gebhart/patrepeval huggingface dataset:
Three Neuropeptide Y Receptor Genes in the Spiny Dogfish, Squalus acanthias, Support en Bloc Duplications in Early Vertebrate Evolution (2003)

It has been debated whether the increase in gene number during early vertebrate evolution was due to multiple independent gene duplications or synchronous duplications of many genes. We describe here the cloning of three neuropeptide Y (NPY) receptor genes belonging to the Y1 subfamily in the spiny dogfish, Squalus acanthias, a cartilaginous fish. The three genes are orthologs of the mammalian subtypes Y1, Y4, and Y6, which are located in paralogous gene regions on different chromosomes in mammals. Thus, these genes arose by duplications of a chromosome region before the radiation of gnathostomes (jawed vertebrates). Estimates of duplication times from linearized trees together with evidence from other gene families supports two rounds of chromosome duplications or tetraploidizations early in vertebrate evolution. The anatomical distribution of mRNA was determined by reverse-transcriptase PCR and was found to differ from mammals, suggesting differential functional diversification of the new gene copies during the radiation of the vertebrate classes.
THE KINETICS AND MECHANISM OF THE REACTION OF TRICO-ORDINATE PHOSPHORUS COMPOUNDS WITH TETRACYANOQUINODIMETHANE AND TETRACYANOETHYLENE (1995)

Abstract Trico-ordinate phosphorus compounds, ArηP(OPri)3-η where n = 0–3, react with tetracyanoquino-dimethane (TCNQ) in acetonitrile in the presence of water to give the corresponding phosphoryl compounds, ArηP(O)(OPri)3-η and 1,4-bis-dicyanomethylbenzene (TCNQH2) in quantitative yield. The kinetics of these reactions are reported together with the Hammett ρ-parameters from variation of substituents in the aryl group for n = 1,2 and 3. On the basis of the available evidence, a mechanism is proposed involving one electron transfer from phosphorus (the donor) to TCNQ. A kinetic study of the reaction of triarylphosphines with TCNE in aqueous acetonitrile, however, suggests rate-limiting nucleophilic attack on nitrogen rather than the radical cation mechanism.
IR-Spectromicroscopy for Subcellular Imaging: Cellular Mapping of a Metal-Carbonyl Exogenous Compound Using AFM-IR and SR-FTIR (2011)

International audience
Pathological anatomy of the bacterial phloem canker disease of <i>Juglans regia</i> (1970)

Erwinia rubrifaciens Wilson, Zeitoun, and Fredrickson invades sieve tubes and parenchyma cells of the nonfunctional secondary phloem of Persian walnut, Juglans regia L. Because the sieve plate pores are great enough in diameter to allow passage of the bacteria, the nonfunctional phloem system provides an avenue along which the bacteria moves long distances up and down the bark. Functional phloem, on the other hand, does not exhibit symptoms of the disease nor is it found to contain the bacteria. Although the bacteria invade the ray parenchyma and move radially through these elements to the outer xylem, bacteria are not found to enter the xylem vessels. In culture, E. rubrifaciens produces long flexuous flagella. When taken from inoculated leaf tissue, however, it does not possess flagella. Hence, transport of bacteria from one sieve tube to another appears to be by apoplastic movement. Internal symptoms develop in two stages: a primary stage due to invasion of degenerate sieve tubes, and a secondary stage due to invasion of parenchyma cells and subsequent formation of wound callus. Pressure from wound callus induces vertical cracks in the bark. A slimy substance containing the bacteria exudes through the cracks to the bark surface, thereby allowing dispersion of the bacteria.
Detection and Characterization of Stress-Induced Defects in Gate SiO<sub>2</sub> Films by Conductive Atomic Force Microscopy (2004)

We have demonstrated the detection of nanometer-scale current-leakage sites in electrically stressed gate SiO 2 films using a conductive atomic force microscope (C-AFM). Prior to C-AFM observations, the gate SiO 2 films in metal-oxide-semiconductor capacitors were subjected to constant-current Fowler-Nordheim (FN) stress. Details of image contrasts and the relationship between the surface topography and the current image of the SiO 2 films were examined. Two types of contrast were clearly observed in the current image: a sharp bright spot reflecting local current leakage were caused by hole trapping at stress-induced defects and a fuzzy bright contrasts originating from the SiO 2 thickness fluctuation. The dependence of C-AFM images on the electron injection direction during FN stress application and the SiO 2 film thickness clearly reveals that the stress-induced defects are distributed in the region within 2.6 nm from the SiO 2 /Si substrate interface.
Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach (2009)

With the severe acute respiratory syndrome epidemic of 2003 and renewed attention on avian influenza viral pandemics, new surveillance systems are needed for the earlier detection of emerging infectious diseases. We applied a "next-generation" parallel sequencing platform for viral detection in nasopharyngeal and fecal samples collected during seasonal influenza virus (Flu) infections and norovirus outbreaks from 2005 to 2007 in Osaka, Japan. Random RT-PCR was performed to amplify RNA extracted from 0.1-0.25 ml of nasopharyngeal aspirates (N = 3) and fecal specimens (N = 5), and more than 10 microg of cDNA was synthesized. Unbiased high-throughput sequencing of these 8 samples yielded 15,298-32,335 (average 24,738) reads in a single 7.5 h run. In nasopharyngeal samples, although whole genome analysis was not available because the majority (>90%) of reads were host genome-derived, 20-460 Flu-reads were detected, which was sufficient for subtype identification. In fecal samples, bacteria and host cells were removed by centrifugation, resulting in gain of 484-15,260 reads of norovirus sequence (78-98% of the whole genome was covered), except for one specimen that was under-detectable by RT-PCR. These results suggest that our unbiased high-throughput sequencing approach is useful for directly detecting pathogenic viruses without advance genetic information. Although its cost and technological availability make it unlikely that this system will very soon be the diagnostic standard worldwide, this system could be useful for the earlier discovery of novel emerging viruses and bioterrorism, which are difficult to detect with conventional procedures.
Fenton Oxidation of Polycyclic Aromatic Hydrocarbons After Surfactant-Enhanced Soil Washing (2000)

The feasibility of using a combination of two well-studied technologies - soil washing and Fenton oxidation - to remove polycyclic aromatic hydrocarbons (PAH) from soil and subsequently destroy them in the resulting waste water solution was investigated. Three well-characterized New Jersey soils, representing a wide range of organic carbon content, were artificially contaminated with a mixture of anthracene, phenanthrene, and fluoranthene to simulate PAH-contaminated field soil. Batch laboratory-scale surfactant-enhanced soil washing was used to remove PAH from these soils. Two nonionic octylphenyl ethoxylate-type surfactants - Triton X-100 and Igepal CA-720 - were employed. PAH concentration in wash solution containing 1% surfactant was increased by over an order of magnitude above the level possible with water alone. The resulting solutions were treated with Fenton's reagent (H2O2 plus Fe2+) to destroy PAH in solution. Greater than 99% of PAH parent material was destroyed in the Triton X-100 wash solution from the low organic sandy soil. Mass spectrometric analysis of the treated material indicated that partially degraded surfactant molecules constituted the major reaction residuals. The extent of disappearance of parent PAH in soil-washing waste water for a given dose of Fenton's reagent was inversely proportional to the water solubility of the species (anthracene greater than fluoranthene greater than phenanthrene). Surfactant and soil organic matter in spent soil-washing solutions represented significant Fenton's reagent sinks, and would likely be the limiting cost factor in determining the feasibility of this method for a given soil-surfactant system.
Dehalogenation of Chloroarenes with Sodium Dihydridobis(2-methoxyethoxo)aluminate in the Presence of Transition Metal Compounds (1994)

Dehalogenation of low-chlorinated arenes such as p -dichlorobenzene or chlorobenzene with the title hydride is accelerated in the presence of transition metal species formed in situ from the corresponding 2,4-pentanedionates. Their efficiency decreases in the order: Co ≈ Ni ≈ Pd > Cu >> Mn > Fe which results from changes of their activity and stability. The dehalogenation is well described by a kinetic model consisting of the set of dehalogenation steps which are first order in the chloroarene combined with the catalyst deactivation which is second order in the transition metal compound.
<title>Measured performance of an airborne Fourier-transform hyperspectral imager</title> (1996)

A new hyperspectral imager has recently been developed by Kestrel Corporation for use in light aircraft platforms. The instrument provides 256 spectral channels with 87 cm<SUP>-1</SUP> spectral bandwidth over the 450 nm to 1000 nm portion of the spectrum. Operated as a pushbroom imager, the FTVHSI has been shown to have a IFOV of 0.75 mrad, and a FOV of 0.23 rad. The sensor includes an internal spectral/radiometric calibration source, a self contained spectrally resolved downwelling sensor, and complete line of sight and GPS positioning information. The instrument is now operating from a Cessna TU-206 single engine aircraft.
PERMANENT ELECTRIC DIPOLE MOMENT OF CH (1989)

Spectra in the $A^{2}\\Delta -X^{2}\\Pi (\\lambda =431 nm)$ band system of the CH radical were recorded by the intermodulated fluorescence technique. The Stark effect on the $Q_{2e}(2)$ and $R_{1}(1)$ branch features was measured, and a determination of the value of the permanent electric dipole moment of the ground state was made. In this determination, a $(2F + 1)X(2F + 1), \\Delta F= \\pm 1$ Hamiltonian matrix, including Stark effect, was set up in a Hund's case ($a_{\\beta}$) basis set and diagonalized to produce eigenvectors and eigenvalues. The calculated spectra were optimized to the experimental observations in a least-squares fashion to give the predicted value of $\\mu(X^{2}\\Pi)$. The determined value will be given, and compared with the previous $determination^{1}$.
Resonant<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>α</mml:mi></mml:math>scattering of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msup><mml:mrow/><mml:mn>6</mml:mn></mml:msup></mml:math>He: Limits of clustering in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msup><mml:mrow/><mml:mn>10</mml:mn></mml:msup></mml:math>Be (2013)

The structure of ${}^{10}$Be was studied via resonant $\ensuremath{\alpha}$-particle scattering of a neutron-rich ${}^{6}$He beam. A time projection chamber, PAT-TPC, was operated in an active-target mode to provide a gaseous ${}^{4}$He target and trace the beam and reaction products traversing its active tracking volume. This significantly lowered the detection threshold of reaction products at low energies. Elastic scattering, inelastic scattering to the ${}^{6}$He 2${}^{+}$ state, and the ${}^{6}$He($\ensuremath{\alpha}$, 2$n$)${}^{8}$Be reaction were measured below an energy of 6 MeV in the center-of-mass frame. Continuous spectra of excitation functions and angular distributions were obtained from unambiguously-identified recoiling $\ensuremath{\alpha}$ particles for the elastic and inelastic channels. While a resonance of the 4${}^{+}$ state at 10.15 MeV in ${}^{10}$Be previously reported was confirmed, no other resonances were identified in the elastic channel over the measured energy region. The results are in line with antisymmetric molecular dynamics calculations that predict the limits of $\ensuremath{\alpha}$ clustering in high-spin states due to a spin-orbit force.
Interaction of eukaryotic threonyl-tRNA synthetase with high-Mr RNAs and tRNAThr (1987)

Threonyl-tRNA synthetase of rabbit reticulocytes was purified to homogeneity. We have found that this enzyme can interact not only with cognate tRNA(Thr), but also with high-Mr RNAs. tRNA(Thr) removes rRNA from the complexes with threonyl-tRNA synthetase. On the other hand, rRNA is unable to dissociate tRNA(Thr) from the complexes with the enzyme. Despite its dimeric organization, threonyl-tRNA synthetase is unable to form stable ternary complexes with tRNA(Thr) and rRNA. In the extract of rabbit reticulocytes about one-third of the threonyl-tRNA synthetase molecules are in association with cognate tRNA(Thr) and thus are unable to interact with high-Mr RNAs.
Preparation of Protoplasts of Hydrocarbon-utilizing Yeast Cells and Their Respiratory Activities (1975)

Journal Article Preparation of Protoplasts of Hydrocarbon-utilizing Yeast Cells and Their Respiratory Activities Get access Midori Yamamura, Midori Yamamura Laboratory of Industrial Biochemistry, Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Kyoto Search for other works by this author on: Oxford Academic Google Scholar Yutaka Teranishi, Yutaka Teranishi Laboratory of Industrial Biochemistry, Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Kyoto Search for other works by this author on: Oxford Academic Google Scholar Yutaka Tanaka, Yutaka Tanaka Laboratory of Industrial Biochemistry, Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Kyoto Search for other works by this author on: Oxford Academic Google Scholar Saburo Fukui Saburo Fukui Laboratory of Industrial Biochemistry, Department of Industrial Chemistry, Faculty of Engineering, Kyoto University, Kyoto To whom correspondence and reprint request should be addressed. Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 39, Issue 1, 1 January 1975, Pages 13–20, https://doi.org/10.1080/00021369.1975.10861574 Published: 01 January 1975 Article history Received: 05 February 1974 Published: 01 January 1975
Modeling unfolded states of peptides and proteins (1995)

The hydrophobic effect is the major factor that drives a protein molecule toward collapse and folding. In this process, residues with apolar side chains associate to form a solvent-shielded hydrophobic core. Often, this hydrophobic contribution to folding is quantified by measuring buried apolar surface area, reckoned as the difference in area between hydrophobic groups in the folded protein and in a standard state. Typically, the standard state area of a residue is obtained from tripeptide models, with the results taken to implicitly represent values appropriate for the unfolded state. Here, we show that a tripeptide is a poor descriptor of the unfolded state, and its widespread use has prompted erroneous conclusions about folding. As an alternative, we explore two limiting models, chosen to bracket the expected behavior of the unfolded chain between reliable extremes. One extreme is represented by simulated hard-sphere peptides and shown to behave like a homopolymer with excluded volume in a good solvent. The other extreme is represented by fragments excised from folded proteins and conjectured to approximate the time-average behavior of a thermally denatured protein at Tm, the midpoint of the unfolding transition. Using these models, it is shown that the area buried by apolar side chains upon folding is considerably less than earlier estimates. For example, upon transfer from the unfolded state to the middle of an alpha-helix, an alanine side chain buries negligible area and, surprisingly, a valine side chain actually gains area. Among other applications, an improved model of the unfolded state can be used to better evaluate the driving force for helix formation in peptides and proteins.
SS: Unlocking the Unconventional Oil and Gas Reservoirs: Utilization of Real Time Microseismic Monitoring and Hydraulic Fracture Diversion Technology in the Completion of Barnett Shale Horizontal Wells (2009)

Abstract It is now well documented that hydraulically fractured horizontal wells are effective at stimulating shale reservoirs. Most commercial shale wells utilize cement or open hole packers to achieve some form of annular isolation. With annular isolation now commonly accepted, the general evolution of these completions has been to stimulate ever shorter sections of the lateral with multiple perforation clusters placed closely together. The objective being to create closely spaced fractures, thereby increasing the reservoir contact area that more effectively imposes a pressure drawdown within the ultra-low permeability reservoir, resulting in a higher recovery factor. The heterogeneous nature of unconventional shale reservoirs makes achieving a complex, closely spaced fracture network problematic. Frequently, geologic structure impacts the created fracture network to such a degree that fluid entry points into the reservoir are of secondary importance. Horizontal well evaluation can be utilized to optimize perforation placement and fracture staging for near-wellbore fracture geometry generation. This has proven to improve well performance. An additional productivity step can be achieved if the far field fracture geometry can be influenced by techniques other than perforation and fracture staging, especially if this technique can be applied in real time during the stimulation treatment. One method that has been successful at altering the created hydraulic fracture geometry is real time microseismic fracture mapping coupled with fracture diversion packages incorporated into the fracturing treatment. Evaluating microseismic events in real time allows one to determine the need to change the fracture geometry being generated. The introduction of diversion packages to achieve this fracture geometry alteration can immediately be evaluated for effectiveness via the microseismic activity. This feedback allows the completions engineer to appropriately use these diversion packages so that effective stimulation along the whole lateral can be achieved. Examples of the use of real time microseismic fracture mapping and fracture diversion packages are shown from the Ft. Worth Basin Barnett Shale formation. Both initial well completions and recompletions are shown. The importance of integrating well, geologic, log, and seismic information, is emphasized so that decisions can be made effectively in real time using the microseismic activity from the treatments. These examples demonstrate that hydraulic fracture geometries can be influenced by the introduction of these diversion packages. Resulting well productivity and fracture pressure responses validate the effectiveness of this real time diversion and evaluation process.
Serotonin Transporter Gene Polymorphism in Women With Suspected Ischemia (2018)

Introduction: Association of serotonin transporter gene ( 5-HTTLPR) polymorphisms with adverse cardiovascular (CV) events in women with suspected ischemia has not yet been reported. We hypothesized an association of 5-HTTLPR polymorphisms with risk of adverse CV events in women with suspected ischemic heart disease (IHD) referred for coronary angiography enrolled in the Women’s Ischemia Syndrome Evaluation (WISE). Method: We studied clinical and angiographic data and DNA from a cohort of 437 Caucasian women enrolled in the WISE genotyped for the long (L) and short (S) variant of the 5-HTTLPR polymorphism. Women were followed yearly for adverse CV events (defined as first occurrence of all-cause death, myocardial infarction, stroke, or heart failure hospitalization) with data collected at WISE 10-year follow-up. Exploratory analyses compared outcomes between genotype groups. Results: A total of 437 women, with baseline, angiographic, and long-term follow-up data, were successfully genotyped. Their mean age was 58 ± 11 years and body mass index 29 ± 6; 54% had hypertension, 18% diabetes, 50% dyslipidemia, 20% depression history, and only 34% had obstructive CAD. At 8.9 years median follow-up, the SS genotype was associated with significantly increased risk of adverse CV event versus LL + LS (1.93, confidence interval [CI]: 1.03-3.61, P = .03). Results were not significant for all-cause death (hazard ratio: 1.63, CI: 0.91-2.93, P = .09). Conclusion: Among a cohort of Caucasian women with suspected IHD enrolled in the WISE, the SS homozygous genotype for the 5-HTTLPR polymorphism was associated with increased risk of adverse CV outcomes.
The development of ATM standards and technology: a retrospective (1993)

The evolution of the ATM (asynchronous transfer mode) from its inception in early trials through to the current developments is reviewed. Strong emphasis is placed on the role of standards development in the development of the technology, as it is the opinion of the author that ATM could never have reached the status that it has today without the development effort put into the standards over the period between 1986 and 1992. The standards development process has also been a learning process. Technical differences seem to get resolved more quickly with more interaction at informal workshops. The creation of the ATM Forum has taken ATM one step closer to the end user. However, the standards community is aware of a need to improve its process, to develop standards that are less ambiguous and less subject to error, and to ensure interoperability of different networks and different vendor products. The author notes that over the next few years one will see major changes in these areas to improve the product of standards development.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High type II error and interpretation inconsistencies when attempting to refute transgenerational epigenetic inheritance (2016)

A recently published article in Genome Biology attempts to refute important aspects of the phenomenon of transgenerational epigenetic inheritance (TEI). An alternative explanation of the data is offered here, showing that TEI is indeed not contradicted.Please see related Correspondence article: www.dx.doi.org/10.1186/s13059-016-0981-5 and related Research article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0619-z.