gebhart/patrepeval huggingface dataset:
The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function (2003)

A new microarray method, the isotope array approach, for identifying microorganisms which consume a (14)C-labeled substrate within complex microbial communities was developed. Experiments were performed with a small microarray consisting of oligonucleotide probes targeting the 16S rRNA of ammonia-oxidizing bacteria (AOB). Total RNA was extracted from a pure culture of Nitrosomonas eutropha grown in the presence of [(14)C]bicarbonate. After fluorescence labeling of the RNA and microarray hybridization, scanning of all probe spots for fluorescence and radioactivity revealed that specific signals were obtained and that the incorporation of (14)C into rRNA could be detected unambiguously. Subsequently, we were able to demonstrate the suitability of the isotope array approach for monitoring community composition and CO(2) fixation activity of AOB in two nitrifying activated-sludge samples which were incubated with [(14)C]bicarbonate for up to 26 h. AOB community structure in the activated-sludge samples, as predicted by the microarray hybridization pattern, was confirmed by quantitative fluorescence in situ hybridization (FISH) and comparative amoA sequence analyses. CO(2) fixation activities of the AOB populations within the complex activated-sludge communities were detectable on the microarray by (14)C incorporation and were confirmed independently by combining FISH and microautoradiography. AOB rRNA from activated sludge incubated with radioactive bicarbonate in the presence of allylthiourea as an inhibitor of AOB activity showed no incorporation of (14)C and thus was not detectable on the radioactivity scans of the microarray. These results suggest that the isotope array can be used in a PCR-independent manner to exploit the high parallelism and discriminatory power of microarrays for the direct identification of microorganisms which consume a specific substrate in the environment.
Nucleotide sequence of one component of the banana bunchy top virus genome contains a putative replicase gene (1993)

One DNA component of the banana bunchy top virus (BBTV) genome was cloned and sequenced. This component is present as a circular, ssDNA in the virions and consists of 1111 nucleotides. It contains one large open reading frame (ORF) of 858 nucleotides in the virion sense; this ORF encodes a putative replicase based on the presence of a dNTP-binding motif (GGEGKT). Two smaller ORFs (249 and 366 nucleotides), in the complementary orientation, could not be assigned any obvious function. Neither of these ORFs had significant sequence homology with any known DNA plant virus gene or gene product. Computer analysis of this component-predicted a strong stem-loop structure in the virion sense putative untranslated region; a nonanucleotide sequence in the loop was nearly identical to the nonanucleotide invariant loop sequence of geminiviruses and coconut foliar decay virus. There is strong evidence that the genome of BBTV consists of more than one component because no ORF was found that would encode a protein the size of the BBTV coat protein. BBTV has some characteristics in common with geminiviruses but cannot be classified as one. Rather, BBTV probably belongs to an undescribed plant virus group which could also include subterranean clover stunt virus and coconut foliar decay virus.
Development of A Novel Dual-Layer Thick Ag Substrate for Surface-Enhanced Raman Scattering (SERS) of Self-Assembled Monolayers (2002)

A dual-layer, thick (∼70 nm) vapor-deposited Ag substrate has been developed that gives enhancement factors on the order of 104 for surface-enhanced Raman scattering (SERS) experiments. This substrate has a total thickness of ∼70 nm but also has an outermost surface morphology that approximates that of a thin Ag island film (AgIF) substrate. This is accomplished using a dual overlayer/underlayer structure in which a thick underlayer of 45-nm Ag is vapor-deposited onto a treated glass slide. This Ag underlayer is exposed to ambient conditions under which the surface chemisorbs oxygen, leading to the thermodynamically favorable formation of an active Ag2O interface. An overlayer of 25-nm Ag is vapor-deposited on top of this structure. The first Ag/Ag2O underlayer produces an active interface that decreases the diffusion of the Ag atoms from the second vapor-deposited overlayer, thereby forming Ag particles with shapes favorable for SERS enhancement. Atomic force microscopy results show that the Ag overlayer particles have ideal shapes for SERS enhancement with morphology comparable to thin, vapor-deposited AgIFs. X-ray photoelectron spectroscopy in the O(1s) region showed the presence of multiple forms of oxygen in the Ag/Ag2O underlayer; the main forms were identified as dissolved bulk oxygen and chemisorbed oxygen. Using self-assembled monolayers (SAMs) of 1-dodecanethiol, a SERS intensity increase of ∼400% was obtained for this new overlayer/underlayer Ag substrate when compared to SAMs formed on traditional thick Ag substrates. Enhancement factors calculated from the Raman intensity of trans-1,2-bis(4-pyridyl)ethane showed a SERS enhancement of approximately 104 for this new Ag/Ag2O/Ag substrate compared with the bulk. This compares favorably with the SERS enhancements obtained using thin AgIF substrates. The Ag/Ag2O/Ag substrates showed reproducible SERS intensities (RSD = 0.45−5%). The mechanisms responsible for the overall enhancement on this new substrate are proposed to be the ideal surface morphology of the Ag overlayer particles as well as a combined enhanced electromagnetic field produced by both the Ag/Ag2O underlayer and the Ag overlayer.
Future influenza vaccines and the use of genetic recombinants. (1969)

Genetic recombination of influenza viruses provides the possibility of immediate reassortment and combination of genes and gene products in a single step. Thus, genetic variants with desirable attributes for vaccine production can be produced by deliberate genetic manipulation of viruses rather than by the empirical "hit or miss" methods of the past. Recombination of a high-yield laboratory strain (A0/PR/8) with a low-yield Hong Kong virus (Aichi strain) produced a high-yield recombinant virus (X-31) of Hong Kong antigenicity suitable for vaccine production. It is proposed that a prefabricated "library" of recombinants might anticipate the mutations which may arise in the future and also that live virus vaccines of greater stability may be produced by recombination of new and old viruses.
Nonmotility and phagocytic resistance of Pseudomonas aeruginosa isolates from chronically colonized patients with cystic fibrosis (1994)

Although Pseudomonas aeruginosa chronically colonizes most older patients with cystic fibrosis (CF), bacterial features responsible for its persistence are understood poorly. We observed that many P. aeruginosa isolates from chronically colonized patients were nonmotile and resistant to phagocytosis by macrophages. P. aeruginosa isolates were collected from 20 CF patients for up to 10 years. Isolates from early colonization were highly motile and expressed both flagellin and pilin. However, many isolates from chronically colonized patients lacked flagellin expression and were nonmotile; a total of 1,030 P. aeruginosa CF isolates were examined, of which 39% were nonmotile. Moreover, sequential isolates recovered from several of the CF patients were consistently nonmotile for up to 10 years. Lack of motility was rare among environmental isolates (1.4%) and other clinical isolates (3.7%) of P. aeruginosa examined. Partial complementation of motility in nonmotile P. aeruginosa isolates was achieved by introduction of extra copies of the rpoN locus carried on plasmid pPT212, indicating that the alternate sigma factor, RpoN, may be involved in the coordinate regulation of virulence factors during CF infection. We hypothesize that the nonmotile phenotype may provide P. aeruginosa a survival advantage in chronic CF infection by enabling it to resist phagocytosis and conserve energy.
Evaluation of carcinoembryonic antigen, tissue polypeptide antigen, and squamous cell carcinoma antigen in the detection of cervical cancers. (1992)

Cervical cancer is a predomiannt gynecologic neoplasia in Taiwan. The associations of carcinoembryonic antigen (CEA), tissue polypeptide antigen (TPA) and squamous cell carcinoma antigen (SCC-Ag) for detection of cervical cancers with type of cancer, clinical stage and lymph node metastasis were studied. Serum samples were collected from 395 patients with cervical cancers (61 CIN3, 334 squamous cell carcinoma, 18 adenocarcinoma), 72 patients with benign gynecologic diseases and 115 healthy controls. The sensitivities of CEA, TPA, and SCC-Ag were 15.2%, 33.6%, and 49.3%. The specificities were 89.3%, 96.2%, and 95.1%, respectively. The positive rate of CEA was found significantly higher among patients with adenocarcinoma than those with squamous cell carcinoma. The positive rate of CEA and SCC-Ag increased with advance of the clinical stages. There was no significant difference in the rate of each tumor marker between patients with lymph node metastasis and those without metastasis. The positive rate obtained by SCC-Ag alone was comparable to those by the combinations of two or three antigens. The result of the present study indicates that SCC-Ag is the most useful tumor marker in the detection of cervical cancers.
Inhibition of lysophosphatidate- and thrombin-induced neurite retraction and neuronal cell rounding by ADP ribosylation of the small GTP-binding protein Rho. (1994)

Addition of the bioactive phospholipid lysophosphatidic acid (LPA) or a thrombin receptor-activating peptide (TRP) to serum-starved N1E-115 or NG108-15 neuronal cells causes rapid growth cone collapse, neurite retraction, and transient rounding of the cell body. These shape changes appear to be driven by receptor-mediated contraction of the cortical actomyosin system independent of classic second messengers. Treatment of the cells with Clostridium botulinum C3 exoenzyme, which ADP-ribosylates and thereby inactivates the Rho small GTP-binding protein, inhibits LPA- and TRP-induced force generation and subsequent shape changes. C3 also inhibits LPA-induced neurite retraction in PC12 cells. Biochemical analysis reveals that the ADP-ribosylated substrate is RhoA. Prolonged C3 treatment of cells maintained in 10% serum induces the phenotype of serum-starved cells, with initial cell flattening being followed by neurite outgrowth; such C3-differentiated cells fail to retract their neurites in response to agonists. We conclude that RhoA is essential for receptor-mediated force generation and ensuing neurite retraction in N1E-115 and PC12 cells, and that inactivation of RhoA by ADP-ribosylation abolishes actomyosin contractility and promotes neurite outgrowth.
SSBI Mitigation and the Kramers–Kronig Scheme in Single-Sideband Direct-Detection Transmission With Receiver-Based Electronic Dispersion Compensation (2017)

The performance of direct-detection transceivers employing electronic dispersion compensation combined with DSP-based receiver linearization techniques is assessed through experiments on a 4 × 112 Gb/s wavelength-division multiplexing direct-detection single-sideband 16 quadratic-amplitude modulation Nyquist-subcarrier-modulation system operating at a net optical information spectral density of 2.8 b/s/Hz in transmission over standard single mode fiber links of up to 240 km. The experimental results indicate that systems with receiver-based dispersion compensation can achieve similar performance to those utilizing transmitter-based dispersion compensation, provided it is implemented together with an effective digital receiver linearization technique. The use of receiver-based compensation would simplify the operation of a fiber link since knowledge of the link dispersion is not required at the transmitter. The recently proposed Kramers-Kronig receiver scheme was found to be the best performing among the receiver linearization techniques assessed. To the best of our knowledge, this is the first experimental demonstration of the Kramers-Kronig scheme.
Recyclable, Strong Thermosets and Organogels via Paraformaldehyde Condensation with Diamines (2014)

Nitrogen-based thermoset polymers have many industrial applications (for example, in composites), but are difficult to recycle or rework. We report a simple one-pot, low-temperature polycondensation between paraformaldehyde and 4,4'-oxydianiline (ODA) that forms hemiaminal dynamic covalent networks (HDCNs), which can further cyclize at high temperatures, producing poly(hexahydrotriazine)s (PHTs). Both materials are strong thermosetting polymers, and the PHTs exhibited very high Young's moduli (up to ~14.0 gigapascals and up to 20 gigapascals when reinforced with surface-treated carbon nanotubes), excellent solvent resistance, and resistance to environmental stress cracking. However, both HDCNs and PHTs could be digested at low pH (<2) to recover the bisaniline monomers. By simply using different diamine monomers, the HDCN- and PHT-forming reactions afford extremely versatile materials platforms. For example, when poly(ethylene glycol) (PEG) diamine monomers were used to form HDCNs, elastic organogels formed that exhibited self-healing properties.
Modulation of Endothelial Cell Apoptosis : Mechanisms and Pathophysiological Roles (1996)

Apoptosis is a mode of cell death in which intrinsic cellular mechanisms participate in the demise of the cell. The modulation of endothelial apoptosis may play a role in atherosclerosis, angiogenesis, vascular remodeling and other pathophysiological states. Control of cell death is mediated by the state of activation of a death pathway as well as by the levels of anti apoptotic proteins. The final common pathway of many, if not all, triggers of apoptosis involves activation of cysteine proteases. The Bcl 2 family, in contrast, appears to play a major role in protection against apoptosis. The role of these mechanisms in modulating endothelial cell apoptosis under various conditions is discussed.
A randomized study of intranasal vs. intravenous infusion of dexmedetomidine in gastroscopy (2014)

Intranasal dexmedetomidine is a new, safe, and effective approach for gastroscopy because it has more stable respiratory and circulatory parameters and less adverse reactions than intravenous dexmedetomidine.
Ecological Aspects of the Distribution of Different Autotrophic CO 2 Fixation Pathways (2011)

Autotrophic CO(2) fixation represents the most important biosynthetic process in biology. Besides the well-known Calvin-Benson cycle, five other totally different autotrophic mechanisms are known today. This minireview discusses the factors determining their distribution. As will be made clear, the observed diversity reflects the variety of the organisms and the ecological niches existing in nature.
CD4+ T-cell induction of Fas-mediated apoptosis in Burkitt's lymphoma B cells (1996)

Cytotoxic function of CD4+ Th1 cells is mediated by Fas (CD95, APO-1) and its ligand (Fas ligand). Recent studies using nontransformed B cells and the Ramos Burkitt's lymphoma (BL) B-cell line cells show that CD40 ligation at the B-cell surface by activated, CD40 ligand (CD40L)-bearing, CD4+ T cells upregulates Fas expression on B cells and primes B cells for Fas-mediated death signals. In this work, we examine whether this CD4+ T-cell-dependent molecular pathway for Fas upregulation and B-cell apoptosis reflects a peculiarity of the Ramos B-cell line or is applicable to other Burkitt's tumors as well. In 5 of the 6 Epstein-Barr virus-negative BL cell lines examined, the cells constitutively express undetectable or low levels of Fas and are resistant to Fas-mediated signals induced by monoclonal anti-Fas antibody. All 6 of the BL cell line B cells upregulate Fas in response to CD40 ligation, and in 4 of the cases they become sensitive to Fas-mediated death signals. In one BL cell line, the cells are constitutively sensitive to Fas-mediated cytolysis and are unaffected by CD40 signals. Next, we applied these immunologic manipulations to cells from a refractory clinical sample and observed that the tumor cells could be induced to express Fas and undergo apoptosis in our system. These results establish CD4+ T cells and the Fas-Fas ligand system as important immune regulators of Burkitt's lymphoma B cells and indicate that the susceptibility of tumor cells to Fas-mediated death signals can be modulated by specific activation events at the cell surface.
The 17-Gene Ethanolamine ( eut ) Operon of Salmonella typhimurium Encodes Five Homologues of Carboxysome Shell Proteins (1999)

The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. Previous genetic analysis revealed six eut genes that are needed for aerobic use of ethanolamine; one (eutR), encodes a positive regulator which mediates induction of the operon by vitamin B12 plus ethanolamine. The DNA sequence of the eut operon included 17 genes, suggesting a more complex pathway than that revealed genetically. We have correlated an open reading frame in the sequence with each of the previously identified genes. Nonpolar insertion and deletion mutations made with the Tn10-derived transposable element T-POP showed that at least 10 of the 11 previously undetected eut genes have no Eut phenotype under the conditions tested. Of the dispensable eut genes, five encode apparent homologues of proteins that serve (in other organisms) as shell proteins of the carboxysome. This bacterial organelle, found in photosynthetic and sulfur-oxidizing bacteria, may contribute to CO2 fixation by concentrating CO2 and excluding oxygen. The presence of these homologues in the eut operon of Salmonella suggests that CO2 fixation may be a feature of ethanolamine catabolism in Salmonella.
Apogossypol Derivatives as Pan-Active Inhibitors of Antiapoptotic B-Cell Lymphoma/Leukemia-2 (Bcl-2) Family Proteins (2009)

Guided by nuclear magnetic resonance (NMR) binding assays and computational docking studies, a series of 5,5' substituted apogossypol derivatives was synthesized that resulted in potent pan-active inhibitors of antiapoptotic Bcl-2 family proteins. Compound 8r inhibits the binding of BH3 peptides to Bcl-X(L), Bcl-2, Mcl-1, and Bfl-1 with IC(50) values of 0.76, 0.32, 0.28, and 0.73 microM, respectively. The compound also potently inhibits cell growth of human lung cancer and BP3 human B-cell lymphoma cell lines with EC(50) values of 0.33 and 0.66 microM, respectively. Compound 8r shows little cytotoxicity against bax(-/-)bak(-/-) cells, indicating that it kills cancers cells via the intended mechanism. The compound also displays in vivo efficacy in transgenic mice in which Bcl-2 is overexpressed in splenic B-cells. Together with its improved chemical, plasma, and microsomal stability relative to compound 2 (apogossypol), compound 8r represents a promising drug lead for the development of novel apoptosis-based therapies for cancer.
Systematic Synthesis and Characterization of Single-Crystal Lanthanide Orthophosphate Nanowires (2003)

A simple hydrothermal method has been developed for the systematic synthesis of lanthanide orthophosphate crystals with different crystalline phases and morphologies. It has been shown that pure LnPO(4) compounds change structure with decreasing Ln ionic radius: i.e., the orthophosphates from Ho to Lu as well as Y exist only in the tetragonal zircon (xenotime) structure, while the orthophosphates from La to Dy exist in the hexagonal structure under hydrothermal treatment. The obtained hexagonal structured lanthanide orthophosphate LnPO(4) (Ln = La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, and Dy) products have a wirelike morphology. In contrast, tetragonal LnPO(4) (Ln = Ho, Er, Tm, Yb, Lu, Y) samples prepared under the same experimental conditions consist of nanoparticles. The obtained hexagonal LnPO(4) (Ln = La --> Tb) can convert to the monoclinic monazite structured products, and their morphologies remained the same after calcination at 900 degrees C in air (Hexagonal DyPO(4) is an exceptional case, it transformed to tetragonal DyPO(4) by calcination), while the tetragonal structure for (Ho--> Lu, Y)PO(4) remains unchanged by calcination. The resulting LnPO(4) (Ln = La --> Dy) products consist almost entirely of nanowires/nanorods with diameters of 5-120 nm and lengths ranging from several hundreds of nanometers to several micrometers. Europium doped LaPO(4) nanowires were also prepared, and their photoluminescent properties were reported. The optical absorption spectrum of CePO(4) nanowires was measured and showed some differences from that of bulk CePO(4) materials. The possible growth mechanism of lanthanide phosphate nanowires was explored in detail. X-ray diffraction, field-emission scanning electron microscopy, transmission electron microscopy, electron diffraction, infrared absorption spectra, X-ray photoelectron spectroscopy, optical absorption spectra, and photoluminescence spectra have been employed to characterize these materials.
Pteridines CV (1995)

Summary Treatment of L-biopterin (I) with N,N-dimethyformamide dimethyl- (or diethyl)acetal and then with acetic anhydride in pyridine gave 1',2'-di-O-acetyl-N'-(N,N-dimethylaminomethylene)-L-biopterin (4), which was converted by the Mitsunobu reaction into 3-methyl (5) and 3-p-nitrophenetyl derivatives (7). The protective groups on the side chain diols and N2 of these compounds were selectively cleaved to furnish products 6, 8-10, among which 9 is naturally occurring 3-methyl-L-biopterin and 8 is N',N(3)-protected biopterin, a versatile intermediate for various reactions on the side-chain diol. In contrast, the same Mitsunobu reactions of tri-N2:I',2'-0-acetyl-L-biopterin (II) afforded 04-methyl (12) and 04-NPE derivatives (13), both of which yielded 0 4-methyl-L-biopterin (14) and subsequently led to 4-amino-L-biopterin (18).
Vascular reactivity in alcoholic rat aortas: in vitro interactions between catecholamines and alcohol. (1995)

To understand the nature of vascular problems of hypertensive and alcoholic subjects, an in vitro interaction between catecholamine and alcohol was investigated in male Sprague-Dawley rats. The descending aortas were isolated from either the control or alcohol treated rats. The aortic strips were cooled rapidly in ice-chilled Krebs-Henseleit (K-H) solution and the aorta was cut into a series of rings of approximately 1 mm width. The rings were fixed under 1 g of resting tension between a force-displacement transducer and anchoring electrodes at 37 degrees C. The rings were equilibrated for an hour with frequent changes of the K-H solution before testing. There was norepinephrine (NE) dose-dependent contraction of the rings, which showed the maximum tension with 1 microM NE. Acetylcholine or carbachol produced slow relaxation. Pretreatment of the rings with 10 microM prazocin prevent the contraction induced by 1 microM NE. Even in the presence of prazocin, 60 mM KCI was able to generate the maximum tension. NE-induced contraction was analyzed in the control K-H solution or in the presence of 1.5, 3.0 and 5.0% of ethanol. Ethanol (1.5%) slowed the rate of rise of the aortic tension without a remarkable compromise of the maximum tension. But, there was a significant reduction in contraction with 3% ethanol. A complete inhibition of contraction was noted with 5% ethanol. However, the effect of ethanol was fully reversible upon washings the aortic rings with K-H solution. Aortic rings prepared from the rats that were fed with alcohol for 30 days were not able to generate the maximum tension with 1 microM NE.(ABSTRACT TRUNCATED AT 250 WORDS)