gebhart/patrepeval huggingface dataset:
Characterization of an Improved Electrodynamic Ion Funnel Interface for Electrospray Ionization Mass Spectrometry (1999)

An improved electrodynamic ion funnel for ion focusing at high pressure (> 1 Torr) has been developed for a triple quadrupole mass spectrometer and its performance compared with that of an earlier prototype previously reported. The ion funnel consists of a series of ring electrodes of progressively smaller internal diameters to which rf and dc electric potentials are co-applied. The new design utilizes ring electrodes possessing larger internal diameters that taper down to a relatively larger exit aperture. In the 1-10 Torr pressure range, the new design provides significant improvement in low m/z ion transmission. Additionally, the overall ion transmission range is improved by linked scanning of the ion funnel's rf voltage concomitantly with the scanning of the quadrupole mass analyzer. Transmission of a noncovalent complex through the interface demonstrated that excessive ion heating was not problematic. Computer simulations of ion transport support the ion funnel design and help explain the relative performance of both designs. Both ion simulations and experimental results are in accord and indicate close to 100% ion transmission efficiency for electrosprayed biopolymer ions through the interface and into the mass analyzer.
A Special Fondness for Lactobacilli (2004)

physiologist, and popularizer of science, established new paths of research in population genetics and evolution.Emphasizing the immensity of the Milky Way in the night sky and the fact that there were 400,000 species of beetles but only 8,000 species of mammals, he is reported to have said, "If one could conclude as to the nature of the Creator from the study of his creation, it would appear that God has a special fondness for stars and beetles."In a similar vein of thought, perusal of the issues of American Society for Microbiology journals and others published in recent years might cause the reader to conclude that microbiologists have a special fondness for lactobacilli.Fifty-two publications concerning lactobacilli (with "lactobacillus" or "lactobacilli" appearing in the article title or abstract) have appeared in Applied and Environmental Microbiology alone during 2003.It is no wonder: these are fascinating and useful bacteria.
Inhibition of Microbial Sialidases - What has Happened Beyond the Influenza Virus? (2004)

Involvement of sialidases in a variety of microbial infections apart from that by influenza virus has been demonstrated but in contrast to the latter, where potent inhibitors have been developed on the basis of the lead compound 2-deoxy-2,3-didehydro-N-acetylneuraminic acid, inhibitor design for bacterial or trypanosomal sialidases has proven to be much less straightforward. This review intends to give an overview of the attempts, which have been made, including both substrate analogues and transition-state analogues of the sialidase reaction as well as structurally unrelated compounds. The bifunctionality of the viral haemagglutininneuraminidases, supported by recently obtained crystal structure data, or the modular architecture of some bacterial enzymes provide useful starting points for improvement of inhibitors through additional interactions beyond the active site itself. This seems especially to be the case for trypanosomal trans-sialidases the inhibition of which might require some sort of acceptor mimic in addition to the sialic acid analogue. Keywords: neuraminidase, sialidase, inhibitors, n-acetylneuraminic acid, sialic acid, bacteria, influenza virus, parasites
Comparison of Contact and Spatial Repellency of Catnip Oil andN,N-Diethyl-3-methylbenzamide (Deet) Against Mosquitoes (2005)

Nepetalactone, the primary component of catnip oil, was compared with the repellent N,N-diethyl-3-methylbenzamide (deet) for its ability to affect the host-seeking ability of Aedes aegypti (L.). A triple cage olfactometer was used to bioassay each substance and to assess its attraction inhibition (spatial repellent) attributes when combined with the following attractants: carbon dioxide, acetone, a blend of L-lactic acid and acetone, and human odors. Repellent tests were conducted with each substance against female Ae. aegypti, Anopheles albimanus Weidemann, and Anopheles quadrimaculatus Say. Catnip oil and deet were both weakly attractive to Ae. aegypti, catnip oil was the better spatial repellent, whereas deet was a more effective contact repellent in tests with all three species of mosquitoes.
Cold-induced brain edema in mice. Involvement of extracellular superoxide dismutase and nitric oxide (1993)

The role of extracellular superoxide in the pathogenesis of vasogenic edema was studied using transgenic mice expressing a 5-fold increase in extracellular superoxide dismutase (EC-SOD) activity in their brains. Increased EC-SOD expression offered significant protection against edema development after cold-induced injury (44% less edema than nontransgenic littermates, p < 0.05). Since iron may contribute to vasogenic edema by catalyzing the production of hydroxyl radical from superoxide and hydrogen peroxide, the effects of the chelator deferoxamine were studied. Deferoxamine reduced edema formation after cold-induced injury (43% less edema than controls, p < 0.05); however, treatment with iron-saturated deferoxamine also reduced edema development in mice (32-48% less edema, p < 0.05). This suggested that the protection offered by deferoxamine was independent of its ability to chelate iron. An iron-independent mechanism by which superoxide can contribute to vasogenic edema is via reaction with nitric oxide to produce the potentially toxic peroxynitrite anion, which is also scavenged by deferoxamine. Mice treated with an inhibitor of nitric oxide synthase were protected against cold-induced edema (37% less edema, p < 0.05). EC-SOD transgenic mice received no additional protection by inhibition of nitric oxide synthesis, supporting this novel alternative mechanism of edema formation.
Materials issues for layered tunnel barrier structures (2002)

Layered dielectric tunnel barriers are expected to greatly increase the program/erase speeds of nonvolatile floating gate memory devices and could allow both nanosecond program/erase times as well as archival data storage. We have correlated dielectric constants and band offsets with respect to silicon in order to help identify possible materials from which to construct these devices. A numerical model has been developed to assess potential layered tunnel barrier materials and structures suitable for integration into silicon electronics. With this model, we explore the relative dominance of Fowler–Nordheim tunneling and thermionic emission and we present simulated I–V curves for some candidate materials.
Metabolic enzymes that bind RNA: yet another level of cellular regulatory network? (2006)

Several enzymes that were originally characterized to have one defined function in intermediatory metabolism are now shown to participate in a number of other cellular processes. Multifunctional proteins may be crucial for building of the highly complex networks that maintain the function and structure in the eukaryotic cell possessing a relatively low number of protein-encoding genes. One facet of this phenomenon, on which I will focus in this review, is the interaction of metabolic enzymes with RNA. The list of such enzymes known to be associated with RNA is constantly expanding, but the most intriguing question remains unanswered: are the metabolic enzyme-RNA interactions relevant in the regulation of cell metabolism? It has been proposed that metabolic RNA-binding enzymes participate in general regulatory circuits linking a metabolic function to a regulatory mechanism, similar to the situation of the metabolic enzyme aconitase, which also functions as iron-responsive RNA-binding regulatory element. However, some authors have cautioned that some of such enzymes may merely represent "molecular fossils" of the transition from an RNA to a protein world and that the RNA-binding properties may not have a functional significance. Here I will describe enzymes that have been shown to interact with RNA (in several cases a newly discovered RNA-binding protein has been identified as a well-known metabolic enzyme) and particularly point out those whose ability to interact with RNA seems to have a proven physiological significance. I will also try to depict the molecular switch between an enzyme's metabolic and regulatory functions in cases where such a mechanism has been elucidated. For most of these enzymes relations between their enzymatic functions and RNA metabolism are unclear or seem not to exist. All these enzymes are ancient, as judged by their wide distribution, and participate in fundamental biochemical pathways.
Opportunistic beamforming using dumb antennas (2002)

Multiuser diversity is a form of diversity inherent in a wireless network, provided by independent time-varying channels across the different users. The diversity benefit is exploited by tracking the channel fluctuations of the users and scheduling transmissions to users when their instantaneous channel quality is near the peak. The diversity gain increases with the dynamic range of the fluctuations and is thus limited in environments with little scattering and/or slow fading. In such environments, we propose the use of multiple transmit antennas to induce large and fast channel fluctuations so that multiuser diversity can still be exploited. The scheme can be interpreted as opportunistic beamforming and we show that true beamforming gains can be achieved when there are sufficient users, even though very limited channel feedback is needed. Furthermore, in a cellular system, the scheme plays an additional role of opportunistic nulling of the interference created on users of adjacent cells. We discuss the design implications of implementing. this scheme in a complete wireless system.
Consumption of Green Tea Causes Rapid Increase in Plasma Antioxidant Power in Humans (1999)

Green tea contains polyphenolic antioxidants that have shown anticarcinogenic properties in animal and in vitro experimental studies. Current data regarding absorption and bioavailability of tea antioxidants in humans, however, are conflicting. In this study, plasma and urine antioxidant power after ingestion of green tea was measured using the ferric reducing/antioxidant power (FRAP) assay (US patent pending) to assess absorption, systemic distribution, and renal excretion of green tea antioxidants in healthy adults. Results showed that absorption of green tea antioxidants was rapid, with peak increase in plasma FRAP of around 4% at 40 minutes after ingestion: mean increase was 44 +/- 9 (SE) mumol/l. Excretion of polyphenolic antioxidants was also fast, peaking at 60-90 minutes, with significant correlation between urinary FRAP values and urinary total phenolic concentrations (r = 0.845, p < 0.001). In control studies, no increase in plasma or urine FRAP values was seen after intake of water. Although the amount of antioxidants absorbed was relatively small and the increase in plasma antioxidant power was of short duration, results demonstrate that some potentially anticarcinogenic polyphenolic antioxidants in green tea enter the systemic circulation soon after ingestion and cause a significant increase in plasma antioxidant status. This increase may, in turn, lower oxidative damage to DNA and so decrease risk of cancer.
Development of a dural substitute from synthetic bioabsorbable polymers (1997)

✓ A new bioabsorbable composite sheet was developed to provide a substitute for the dura mater and was evaluated histologically and biomechanically using rats and rabbits. This composite, composed of two l -lactic acid-ϵ-caprolactone (50% l -lactic acid, 50% ϵ-caprolactone) copolymer films and a poly(glycolic acid) nonwoven fabric, displayed good mechanical properties and was completely absorbed 24 weeks after implantation in the back of rats. Histological evaluation of the composite sheet was undertaken by implanting it in 31 rabbits with dural defects and examining the sites of implantation 2 weeks to 26 months later. No infection, cerebrospinal fluid leakage, evidence of convulsive disorders, significant adhesion to underlying cortex, or calcification was noticed in any cases. In addition, the regenerated duralike tissue had a high pressure-resistant strength 2 weeks after implantation. The authors conclude that this new bioabsorbable composite sheet can be successfully used as a dural substitute.
Nucleotide sequences of integrated Moloney sarcoma provirus long terminal repeats and their host and viral junctions. (1980)

Integrated Moloney murine sarcoma provirus (MSV) has direct terminal repeat sequences (TRS). We determined the nucleotide sequence of both 588-base-pair TRS elements and the adjacent host and viral junctions of an integrated MSV cloned in bacteriophage lambda. Sequences were identified corresponding to the tRNAPro primer binding site in genomic RNA and the reverse-transcribed minus strong stop DNA. Each 588-base-pair repeat contains putative sites for promoting RNA synthesis and RNA polyadenylylation. The first and last 11 nucleotides of the TRS are inverted with respect to each other, and the same four-nucleotide host sequence is found bracketing integrated MSV. Some similarities of TRS and prokaryotic insertion sequence elements are discussed.
Subtypes of P2‐Purinoceptors (1990)

Studies using analogues of ATP have allowed a comparison of structure-activity relationships that has provided ample evidence for the existence of at least four subtypes of P2-purinoceptors responsive to adenine nucleotides. Competitive antagonists have defined clearly the P2T subtype, specific agonists are now available for the P2X and P2Y subtypes, and leads have been given for development of reversible specific antagonists for the P2X and P2Z subtypes. The availability especially of inhibitors of ectonucleotidases and of specific antagonists for each P2-purinoceptor subtype would enable the roles of endogenous extracellular nucleotides to be ascertained, as has already been shown for the interaction of platelets with the vasculature.
The Human Gut Chip ‘‘HuGChip’’, an Explorative Phylogenetic Microarray for Determining Gut Microbiome Diversity at Family Level (2013)

International audience
QapR (PA5506) Represses an Operon That Negatively Affects the Pseudomonas Quinolone Signal in Pseudomonas aeruginosa (2013)

Pseudomonas aeruginosa is a Gram-negative, opportunistic pathogen that can cause disease in varied sites within the human body and is a significant source of morbidity and mortality in those afflicted with cystic fibrosis. P. aeruginosa is able to coordinate group behaviors, such as virulence factor production, through the process of cell-to-cell signaling. There are three intercellular signaling systems employed by P. aeruginosa, and one of these systems utilizes the small molecule 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas quinolone signal [PQS]). PQS is required for virulence in multiple infection models and has been found in the lungs of cystic fibrosis patients colonized by P. aeruginosa. In this study, we have identified an RpiR family transcriptional regulator, QapR, which is an autoregulatory repressor. We found that mutation of qapR caused overexpression of the qapR operon. We characterized the qapR operon to show that it contains genes qapR, PA5507, PA5508, and PA5509 and that QapR directly controls the transcription of these genes in a negative manner. We also show that derepression of this operon greatly reduces PQS concentration in P. aeruginosa. Our results suggest that qapR affects PQS concentration by repressing an enzymatic pathway that acts on PQS or a PQS precursor to lower the PQS concentration. We believe that this operon comprises a novel mechanism to regulate PQS concentration in P. aeruginosa.
Synthesis of 2‘-Aminomethyl Derivatives of N-(2-(Phosphonomethoxy)ethyl) Nucleotide Analogues as Potential Antiviral Agents (1996)

A series of purine and pyrimidine N-(2-(phosphonomethoxy)ethyl) derivatives bearing aminomethyl, (dimethylamino)methyl, morpholinomethyl, and (trimethylammonio)methyl groups at the 2'-position were synthesized. The compounds were prepared by alkylation of the heterocyclic bases with appropriately substituted (aminoalkyl)oxiranes followed by condensation of the resulting intermediates with dialkyl ((p-tolylsulfonyl)oxy)methanephosphonate and subsequent treatment of the obtained diester with bromotrimethylsilane. 9-(3-Amino-2-(phosphonomethoxy)propyl)adenine (2a) proved active against varicella zoster virus (VZV), cytomegalovirus (CMV), and Moloney murine sarcoma virus (MSV) in the concentration range of 7-35 micrograms/mL. None of the other aminoalkyl derivatives demonstrated significant antiviral activity against herpes simplex virus type 1 and 2 (HSV-1 and HSV-2), VZV, (CMV), vaccinia virus (VV), MSV, and human immunodeficiency virus type 1 and 2 (HIV-1 and HIV-2).
Somatic mutations in the notch, NF‐KB, PIK3CA, and hedgehog pathways in human breast cancers (2012)

Exome sequencing of human breast cancers has revealed a substantial number of candidate cancer genes with recurring but infrequent somatic mutations. To determine more accurately their mutation prevalence, we performed a mutation analysis of 36 novel candidate cancer genes in 96 human breast cancers. Somatic mutations with potential impact on protein function were observed in the genes ADAM12, CENTB1, CENTG1, DIP2C, GLI1, GRIN2D, HDLBP, IKBKB, KPNA5, NFKB1, NOTCH1, and OTOF. These findings strengthen the evidence for involvement of the Notch, Hedgehog, NF-KB, and PIK3CA pathways in breast cancer development, and point to novel processes that likely are involved.
An Analog Modulation Using a Spiral Mapping (2006)

This work presents the spiral analog modulation, which is a mapping scheme for continuous in value discrete in time samples based on the spiral locus S (x) = xeix. A mapping function is used to map the source onto the spiral. The Maximum Likelihood (M.L.) optimal demodulator is presented followed by approximated demodulators. The SNR gain and the threshold SNR are analyzed and simulated. Finally we optimize classes of mapping functions with regard to maximum SNR for a given threshold SNR.
Improvement of Dissolution Rate and Oral Bioavailability of a Sparingly Water-Soluble Drug, (.+-.)-5-((2-(2 Naphthalenylmethyl)-5-benzoxazolyl)-methyl)-2,4-thiazolidinedione, in Co-ground Mixture with D-Mannitol. (1997)

We investigated the usefulness and efficiency of the co-grinding method with D-mannitol to improve the bioavailability of a sparingly water-soluble drug, (+/-)-5-[[2-(2-naphthalenylmethyl)-5-benzoxazolyl]methyl]-2, 4-thiazolidinedione (174), and compared it with those of the single-grinding method. The co-ground mixtures in drug/carrier weight ratios up to 1:5 gave fine particle sizes of less than about 3 microns, which showed a marked increase in the dissolution rate with reduction of particle size, compared with the single-ground powder, even with a similar particle size. The oral bioavailability study of co-ground powders in beagle dogs exhibited a dramatic increase, as did the dissolution rate, according to finer particle size. Finally, complete bioavailability was obtained at the finest particle size of 1.2 microns (drug/carrier ratio of 1:5, w/w) as was a solution of the drug. Bioavailability had a good linear correlation with the dissolution rate. These findings suggested that the co-grinding method with D-mannitol dramatically increased the available surface area, caused by a reduction of particle size, which not only accelerated the dissolution rate but also resulted in greater enhancement of the bioavailability of 174.
Effects on Weight and Outcome of Long-term Olanzapine-Topiramate Combination Treatment in Bipolar Disorder (2004)

Olanzapine is an effective drug for the long-term treatment of bipolar disorder but is associated with burdensome weight gain. Topiramate is a novel anticonvulsant that may induce weight loss in some patients. This is the first study to address the long-term efficacy and impact on weight of the combination of olanzapine and topiramate in bipolar patients. Twenty-six Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition bipolar spectrum patients received olanzapine plus topiramate cotherapy for treatment of their manic (n = 14), hypomanic (n = 6), depressive (n = 2), and mixed (n = 1) symptoms for 1 year. Three rapid cycling patients were also enrolled despite being euthymic. Efficacy was assessed with the Young Mania Rating Scale, the Hamilton Depression Rating Scale, and the Modified Clinical Global Impressions for Bipolar Disorder. Weight, body mass index, and side effects were collected at every visit. Thirteen (50%) patients completed the 1-year follow-up. By intent-to-treat, patients significantly improved from baseline in Young Mania Rating Scale scores (P < 0.0001), Hamilton Depression Rating Scale (P < 0.05), and Modified Clinical Global Impressions for Bipolar Disorder subscales (mania P < 0.0001, depression P < 0.05, overall P < 0.0001). Most patients gained weight during the first month of combined treatment (mean weight gain 0.7 +/- 0.6 kg), but at the 12-month endpoint, the mean weight change was -0.5 +/- 1.1 kg. The combination of olanzapine and topiramate was efficacious for the long-term treatment of bipolar patients and appeared to carry some benefits for controlling weight gain. Given the limitations of the open, uncontrolled design, further trials are warranted with this combination.
A Highly Efficient and Practical Synthesis of Chromene Derivatives Using Ring-Closing Olefin Metathesis (1998)

Chromenes (2H-1-benzopyran derivatives) have been widely employed as important intermediates in the synthesis of many natural products and medicinal agents. There has been recent interest in the use of these common structural elements for a new family of potassium-channel activating drugs. They also serve as the framework of a range of tannins, which are becoming increasingly important because of their health-promoting effects found in teas, vegetables, fruits, fruit juices, and red wines. Despite the several existing methods for the synthesis of chromene derivatives, there still is demand for general strategies which can efficiently provide variously substituted chromene systems. &#13;\n&#13;\nIn this note, we report a practical and highly efficient procedure for preparing diverse chromene derivatives using ring-closing metathesis (RCM), a methodology emerging as a new tool in synthetic organic chemistry
Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolution (1975)

The model of pancreatic trypsin inhibitor determined by Huber, Kukla, Rtihlmann, Epp & Formanek [Naturwissenschaften (1970). 57, 389-392] was fitted to an electron-density map of 1.9 A resolution calculated with isomorphous-replacement phases by application of the real-space refinement procedure of Diamond [Acta Cryst. (1971). A27, 436-452]. Further refinement was done at 1.5 A resolution by cyclic real-space refinement against electron-density maps computed with observed structure-factor amplitudes and phases calculated from the preceding model. Five difference Fourier maps helped to correct severe errors in the model, and to locate solvent molecules. After 15 cycles of constrained crystallographic refinement the R value for all 8079 independent reflexions was 0.225. The R value for 6893 reflexions with intensities above the 2o significance level determined from counting statistics within the range 7.0 A > d> 1-5 A was 0-197. Details of the refined model are presented in terms of hydrogen bonds and conformational angles.