gebhart/patrepeval huggingface dataset:
Use of recA as an alternative phylogenetic marker in the family Vibrionaceae (2004)

This study analysed the usefulness of recA gene sequences as an alternative phylogenetic and/or identification marker for vibrios. The recA sequences suggest that the genus Vibrio is polyphyletic. The high heterogeneity observed within vibrios was congruent with former polyphasic taxonomic studies on this group. Photobacterium species clustered together and apparently nested within vibrios, while Grimontia hollisae was apart from other vibrios. Within the vibrios, Vibrio cholerae and Vibrio mimicus clustered apart from the other genus members. Vibrio harveyi- and Vibrio splendidus-related species formed compact separated groups. On the other hand, species related to Vibrio tubiashii appeared scattered in the phylogenetic tree. The pairs Vibrio coralliilyticus and Vibrio neptunius, Vibrio nereis and Vibrio xuii and V. tubiashii and Vibrio brasiliensis clustered completely apart from each other. There was a correlation of 0.58 between recA and 16S rDNA pairwise similarities. Strains of the same species have at least 94 % recA sequence similarity. recA gene sequences are much more discriminatory than 16S rDNA. For 16S rDNA similarity values above 98 % there was a wide range of recA similarities, from 83 to 99 %.
Human Thermoregulation and Measurement of Body Temperature in Exercise and Clinical Settings (2008)

This review discusses human thermoregulation during exercise and the measurement of body temperature in clinical and exercise settings. The thermoregulatory mechanisms play important roles in maintaining physiological homeostasis during rest and physical exercise. Physical exertion poses a challenge to thermoregulation by causing a substantial increase in metabolic heat production. However, within a non-thermolytic range, the thermoregulatory mechanisms are capable of adapting to sustain physiological functions under these conditions. The central nervous system may also rely on hyperthermia to protect the body from "overheating." Hyperthermia may serve as a self-limiting signal that triggers central inhibition of exercise performance when a temperature threshold is achieved. Exposure to sub-lethal heat stress may also confer tolerance against higher doses of heat stress by inducing the production of heat shock proteins, which protect cells against the thermolytic effects of heat. Advances in body temperature measurement also contribute to research in thermoregulation. Current evidence supports the use of oral temperature measurement in the clinical setting, although it may not be as convenient as tympanic temperature measurement using the infrared temperature scanner. Rectal and oesophagus temperatures are widely accepted surrogate measurements of core temperature (Tc), but they cause discomfort and are less likely to be accepted by users. Gastrointestinal temperature measurement using the ingestible temperature sensor provides an acceptable level of accuracy as a surrogate measure of Tc without causing discomfort to the user. This form of Tc measurement also allows Tc to be measured continuously in the field and has gained wider acceptance in the last decade.
Carbon nanotube reinforced metal matrix composites - a review (2010)

<title/>This review summarises the research work carried out in the field of carbon nanotube (CNT) metal matrix composites (MMCs). Much research has been undertaken in utilising CNTs as reinforcement for composite material. However, CNT-reinforced MMCs have received the least attention. These composites are being projected for use in structural applications for their high specific strength as well as functional materials for their exciting thermal and electrical characteristics. The present review focuses on the critical issues of CNT-reinforced MMCs that include processing techniques, nanotube dispersion, interface, strengthening mechanisms and mechanical properties. Processing techniques used for synthesis of the composites have been critically reviewed with an objective to achieve homogeneous distribution of carbon nanotubes in the matrix. The mechanical property improvements achieved by addition of CNTs in various metal matrix systems are summarised. The factors determining strengthening achieved by CNT reinforcement are elucidated as are the structural and chemical stability of CNTs in different metal matrixes and the importance of the CNT/metal interface has been reviewed. The importance of CNT dispersion and its quantification is highlighted. Carbon nanotube reinforced MMCs as functional materials are summarised. Future work that needs attention is addressed.
Magnetic bearings using high-temperature superconductors: some practical considerations (1990)

An experimental study of Meissner effect levitation involving high-temperature superconductors is presented. Two simple apparatuses are described for quantifying the static and dynamic characteristics of levitated systems. The levitation properties of Y-Ba-Cu-O in conventional pressed ceramic form and in insulating matrix composites are compared. Temperature-dependent force measurements are correlated with SQUID magnetometry data. A preliminary assessment of the practical potential of magnetic levitation using high-temperature superconductors is provided.
Disulfide Cross-Linked Polymer Capsules:  En Route to Biodeconstructible Systems (2005)

Hydrogen-bonded multilayer thin films were constructed using poly(vinylpyrrolidone) and poly(methacrylic acid) functionalized with cysteamine. The resulting films included thiol moieties that were cross-linked to render the films stable at physiological pH. Film buildup was followed using quartz crystal microgravimetry, which was also used to demonstrate the improved stability imparted by reacting the thiol moieties to form disulfide bonds. Films without disulfide bonds were readily deconstructed at physiological pH, while those with disulfide bonds were swollen upon exposure to this pH (7) but remained intact. Addition of a common thiol-disulfide exchange reagent, dithiothreitol (DTT) at pH 7 led to disassembly of the multilayer films. The films were also prepared on colloidal substrates (as demonstrated using confocal microscopy) and were used to retain a model drug (fluorescently labeled transferrin) and release this molecule when triggered by the addition of DTT. This approach has potential for the in vivo applications of hollow capsules, as thiol-disulfide exchange leading to deconstruction of the capsules can occur with the assistance of intracellular proteins.
Sequence Diversity in the Tetraploid Zea perennis and the Closely Related Diploid Z. diploperennis: Insights From Four Nuclear Loci (2001)

Polyploidy has been an extremely common phenomenon in the evolutionary history of angiosperms. Despite this there are few data available to evaluate the effects of polyploidy on genetic diversity and to compare the relative effects of drift and selection in polyploids and related diploids. We investigated DNA sequence diversity at four nuclear loci (adh1, glb1, c1, and waxy) from the tetraploid Zea perennis and the closely related diploid Z. diploperennis. Contrary to expectations, we detected no strong evidence for greater genetic diversity in the tetraploid, or for consistent differences in the effects of either drift or selection between the tetraploid and the diploid. Our failure to find greater genetic diversity in Z. perennis may result from its relatively recent origin or demographic factors associated with its origin. In addition to comparing genetic diversity in the two species, we constructed genealogies to infer the evolutionary origin of Z. perennis. Although these genealogies are equivocal regarding the mode of origin, several aspects of these genealogies support an autotetraploid origin. Consistent with previous molecular data the genealogies do not, however, support the division of Zea into two sections, the section Zea and the section Luxuriantes.
Optimized labeling of NOTA-conjugated octreotide with F-18 (2011)

We recently reported a facile method based on the chelation of [(18)F]aluminum fluoride (Al(18)F) by NOTA (1,4,7-triazacyclononane-1,4,7-triacetic acid). Here, we present a further optimization of the (18)F labeling of NOTA-octreotide (IMP466). Octreotide was conjugated with the NOTA chelate and was labeled with (18)F in a two-step, one-pot method. The labeling procedure was optimized with regard to the labeling buffer, ionic strength, peptide concentration, and temperature. Radiochemical yield, specific activity, in vitro stability, and receptor affinity were determined. Biodistribution of (18)F-IMP466 was studied in AR42J tumor-bearing mice. In addition, microPET/CT images were acquired. IMP466 was labeled with Al(18)F in a single step with 97% yield in the presence of 80% (v/v) acetonitrile or ethanol. The labeled product was purified by HPLC to remove unlabeled peptide and unbound Al(18)F. The radiolabeling, including purification, was performed for 45 min. Specific activities of 48,000 GBq/mmol could be obtained. (18)F-IMP466 showed a high tumor uptake and excellent tumor-to-blood ratios at 2 h post-injection. In addition, the low bone uptake indicated that the Al(18)F-NOTA complex was stable in vivo. PET/CT scans revealed excellent tumor delineation and specific accumulation in the tumor. Uptake in receptor-negative organs was low. NOTA-octreotide could be labeled with (18)F in quantitative yields using a rapid two-step, one-pot, method. The compound was stable in vivo and showed rapid accretion in SSTR(2)-receptor-expressing AR42J tumors in nude mice. This method can be used to label other NOTA-conjugated compounds such as RGD peptides, GRPR-binding peptides, and Affibody molecules with (18)F.
Decreased frequency of rearrangement due to the synergistic effect of nucleotide changes in the heptamer and nonamer of the recombination signal sequence of the V kappa gene A2b, which is associated with increased susceptibility of Navajos to Haemophilus influenzae type b disease. (1998)

Navajos and genetically related populations have a 10-fold increased incidence of Haemophilus influenzae type b (Hib) disease compared with control populations. The Vkappa gene A2 is used to encode the majority of anti-Hib Abs, and these are the highest affinity anti-Hib Abs. Navajos carry a different allele of the A2 gene segment (A2b) that is defective in its ability to undergo V-J recombination. The A2b allele has only three nucleotide changes from the commonly occurring A2a allele, two of which could potentially affect its ability to recombine. In this study we used two independent in vitro assays to test whether the nucleotide change found in the A2b promoter and/or in the A2b recombination signal sequence (RSS) might be responsible for the decrease in recombination frequency observed in vivo. Using a luciferase reporter gene assay, we found no significant difference between A2a and A2b promoter activities. However, the competition recombination substrate assay showed a 4.5-fold reduction in the relative frequency of recombination of the A2b RSS compared with A2a. We show that this decreased frequency is due to a synergistic effect of the unique nucleotide change present in the heptamer of the A2b RSS and the shared nucleotide change present in the nonamer of both A2b and A2a. This in vitro relative frequency of rearrangement is not significantly different from that observed in vivo; therefore, the A2b RSS is probably the factor associated with the increased susceptibility to Hib disease among individuals carrying the A2b allele.
Natural Antioxidants: Sources, Compounds, Mechanisms of Action, and Potential Applications (2011)

Abstract: While use of synthetic antioxidants (such as butylated hydroxytoluene and butylated hydroxyanisole) to maintain the quality of ready‐to‐eat food products has become commonplace, consumer concern regarding their safety has motivated the food industry to seek natural alternatives. Phenolic antioxidants can inhibit free radical formation and/or interrupt propagation of autoxidation. Fat‐soluble vitamin E (α‐tocopherol) and water‐soluble vitamin C (L‐ascorbic acid) are both effective in the appropriate matrix. Plant extracts, generally used for their flavoring characteristics, often have strong H‐donating activity thus making them extremely effective antioxidants. This antioxidant activity is most often due to phenolic acids (gallic, protocatechuic, caffeic, and rosmarinic acids), phenolic diterpenes (carnosol, carnosic acid, rosmanol, and rosmadial), flavonoids (quercetin, catechin, naringenin, and kaempferol), and volatile oils (eugenol, carvacrol, thymol, and menthol). Some plant pigments (anthocyanin and anthocyanidin) can chelate metals and donate H to oxygen radicals thus slowing oxidation via 2 mechanisms. Tea and extracts of grape seeds and skins contain catechins, epicatechins, phenolic acids, proanthocyanidins, and resveratrol, all of which contribute to their antioxidative activity. The objective of this article is to provide an overview of natural antioxidants, their mechanisms of action, and potential applications.
[[.omega.-(Heterocyclylamino)alkoxy]benzyl]-2,4-thiazolidinediones as potent antihyperglycemic agents (1994)

A series of [(ureidoethoxy)benzyl]-2,4-thiazolidinediones and [[(heterocyclylamino)alkoxy]-benzyl]-2,4-thiazolidinediones was synthesized from the corresponding aldehydes. Compounds from the urea series, exemplified by 16, showed antihyperglycemic potency comparable with known agents of the type such as pioglitazone and troglitazone (CS-045). The benzoxazole 49, a cyclic analogue of 16, was a very potent enhancer of insulin sensitivity, and by modification of the aromatic heterocycle, an aminopyridine, 37, was identified as a lead compound from SAR studies. Evaluation of antihyperglycemic activity together with effects on blood hemoglobin content, to determine the therapeutic index, was performed in 8-day repeat administration studies in genetically obese C57 Bl/6 ob/ob mice. From these studies, BRL 49653 (37) has been selected, on the basis of antihyperglycemic potency combined with enhanced selectivity against reductions in blood hemoglobin content, for further evaluation.
Sounds and beyond: multisensory and other non-auditory signals in the inferior colliculus (2012)

The inferior colliculus (IC) is a major processing center situated mid-way along both the ascending and descending auditory pathways of the brain stem. Although it is fundamentally an auditory area, the IC also receives anatomical input from non-auditory sources. Neurophysiological studies corroborate that non-auditory stimuli can modulate auditory processing in the IC and even elicit responses independent of coincident auditory stimulation. In this article, we review anatomical and physiological evidence for multisensory and other non-auditory processing in the IC. Specifically, the contributions of signals related to vision, eye movements and position, somatosensation, and behavioral context to neural activity in the IC will be described. These signals are potentially important for localizing sound sources, attending to salient stimuli, distinguishing environmental from self-generated sounds, and perceiving and generating communication sounds. They suggest that the IC should be thought of as a node in a highly interconnected sensory, motor, and cognitive network dedicated to synthesizing a higher-order auditory percept rather than simply reporting patterns of air pressure detected by the cochlea. We highlight some of the potential pitfalls that can arise from experimental manipulations that may disrupt the normal function of this network, such as the use of anesthesia or the severing of connections from cortical structures that project to the IC. Finally, we note that the presence of these signals in the IC has implications for our understanding not just of the IC but also of the multitude of other regions within and beyond the auditory system that are dependent on signals that pass through the IC. Whatever the IC "hears" would seem to be passed both "upward" to thalamus and thence to auditory cortex and beyond, as well as "downward" via centrifugal connections to earlier areas of the auditory pathway such as the cochlear nucleus.
Highly sensitive and specific detection of E. coli by a SERS nanobiosensor chip utilizing metallic nanosculptured thin films (2015)

A nanobiosensor chip, utilizing surface enhanced Raman spectroscopy (SERS) on nanosculptured thin films (nSTFs) of silver, was shown to detect Escherichia coli (E. coli) bacteria down to the concentration level of a single bacterium. The sensor utilizes highly enhanced plasmonic nSTFs of silver on a silicon platform for the enhancement of Raman bands as checked with adsorbed 4-aminothiophenol molecules. T-4 bacteriophages were immobilized on the aforementioned surface of the chip for the specific capture of target E. coli bacteria. To demonstrate that no significant non-specific immobilization of other bacteria occurs, three different, additional bacterial strains, Chromobacterium violaceum, Paracoccus denitrificans and Pseudomonas aeruginosa were used. Furthermore, experiments performed on an additional strain of E. coli to address the specificity and reusability of the sensor showed that the sensor operates for different strains of E. coli and is reusable. Time resolved phase contrast microscopy of the E. coli-T4 bacteriophage chip was performed to study its interaction with bacteria over time. Results showed that the present sensor performs a fast, accurate and stable detection of E. coli with ultra-small concentrations of bacteria down to the level of a single bacterium in 10 μl volume of the sample.
23S rRNA Similarity from Selection for Peptidyl Transferase Mimicry (1997)

RNAs from a randomized pool were selected by affinity elution for binding to the molecule CCdApPuro, a high-affinity ligand of ribosomal peptidyl transferase designed as a transition-state analogue of peptide formation. The selected RNAs show affinity for CCdApPuro comparable to that of the peptidyl transferase center itself (Kd approximately 10 nM). Chemical modification/protection experiments implicate bases completely conserved among the selected RNAs in CCdApPuro interaction, which appears to involve both CCdA and puromycin moieties, that is, both A- and P-site homologues. The apparent selected binding site shows up to 17 nucleotides with similarity to conserved nucleotides of the peptidyl transferase loop domain of 23S rRNA and is conserved when reselected under mutagenesis. Thus, these nucleotides of 23S rRNA likely provide elements of the peptidyl transferase active center that bind the reactants near the site of peptide bond formation. Binding of CCdApPuro by a peptidyl transferase-like motif in the absence of protein strengthens the hypothesis that peptidyl transfer originated in an RNA world.
Isolation of renin-rich rat kidney cells. (1987)

Enzymatic dispersion and density gradient (Percoll) sedimentation were used to isolate a population of renin-containing, granule-laden cells (density 1.067 g/ml) from rat kidney cortex. Using immunohistochemistry (light microscopy) and electron microscopy, we defined the presence and ability of these cells to store renin protein(s). A 1000 base pair rat renin complementary DNA was used to show that these cells express the renin gene. The reverse hemolytic plaque assay defined the functional properties of the renin-containing cell. The data are consistent with the postulated inverse relationship between calcium concentration and release of renin. Thus, we have isolated a population of functional rat kidney cells that synthesize, store, and release renin.
Long-term expression of human adenosine deaminase in vascular smooth muscle cells of rats: a model for gene therapy. (1992)

Gene transfer into vascular smooth muscle cells in animals was examined by using recombinant retroviral vectors containing an Escherichia coli beta-galactosidase gene or a human adenosine deaminase (adenosine aminohydrolase, EC 3.5.4.4) gene. Direct gene transfer by infusion of virus into rat carotid arteries was not observed. However, gene transfer by infection of smooth muscle cells in culture and seeding of the transduced cells onto arteries that had been denuded of endothelial cells was successful. Potentially therapeutic levels of human adenosine deaminase activity were detected over 6 months of observation, indicating the utility of vascular smooth muscle cells for gene therapy in humans.
Enzyme-linked immunosorbent assay to evaluate the immunogenicity of a polyvalent Klebsiella capsular polysaccharide vaccine in humans (1988)

A highly sensitive enzyme-linked immunosorbent assay was developed for Klebsiella capsular polysaccharide (CPS) and used to evaluate the immunoglobulin G (IgG) antibody response to a 24-valent CPS vaccine in seven adult volunteers. The median rise in titer to all vaccine antigens in samples from the volunteers was significant (twofold or greater). Significant IgG responses to 11 immunologically related serotypes not included in the vaccine were also noted. The mean cross-reacting IgG titer of 127.2 was only slightly lower than the mean titer of 175.7 to the serotypes in the vaccine (P less than 0.05). The mean 29.9-fold increase in titer to the serotypes in the vaccine was significantly higher than the mean 13.5-fold increase in titer to the additional antigens (P less than 0.001). The difference was partly because of the significantly lower (P less than 0.01) natural antibody titers in the preimmune sera to the serotypes in the vaccine, compared with those to serotypes not included in the vaccine. The selection of vaccine serotypes was based on the frequency of serotype isolation from cases of Klebsiella bacteremia. The above findings, which show low levels of natural antibody to these serotypes, support the hypothesis that anti-CPS antibody is protective against bacteremic disease.
Microfluidic origami for point-of-care extraction of nucleic acids from viscous samples (2011)

We present a low-cost microfluidic origami device for point-of-care extraction of bacterial DNA from raw viscous samples-a challenge for conventional microfluidic systems. The core idea is a novel method for sequencing arbitrarily complex chemical and physical processing steps through sequential folding of 2D surfaces. This folding creates temporary paper fluidic circuits substituting capillary flow for pumps, and folding and unfolding for valves. Demonstrated here is room temperature cell lysis and DNA extraction from E. coli spiked pig mucin (simulating sputum) without the use of external power. Device fabrication takes less than 30 min, and can be adapted for mass production in the developing world.
Selection for improved subtiligases by phage display (1999)

Engineering enzyme activity has been challenging because of uncertainties in structure-function relationships and difficulties in screening a large number of mutant enzymes. A product capture strategy using phage display is presented here for the selection of improved enzymes from a large library of variants (>10(9) independently derived mutants). Subtiligase, a double mutant of subtilisin BPN' that catalyzes the ligation of peptides, was displayed on phage. Twenty-five active site residues were randomly mutated in groups of four or five to yield six different libraries that were independently sorted. Variants that ligated a biotin peptide onto their own extended N termini were selectively captured. Mutant subtiligases were identified that had increased ligase activity. The selection also yielded unexpected subtiligase mutants having residues known to improve the stability and oxidative resistance of wild-type subtilisin. These studies are exemplary for the use of phage to improve enzyme function when it is closely linked to a selectable catalytic event.