gebhart/patrepeval huggingface dataset:
Antigenic comparison of feline coronavirus isolates: evidence for markedly different peplomer glycoproteins (1987)

The antigenic relationships among seven feline coronavirus isolates were investigated by using a panel of 26 monoclonal antibodies (MAbs). The MAbs were categorized into five immunoreactive groups which were used to delineate two antigenic types of feline coronaviruses. One antigenic type included the more virulent feline infectious peritonitis virus (FIPV) isolates (FIPV-UCD-1, FIPV-UCD-4, FIPV-TN406, FIPV-DF2, and FIPV-79-1146), whereas the second antigenic type was composed of the avirulent isolate FIPV-UCD-2. The feline enteric coronavirus isolate FECV-79-1683 shared some characteristics of both of the major antigenic groups. Epitopes on the nucleocapsid and envelope polypeptides were in general highly conserved among both antigenic types, although a few type-specific antigenic sites were discriminated. The most striking finding was the marked antigenic difference in the peplomer (E2) glycoproteins between the two antigenic types. Seven anti-E2 MAbs reacted with one antigenic type of E2, whereas seven other anti-E2 MAbs recognized a different antigenic form of E2. None of the 14 anti-E2 MAbs reacted with all of the isolates.
Comparison of Antiviral Effects of Zidovudine Phosphoramidate and Phosphorodiamidate Derivatives against HIV and ULV in vitro (1992)

A number of zidovudine phosphoramidate and phosphorodiamidate derivatives were prepared, including some previously unreported benzyl esterified amino acyl compounds. These were found to be active in vitro against the human immunodeficiency virus (HIV-1), and were tested subsequently in the S+L-tissue culture assay against urethane leukaemia virus (ULV), a murine leukaemia virus (MuLV). The fifteen compounds tested showed a similar range of activity against the two viruses. No active compounds were missed in the MuLV system which was usually more sensitive to antiviral effects. Five compounds showed some toxicity to the mouse cells only. We are using this system in parallel with HIV assays to identify those derivatives which will be tested subsequently against a murine retrovirus in vivo.
Aggregative adherence fimbria II, a second fimbrial antigen mediating aggregative adherence in enteroaggregative Escherichia coli (1997)

Enteroaggregative Escherichia coli (EAEC) has been implicated as an agent of pediatric diarrhea in the developing world. We have shown previously that EAEC adheres to HEp-2 cells by virtue of a plasmid-encoded fimbrial adhesin designated aggregative adherence fimbria I (AAF/I), the genes for which have been cloned and sequenced. However, not all EAEC strains express AAF/I. Using TnphoA mutagenesis, we have characterized a novel fimbria (designated AAF/II) which mediates HEp-2 adherence of the human-pathogenic strain 042. AAF/II is 5 nm in diameter and does not bind AAF/I antiserum, as determined by immunogold transmission electron microscopy. TnphoA identified a gene (designated aafA) which bears significant homology to aggA, the fimbrial subunit of AAF/I (25% identity and 47% similarity at the amino acid level). When hyperexpressed and purified by polyhistidine tagging, the AafA protein assembled into 5-nm-diameter filaments which bound anti-AAF/II antiserum. The cloned aafA gene complemented a mutation in the aggA gene to confer fimbrial expression from the AAF/I gene cluster, manifesting phenotypes characteristic of AAF/II but not AAF/I. The aafA mutant did not adhere to human intestinal tissue in culture, suggesting a role for AAF/II in intestinal colonization. By using DNA probes for AAF/I and AAF/II derived from fimbrial biosynthesis genes, we show that AAF/I and AAF/II are each found in only a minority of EAEC strains, suggesting that still more EAEC adhesins exist. Our data suggest that AAF adhesins represent a new family of fimbrial adhesins which mediate aggregative adherence in EAEC.
The carbon nanotube-silicon heterojunction as infrared detector (2006)

Carbon nanotubes are a unique material that can be either metallic or semiconducting, usually with a small bandgap inversely proportional to tube diameter and with interesting optical properties. However, their general randomness in length, diameter, and chirality, and the challenges in aggregating sufficiently large quantities of precisely uniform nanotubes, render its applications in optical detection so far unattainable beyond simple absorptive coating. The highly-ordered carbon nanotube array, as grown by the non-lithographic methods described here, surmounts many of these obstacles while presenting a geometry that is useful for focal plane array applications. A nanoporous alumina template assists the nanotube growth, which proceeds by carbon vapor deposition in a technique that is compatible with integration on silicon. We report on the experimental treatment of one possible platform for applying carbon nanotubes in infrared detection: a heterojunction photodiode with silicon. The nanotube-silicon heterojunction has rectifying characteristics that are consistent with silicon doping type, nanotube work function, and silicon-nanotube bandgaps. We investigate this hybrid nanostructure with spectral photocurrent measurements in the near and mid-infrared regime in both cooled and uncooled modes of detection. Transient photocurrent analysis suggests that both pyroelectric and direct optoelectronic effects are sources of photoresponse. First-principle theoretical treatments of nanotube-silicon heterojunction detection imply that performance parameters such as D* could be greatly optimized in future generations of samples. We explore the suitability of this detector prototype for spaceborne applications where many known properties of carbon, such as chemical and mechanical durability as well as strong covalent bonding and therefore radiation hardness, merit its consideration.
In vivo label-free photoacoustic microscopy of cell nuclei by excitation of DNA and RNA (2010)

Imaging of cell nuclei plays a critical role in cancer diagnosis and prognosis. To image noninvasively cell nuclei in vivo without staining, we developed UV photoacoustic microscopy (UV-PAM), in which 266 nm wavelength UV light excites unlabeled DNA and RNA in cell nuclei to produce photoacoustic waves. We applied UV-PAM to ex vivo imaging of cell nuclei in a mouse lip and a mouse small intestine and to in vivo imaging of the cell nuclei in the mouse skin. The UV-PAM images of unstained cell nuclei match the optical micrographs of the histologically stained cell nuclei. Given intrinsic optical contrast and high spatial resolution, in vivo label-free UV-PAM has potential for unique biological and clinical application.
Interleukin-8 and related chemotactic cytokines--CXC and CC chemokines. (1994)

Publisher Summary This chapter focuses on interleukin-8 (IL-8) and related chemotactic cytokines—namely, CXC and CC chemokines. IL-8 is the best known member of a new class of cytokines that are widely studied because of their ability to attract and activate leukocytes, and their potential role as mediators of inflammation. IL-8 was originally isolated from the culture supernatants of stimulated human blood monocytes and was identified as a protein of 72 amino acids with a molecular weight of 8383. The three-dimensional structure of IL-8 has been studied by nuclear magnetic resonance spectroscopy and X-ray crystallography. In concentrated solution, and on crystallization, IL-8 is present as a dimer. The first CC chemokine was identified after cloning by differential hybridization from human tonsillar lymphocytes and was termed LD78. The CC and CXC chemokines are similar in size and have an overall structure that is characterized by the two intrachain disulfide bonds, short N-terminal and long C-terminal sequences. It discusses the role of chemokines in pathology with skin inflammation because psoriasis was the first disease to be linked to overproduction of IL-8. Several independent studies document the occurrence of high levels of IL-8 in the synovial fluid of inflamed joints of patients with different forms of rheumatic diseases, osteoarthritis, and gout.
Effects of interfacial layer growth on the electrical characteristics of thin titanium oxide films on silicon (1999)

Effects of interfacial layer growth on reactively sputter-deposited TiO2 films were studied. Leakage current was reduced to 10−8 A/cm2 at +1 V after annealing in oxygen ambient and showed tunneling-like temperature dependence. As the interfacial layer grew, interface states and hysteresis were improved significantly. However, the reliability was degraded as the annealing temperature increased.
An Evaluation of Non-Equijoin Algorithms (1991)

A non-equijoin of relations R and S is a band join if the join predicate requires values in the join attribute of R to fall within a specified band about the values in the join attribute of S. We propose a new algorithm, termed a partitioned band join, for evaluating band joins. We present a comparison between the partitioned band join algorithm and the classical sort-merge join algorithm (optimized for band joins) using both an analytical model and an implementation on top of the WiSS storage system. The results show that the partitioned band join algorithm outperforms sortmerge unless memory is scarce and the operands of the join are of equal size. We also describe a parallel implementation of the partitioned band join on the Gamma database machine, and present data from speedup and scaleup experiments demonstrating that the partitioned band join is efficiently parallelizable.
Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria (2002)

Fluorescence in situ hybridization (FISH) with horseradish peroxidase (HRP)-labeled oligonucleotide probes and tyramide signal amplification, also known as catalyzed reporter deposition (CARD), is currently not generally applicable to heterotrophic bacteria in marine samples. Penetration of the HRP molecule into bacterial cells requires permeabilization procedures that cause high and most probably species-selective cell loss. Here we present an improved protocol for CARD-FISH of marine planktonic and benthic microbial assemblages. After concentration of samples onto membrane filters and subsequent embedding of filters in low-gelling-point agarose, no decrease in bacterial cell numbers was observed during 90 min of lysozyme incubation (10 mg ml(-1) at 37 degrees C). The detection rates of coastal North Sea bacterioplankton by CARD-FISH with a general bacterial probe (EUB338-HRP) were significantly higher (mean, 94% of total cell counts; range, 85 to 100%) than that with a monolabeled probe (EUB338-mono; mean, 48%; range, 19 to 66%). Virtually no unspecific staining was observed after CARD-FISH with an antisense EUB338-HRP. Members of the marine SAR86 clade were undetectable by FISH with a monolabeled probe; however, a substantial population was visualized by CARD-FISH (mean, 7%; range, 3 to 13%). Detection rates of EUB338-HRP in Wadden Sea sediments (mean, 81%; range, 53 to 100%) were almost twice as high as the detection rates of EUB338-mono (mean, 44%; range, 25 to 71%). The enhanced fluorescence intensities and signal-to-background ratios make CARD-FISH superior to FISH with directly labeled oligonucleotides for the staining of bacteria with low rRNA content in the marine environment.
Stereospecific Alkane Hydroxylation by Non-Heme Iron Catalysts:  Mechanistic Evidence for an FeVO Active Species (2001)

High-valent iron-oxo species have frequently been invoked in the oxidation of hydrocarbons by both heme and non-heme enzymes. Although a formally Fe(V)=O species, that is, [(Por(*))Fe(IV)=O](+), has been widely accepted as the key oxidant in stereospecific alkane hydroxylation by heme systems, it is not established that such a high-valent state can be accessed by a non-heme ligand environment. Herein we report a systematic study on alkane oxidations with H(2)O(2) catalyzed by a group of non-heme iron complexes, that is, [Fe(II)(TPA)(CH(3)CN)(2)](2+) (1, TPA = tris(2-pyridylmethyl)amine) and its alpha- and beta-substituted analogues. The reactivity patterns of this family of Fe(II)(TPA) catalysts can be modulated by the electronic and steric properties of the ligand environment, which affects the spin states of a common Fe(III)-OOH intermediate. Such an Fe(III)-peroxo species is high-spin when the TPA ligand has two or three alpha-substituents and is proposed to be directly responsible for the selective C-H bond cleavage of the alkane substrate. The thus-generated alkyl radicals, however, have relatively long lifetimes and are susceptible to radical epimerization and trapping by O(2). On the other hand, 1 and the beta-substituted Fe(II)(TPA) complexes catalyze stereospecific alkane hydroxylation by a mechanism involving both a low-spin Fe(III)-OOH intermediate and an Fe(V)=O species derived from O-O bond heterolysis. We propose that the heterolysis pathway is promoted by two factors: (a) the low-spin iron(III) center which weakens the O-O bond and (b) the binding of an adjacent water ligand that can hydrogen bond to the terminal oxygen of the hydroperoxo group and facilitate the departure of the hydroxide. Evidence for the Fe(V)=O species comes from isotope-labeling studies showing incorporation of (18)O from H(2)(18)O into the alcohol products. (18)O-incorporation occurs by H(2)(18)O binding to the low-spin Fe(III)-OOH intermediate, its conversion to a cis-H(18)O-Fe(V)=O species, and then oxo-hydroxo tautomerization. The relative contributions of the two pathways of this dual-oxidant mechanism are affected by both the electron donating ability of the TPA ligand and the strength of the C-H bond to be broken. These studies thus serve as a synthetic precedent for an Fe(V)=O species in the oxygen activation mechanisms postulated for non-heme iron enzymes such as methane monooxygenase and Rieske dioxygenases.
Complete nucleotide and deduced protein sequence of CMP-NeuAc: poly-α-2,8 sialosyl sialyltransferase of Escherichia coli K1 (1991)

Poly-alpha-2,8 N-acetylneuraminic acid (polySia) is an important virulence factor in infections caused by Escherichia coli K1 and Neisseria meningitidis B. In E. coli K1 a membranous CMP-NeuAc: poly-alpha-2,8 sialosyl sialyltransferase (polysialyltransferase) complex catalyses the synthesis of linear polySia chains. The complex also elongates sialyl oligomers that serve as exogenous acceptors. The gene encoding a polysialyltransferase of E. coli has been identified by subcloning and DNA sequence analysis. The subcloned DNA fragment codes for a polypeptide with a molecular mass of 47 kDa catalysing the in vitro synthesis of polySia by elongation of exogenous acceptors.
Triage: performance isolation and differentiation for storage systems (2004)

Ensuring performance isolation and differentiation among workloads that share a storage infrastructure is a basic requirement in consolidated data centers. Existing management tools rely on resource provisioning to meet performance goals; they require detailed knowledge of the system characteristics and the workloads. Provisioning is inherently slow to react to system and workload dynamics, and in the general case, it is impossible to provision for the worst case. We propose a software-only solution that ensures predictable performance for storage access. It is applicable to a wide range of storage systems and makes no assumptions about workload characteristics. We use an on-line feedback loop with an adaptive controller that throttles storage access requests to ensure that the available system throughput is shared among workloads according to their performance goals and their relative importance. The controller considers the system as a "black box" and adapts automatically to system and workload changes. The controller is distributed to ensure high availability under overload conditions, and it can be used for both block and file access protocols. The evaluation of Triage, our experimental prototype, demonstrates workload isolation and differentiation, in an overloaded cluster file-system where workloads and system components are changing.
In situ hybridization to chromosomes stabilized in gel microdrops (1995)

Conventional chromosome in situ hybridization procedures rely on fixation to glass slides followed by microscopic evaluation. This report describes the development of a microdrop in situ hybridization to chromosomes in suspension. Chromosomes encapsulated in gel microdrops (GMDs) composed of an agarose matrix withstood stringent hybridization and denaturation conditions. Because of the increased stability, hybridization to encapsulated chromosomes was detected by flow cytometry as well as conventional microscopy. Thus, the MISH method offers a means for chromosome hybridization without slides and may enable identification and isolation of chromosome using hybridization rather than nucleic acid binding dyes.
Cell Contact–dependent Activation of α3β1 Integrin Modulates Endothelial Cell Responses to Thrombospondin-1 (2000)

Thrombospondin-1 (TSP1) can inhibit angiogenesis by interacting with endothelial cell CD36 or proteoglycan receptors. We have now identified alpha3beta1 integrin as an additional receptor for TSP1 that modulates angiogenesis and the in vitro behavior of endothelial cells. Recognition of TSP1 and an alpha3beta1 integrin-binding peptide from TSP1 by normal endothelial cells is induced after loss of cell-cell contact or ligation of CD98. Although confluent endothelial cells do not spread on a TSP1 substrate, alpha3beta1 integrin mediates efficient spreading on TSP1 substrates of endothelial cells deprived of cell-cell contact or vascular endothelial cadherin signaling. Activation of this integrin is independent of proliferation, but ligation of the alpha3beta1 integrin modulates endothelial cell proliferation. In solution, both intact TSP1 and the alpha3beta1 integrin-binding peptide from TSP1 inhibit proliferation of sparse endothelial cell cultures independent of their CD36 expression. However, TSP1 or the same peptide immobilized on the substratum promotes their proliferation. The TSP1 peptide, when added in solution, specifically inhibits endothelial cell migration and inhibits angiogenesis in the chick chorioallantoic membrane, whereas a fragment of TSP1 containing this sequence stimulates angiogenesis. Therefore, recognition of immobilized TSP1 by alpha3beta1 integrin may stimulate endothelial cell proliferation and angiogenesis. Peptides that inhibit this interaction are a novel class of angiogenesis inhibitors.
Frequent alterations of chromosome 1 in ductal carcinoma in situ of the breast. (1995)

Ductal carcinoma in situ (DCIS) of the breast is commonly described as a premalignant lesion. Using PCR to amplify DNA from areas of tumour cells which have been microdissected from fixed material, we have studied the involvement of chromosome 1 in 19 cases of DCIS. A series of microsatellite repeat polymorphisms has been used to define regions of allelic imbalance and this has confirmed the involvement in DCIS of six of the regions previously implicated in studies of invasive breast tumours. This suggests that these regions may harbour tumour suppressor genes, the inactivation of which is important for the early stages of breast tumour development. Analysis of separate ducts from within the same tumour has revealed that the same genetic alterations are not necessarily present throughout the lesion. In addition we have found that in three cases where frank invasive carcinoma is also present, similar alterations can be detected in the in situ and invasive component.
Cognitive Networking for Next-G Wireless Communications (2016)

With the development and the promising future of nextgeneration wireless communications, cognitive networking has emerged as a promising technology to address spectrum scarcity and achieve higher data rate. Despite of its benefit, the employment of cognitive techniques at different layers brings nontrivial design challenges to many networking functionalities. In such context, this special issue is aimed at investigating and seeking potential solutions to various challenges in cognitive networking for next-generation (Next-G) wireless communications, such as cognitive communication architecture and topology control, spectrum sensing, sharing, andmanagementmechanisms, cognitive techniques and networking for Next-G wireless communications, and security and privacy in Next-G wireless communications. Specifically, the special issue is composed of the following papers. Here we present a high-level overview of them.
Bovine Serum Estrogens, Progestins and Glucocorticoids during Late Pregnancy, Parturition and Early Lactation (1973)

Jugular blood was collected from 10 Holstein heifers twice weekly from 26 to 6 days before parturitiion, twice daily from 6 days before to 5 days after parturition and on day 9 after parturition. Progestins were extracted from blood serum with trimethyl pentane, glucocorticoids were extracted with dichloromethane, and each was quantified by competitive protein binding assay. Estradiol and estrone were extracted with ether, isolated by column chromatography and determined by radioimmunoassays. Progesterone remained high until —2 days (7.6±.9 ng/ml), fell to 3.0±.7 ng/ml at —1 day and to 0.6±.1 ng/ml at parturition, and remained near this low level for 9 days postpartum. Glucocorticoids remained low until —1 day (6.4±.9 ng/ml), increased dramatically to 10.3±1.5 ng/ml at —.5 day, to 16.7±3.5 ng/ml at parturition, and then fell to 5.1±.8 at 0.5 day after parturition and remained near that basal level for 9 days postpartum. Estradiol increased linearly from 32±6 pg/ml at —26 days to 150±24 pg/ml at —5 days, and jumped to 295±53 pg/ml at —2 and —1.5 days. Then estradiol fell to 52±11 pg/ml at 1 day postpartum and averaged 14±10 pg/ml until day 9 postpartum. Changes in serum estrone generally followed those for estradiol, but estrone was about eight-fold higher. Thus, a 10-fold increase in blood serum estrogens during the month before parturition was the first major change in steroid hormones in advance of parturition. Estradiol, estrone and progesterone all declined precipitously during the final 2 days of pregnancy, while glucocorticoid increased to a peak at parturition.
Elicitation of anti-H-2 cytotoxic T lymphocytes with antigen-modified H-2 negative stimulator cells. (1981)

By a newly developed technique, we have modified H-2k-negative cells in such a way as to render them capable of elicitation of anti-H-2 CTL. Purified H-2Kk and/or partially purified Iak glycoproteins were incorporated into lipid vesicles that contained the hemagglutinin-neuraminidase (HN) glycoprotein and the fusion (F) glycoprotein of Sendai virus. These lipid vesicles were incubated with H-2-negative tumor cells (R1-) in a manner that resulted in rendering these cells capable of eliciting anti-H-2Kk CTL. The presence of Iak on the surface of the modified stimulator cell had a significant effect on the proportion of anti-H-2Kk CTL possessing a particular Lyt phenotype. Primary effector cells elicited by an H-2Kk-Iak difference were primarily Lyt 1-, 2+, whereas primary anti-H-2Kk CTL elicited by an H-2Kk difference alone were predominantly Lyt 1+, 2+.
Microglial inflammation in the parkinsonian substantia nigra: relationship to alpha-synuclein deposition (2005)

While microglia appeared to respond to alpha-synuclein deposition, MHC class II antigen expression by microglia in the substantia nigra cannot be used as an indicator of clinical PD severity or disease progression. In addition, a contributory or even causative role for microglia in the neuronal loss associated with PD as suggested by some authors seems unlikely. Our data further suggest that an assessment of microglial activation in the aged brain on the basis of immunohistochemistry for MHC class II antigens alone should be done with caution.