gene did not have a complete catalytic domain, indicating that engN is a truncated gene. This large gene cluster is flanked at the 5' end by a putative noncellulosomal operon consisting of nifV-orf1-sigX-regA and at the 3' end by noncellulosomal genes with homology to transposase (trp) and malate permease (mle). Since gene clusters for the cellulosome are also found in C. cellulolyticum and C. josui, they seem to be typical of mesophilic clostridia, indicating that the large gene clusters may arise from a common ancestor with some evolutionary modifications.
A Mathematical Model of Heat Transfer in a Rotary Kiln Thermo‐Reactor (2005)

Abstract Rotary kilns are used ubiquitously in the chemical and metallurgical industries. The mechanism of heat transfer in a rotary kiln is discussed in this paper, in which the effect of rotation is considered in determining heat transfer coefficients. In particular, an extended penetration theory is successfully developed to describe the heat transfer coefficient of the covered wall to the bulk solid in a rotary kiln, i.e., h cw–cb = (χ d p / k g + 0.5/ $ \sqrt {2k_b \rho_bc_{pb} n/\phis_0} $ ) –1 (0.096 < χ < 0.198). A one‐dimensional axial heat transfer model for an internally heated rotary kiln has been developed. Both predicted temperature profiles and heat transfer fluxes agree well with the experimental data of Barr et al. The simulated results are used to successfully explain for the first time the coupling phenomenon of the bulk bed and covered wall temperatures discussed in previous publications.
Extracellular signal-regulated protein kinases (ERKs) and ERK kinase (MEK) in brain: regional distribution and regulation by chronic morphine (1995)

Quantitative blot immunolabeling techniques were used to determine the concentrations of ERK1 (M(r) 44 kDa) and ERK2 (M(r) 42 kDa), the two major extracellular signal-regulated protein kinases, in different regions of rat brain. The aggregate ERK concentrations (ERK1 and ERK2) were relatively high in each of the brain regions studied, ranging from approximately 0.35 ng/microgram protein in cerebellum to approximately 1.2 ng/microgram protein in nucleus accumbens. However, differences in the regional distributions of ERK1 and ERK2 resulted in ratios of their relative abundance that differed by close to 10-fold among the regions studied. The ratios of ERK1 protein to ERK2 protein varied along a rostral-caudal gradient from a low of 0.16 in frontal cortex to a high of 1.5 in pons/medulla. In hypotonic homogenates from regions at either extreme of the gradient, ERK1 and ERK2 were both found to be predominantly (> 80%) soluble. In subcellular fractions prepared from sucrose homogenates of frontal cortex and pons/medulla, both ERK1 and ERK2 were enriched in the synaptosomal and cytosolic fractions, whereas ERK2 was also enriched in the microsomal fraction. By contrast, in subfractions containing purified nuclei, levels of ERK1 and ERK2 were about one-third of those seen in homogenates and, in subfractions enriched in mitochondria, both ERK1 and ERK2 were barely detectable. The catalytic activity of the ERKs paralleled their protein levels in all of the brain regions except the hippocampus, in which the activity and phosphotyrosine content were disproportionately high. As a possible explanation for this apparent disparity, the regional distribution of ERK kinase (MEK), which phosphorylates and activates the ERKs, was also investigated. The levels of immunoreactivity of the M(r) 45 kDa ERK kinase band differed by about threefold among the brain regions, with the highest levels being present in nucleus accumbens, hippocampus, substantia nigra, and caudate/putamen. Therefore, a higher concentration of ERK kinase immunoreactivity did not appear to account for the disproportionate levels of ERK activity and phosphotyrosine content in the hippocampus. Potential regulation of ERK and ERK kinase levels was also investigated in rats subjected to chronic morphine treatment. ERK1 and ERK2 levels were increased selectively in locus coeruleus and caudate/putamen after chronic morphine treatment, whereas ERK kinase immunoreactivity remained unchanged in all of the brain regions analyzed. In summary, the regional differences in ERK and ERK kinase expression and the region-specific regulation of ERK expression suggest that ERK-related signaling may play an important role in CNS function and its adaptive responses.
Compositions of commercial corn and soybean lecithins (1981)

Abstract The lipid and fatty acid compositions of commercial corn and soybean lecithins were compared. The types of lipids were similar, but the proportions varied. The ratio of glycolipids to phospholipids was 0.36 for corn lecithin and 0.14 for soybean. Phosphatidylcholine and phosphatidylinositol were major phospholipids in both lecithins. In soybean lecithin, the percentage of phosphatidyleth‐anolamine equaled that of phosphatidylinositol, but in corn, the percentage of phosphatidylethanolamine was only about one‐fourth the percentage of phosphatidylinositol. High levels of phosphatidic acid in both the corn and soybean preparations indicated some degradation of the phospholipids during processing. The major differences in fatty acid compositions were a higher percentage of oleic acid and lower percentages of stearic and linolenic acids in corn compared to soybean. The lower level of linolenic acid should give corn lecithin greater resistance toward autoxidation and the development of off‐flavors.
Stable isotope dilution analysis of hydrologic samples by inductively coupled plasma mass spectrometry (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStable isotope dilution analysis of hydrologic samples by inductively coupled plasma mass spectrometryJohn R. Garbarino and Howard E. TaylorCite this: Anal. Chem. 1987, 59, 11, 1568–1575Publication Date (Print):June 1, 1987Publication History Published online1 May 2002Published inissue 1 June 1987https://pubs.acs.org/doi/10.1021/ac00138a018https://doi.org/10.1021/ac00138a018research-articleACS PublicationsRequest reuse permissionsArticle Views97Altmetric-Citations55LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
c-myc amplification and expression in newly established human osteosarcoma cell lines. (1987)

Three cell lines were isolated from a patient with osteosarcoma of the femur. These lines were obtained from the primary neoplasm before (HTLA145) and after (HTLA161) chemotherapy and from a metastasis of the lung (HTLA195) in the same patient. The three cell lines exhibited a similar morphology in culture and formed tumors in nude mice which demonstrated a histopathology similar to that which had been observed in the patient. High expression of the genes coding for the alpha-1 and alpha-2 chain of collagen Type I was found in vitro and in s.c. tumors growing in nude mice. The c-myc protooncogene was amplified in all three cell lines and extensive expression of c-myc was found in vitro and in vivo. No heterogeneity in regard to c-myc expression in vivo was detected by in situ localization in tumors growing in nude mice.
A Prosodic Model of Sign Language Phonology (1999)

Superior to any other book on the subject that I have seen. I can see it being used as a class text or reference for current theory in sign language phonology. This book is intended in part to provide linguists and cognitive scientists who do not know sign language with a point of entry into the study of sign language phonology. At the same time, it presents a comprehensive theory of American Sign Language (ASL) phonology, while reviewing and building on alternative theories. One claim of this theoretical framework is that, because of sign language's visual/gestural phonetic basis, the consonant-like units and vowel-like units are expressed simultaneously with one another, rather than sequentially as in spoken languages. A second claim is that movements operate as the most basic prosodic units of the language. The author is concerned to show both the similarities and differences between signed and spoken languages, and to indicate some directions for future work in cognitive science that can be derived from her phonological model. Bradford Books imprint
A new simplified NO/NO2 conversion model under consideration of direct NO2-emissions (2010)

Although many German monitoring sites report declines of NOx concentrations, NO2-concentrations actually stagnate or even increase quite often. Various analyses have identified the altered compositions of nitrogen oxides (NO2/NOx-ratio) emitted by motor vehicles (resulting in an increase of primary NO2-emissions) as well as the chemical environmental conditions (mainly ground level ozone) as the main causes. The chemical conversion of NO to NO2 is often parameterized in dispersion calculations of exhaust emissions. A widely applied conversion model is the so-called Romberg approach from 1996. However, the Romberg approach has to be re-evaluated to accommodate the above-mentioned conditions. This article presents an adjustment to the Romberg approach in accordance with the measured data from 2000 to 2006, taking into consideration substantially higher NO2/NOx-ratios especially for higher NOx-concentrations. Model calculations with OSPM (Operational Street Pollution Model) including its internal chemistry module are able to reproduce very well the trends in the measured annual NO2-concentrations over a 10 year period. The relevant parameters for variations between the years are the NOx-emissions, primary NO2-emissions, ozone concentrations, wind conditions, and background concentrations. A simplified chemistry model based on annual mean NOx- and NO2-concentrations, and background ozone concentrations, as well as primary NO2-emissions is presented as a better method than the updated Romberg approach. This model simulates the annual mean NO2-concentrations much more accurately than the conventional and the updated Romberg approaches.
All-optical time-division demultiplexing experimentwithsimultaneous output of all constituent channels from 100 Gbit/s OTDM signal (2001)

The successful demonstration of all-optical time-division demultiplexing is reported, wherein all 10 Gbit/s constituent channels are simultaneously demultiplexed with no error from a 10 × 10 Gbit/s OTDM signal. A multichannel demultiplexer based on XPM-induced frequency shift in an optical fibre, called MOXIC, is used.
<i>N,O</i>-Dimethylhydroxylamine (2001)

(·HCl) [1117-97-1] C2H7NO (MW 61.10) [6638-79-5] C2H8ClNO (MW 97.56) (used extensively in the formation of N-methoxy-N-methylamides2 and ureas,3 which are valuable acylating agents) Physical Data: mp −97 °C; bp 43.2 °C. ·HCl salt, mp 115–116 °C. Form Supplied in: commercially available as the HCl salt. Handling, Storage, and Precautions: the free amine decomposes readily. However, the HCl salt is stable indefinitely.
Monocular Depth Estimation Using Neural Regression Forest (2016)

This paper presents a novel deep architecture, called neural regression forest (NRF), for depth estimation from a single image. NRF combines random forests and convolutional neural networks (CNNs). Scanning windows extracted from the image represent samples which are passed down the trees of NRF for predicting their depth. At every tree node, the sample is filtered with a CNN associated with that node. Results of the convolutional filtering are passed to left and right children nodes, i.e., corresponding CNNs, with a Bernoulli probability, until the leaves, where depth estimations are made. CNNs at every node are designed to have fewer parameters than seen in recent work, but their stacked processing along a path in the tree effectively amounts to a deeper CNN. NRF allows for parallelizable training of all "shallow" CNNs, and efficient enforcing of smoothness in depth estimation results. Our evaluation on the benchmark Make3D and NYUv2 datasets demonstrates that NRF outperforms the state of the art, and gracefully handles gradually decreasing training datasets.
Preparation of Petaloid Microspheres of Basic Magnesium Carbonate (2007)

The synthesis of basic magnesium carbonate was examined under ultrasonic irradiation and was performed by the soda ash method using magnesium sulfate and sodium carbonate as starting materials. The particulate product was evaluated using SEM observations. Ultrasonic irradiation in the preparation of basic magnesium carbonate was found to give fine petaloid microspheres of about 3 mum in primary particle size.
Effect of estrogen and progesterone on macrophage activation during wound healing (2009)

Age-related impaired wound healing leads to substantial morbidity and mortality along with a large financial burden to health services. There is accumulating evidence that the tissue damage associated with chronic wounds is initiated and propagated by an inappropriately excessive inflammatory response. Research on age-related impaired wound healing suggests that the decline in sex steroid hormones with age may have a substantial influence on the inflammatory response in vivo. Topical and systemic estrogen treatments have shown an increased rate of healing by reducing inflammation, however the underlying mechanisms are little understood. In vitro studies also suggest progesterone may play a role in modulating inflammation. Macrophages are essential mediators of inflammation and wound healing. Macrophages can be activated in a classical or alternative manner in parallel with the T(H)1/T(H)2 dichotomy, respectively. Using a murine incisional wound healing model this study was carried out to investigate the roles of estrogen and progesterone on macrophage activation during the wound healing response. Our findings suggest with a reduction of steroid hormones following ovariectomy, alternatively activated macrophage markers (Fizz1 and Ym1) were reduced, with this effect being reversed with the administration of estrogen or progesterone; suggesting that with the reduction of steroid hormones macrophages are activated in a classical manner, promoting inflammation, whereas estrogen or progesterone are contributing toward macrophage activation in an alternative manner, driving wound repair, angiogenesis, and remodeling.
A STUDY ON THE CHARACTERISTICS OF OUTER SPACE OF DAEBANG BUILDING IN BUDDHIST TEMPLES OF SEOUL AND GYEONGGI PROVINCE FROM THE 19TH TO THE MID-20TH CENTURY (2003)

The study on the characteristics of outer space of daebang in Seoul and Gyeonggi province could be summarized as follows : 1. In the central domain of temples having been composed of both a main temple and a daebang, the former was regarded as a practical or symbolic worship object of the latter and these two buildings were settled within the distance of 75ft each other. It is the maximum length between a stage and an auditorium that we can see and listen to the actors on the stage. 2. In case of daebang with side wing room (s), the degree of view looking downward at the front window of it was usually within the limit of 30°, which was the downward angle of easy view permitting us to look out without any movement of one's head or eyes.
<i>Actinobacillus actinomycetemcomitans</i> fimbriae (1988)

Freshly isolated Actinobacillus actinomycetemcomitans strains were found to possess fimbriae. These appendages appeared to be irreversibly lost after 30 to 40 subcultures in the laboratory. The fimbriated strains were associated with a specific type of colonial morphology designated SP (Star Positive); the non‐fimbriated variant colony was designated SN (Star Negative). The fimbriae were approximately 5 nm wide and could be several μm in length. The fimbriated cells tended to aggregate readily whereas the non‐fimbriated cells formed uniform suspensions. Three stains of fimbriated A. actinomycetemcomitans isolated from different patients were compared to their non‐fimbriated variants for attachment to hydroxyapatite (HA) and saliva coated hydroxyapatite (SHA). Two of the fimbriated variants exhibited a 3‐ to 4‐fold enhancement of attachment to HA and SHA over their non‐fimbriated variant. However, there did not appear to be any specificity for SHA over HA. One strain (Pag) showed no major differences in attachment of the fimbriated or non‐fimbriated variant, albeit the fimbriae were indistinguishable from those of the other A. actinomycetemcomitans strains. Thus, there may be molecular differences among fimbriae of various A. actinomycetemcomitans strains which determine both their tissue specificity and their affinity for particular substrates.
Design of a monolithic Michelson interferometer for fringe imaging in a near-field, UV, direct-detection Doppler wind lidar (2016)

The low-biased, fast, airborne, short-range, and range-resolved determination of atmospheric wind speeds plays a key role in wake vortex and turbulence mitigation strategies and would improve flight safety, comfort, and economy. In this work, a concept for an airborne, UV, direct-detection Doppler wind lidar receiver is presented. A monolithic, tilted, field-widened, fringe-imaging Michelson interferometer (FWFIMI) combines the advantages of low angular sensitivity, high thermo-mechanical stability, independence of the specific atmospheric conditions, and potential for fast data evaluation. Design and integration of the FWFIMI into a lidar receiver concept are described. Simulations help to evaluate the receiver design and prospect sufficient performance under different atmospheric conditions.
Coder/Decoder Units for RGB and NTSC Signals (1981)

This paper contains a brief description of the RGB and the NTSC codecs used during the First SMPTE Component-Coded Demonstration of Digital Video. Each unit operates at the luminance/chrominance sampling ratio of 4:4:4 and is capable of running at any of three demonstration clock rates. Operating the above units in any tandem combination, as well as with a digital interface with units of the other Demonstration participants, yielded acceptable picture quality. In the Appendix the codec matrices between RGB, YUV, YIQ, and Y, R - Y, and B - Y of the digital interface are postulated. The relationship of Y, R - Y, and B - Y to the composite video signal is indicated. The numerical relationships described in this paper are independent of clock frequencies and luminance/chrominance sampling ratios.