gebhart/patrepeval huggingface dataset:
Examination of the Premelting Transition of DNA A-Tracts Using a Fluorescent Adenosine Analogue (2006)

The fluorescent adenosine analogue 4-amino-8-(2-deoxy-beta-d-ribofuranosyl)-5'-O-dimethoxytrityl-6-methyl-7(8H)-pteridone (6MAP) has been used to perform residue specific analyses of DNA A-tracts during the premelting transition. DNA A-tracts, which exhibit sequence-induced curvature, adopt a B-DNA conformation as a function of increasing temperature. Fluorescence melting curves indicate that 6MAP is a more sensitive reporter of the premelting transition than UV absorption spectroscopy. Further, residue specific fluorescence analyses of A-tract and control duplexes reveal that some of the conformational changes associated with the premelting transition occur within A-tract regions. Analyses of the energetics of the premelting transition indicate that ApA steps make a larger enthalpic contribution to the premelting transition than ApT steps. To explore the effect of cations on the premelting transition, fluorescence melts were performed in the presence of NH(4)(+), Mg(2+), and low (0.05 M) and high (0.5 M) concentrations of Na(+). These studies show that the fluorescence intensity changes associated with the premelting transition are sensitive to cation type and concentration and are larger and more pronounced in the presence of 0.5 M Na(+), NH(4)(+), and Mg(2+). Incorporation of 6MAP into longer duplexes containing phased A-tracts shows that the local environment of adenosines in phased A-tracts is similar to that of individual A-tracts. Fluorescence quenching results indicate that ApA and ApT steps within A-tracts are less solvent exposed than their counterparts in control sequence isomers, possibly because of the narrowed minor groove of A-tract sequences.
Nanopatterning of diblock copolymer directed self-assembly lithography with wet development (2012)

A method for using wet development in a directed self-assembly lithography (DSAL) application is reported. For the typical diblock copolymer poly(styrene-block-methyl methacrylate) (PS-b-PMMA), the PMMA area is removed by an oxygen plasma. However, the oxygen plasma has poor selectivity for the PS portion of the block polymer and etches it simultaneously. As a result, the thickness of the residual PS pattern is thinner than desired and creates a challenge for subsequent pattern transfer. A wet development technique is discussed which offers higher selectivity between the PMMA and PS blocks in the assembled pattern. Specifically, a method using a low pressure mercury lamp and conventional tetramethylammonium hydroxide (TMAH, 2.38%) developer is proposed. Using this method, DSA pattern formation is completed in a single track having coating, baking, exposure, and development modules.
ChemInform Abstract: A Novel Nucleoside Phosphoramidite Synthon Derived from (1R,2S)‐ Ephedrine. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Magnetic properties of amorphous Fe93Zr7 films: Effect of light ion implantation (2015)

The Curie temperature (Tc) of amorphous FeZr alloys can be greatly enhanced by doping with light elements. In this investigation, ion implantation is used to dope Fe93Zr7 thin films with H, He, B, C, and N. Extended X-ray absorption fine structure measurements confirm that the amorphous structure is preserved upon implantation for all samples, except for the N-implanted sample which is partially crystallized. The Curie temperature increases from 124 K for the pristine FeZr sample to about 400 K for the (FeZr)B0.11 sample. The increase of Tc is proportional to the increase in the average Fe-Fe distance, which allows us to conclude that the dominant cause of the Tc enhancement of amorphous Fe93Zr7 upon doping is a volume effect.
Two-photon excited fluorescence properties of glycation-associated collagen crosslinks that are correlated with tissue stiffness (Conference Presentation) (2019)

Collagen is a main constituent of the extracellular matrix, and its content, organization, and crosslinking status affect significantly tissue mechanical properties. Cells continuously sense their local mechanical environment via interactions that impact significantly cell fate and the development and progression of numerous diseases. Non-linear imaging, especially through the combined use of second harmonic generation (SHG) and two-photon excited fluorescence (TPEF), has the potential to provide detailed information regarding collagen organization, content, and crosslinking with sub-micron level resolution in a non-invasive and label-free manner. However, the crosslink fluorescence properties that are correlated with tissue stiffness aren’t well understood. Thus, we characterized the TPEF emission over 680 to 920 nm excitation and 400 to 780 nm emission of three types of collagen gels: a) plain collagen gels, b) collagen gels with a 250 mM ribose solution for five days prior to gelation, and c) following gelation. Uniaxial tensile testing of gels created using the same protocols was performed by a custom-built testing system. We identified two components, which peak at 440 nm and 510 nm, that were significantly correlated with the exponential stiffening detected in collagen gels treated with ribose following gelation. Thus, TPEF information acquired at these emission ranges can be used in future studies and in combination with SHG measurements to develop detailed mathematical models that aim to predict tissue micromechanical properties. The latter will be useful in helping us to understand mechanosensitive cell behaviors that ultimately dictate the progress of diseases such as fibrosis and cancer.
A microfluidic method for dopamine uptake measurements in dopaminergic neurons (2016)

Dopamine (DA) is a classical neurotransmitter and dysfunction in its synaptic handling underlies many neurological disorders, including addiction, depression, and neurodegeneration. A key to understanding DA dysfunction is the accurate measurement of dopamine uptake by dopaminergic neurons. Current methods that allow for the analysis of dopamine uptake rely on standard multiwell-plate based ELISA, or on carbon-fibre microelectrodes used in in vivo recording techniques. The former suffers from challenges associated with automation and analyte degradation, while the latter has low throughput and is not ideal for laboratory screening. In response to these challenges, we introduce a digital microfluidic platform to evaluate dopamine homeostasis in in vitro neuron culture. The method features voltammetric dopamine sensors with limit of detection of 30 nM integrated with cell culture sites for multi-day neuron culture and differentiation. We demonstrate the utility of the new technique for DA uptake assays featuring in-line culture and analysis, with a determination of uptake of approximately ∼32 fmol in 10 min per virtual microwell (each containing ∼200 differentiated SH-SY5Y cells). We propose that future generations of this technique will be useful for drug discovery for neurodegenerative disease as well as for a wide range of applications that would benefit from integrated cell culture and electroanalysis.
Site- and Enantioselective Formation of Allene-Bearing Tertiary or Quaternary Carbon Stereogenic Centers through NHC–Cu-Catalyzed Allylic Substitution (2012)

Catalytic enantioselective allylic substitutions that result in addition of an allenyl group (<2% propargyl addition) and formation of tertiary or quaternary C-C bonds are described. Commercially available allenylboronic acid pinacol ester is used. Reactions are promoted by a 5.0-10 mol % loading of sulfonate-bearing chiral bidentate N-heterocyclic carbene (NHC) complexes of copper, which exhibit the unique ability to furnish chiral products arising from the S(N)2' mode of addition. Allenyl-containing products are generated in up to 95% yield, >98% S(N)2' selectivity, and 99:1 enantiomeric ratio (er). Site-selective NHC-Cu-catalyzed hydroboration of enantiomerically enriched allenes and conversion to the corresponding β-vinyl ketones demonstrates the method's utility.
Investigation of a UWB Wind Turbine Blade Deflection Sensing System With a Tip Antenna Inside a Blade (2016)

An ultra-wideband (UWB) blade deflection sensing system with a tip antenna inside a blade is investigated in this paper. The lower UWB band of 3.1-5.3 GHz is utilized. This system composes of two UWB radio links between one antenna inside the blade tip and two antennas outside the blade root. Blade deflections are tracked via two radio links using delay-based distance estimation and triangulation. In order to build reliable radio links, time-domain pulse field distributions are simulated to optimize the in-blade tip antenna polarization and the locations of the two root antennas around the root surface. Full-blade time-domain measurements are proposed to verify the simulations and realize the blade deflection sensing with an in-blade tip antenna. With the optimized in-blade tip antenna polarization and two root antenna locations, an accuracy of 2 cm is achieved for the tip-root antenna distance estimation, and the sensing system can realize the deflection tracking with a maximum deviation of 0.21 m and a root mean squared error of 0.11 m.
Coherent Electronic Compensation Techniques for Long-Haul Optical Fibre Transmission - Opportunities and Challenges (2009)

We review recent advances in the use coherent detection and digital signal processing to compensate for dispersion and nonlinearity in long-haul WDM links, and assess the use of these techniques for long-haul and subsea applications. © VDE VERLAG GMBH.
An MMI-Based 4-Beam Combiner with Spline-Curved Index Step (2015)

We propose a compact MMI-based 4-beam combiner with a spline-curved index step. The 1.74 mm-long device designed in InP material systems offers 3 dB better transmittance than power combiners at a 4.5 nm wavelength spacing.
Intramedullary Nailing of Metacarpal Shaft Fractures (2005)

Uncorrected bony deformity or stiffness resulting from a metacarpal shaft fracture can produce a significant functional or cosmetic deficit. Intramedullary fixation of metacarpal shaft fractures using small flexible rods can provide stable internal fixation while minimizing the extent of soft tissue trauma that is associated with more extensive surgical techniques such as plate or screw fixation. The flexible rod is usually introduced in a proximal to distal direction to avoid injury to the metacarpophalangeal joint and extensor mechanism. Closed reduction of the fracture and percutaneous insertion of the rod improve operative efficiency and allow what is truly a minimally invasive procedure. The use of a proximal locking pin greatly enhances fixation and has resulted in an expansion of the surgical indications to include spiral and comminuted fractures. Usually a single locked nail is used, although it is possible to insert multiple nails if necessary. A radiopaque plastic cap can be applied over the cut end of the nail to minimize irritation of the adjacent soft tissues during rehabilitation. Post-operatively, splint or cast immobilization is often unnecessary. The nails are routinely removed after the fracture has completely healed.
Analysis of cell surface proteins delineates a differentiation pathway linking endocrine and nonendocrine human lung cancers. (1983)

We have previously determined that the cell surface protein phenotype distinguishes human small cell lung carcinoma (SCC), a neoplasm with endocrine properties, from non-SCC in culture. We now demonstrate that cloned cell cultures of human large cell undifferentiated lung carcinoma, established directly from a patient with mixed SCC and non-SCC, simultaneously express surface proteins characteristic of SCC and non-SCC lung cancer cells. Hence, SCC and a form of large cell carcinoma appear linked through a continuum of differentiation events that: (i) may explain clinically important transitions that occur between the major types of human lung cancer and (ii) provide evidence for a common cellular origin of endocrine and nonendocrine cells in the bronchial mucosa.
Methods of forming electrode structures (2023)

An electrode structure and its method of manufacture are disclosed. The disclosed electrode structures may be manufactured by depositing a first release layer on a first carrier substrate. A first protective layer may be deposited on a surface of the first release layer and a first electroactive material layer may then be deposited on the first protective layer. Subsequently, the first carrier substrate may be delaminated from the first release layer. The first release layer may then be removed from the first protective layer by dissolution in an electrolyte. The first protective layer may have a low mean peak to valley surface roughness and/or may be thin. In some embodiments, an interface between the first protective layer and the first electroactive material layer has a low mean peak to valley surface roughness. In some embodiments, a thickness of the first protective layer is greater than a mean peak to valley roughness of the first release layer. In some embodiments, an adhesive strength between the first release layer and the first protective layer is greater than an adhesive strength between the first release layer and the first carrier substrate.
Developmental synaptic regulator, TWEAK/Fn14 signaling, is a determinant of synaptic function in models of stroke and neurodegeneration (2021)

Identifying molecular mediators of neural circuit development and/or function that contribute to circuit dysfunction when aberrantly reengaged in neurological disorders is of high importance. The role of the TWEAK/Fn14 pathway, which was recently reported to be a microglial/neuronal axis mediating synaptic refinement in experience-dependent visual development, has not been explored in synaptic function within the mature central nervous system. By combining electrophysiological and phosphoproteomic approaches, we show that TWEAK acutely dampens basal synaptic transmission and plasticity through neuronal Fn14 and impacts the phosphorylation state of pre- and postsynaptic proteins in adult mouse hippocampal slices. Importantly, this is relevant in two models featuring synaptic deficits. Blocking TWEAK/Fn14 signaling augments synaptic function in hippocampal slices from amyloid-beta-overexpressing mice. After stroke, genetic or pharmacological inhibition of TWEAK/Fn14 signaling augments basal synaptic transmission and normalizes plasticity. Our data support a glial/neuronal axis that critically modifies synaptic physiology and pathophysiology in different contexts in the mature brain and may be a therapeutic target for improving neurophysiological outcomes.
Acid-sensing ion channel 1a is a postsynaptic proton receptor that affects the density of dendritic spines (2006)

Extracellular proton concentrations in the brain may be an important signal for neuron function. Proton concentrations change both acutely when synaptic vesicles release their acidic contents into the synaptic cleft and chronically during ischemia and seizures. However, the brain receptors that detect protons and their physiologic importance remain uncertain. Using organotypic hippocampal slices and biolistic transfection, we found the acid-sensing ion channel 1a (ASIC1a), localized in dendritic spines where it functioned as a proton receptor. ASIC1a also affected the density of spines, the postsynaptic site of most excitatory synapses. Decreasing ASIC1a reduced the number of spines, whereas overexpressing ASIC1a had the opposite effect. Ca(2+)-mediated Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) signaling was probably responsible, because acid evoked an ASIC1a-dependent elevation of spine intracellular Ca(2+) concentration, and reducing or increasing ASIC1a levels caused parallel changes in CaMKII phosphorylation in vivo. Moreover, inhibiting CaMKII prevented ASIC1a from increasing spine density. These data indicate that ASIC1a functions as a postsynaptic proton receptor that influences intracellular Ca(2+) concentration and CaMKII phosphorylation and thereby the density of dendritic spines. The results provide insight into how protons influence brain function and how they may contribute to pathophysiology.
The Immunosuppressive Agent Mizoribine Monophosphate Forms a Transition State Analogue Complex with Inosine Monophosphate Dehydrogenase (2003)

Mizoribine monophosphate (MZP) is the active metabolite of the immunosuppressive agent mizoribine and a potent inhibitor of IMP dehydrogenase (IMPDH). This enzyme catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD via a covalent intermediate at Cys319 (E-XMP). Surprisingly, mutational analysis indicates that MZP is a transition state analogue although its structure does not resemble that of the expected transition state. Here we report the X-ray crystal structure of the E.MZP complex at 2.0 A resolution that reveals a transition state-like structure and solves the mechanistic puzzle of the IMPDH reaction. The protein assumes a new conformation where a flap folds into the NAD site and MZP, Cys319, and a water molecule are arranged in a geometry resembling the transition state. The water appears to be activated by interactions with a conserved Arg418-Tyr419 dyad. Mutagenesis experiments confirm that this new closed conformation is required for the hydrolysis of E-XMP, but not for the reduction of NAD. The closed conformation provides a structural explanation for the differences in drug selectivity and catalytic efficiency of IMPDH isozymes.
Computed Tomography in Color: NanoK‐Enhanced Spectral CT Molecular Imaging (2010)

Multicolored imaging: A new class of molecular imaging agent has been developed based on low-molecular-weight organically soluble bismuth to detect and quantify intraluminal fibrin presented by ruptured plaque in the context of computed tomography angiograms without calcium interference. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Fabrication Process for High-Density Wiring Interposer Using Photosensitive Multiblock Copolyimide Insulation Layers for 3D Packaging (2006)

We have developed a high-density wiring interposer for 10 Gbps signal propagation using a photosensitive polyimide. We optimized the basic properties of the photosensitive polyimide film and the lift-off process for the metal layer using an image-reversal-patterned negative photoresist for the fabrication of the interposer. We experimentally confirmed that the high-density wiring interposer could be fabricated using the polyimide and gold multilayered structure. Fine metal wiring was smoothly covered by the polyimide, as confirmed by scanning electron microscopy (SEM) of the cross section of the fabricated balance pair strip line structure.
Observation of a Resonance inB+→K+μ+μ−Decays at Low Recoil (2013)

A broad peaking structure is observed in the dimuon spectrum of B+ → K+ μ+ μ- decays in the kinematic region where the kaon has a low recoil against the dimuon system. The structure is consistent with interference between the B+ → K+ μ+ μ- decay and a resonance and has a statistical significance exceeding six standard deviations. The mean and width of the resonance are measured to be 4191(-8)(+9) MeV/c2 and 65(-16)(+22) MeV/c2, respectively, where the uncertainties include statistical and systematic contributions. These measurements are compatible with the properties of the ψ(4160) meson. First observations of both the decay B+ → ψ(4160)K+ and the subsequent decay ψ(4160) → μ+ μ- are reported. The resonant decay and the interference contribution make up 20% of the yield for dimuon masses above 3770 MeV/c2. This contribution is larger than theoretical estimates.
Comparison of the Effects of Glibenclamide on Metabolic Parameters, GLUT1 Expression, and Liver Injury in Rats With Severe and Mild Streptozotocin-Induced Diabetes Mellitus (2012)

The GLUT1 expression was found to be affected by the glucose and insulin levels and can be modulated by glibenclamide in severely and mildly diabetic rats. Glibenclamide can prevent the liver damage caused by severe hyperglycemia.
Abstract 1841: Stromal Cell Derived Factor-1 Increases Capillary Density But Does Not Contribute To Cardiomyocyte Replacement After Experimental Myocardial Infarction (2008)

Background. The mechanisms by which regenerative therapies improve cardiac function are incompletely defined. Numerous laboratories have demonstrated that the stem cell chemoattractant Stromal cell derived factor-1 (SDF-1) improves cardiac function after myocardial infarction (MI). This study used a genetic fate-mapping approach to ask the question: Is the beneficial effect of SDF-1 delivery due to cardiomyocyte regeneration, increased capillary density, or both? Methods. We used a genetic fate-mapping system that allows “pulse-chase” studies of cardiomyocyte turnover in mice. We crossed an inducible cardiomyocyte-specific Mer-Cre-Mer transgenic mouse with Z/EG reporter mice. Using a high-efficiency 4-OH-tamoxifen protocol, we then induced Cre recombination and expression of GFP in cardiomyocytes only. SDF-1(S4V), a protease-resistant form of SDF-1, was delivered with nanofibers after coronary ligation. Results. The percentage of pulse-labeled GFP+ cardiomyocytes was 81±4% (n=6) in sham-operated mice, as anticipated with this system. GFP+ cardiomyocytes were 60±5% and 69±4% (n=11) respectively at MI border and MI remote areas of the control nanofiber group, consistent with our previous study and suggesting a significant stem/precursor cell contribution to cardiomyocyte replacement after injury (P&lt;0.0001). GFP+ cardiomyocytes were 65±9% and 76±6% (n=10) respectively at MI border and MI remote areas of the SDF-1(S4V)-RAD group (p=ns vs nanofiber control group), indicating no significantly increase in cardiomyocyte refreshment attributable to SDF-1. However, capillary density increased from 204.7 ± 10.1/mm2 in the nanofiber control group to 308.9 ± 21.9/mm2 in SDF-1(S4V)-RAD + nanofiber group (p =0.0003). Conclusion. Using genetic “pulse-chase” fate mapping, these data indicate that the stem cell chemoattractant SDF-1 does not induce measurable adult mammalian cardiomyocyte replacement by stem/precursor cells following injury. However, SDF-1 significantly increases myocardial capillary density, suggesting that increased angiogenesis but not cardiogenesis is responsible for the beneficial effects of SDF-1 on cardiac function.
A dual-mode 802.11b/bluetooth radio in 0.35-/spl mu/m CMOS (2005)

A fully integrated dual-mode CMOS transceiver tuned to 2.4 GHz consumes 65 mA in receive mode and 78 mA in transmit mode from a 3-V supply. The radio includes all the receive and transmit building blocks, such as frequency synthesizer, voltage-controlled oscillator (VCO), and power amplifier, and is intended for use in 802.11b and Bluetooth applications. The Bluetooth receiver uses a low-IF architecture for higher level of integration and lower power consumption, while the 802.11b receiver is direct conversion. The receiver achieves a typical sensitivity of -88 dBm at 11 Mb/s for 802.11b, and -83 dBm for Bluetooth mode. The receiver minimum IIP3 is -8 dBm. Both transmitters use a direct-conversion architecture, and deliver a nominal output power of 0 dBm, with a power range of 20 dB in 2-dB steps.
Supplementary Figure 7 from Tumor-Promoting Desmoplasia Is Disrupted by Depleting FAP-Expressing Stromal Cells (2023)

&lt;p&gt;Identification of tumor stroma by FAP and SMA reveals stromal cell heterogeneity in human and murine PDA.&lt;/p&gt;