gebhart/patrepeval huggingface dataset:
Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes (2002)

Previous molecular phylogenetic studies have failed to resolve the branching order among the major cotton (Gossypium) lineages, and it has been unclear whether this reflects actual history (rapid radiation) or sampling properties of the genes evaluated. In this paper, we reconsider the phylogenetic relationships of diploid cotton genome groups using DNA sequences from 11 single-copy nuclear loci (10 293 base pairs [bp]), nuclear ribosomal DNA (695 bp), and four chloroplast loci (7370 bp). Results from individual loci and combined nuclear and chloroplast DNA partitions reveal that the cotton genome groups radiated in rapid succession following the formation of the genus. Maximum likelihood analysis of nuclear synonymous sites shows that this radiation occurred within a time span equivalent to 17% of the time since the separation of Gossypium from its nearest extant relatives in the genera Kokia and Gossypioides. Chloroplast and nuclear phylogenies differ significantly with respect to resolution of the basal divergence in the genus and to interrelationships among African cottons. This incongruence is due to limited character evolution in cpDNA and either previously unsuspected hybridization or unreliable phylogenetic performance of the cpDNA characters. This study highlights the necessity of using multiple, independent data sets for resolving phylogenetic relationships of rapidly diverged lineages.
Patterned selective growth of carbon nanotubes and large field emission from vertically well-aligned carbon nanotube field emitter arrays (2001)

We have grown well-aligned carbon nanotube arrays by thermal chemical vapor deposition at 800 °C on Fe nanoparticles deposited by a pulsed laser on a porous Si substrate. We also attain a selective growth of carbon nanotubes on a patterned Fe film on Si substrates in terms of pulsed laser deposition and a liftoff patterning method. Field emission measurement has been made on the carbon nanotube (CNT)-cathode diode device at room temperature and in a vacuum chamber below 10−6 Torr. The distance between the CNT cathode and the anode is 60 μm and is kept through an insulating spacer of polyvinyl film. The measured field emitting area is 4.0×10−5 cm2. Our vertically well-aligned carbon nanotube field emitter arrays on the Si-wafer substrate emit a large current density as high as 80 mA/cm2 at 3 V/μm. The transmission electron microscope image shows that they are multiwalled and bamboolike structures and that the tips of some of the carbon nanotube emitters are open. The open tip structure of our CNTs and their good adhesion via Fe nanoparticles to the Si substrate are part of the reason why we can attain a large field emission current density within a low field.
Insights into bone health in Duchenne muscular dystrophy (2012)

Poor bone health is a significant problem for patients with Duchenne muscular dystrophy (DMD), a progressive, disabling disease. Although the primary focus of DMD disease pathogenesis is degeneration of striated muscle, impairment of bone health likely has a role in the disease that has only been superficially examined to date. Deficiency of bone mineral density and increased incidence of bone fractures are well-recognized clinical components of the DMD phenotype. Furthermore, therapy with corticosteroids, an approved treatment for DMD that prolongs ambulation, may have multiple effects on bone health in DMD patients. This review examines the evidence in preclinical models and in human DMD disease that provides insight into the role performed by bone in the disease pathogenesis and phenotype of DMD. The information reviewed here points toward the need for mechanistic and therapeutic studies to optimize bone health in DMD patients.
The prognostic value of overexpression of Skp2 mRNA in non-small cell lung cancer (2005)

Skp2 putatively plays a critical role in regulating cell cycle progression. A high level of Skp2 expression is observed in a variety of cancer. No previous report describes the prognostic value of Skp2 mRNA in non-small cell lung cancer (NSCLC). Therefore, the purpose of this study was to examine overexpression of Skp2 mRNA in NSCLC and identify the association of Skp2 expression level with patient survival. We investigated Skp2 expression in 79 patients with NSCLC by means of reverse transcription-polymerase chain reaction (RT-PCR) and immunohistochemistry. The Skp2 expression was significantly associated with tumor status, lymph node metastasis, stage, vascular invasion, histology and Skp2 protein. With regard to prognosis, the overall and stage I survival rates for patients in the high Skp2 mRNA group were significantly poorer when compared with the low Skp2 mRNA group. Furthermore, expression of Skp2 mRNA was an independent predictor of prognosis by multivariate analysis. Skp2 expression might play an important role in the development and progression in NSCLC and Skp2 gene expression can serve as a useful prognostic marker in NSCLC patients.
Thermodynamics of RNA−RNA Duplexes with 2- or 4-Thiouridines:  Implications for Antisense Design and Targeting a Group I Intron (1999)

Antisense compounds are designed to optimize selective hybridization of an exogenous oligonucleotide to a cellular target. Typically, Watson-Crick base pairing between the antisense compound and target provides the key recognition element. Uridine (U), however, not only stably base pairs with adenosine (A) but also with guanosine (G), thus reducing specificity. Studies of duplex formation by oligonucleotides with either an internal or a terminal 2- or 4-thiouridine (s(2)U or s(4)U) show that s(2)U can increase the stability of base pairing with A more than with G, while s(4)U can increase the stability of base pairing with G more than with A. The latter may be useful when binding can be enhanced by tertiary interactions with a s(4)U-G pair. To test the effects of s(2)U and s(4)U substitutions on tertiary interactions, binding to a group I intron ribozyme from mouse-derived Pneumocystis carinii was measured for the hexamers, r(AUGACU), r(AUGACs(2)U), and r(AUGACs(4)U), which mimic the 3' end of the 5' exon. The results suggest that at least one of the carbonyl groups of the 3' terminal U of r(AUGACU) is involved in tertiary interactions with the catalytic core of the ribozyme and/or thio groups change the orientation of a terminal U-G base pair. Thus thio substitutions may affect tertiary interactions. Studies of trans-splicing of 5' exon mimics to a truncated rRNA precursor, however, indicate that thio substitutions have negligible effects on overall reactivity. Therefore, modified bases can enhance the specificity of base pairing while retaining other activities and, thus, increase the specificity of antisense compounds targeting cellular RNA.
Infrared Spectroscopic Characterization of Chromium Carbonyl Species Formed by Ultraviolet Photoreduction of Silica-Supported Chromium(VI) in Carbon Monoxide (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfrared Spectroscopic Characterization of Chromium Carbonyl Species Formed by Ultraviolet Photoreduction of Silica-Supported Chromium(VI) in Carbon MonoxideSteven D. Kohler and John G. EkerdtCite this: J. Phys. Chem. 1994, 98, 16, 4336–4342Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/j100067a021https://doi.org/10.1021/j100067a021research-articleACS PublicationsRequest reuse permissionsArticle Views390Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Telomerase protein rather than its RNA is the target of phosphorothioate-modified oligonucleotides (1999)

Human telomerase is a ribonucleoprotein which uses its internal RNA moiety as a template for telomeric DNA synthesis. This enzyme is up-regulated in most malignant tumors and is therefore considered as a possible cancer target. Here we examined the effects of differently modified oligomers on telomeraseactivity from HL-60 cell extracts (TRAP-ezetrade mark assay). Phosphorothioate-modified oligonucleotides (PS-ODNs) inhibited telomerase activity at subnanomolar concen-trations and proved to be more efficient than peptide nucleic acids. In contrast to all the investigated oligomers, PS-ODNs were found to bind to the protein motif of telomerase called the primer binding site but poorly to its RNA. This is suggested by kinetic investigations demonstrating a competitive interaction of PS-ODNs and TS primer at the primer binding site. The K m value of the TS primer was 10.8 nM, the K i value of a 20mer PS-ODN was 1.6 nM. When the TS primer was PS-modified a striking increase in the telomerase activity was found which correlates with the number of phosphodiesters replaced. The K m value of a completely PS-modified TS primer was 0.56 nM. Based on these results the design of chimeric ODNs is proposed consisting of a 5'-PS-modified part targeting the primer binding site and a 3'-terminus part targeting the telomerase RNA.
Isocyanates, Part 4. Convenient Phosgene-Free Method for the Synthesis and Derivatization of Enantiopure α-Isocyanato Carboxylic Acid Esters (1997)

A novel phosgene-free procedure for the synthesis of α-isocyanato carboxylic acid esters starting from α-amino acid esters has been achieved. The isocyanates are obtained enantiomerically pure (>99% ee) by a DMAP-catalyzed isocyanation with di-tert-butyl dicarbonate, which proceeds in 10 min at room temperature. In situ derivatization of the isocyanates by reaction with amines and alcohols affords the corresponding enantiopure ureas and carbamates.
Novel solvent properties of choline chloride/urea mixturesElectronic supplementary information (ESI) available: spectroscopic data. See http://www.rsc.org/suppdata/cc/b2/b210714g/ (2002)

Eutectic mixtures of urea and a range of quaternary ammonium salts are liquid at ambient temperatures and have interesting solvent properties.
RADIUS Accounting Client MIB (1999)

This memo provides information for the Internet community. This memo does not specify an Internet standard of any kind. Distribution of this memo is unlimited. Copyright Notice Copyright (C) The Internet Society (1999). All Rights Reserved. This memo defines a set of extensions which instrument RADIUS accounting client functions. These extensions represent a portion of the Management Information Base (MIB) for use with network management protocols in the Internet community. Using these extensions IP-based management stations can manage RADIUS accounting clients. 1.
A 3D paired microelectrode array for accumulation and separation of microparticles (2006)

This paper presents a microfluidic system comprising a three-dimensional microelectrode structure for accumulation and separation of micro-sized particles based on the combination of negative dielectrophoresis (DEP) and hydrodynamic force. The paired electrode array is constructed by aligning two layers of microelectrode structure face to face on the top and bottom sides of the microchannel. Dielectrophoretic gates are generated between the top and bottom electrodes with high-frequency ac voltage. These gates are designed to study the behavior of microparticles such as polystyrene beads or cells carried by a laminar flow past the electrodes. Depending on the relative strength of the DEP force and hydrodynamic force acting on the particles, the particles can either penetrate the gates or settle by the gates. The threshold velocity at which the particles begin to penetrate the gates depends on a number of parameters such as channel height, particle size, dielectric properties, electrode width and local heating, etc. A wide range of these parameters give rise to approaches of accumulating and separating microparticles. For this purpose, a microfluidic device with the paired microelectrode array sitting on the channel has been designed and fabricated using microfabrication techniques. Polystyrene beads were used to study the performance of the device and particle behavior. Using a proper range of flow rates, particle accumulation and separation are successfully achieved with the microsystem.
Time domain analysis and its practical application to the measurement of phase noise and jitter (1997)

The precise determination of phase is necessary for a very large set of measurements. Traditionally, phase measurements have been made using analog phase detectors which suffer from limited accuracy and dynamic range. This paper describes how phase digitizing, which uses time domain techniques, removes these limitations. Phase digitizing is accomplished using a time interval analyzer, which measures the signal zero-crossing times. These zero-crossing times are processed to compute phase deviation, with the reference frequency specified as a numerical value or derived from the times themselves. Phase digitizing can be applied even in the presence of modulation, as the underlying clock can be reconstructed in software to fit the data. Measurements derived from this phase data such as phase noise, jitter analysis, Allan variance (AVAR), maximum time interval error (MTIE), and time deviation (TDEV) are applied to such applications as the characterization of oscillators, computer clocks, chirp radar, token ring networks, and tributaries in communication systems.
Lack of pressure pain modulation by heterotopic noxious conditioning stimulation in patients with painful osteoarthritis before, but not following, surgical pain relief (2000)

To investigate the influence of chronic nociceptive pain on endogenous pain modulation, the effect of heterotopic noxious conditioning stimulation (HNCS) on perception of various somatosensory modalities was assessed in 15 patients with painful osteoarthritis of the hip. Thirteen patients were re-assessed when pain-free 6-14 months following surgery. Sex- and age matched healthy subjects assessed at similar time intervals served as controls. The effects of HNCS were tested using the upper extremity submaximal effort tourniquet test. Subjects rated tourniquet-induced pain intensity on a visual analogue scale (VAS). Quantitative sensory testing (QST) was performed contralaterally to the maximally painful area in 13 patients and contralaterally to the second most painful area in two patients (i.e. lateral thigh n = 12, frontal thigh n = 1, lateral calf n = 2). Sensibility was assessed before, during and 45 min following the tourniquet test. Perception thresholds to light touch were assessed using von Frey filaments and pressure pain thresholds by pressure algometry. Perception thresholds to non-painful and painful warmth and cold were determined using a Thermotest. In both sessions, patients rated the tourniquet-induced pain higher than controls at the start (P < 0.003 and P < 0.006, respectively), but not at the end of the tourniquet test. Decreased sensitivity to light touch (P < 0.001) and innocuous cold (P < 0.002) was seen during the tourniquet in patients and controls alike, on both occasions, while perception thresholds to innocuous warmth and heat pain remained unaffected. In the first session, pressure pain thresholds increased during the tourniquet test in controls (P < 0.002), but not in patients. In the second session, pressure pain thresholds increased during the tourniquet test in controls (P < 0.001) and in patients (P < 0.02). In conclusion, no pressure pain modulation was induced by HNCS in patients before surgery, as opposed to controls, suggesting a dysfunction in systems subserving 'diffuse noxious inhibitory controls' (DNIC). Normal pressure pain modulation induced by HNCS was seen when patients were re-assessed in a pain-free state following surgery, indicating that the dysfunction of DNIC had been maintained by chronic nociceptive pain.
Mapping of deletions in the genome of the highly attenuated vaccinia virus MVA and their influence on virulence (1991)

Different passages of the vaccinia virus strain Ankara (CVA wild-type) during attenuation to MVA (modified vaccinia virus Ankara) have been analysed to detect alterations in the genome. Physical maps for the restriction enzymes HindIII and XhoI have been established. Six major deletions relative to the wild-type strain CVA could be localized. They reduce the size of the entire genome from 208 kb (CVA wild-type) to 177 kb for the MVA strain. Four deletions occurred during the first 382 passages and the resulting variant (CVA 382) displays an attenuated phenotype similar to that of the MVA strain. The deletions are located in both terminal fragments, affect two-thirds of the host range gene K1L and eliminate 3.5 kb of a highly conserved region in the HindIII A fragment. During the next 190 passages leading to MVA two additional deletions appeared. Again, one is located in the left terminal fragment, and the other includes the A-type inclusion body gene. Neither of the deletions appear to participate in further attenuation of the virus. Rescue of the partially deleted host range region with the corresponding wild-type DNA restored the ability of the attenuated strains MVA and CVA 382 to grow in some non-permissive tissue cultures. Nevertheless, the complete host range of the wild-type strain was not recovered. Also, plaque-forming behaviour and reduced virulence were not influenced. From the data presented it may be concluded that the partially deleted host range gene is not solely responsible for attenuation.
Lasting cortical activation after repetitive TMS of the motor cortex (2000)

Subthreshold 5-Hz repetitive transcranial magnetic stimulation (rTMS) over the hand area of the primary motor cortex is associated with a persisting neuronal activation in a distinct set of motor cortical areas beyond the time of stimulation. The current findings demonstrate that [18F]FDG-PET can localize and quantify regional net changes in synaptic cortical activity after rTMS and thus might elucidate the mechanisms underlying rTMS-associated therapeutic effects.
Theoretical and experimental studies on tightly focused vector vortex beams (2011)

The high-NA focusing properties of vector vortex beams are studied theoretically and experimentally. The vector vortex beams are generated by space-variant segmented subwavelength metallic gratings first. Then the mathematical expressions for the focused fields are derived based on the vector diffraction theory, and some numerical simulations are presented that show that the focused fields are not dark at the center and the focusing spot size of vector vortex beams with high topological charges approaches the diffraction limitation at high NA. Finally, to verify the theoretical analysis, the tightly focused fields are measured based on a confocal microscopy system when the NA of the objective lens is 0.90. The research results confirm the potential of vector vortex beams in some applications, such as optical trapping, laser printing, lithography, and material processing.
Crystal Structures of a Mutant (βK87T) Tryptophan Synthase α2β2 Complex with Ligands Bound to the Active Sites of the α- and β-Subunits Reveal Ligand-Induced Conformational Changes (1997)

Three-dimensional structures are reported for a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with either the substrate L-serine (betaK87T-Ser) or product L-tryptophan (betaK87T-Trp) at the active site of the beta-subunit, in which both amino acids form external aldimines with the coenzyme, pyridoxal phosphate. We also present structures with L-serine bound to the beta site and either alpha-glycerol 3-phosphate (betaK87T-Ser-GP) or indole-3-propanol phosphate (betaK87T-Ser-IPP) bound to the active site of the alpha-subunit. The results further identify the substrate and product binding sites in each subunit and provide insight into conformational changes that occur upon formation of these complexes. The two structures having ligands at the active sites of both alpha- and beta-subunits reveal an important new feature, the ordering of alpha-subunit loop 6 (residues 179-187). Closure of loop 6 isolates the active site of the alpha-subunit from solvent and results in interaction between alphaThr183 and the catalytic residue alphaAsp60. Other conformational differences between the wild type and these two mutant structures include a rigid-body rotation of the alpha-subunit of approximately 5 degrees relative to the beta-subunit and large movements of part of the beta-subunit (residues 93-189) toward the rest of the beta-subunit. Much smaller differences are observed in the betaK87T-Ser structure. Remarkably, binding of tryptophan to the beta active site results in conformational changes very similar to those observed in the betaK87T-Ser-GP and betaK87T-Ser-IPP structures, with exception of the disordered alpha-subunit loop 6. These large-scale changes, the closure of loop 6, and the movements of a small number of side chains in the alpha-beta interaction site provide a structural base for interpreting the allosteric properties of tryptophan synthase.
Multiwavelength light source with precise frequency spacing using mode-locked semiconductor laser and arrayed waveguide grating filter (2005)

We report here a multiwavelength light source using semiconductor mode-locked lasers with the optical frequency spacing of 100 GHz. In this light source, a mode-locked semiconductor laser was used for the original light source, which gave multimodes with constant frequency spacings. The output from the mode-locked laser was fed into silica-based arrayed waveguide grating filter (AWG) with the free spectral range of 100 GHz and 16 channels of input/output ports.