gebhart/patrepeval huggingface dataset:
Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts (2019)

Numerous, diverse, highly variable defense and offense genetic systems are encoded in most bacterial genomes and are involved in various forms of conflict among competing microbes or their eukaryotic hosts. Here we focus on the offense and self-versus-nonself discrimination systems encoded by archaeal genomes that so far have remained largely uncharacterized and unannotated. Specifically, we analyze archaeal genomic loci encoding polymorphic and related toxin systems and ribosomally synthesized antimicrobial peptides. Using sensitive methods for sequence comparison and the "guilt by association" approach, we identified such systems in 141 archaeal genomes. These toxins can be classified into four major groups based on the structure of the components involved in the toxin delivery. The toxin domains are often shared between and within each system. We revisit halocin families and substantially expand the halocin C8 family, which was identified in diverse archaeal genomes and also certain bacteria. Finally, we employ features of protein sequences and genomic locus organization characteristic of archaeocins and polymorphic toxins to identify candidates for analogous but not necessarily homologous systems among uncharacterized protein families. This work confidently predicts that more than 1,600 archaeal proteins, currently annotated as "hypothetical" in public databases, are components of conflict and self-versus-nonself discrimination systems.<b>IMPORTANCE</b> Diverse and highly variable systems involved in biological conflicts and self-versus-nonself discrimination are ubiquitous in bacteria but much less studied in archaea. We performed comprehensive comparative genomic analyses of the archaeal systems that share components with analogous bacterial systems and propose an approach to identify new systems that could be involved in these functions. We predict polymorphic toxin systems in 141 archaeal genomes and identify new, archaea-specific toxin and immunity protein families. These systems are widely represented in archaea and are predicted to play major roles in interactions between species and in intermicrobial conflicts. This work is expected to stimulate experimental research to advance the understanding of poorly characterized major aspects of archaeal biology.
Measurement of the muonium 1S-2S transition frequency (2002)

A new measurement of the 1S-2S energy splitting of muonium by Doppler-free two-photon spectroscopy has been performed at the Rutherford Appleton Laboratory in Chilton, Didcot, UK. Increased accuracy is expected compared to a previous experiment. Spectroscopy of this transition promises an improvement of the muon mass value.
Cholesteryl Ester Transfer Protein (CETP) Genetic Variation and Early Onset of Non‐Fatal Myocardial Infarction (2008)

Although Cholesteryl Ester Transfer Protein (CETP) mediates the transfer of cholesteryl esters and triglycerides between lipoprotein particles and thus plays a crucial role in reverse cholesterol transport, the association of variations in the CETP gene with acute myocardial infarction (MI) remains unclear. In this study we examined whether common genetic variation in the CETP gene is related to early-onset non-fatal MI risk in a population-based case-control study from western Washington State. Genotyping for the CETP -2708 G/A, -971 A/G, -629 A/C, Intron-I TaqI G/A and exon-14 A/G (I405V) SNPs was performed in 578 cases with first acute non-fatal MI and in 666 demographically similar controls, free of clinical cardiovascular disease, identified randomly from the community. In-person interviews and non-fasting blood specimens provided data on coronary heart disease risk factors. In men, there was little evidence for an association between single SNPs and MI risk, but in women the age- and race-adjusted OR was found to be significant in 4 out of the 5 CETP single variants. Haplotype analysis revealed two haplotypes associated with MI risk among men. As compared to men homozygous for the most common haplotype D (-2708 G, -971 G, -629 C, TaqI G and exon-14 A), the fully-adjusted multiplicative model identified haplotype G (-2708 G, -971 A, -629 A, TaqI G and exon-14 G) was associated with a 4.0-6.0-fold increased risk of MI for each additional copy; [95%CI 2.4-14.8] and haplotype B (-2708 G, -971 G, -629 A, TaqI A and exon-14 A) showed a significant decreased risk for early onset MI [OR = 0.18; 95%CI 0.04 - 0.75]. An evolutionary-based haplotype analysis indicated that the two haplotypes associated with the MI risk are most evolutionarily divergent from the other haplotypes. Variation at the CETP gene locus is associated with the risk of early-onset non-fatal MI. This association was found to be independent of HDL-C levels. These data and the sex-specific findings require confirmation in other populations.
Cross-Linking of Collagen by Singlet Oxygen Generated with UV-A. (1997)

Singlet oxygen (1O2), a highly reactive and toxic intermediate, may play a role in photo-induced aging. We examined singlet oxygen generation from hematoporphyrin (HP) with UV-A, by monitoring the emission at 1,268 nm corresponding to 1O2 --> 3O2. Singlet oxygen was formed HP-dose-dependently in this system. We then investigated the reaction of singlet oxygen generated by UV-A irradiation with collagen, which is related to skin elasticity and softness. Collagen from skin was rapidly and dose-dependently cross-linked by singlet oxygen. The reaction was inhibited by NaN3, a selective quencher of singlet oxygen. In contrast, SOD (superoxide dismutase) and mannitol had no effect. These results suggested that cross-linking of collagen was caused by UV-A-generated singlet oxygen, not by any other reactive oxygen species. Compared with another multisubunit protein, alcohol dehydrogenase, collagen was cross-linked much more efficiently. Further, the finding that semicarbazide inhibited cross-linking of collagen showed that cross-links were formed between photooxidized histidyl residues and amino groups. Singlet oxygen generated by UV-A irradiation may contribute to cross-linking of collagen in the process of skin photoaging.
Solubilization of flurbiprofen into aptamer-modified PEG–PLA micelles for targeted delivery to brain-derived endothelial cells<i>in vitro</i> (2013)

Novel aptamer-functionalized polyethylene glycol-polylactic acid (PEG-PLA) (APP) micelles were developed with the objective to target the transferrin receptor on brain endothelial cells. Flurbiprofen, a potential drug for therapeutic management of Alzheimer's disease (AD), was loaded into the APP micelles using the co-solvent evaporation method. Results indicated that 9.03% (w/w) of flurbiprofen was entrapped in APP with good retention capacity in vitro. Targeting potential of APPs was investigated using the transferring receptor-expressing murine brain endothelial bEND5 cell line. APPs significantly enhanced surface association of micelles to bEND5 cells as quantified by fluorescence spectroscopy. Most importantly, APPs significantly enhanced intracellular flurbiprofen delivery when compared to unmodified micelles. These results suggest that APP micelles may offer an effective strategy to deliver therapeutically effective flurbiprofen concentrations into the brain for AD patients.
Ultrabroadband parametric generation and wavelength conversion in silicon waveguides (2006)

We show that ultrabroadband parametric generation and wavelength conversion can be realized in silicon waveguides in the wavelength region near 1550 nm by tailoring their zero-dispersion wavelength and launching pump wave close to this wavelength. We quantify the impact of two-photon absorption, free-carrier generation, and linear losses on the process of parametric generation and show that it is difficult to realize a net signal gain and transparent wavelength conversion with a continuous-wave pump. By investigating the transient dynamics of the four-wave mixing process initiated with a pulsed pump, we show that the instantaneous nature of electronic response enables highly efficient parametric amplification and wavelength conversion for pump pulses as wide as 1 ns. We also discuss the dual-pump configuration and show that its use permits multiband operation with uniform efficiency over a broad spectral region extending over 300 nm.
Calculation of the electric field resulting from human body rotation in a magnetic field (2012)

A number of recent studies have shown that the electric field and current density induced in the human body by movement in and around magnetic resonance imaging installations can exceed regulatory levels. Although it is possible to measure the induced electric fields at the surface of the body, it is usually more convenient to use numerical models to predict likely exposure under well-defined movement conditions. Whilst the accuracy of these models is not in doubt, this paper shows that modelling of particular rotational movements should be treated with care. In particular, we show that v × B rather than -(v · ∇)A should be used as the driving term in potential-based modelling of induced fields. Although for translational motion the two driving terms are equivalent, specific examples of rotational rigid-body motion are given where incorrect results are obtained when -(v · ∇)A is employed. In addition, we show that it is important to take into account the space charge which can be generated by rotations and we also consider particular cases where neglecting the space charge generates erroneous results. Along with analytic calculations based on simple models, boundary-element-based numerical calculations are used to illustrate these findings.
Crystallization and preliminary crystallographic analysis of the recombinant N-terminal domain of riboflavin synthase (2001)

Riboflavin synthase catalyzes the final step in the biosynthesis of riboflavin. Animals and humans lack this enzyme, whereas many bacteria and certain yeasts are absolutely dependent on endogenous riboflavin synthesis. Riboflavin synthase is therefore an attractive target for chemotherapy. The N-terminal domain of riboflavin synthase forms a dimer in solution and is capable of strongly binding riboflavin. It can serve as a model for the binding site of the native enzyme. Structural information obtained from this domain at high resolution will be helpful in the determination of the binding mode of riboflavin and thus for the development of antimicrobial drugs. Here, the crystallization and preliminary crystallographic analysis of the N-terminal domain of riboflavin synthase are reported. The crystals belong to the space group C222(1), with unit-cell parameters a = 50.3, b = 104.7, c = 85.3 A, alpha = beta = gamma = 90 degrees, and diffract to 2.6 A resolution.
Formation of voids in silicone RTV dispersion under beam-leaded silicon integrated circuits (1990)

The results of a study on void formation under simulated beam-leaded silicon integrated circuits (ICs) (chips) encapsulated with Dow-Corning 96-084 RTV silicone rubber dispersion are described. The simulated chips were made out of glass. Three types of voids were observed: voids originating at the center under a chip and progressively spreading outward (solvent vapor voids), voids formed by air entering under a chip through a tunnel in the RTV dispersion (tunnel voids), and voids originating at the sides under a chip and progressively spreading under it without tunnel formation (air diffusion voids). The process of formation of each void type was documented with the aid of photographs. Analyses have been made of the first two types of voids. The results of the analysis of the solvent vapor voids allow determination of the highest initial encapsulant viscosity for which void-free coverage can be obtained for a chip having a given side length. The results of the analysis of the tunnel voids give the smallest encapsulant height-to-chip-side-length ratio needed for tunnel-free coverage of chips with and without a tilt.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
First‐year growth response of trees in an intact forest exposed to elevated CO<sub>2</sub> (1999)

Summary Although elevated atmospheric CO 2 has been shown to increase growth of tree seedlings and saplings, the response of intact forest ecosystems and established trees is unclear. We report results from the first large‐scale experimental system designed to study the effects of elevated CO 2 on an intact forest with the full complement of species interactions and environmental stresses. During the first year of exposure to ^ 1.5 Ë ambient CO 2 , canopy loblolly pine ( Pinus taeda , L.) trees increased basal area growth rate by 24% but understorey trees of loblolly pine, sweetgum ( Liquidambar styraciflua L.), and red maple ( Acer rubrum L.) did not respond. Winged elm ( Ulmus alata Michx.) had a marginally significant increase in growth rate ( P = 0.069). These data suggest that this ecosystem has the capacity to respond immediately to a step increase in atmospheric CO 2 ; however, as exposure time increases, nutrient limitations may reduce this initial growth stimulation.
Comparison of antisera in the fluorescent antibody test for detection of Bacteroides spp in clinical specimens. (1982)

Twenty-two known strains of the Bacteroides fragilis group of organisms and 67 clinical specimens from a variety of sites were examined by fluorescent antibody test (IFA) using two different antisera fro the rapid detection of B fragilis group of organisms. A previously reported Barts' pooled antisera was compared with a commercially produced Fluoretec kit antisera and the findings were related to routine anaerobic culture and gas liquid chromatography for short chain fatty acids. The Barts' antisera was more sensitive (88%) but less specific (88%) than the kit (sensitivity 50%, specificity 98%). This indicates that Barts' antisera picks up more positive cultures than the kit. The predictive value of a positive test was 82% for Barts' antisera and 93% for the kit. There were higher numbers of false-negatives with the kit (13/26) than with the Barts' (3/26). The predictive value of a negative test was 92% for Barts' antisera and 75% for the kit, indicating that a negative IFA test with Barts' antisera is a reliable index of the absence of the B fragilis group of organisms from clinical specimens. The implications for the use of this test in a routine laboratory are discussed.
Synthesis of Functionalized Spherosilicates: Novel Polyhedral Polyreactive Oligomers (1990)

Abstract Four new compounds [Sin02.5nJ](Si(CH3)2Y)n n = 8,10; Y = -CHCH2, -CH2Cl, were synthesized and characterized. The synthesis involved the use of the adducts (H3C)3NO.ClSi(CH3)2Y (Y = -CHCH2, -CH2Cl) as reagents to convert the [dbnd]Si-H groups in the hydridospherosiloxanes, HnSin01.5n (n=8,10), directly to [dbnd]SiOSi(CH3)2Y (Y[dbnd]-CHCH2, -CH2Cl) groups. These compounds are polyhedral, polyreactive oligomers consisting of a spherosilicate core, [Sin02.5n], of cubic (n=8) or pentagonal prismatic (n=10) symmetry with reactive functional groups, either vinyl or chloromethyl, attached to each vertex.
MicroRNA therapeutics: principles, expectations, and challenges (2011)

MicroRNAs (miRNAs) are a class of highly abundant non-coding RNA molecules that are involved in several biological processes. Many miRNAs are often deregulated in several diseases including cancer. There is substantial interest in exploiting miRNAs for therapeutic applications. In this editorial, we briefly review current advances in the use of miRNAs or antisense oligonucleotides (antagomirs) for such therapies. One of the key issues related to therapy using miRNAs is degradation of naked particles in vivo. To overcome this limitation, delivery systems for miRNA-based therapeutic agents have been developed, which hold tremendous potential for improving therapeutic outcome of cancer patients.
pH-Induced Conformational Change of the Rotavirus VP4 Spike: Implications for Cell Entry and Antibody Neutralization (2005)

The rotavirus spike protein, VP4, is a major determinant of infectivity and neutralization. Previously, we have shown that trypsin-enhanced infectivity of rotavirus involves a transformation of the VP4 spike from a flexible to a rigid bilobed structure. Here we show that at elevated pH the spike undergoes a drastic, irreversible conformational change and becomes stunted, with a pronounced trilobed appearance. These particles with altered spikes, at a normal pH of 7.5, despite the loss of infectivity and the ability to hemagglutinate, surprisingly exhibit sialic acid (SA)-independent cell binding in contrast to the SA-dependent cell binding exhibited by native virions. Remarkably, a neutralizing monoclonal antibody that remains bound to spikes throughout the pH changes (pH 7 to 11 and back to pH 7) completely prevents this conformational change, preserving the SA-dependent cell binding and hemagglutinating functions of the virion. A hypothesis that emerges from the present study is that high-pH treatment triggers a conformational change that mimics a post-SA-attachment step to expose an epitope recognized by a downstream receptor in the rotavirus cell entry process. This process involves sequential interactions with multiple receptors, and the mechanism by which the antibody neutralizes is by preventing this conformational change.
Frontal and Nasal Nerve Blocks in the Treatment of Severe Pain in Acute Ophthalmic Zoster (2002)

To the Editor: Acute ophthalmic zoster (OZ) is frequently accompanied by severe pain in the frontal and nasal branches of the ophthalmic nerve (ON) in elderly patients. Rapid relief is particularly important in these patients because their daily activities are disrupted (1), but is often difficult owing to the iatrogenic effects of antalgics (2). We report an original treatment of this pain: peripheral blockades of the ON. Twenty patients (mean age 76 ± 7 years, range 63–88) were referred to our pain center with severe pain (mean VAS 74 ± 10, range 60–100) stubborn to proper analgesic treatment. We performed daily frontal and/or nasal blocks of 1 mL of bupivacaine with 0.25% adrenaline added to 12.5 μg of clonidine until VAS <40. All patients experienced less pain after the first injection. The number of blocks per patient was 2.3 ± 0.7 (range 1–4). The mean aily VAS fell to 48 ± 10, 41 ± 11, 35 ± 10, 32 ± 6 and 28 ± 9 between days 1 and 5 (P <0.001). All pain-associated symptoms were improved, and sleep disturbance was reduced. All patients’ analgesic medication, especially morphine, could be substantially reduced. No side effects were observed. These findings are preliminary data for a new treatment of pain in acute OZ. A controlled study is necessary for verification. Philippe Gain, MD, PhD Gilles Thuret, MD Christophe Chiquet, MD Marie-Louise Navez, MD Jean Pascal, MD
Thresholdless Lasing of Nitride Nanobeam Cavities (2016)

Exploring the limit of thresholdless operation is a central goal in the development of nanolasers. It goes along with a vivid debate about how to prove and interpret thresholdless lasing. Moreover, it is also relevant regarding future applications of nanolasers and large-scale photonic integration requiring energy-efficient coherent light emitters with small footprint. We present close to ideal lasing behavior of GaN nanobeam cavities grown on silicon. Due to their high optical quality, such nanobeam cavities allow for efficient coupling of spontaneous emission from the quantum well gain material into the laser mode. By performing a comprehensive optical and quantum-optical characterization of these nanolasers, we unambiguously identify high-$\beta$ lasing at room temperature and thresholdless lasing at 156 K. The peculiar thresholdless characteristic is explained in terms of a temperature and excitation power dependent interplay between 0D and 2D gain contributions and the impact of non-radiative recombination.
Esophageal Impaction of Trichobezoar Caused by Endoscopic Removal (2009)

Trichobezoar usually occurs in patients who have trichotillomania combined with trichophagia. Bezoars can result in serious complications including gastric ulceration, bleeding, perforation and small bowel obstruction when undiagnosed. The three main venues of bezoar removal (chemical dissolution, endoscopic removal and surgical removal) are chosen mainly by the size and composition of the bezoar. Trichobezoars generally require endoscopic or surgical removal. An 8-year-old girl visited our emergency room with recurrent epigastric pain and vomiting. Gastroduodenoscopy showed a 210 cm trichobezoar causing pyloric obstruction. During endoscopic removal of trichobezoar, esophageal impaction occurred. The trichobezoar was pushed into the stomach and was removed through surgical gastrostomy under general anesthesia. We report this case as an instructive reference for the proper treatment of trichobezoar in children.
Changes in Cd and Cr fluxes during the bioremediation of phenanthrene (2005)

Abstract. Different types of contaminants such as polycyclic aromatic hydrocarbons (PAHs) and metals coexist in different chemical forms in soil. Although bioremediation of organics has been widely studied, little attention has been paid to changes in metal behaviour during the bioremediation process. In this study, the diffusion gradient in thin-film (DGT) technique was used to assess changes in potentially bioavailable Cd and Cr fluxes in soil during the bioremediation of phenanthrene. Fluxes of Cd were low (< 0.2pgcm−2 s−1) and increased to 0.4–0.9 pg cm−2 s−1, while Cr(III) fluxes showed an approximately tenfold increase. Results showed that there was increased mobilization of metals associated with the fungal reduction of phenanthrene concentrations by Penicillium frequentans.
Alteration of Type II Regulatory Subunit of cAMP‐dependent Protein Kinase in Human Cisplatin‐resistant Cells as a Basis of Collateral Sensitivity to 8‐Chloro‐cAMP (1992)

A cyclic adenosine 3',5'-monophosphate (cAMP) analogue, 8-chloro-cAMP (8-Cl-cAMP), had a collateral growth-inhibitory effect on a cis-diamminedichloroplatinum(II) (CDDP)-resistant human cancer cell lines (PC-14/CDDP). The non-selective analogues dibutyryl-cAMP, 8-bromo-cAMP and forskolin, which are cAMP agonists, showed far less cytotoxicity than 8-Cl-cAMP in both cell lines. There was no significant difference in cAMP content between PC-14 and PC-14/CDDP. Because 8-Cl-cAMP has been shown to bind selectively to the site I receptor of the type II regulatory subunit (RII) of cAMP-dependent protein kinase, we determined the level of expression of regulatory subunits in PC-14 and PC-14/CDDP cells by photoaffinity labeling. PC-14/CDDP cells had a higher RII level, low site I receptor of type I regulatory subunit (RI) level, and a lower RI/RII ratio than the parental PC-14 cells. Exposure to 8-Cl-cAMP increased the RI and RII level in PC-14/CDDP cells in dose- and time-dependent manners. On the other hand, in parental PC-14 cells, RII was not detected and the levels of RI and RII were not increased by exposure to 8-Cl-cAMP. These results suggested that the change in RI and/or RII levels caused by 8-Cl-cAMP was correlated with 8-Cl-cAMP-induced growth inhibition and that the collateral sensitivity to 8-Cl-cAMP in CDDP-resistant cells was due to the increased RII level. Our results suggest that 8-Cl-cAMP can be used in combination with CDDP and that measurement of RI and RII levels and/or the RI/RII ratio is a useful tool to predict CDDP sensitivity.