gebhart/patrepeval huggingface dataset:
A Pneumocystis carinii Group I Intron Ribozyme That Does Not Require 2‘ OH Groups on Its 5‘ Exon Mimic for Binding to the Catalytic Core (1997)

The recent increase in the population of immunocompromised patients has led to an insurgence of opportunistic human fungal infections. The lack of effective treatments against some of these pathogens makes it important to develop new therapeutic strategies. One such strategy is to target key RNAs with antisense compounds. We report the development of a model system for studying the potential for antisense targeting of group I self-splicing introns in fungal pathogens. The group I intron from the large ribosomal subunit RNA of mouse-derived Pneumocystis carinii has been isolated and characterized. This intron self-splices in vitro. A catalytically active ribozyme, P-8/4x, has been constructed from this intron to allow measurement of dissociation constants for potential antisense agents. At 37 degrees C, in 50 mM Hepes (25 mM Na+), 15 mM MgCl2, and 135 mM KCl at pH 7.5, the exogenous 5' exon mimic r(AUGACU) binds about 60 000 times more tightly to this ribozyme than to r(GGUCAU), a mimic of its complementary binding site on the ribozyme. This enhanced binding is due to tertiary interactions. This tertiary stabilization is increased by single deoxynucleotide substitutions in the exon mimic at every position except for the internal A, which is essentially unchanged. Thus 2' OH groups of the 5' exon mimic do not form stabilizing tertiary interactions with the P-8/4x ribozyme, in contrast to the Tetrahymena L-21 ScaI ribozyme. Furthermore, at 37 degrees C, the exogenous 5' exon mimic d(ATGACT) binds nearly 32 000 times more tightly to the P-8/4x ribozyme than to r(GGUCAU). Therefore, oligonucleotides without 2' OH groups can exploit tertiary stabilization to bind dramatically more tightly and with more specificity than possible from base pairing. These results suggest a new paradigm for antisense targeting: targeting the tertiary interactions of structural RNAs with short antisense oligonucleotides.
AlkA Protein Is the Third Escherichia coli DNA Repair Protein Excising a Ring Fragmentation Product of Thymine (2000)

Various forms of oxidative stress lead to the formation of damaged bases including N-(2-deoxy-β-d-erythro-pentofuranosyl)-N-3-(2R-hydroxyisobutyric acid)-urea or αRT, the fragmentation product of thymine formed from 5R-thymidine C5-hydrate upon hydrolysis. It was shown that αRT is excised by Escherichia coli Fpg and Nth proteins. Here we report that when present in DNA, αRT is, in addition, a substrate for the E. coli AlkA protein with an apparent Km value of ≅170 nM. αRT positioned opposite T, dG, dC, and dA were efficiently excised by AlkA protein from duplex oligodeoxynucleotides in the following order: dA ≈ T ≫ dC ≈ dG. This is the first example of the excision of a ring opened form of a pyrimidine by AlkA protein and also the first example where the same DNA base lesion is excised by three different DNA glycosylases of the base excision repair pathway. The present results suggest possible structural similarity of the active site between E. coli AlkA, Fpg, and Nth proteins.
Far-Ultraviolet Reflectance of II-VI Compounds and Correlation with the Penn—Phillips Gap (1973)

Synchrotron radiation and standard light sources have been used to measure the polarization-dependent reflectance spectra of BeO, ZnO, ZnS, ZnSe, ZnTe, MgO, CdO, CdS, CdSe, and CdTe for photon energies $0.6&lt;\ensuremath{\hbar}\ensuremath{\omega}&lt;30$ eV at temperatures $90&lt;T&lt;400$ K. The reflectance was analyzed via the Kramers---Kronig relations. We report curves for ${\ensuremath{\epsilon}}_{1}$, ${\ensuremath{\epsilon}}_{2}$, $\ensuremath{-}\mathrm{Im}(\frac{1}{\ensuremath{\epsilon}})$, and ${N}_{\mathrm{eff}}(\ensuremath{\hbar}\ensuremath{\omega})$ for all of the $\mathrm{II}B\ensuremath{-}\mathrm{V}\mathrm{I}$ compounds studied. Strong structures in the valence-band transition region of the zinc compounds and of the cadmium compounds were found to scale linearly with the Penn---Phillips average energy gap. Reflectance structures corresponding to core excitations were observed. A doublet at about 13.5 eV in CdS, CdSe, and CdTe was identified as a spin-orbit-split transition from the Cd $4d$ level. The observed spin-orbit splitting of this level was 0.6 eV. A shoulder on the low-energy side of this doublet in CdTe at 12.8 eV is identified as originating in the Te $5s$ band.
Crocus sativus Lectin Recognizes Man3GlcNAc in the N-Glycan Core Structure (2000)

<i>Crocus sativus</i> lectin (CSL) is one of the truly mannose-specific plant lectins that has a unique binding specificity that sets it apart from others. We studied sugar-binding specificity of CSL in detail by a solution phase method (fluorescence polarization) and three solid phase methods (flow injection, surface plasmon resonance, and microtiter plate), using a number of different glycopeptides and oligosaccharides. CSL binds the branched mannotriose structure in the <i>N-</i>glycan core. Substitution of the terminal Man in the Manα(1–3)Man branch with GlcNAc drastically decreases binding affinity much more than masking of the terminal Man in the Manα(1–6)Man branch. Most interestingly, the β-Man<i>-</i>linked GlcNAc in <i>N-</i>glycan core structure contributes greatly to the binding. The effect of this GlcNAc is so strong that it can substantially offset the negative effect of substitution on the nonreducing terminal Man residues. On the other hand, the GlcNAc that is usually attached to Asn in<i>N-</i>glycans and the l-Fuc linked at the 6-position of the GlcNAc are irrelevant to the binding. A bisecting GlcNAc neither contributes to nor interferes with the binding. This unique binding specificity of CSL offers many possibilities of its use in analytical and preparative applications.
Inferring the relation between seismic slowness and hydraulic conductivity in heterogeneous aquifers (2000)

Cross‐well seismic tomography can be used to develop high‐resolution seismic slowness (1/velocity) estimates along planes through aquifers. Unfortunately, the relation between seismic slowness and hydraulic conductivity is poorly understood, resulting in poor characterization of hydraulic properties from seismic data. This relation is generally developed from laboratory measurements, but slowness values measured with very high frequencies in the lab are often poorly correlated with lower frequency cross‐well and surface seismic slowness values. To address this problem, we developed an approach to infer the relation between slowness and hydraulic conductivity using field scale geophysical and hydrogeologic measurements. We first develop an a priori relation between the conductivity measurements and the cross‐well slowness estimates. Multiple three‐dimensional slowness realizations, conditioned on the cross‐well estimates, are then generated and remapped into log conductivity fields using the a priori slowness to log conductivity relation. We simulate groundwater flow and tracer transport through these conductivity fields and calculate the residuals between measured and simulated concentration arrival time quantiles and drawdown. The slope and intercept of the relation between slowness and log hydraulic conductivity and the dispersivity are then estimated for each slowness realization to minimize the sum of these squared residuals. We demonstrate this approach for the Kesterson aquifer, California, where seismic tomography provided valuable information about aquifer properties. The groundwater flow and tracer transport simulations, through the estimated conductivity fields, yield reasonable fits to the observed tracer concentration histories for two multiple‐well tracer tests (one of which was not used in the inversion) and to the measured drawdown. This approach provides estimates of seismic slowness and hydraulic conductivity, and information about the relation between slowness and log conductivity for a field site.
Differential Pattern of Integrin Receptor Expression in Differentiated and Anaplastic Thyroid Cancer Cell Lines (2005)

Adhesion of tumor cells to the extracellular matrix (ECM) is a crucial step for the development of metastatic disease and is mediated by specific integrin receptor molecules (IRM). The pattern of metastatic spread differs substantially among the various histotypes of thyroid cancer (TC). However, IRM have only occasionally been characterized in TC until now. IRM expression was investigated in 10 differentiated (FTC133, 236, 238, HTC, HTC TSHr, XTC, PTC4.0/4.2, TPC1, Kat5) and two anaplastic TC cell lines (ATC, C643, Hth74), primary cultures of normal thyroid tissue (Thy1,3), and thyroid cancer specimens (TCS). Expression of 16 IRM (beta1-4, beta7, alpha1-6, alphaV, alphaIIb, alphaL, alphaM, alphaX) and of four IRM heterodimers (alpha2beta1, alpha5beta1, alphaVbeta3, alphaVbeta5), was analyzed by fluorescent-activated cell sorter (FACS) and immunohistochemical staining. Thyroid tumor cell adhesion to ECM proteins and their IRM expression in response to thyrotropin (TSH) was assessed. Follicular TC cell lines presented high levels of integrins alpha2, alpha3, alpha5, beta1, beta3 and low levels of alpha1, whereas papillary lines expressed a heterogenous pattern of IRM, dominated by alpha5 and beta1. ATC mainly displayed integrins alpha2, alpha3, alpha5, alpha6, beta1 and low levels of alpha1, alpha4 and alphaV. Integrin heterodimers correlated with monomer expression. Evaluation of TCS largely confirmed these results with few exceptions, namely alpha4, alpha6, and beta3. The ability of TC cell lines to adhere to purified ECM proteins correlated with IRM expression. TSH induced TC cell adhesion in a dose-dependent fashion, despite an unchanged array of IRM expression or level of a particular IRM. Thyroid carcinoma cell lines of different histogenetic background display profoundly different patterns of IRM expression that appear to correlate with tumor aggressiveness. In vitro adhesion to ECM proteins and IRM expression concur. Finally, TSH-stimulated adhesion of thyroid tumor cell lines to ECM may not be associated with altered IRM expression.
Strand breakage of a (6–4) photoproduct-containing DNA at neutral pH and its repair by the ERCC1–XPF protein complex (2013)

The (6-4) photoproduct is one of the major UV-induced lesions in DNA. We previously showed that hydrolytic ring opening of the 5' base and subsequent hydrolysis of the glycosidic bond of the 3' component occurred when this photoproduct was treated with aqueous NaOH. In this study, we found that another product was obtained when the (6-4) photoproduct was heated at 90 °C for 6 h, in a 0.1 M solution of N,N'-dimethyl-1,2-ethanediamine adjusted to pH 7.4 with acetic acid. An analysis of the chemical structure of this product revealed that the 5' base was intact, whereas the glycosidic bond at the 3' component was hydrolyzed in the same manner. The strand break was detected for a 30-mer oligonucleotide containing the (6-4) photoproduct upon treatment with the above solution or other pH 7.4 solutions containing biogenic amines, such as spermidine and spermine. In the case of spermidine, the rate constant was calculated to be 1.4 × 10(-8) s(-1) at 37 °C. The strand break occurred even when the oligonucleotide was heated at 90 °C in 0.1 M sodium phosphate (pH 7.0), although this treatment produced several types of 5' fragments. The Dewar valence isomer was inert to this reaction. The product obtained from the (6-4) photoproduct-containing 30-mer was used to investigate the enzymatic processing of the 3' end bearing the damaged base and a phosphate. The ERCC1-XPF complex removed several nucleotides containing the damaged base, in the presence of replication protein A.
3,3′-(Hexane-1,6-diyl)bis(1-vinyl-4-imidazoline-2-thione) (2017)

The title compound, C 16 H 22 N 4 S 2 , was obtained by the reaction of sulfur with the corresponding quaternary salt in the presence of K 2 CO 3 . It crystallizes with two half-molecules in the asymmetric unit; the complete molecules are generated by inversion symmetry with the central CH 2 —CH 2 bonds of the hexane bridges being located on inversion centres. In each molecule, the C 6 -alkyl chain adopts a typical antiperiplanar conformation and the two heterocyclic rings are oriented antiparallel to each other. In the crystal, molecules are linked by C—H...π interactions, forming layers lying parallel to the ac plane.
Structure of Alkanoic Acid Stabilized Magnetic Fluids. A Small-Angle Neutron and Light Scattering Analysis (2000)

Small-angle neutron scattering and dynamic and static light scattering measurements were used to probe the structures of aqueous and organic-solvent-based magnetic fluids comprising dispersed magnetite nanoparticles (∼10 nm in diameter) stabilized against flocculation by adsorbed alkanoic acid layers. A core−shell model fitted to a set of neutron scattering spectra obtained from contrast variation experiments allowed the determination of the iron oxide core size and size distribution, the thicknesses of the surfactant shells, and the spatial arrangement of the individual particles. The magnetic colloidal particles appear to form compact fractal clusters with a fractal dimension of 2.52 and a correlation length of ∼350 Å in aqueous magnetic fluids, consistent with the structures of clusters observed directly using cryo-TEM (transmission electron microscopy), whereas chainlike clusters with a fractal dimension of 1.22 and a correlation length of ∼400 Å were found for organic-solvent-based magnetic fluids. The differences in cluster structure were attributed to the relative strengths of the particle−particle interaction energies. Weak interactions in the organic-solvent-based systems dictate the formation of small structures for which the apparent fractal dimensions are naturally small, whereas significantly stronger interparticle interactions in aqueous magnetic fluids result in larger, more compact clusters with higher fractal dimensions. The growth of the aqueous clusters beyond a certain size was inhibited by an increasingly high energy barrier (balance between repulsive electrostatic and attractive van der Waals interactions) with increasing cluster size. The aqueous clusters were stable against further growth when diluted with a surfactant solution but grew in time when diluted with pure water. In the latter case, the loss of part of the stabilizing secondary surfactant layer to the aqueous phase to satisfy thermodynamic partitioning constraints led to a destabilization in its dispersion. Light scattering studies indicated a change in the fractal dimension from 2.52 to about 1.20 as the clusters grew.
Soft, smart contact lenses with integrations of wireless circuits, glucose sensors, and displays (2018)

Recent advances in wearable electronics combined with wireless communications are essential to the realization of medical applications through health monitoring technologies. For example, a smart contact lens, which is capable of monitoring the physiological information of the eye and tear fluid, could provide real-time, noninvasive medical diagnostics. However, previous reports concerning the smart contact lens have indicated that opaque and brittle components have been used to enable the operation of the electronic device, and this could block the user's vision and potentially damage the eye. In addition, the use of expensive and bulky equipment to measure signals from the contact lens sensors could interfere with the user's external activities. Thus, we report an unconventional approach for the fabrication of a soft, smart contact lens in which glucose sensors, wireless power transfer circuits, and display pixels to visualize sensing signals in real time are fully integrated using transparent and stretchable nanostructures. The integration of this display into the smart lens eliminates the need for additional, bulky measurement equipment. This soft, smart contact lens can be transparent, providing a clear view by matching the refractive indices of its locally patterned areas. The resulting soft, smart contact lens provides real-time, wireless operation, and there are in vivo tests to monitor the glucose concentration in tears (suitable for determining the fasting glucose level in the tears of diabetic patients) and, simultaneously, to provide sensing results through the contact lens display.
A Simple Torch Design for a Microwave-Induced Plasma (1988)

This paper describes a simple torch design for use with a microwave-induced plasma (MIP). The torch is constructed from commonly available components with an absolute minimum of machining. The basic torch may be constructed with the use of only hand tools and a drill press. The design is adaptable to a variety of configurations, including a tangential flow torch.
Settlement, Growth, and Survival of Eastern Oysters on Alternative Reef Substrates (2015)

Restoration of the native eastern oyster (Crassostrea virginica) has been severely hindered by the dwindling supply and rising costs of fossil and new oyster shell (OS) for use in reef restoration. Consequently, emphasis has shifted to the use of alternative oyster reef materials, which need to be tested for their effectiveness as settlement substrate. Furthermore, low recruitment of wild larvae has also impeded restoration, indicating a need to assess the potential of field setting of cultured larvae. We experimentally examined oyster settlement, growth and survival on unconsolidated OS, vertically embedded oyster shell (ES) in concrete, and concrete Oyster Castles (OC) in field and mesocosm experiments. In addition, we examined settlement success of cultured larvae in the mesocosm experiment. In the field experiment, juvenile recruitment was 3× higher on castles and unconsolidated shell than on embedded shell. Castles retained 4× the number of oysters and hosted 5× the biomass than embedded shell, and retained 1.5× the oysters and hosted 3× the biomass than unconsolidated shell. The proportion of live oyster recruits on castles was 1.5× that on both embedded and unconsolidated shell. In the mesocosm experiment (90-d postlarval deployment), the castles recruited, retained, and hosted an oyster biomass 4× higher than that of unconsolidated and embedded shell. This study confirms that artificial reef materials, such as OC, are suitable alternative substrates for oyster restoration, and remote setting of larvae can be effective under controlled environmental conditions. Future restoration efforts should consider use of alternative reef substrates and field setting of larvae, where recruitment is limited, to maximize oyster recruitment, while simultaneously minimizing the cost of reef restoration.
Studies of the electronic properties of the tetrathiotungstate(VI) ion, [WS4]2–, by low-temperature absorption and resonance Raman spectroscopy (1983)

The resonance Raman spectrum of the [WS4]2– ion as its [NH4]+ and [NBu4]+ salts has been studied over the range 647.1–350.7 nm. On the basis of the observed ν1(a1) band progressions, values for the harmonic wavenumber (ω1) and anharmonicity constant (x11) are calculated and the bandwidths are discussed in terms of contemporary theories. Computer simulation of the observed excitation profiles of the ν1, 2ν1, and 3ν1, bands in the case of the [NBu4]+ salt allows the deduction that, on excitation from the ground (1A1) to resonant excited (1T2) states, the W–S bond length increases by 0.058 Å.
Surfactant protein D (SP-D) counteracts the inhibitory effect of surfactant protein A (SP-A) on phospholipid secretion by alveolar type II cells. Interaction of native SP-D with SP-A (1991)

The surfactant proteins SP-A and SP-D were obtained from rats given intratracheal instillation of silica. SP-D was isolated from the 33,000 g supernatant of rat bronchoalveolar lavage fluids, and we examined whether SP-D affects surfactant secretion by alveolar type II cells. Native SP-D affected neither basal secretion nor stimulated secretion by type II cells. However, native SP-D counteracted the inhibitory effect of SP-A on surfactant secretion in a concentration-dependent manner; however, SP-D failed to counteract the inhibitory effect of concanavalin A. The activity of SP-D was unaffected by inclusion of excess methyl alpha-mannoside. Excess native SP-D competed with 125I-SP-A for high-affinity binding to type II cells. Heat treatment of SP-D and antibody against SP-D both decreased SP-D activity. Butanol extraction of native SP-D was most effective at destroying SP-D activity and attenuated the ability of the protein to compete with labelled SP-A for binding to type II cells. The butanol-soluble fraction of SP-D possessed the ability to alter the inhibitory effect of SP-A to the same extent as native SP-D. Direct binding of 125I-SP-A on nitrocellulose sheets demonstrated that SP-A could bind native SP-D, but not butanol-extracted SP-D. We conclude that native SP-D alters SP-A activity in type II cells through interaction with it via SP-D-associated lipids.
Quantitative Studies and Taste Re-engineering Experiments toward the Decoding of the Nonvolatile Sensometabolome of Gouda Cheese (2008)

The first comprehensive quantitative determination of 49 putative taste-active metabolites and mineral salts in 4- and 44-week-ripened Gouda cheese, respectively, has been performed; the ranking of these compounds in their sensory impact based on dose-over-threshold (DoT) factors, followed by the confirmation of their sensory relevance by taste reconstruction and omission experiments enabled the decoding of the nonvolatile sensometabolome of Gouda cheese. The bitterness of the cheese matured for 44 weeks was found to be induced by CaCl2 and MgCl2, as well as various bitter-tasting free amino acids, whereas bitter peptides were found to influence more the bitterness quality rather than the bitter intensity of the cheese. The DoT factors determined for the individual bitter peptides gave strong evidence that their sensory contribution is mainly due to the decapeptide YPFPGPIHNS and the nonapeptides YPFPGPIPN and YPFPGPIHN, assigned to the casein sequences beta-CN(60-69) and beta-CN(60-68), respectively, as well as the tetrapeptide LPQE released from alphas1-CN(11-14). Lactic acid and hydrogen phosphate were identified to play the key role for the sourness of Gouda cheese, whereas umami taste was found to be due to monosodium L-glutamate and sodium lactate. Moreover, saltiness was induced by sodium chloride and sodium phosphate and was demonstrated to be significantly enhanced by L-arginine.