gebhart/patrepeval huggingface dataset:
<title>Image formation in near-field infrared microscopy</title> (2000)

In this paper we discuss the mechanisms of image formation in the mid-IR of a transmission mode near-field microscope are studied. It is found that the amount of light propagating from a sub-wavelength aperture through a flat substrate strongly increases the tip nears the same. This effect tends to generate topographic artifacts in near-field images that can be eliminated through the use of flat sample preparation techniques. The transmitted power is strongly influenced by the refractive index of the sample, leading to a substantial difference between a near-field and a far- field spectrum. A phenomenological model, which makes predictions in good agreement with experiment, describing tunneling of light through a sub-wavelength aperture into a substrate is developed. The model predicts spectral sensitivity enhancement with decreasing aperture size.
20(S)‐protopanaxadiol‐aglycone downregulation of the full‐length and splice variants of androgen receptor (2012)

As a public health problem, prostate cancer engenders huge economic and life-quality burden. Developing effective chemopreventive regimens to alleviate the burden remains a major challenge. Androgen signaling is vital to the development and progression of prostate cancer. Targeting androgen signaling via blocking the production of the potent ligand dihydrotestosterone has been shown to decrease prostate cancer incidence. However, the potential of increasing the incidence of high-grade prostate cancers has been a concern. Mechanisms of disease progression after the intervention may include increased expression of androgen receptor (AR) in prostate tissue and expression of the constitutively active AR splice variants (AR-Vs) lacking the ligand-binding domain. Thus, novel agents targeting the receptor, preferentially both the full-length and AR-Vs, are urgently needed. In the present study, we show that ginsenoside 20(S)-protopanaxadiol-aglycone (PPD) effectively downregulates the expression and activity of both the full-length AR and AR-Vs. The effects of PPD on AR and AR-Vs are manifested by an immediate drop in proteins followed by a reduction in transcripts, attributed to PPD induction of proteasome-mediated degradation and inhibition of the transcription of the AR gene. We further show that although PPD inhibits the growth as well as AR expression and activity in LNCaP xenograft tumors, the morphology and AR expression in normal prostates are not affected. This study is the first to show that PPD suppresses androgen signaling through downregulating both the full-length AR and AR-Vs, and provides strong rationale for further developing PPD as a promising agent for the prevention and/or treatment of prostate cancer.
Probing the interaction of the biotin–avidin complex with the relaxivity of biotinylated Gd-DTPA (2004)

A biotinylated Gd-DTPA complex is designed to study the biotin-avidin complexation using the longitudinal relaxivity of this new MRI label, which illustrates the use of MRI contrast agents to probe the formation of supramolecular assemblies in water.
Splice Variants of Superoxide Dismutases in Rice and Their Expression Profiles under Abiotic Stresses (2021)

The superoxide dismutases (SODs) play vital roles in controlling cellular reactive oxygen species (ROS) that are generated both under optimal as well as stress conditions in plants. The rice genome harbors seven SOD genes (CSD1, CSD2, CSD3, CSD4, FSD1, FSD2, and MSD) that encode seven constitutive transcripts. Of these, five (CSD2, CSD3, CSD4, FSD1, and MSD) utilizes an alternative splicing (AS) strategy and generate seven additional splice variants (SVs) or mRNA variants, i.e., three for CSD3, and one each for CSD2, CSD4, FSD1, and MSD. The exon-intron organization of these SVs revealed variations in the number and length of exons and/or untranslated regions (UTRs). We determined the expression patterns of SVs along with their constitutive forms of SODs in rice seedlings exposed to salt, osmotic, cold, heavy metal (Cu+2) stresses, as well as copper-deprivation. The results revealed that all seven SVs were transcriptionally active in both roots and shoots. When compared to their corresponding constitutive transcripts, the profiles of five SVs were almost similar, while two specific SVs (CSD3-SV4 and MSD-SV2) differed significantly, and the differences were also apparent between shoots and roots suggesting that the specific SVs are likely to play important roles in a tissue-specific and stress-specific manner. Overall, the present study has provided a comprehensive analysis of the SVs of SODs and their responses to stress conditions in shoots and roots of rice seedlings.
Thermodynamic Stability of the P4−P6 Domain RNA Tertiary Structure Measured by Temperature Gradient Gel Electrophoresis (1998)

The P4-P6 domain RNA from the Tetrahymena self-splicing group I intron is an independent unit of tertiary structure that, in the kinetic folding pathway, folds before the rest of the intron and then stabilizes the remainder of the intron's tertiary structure. We have employed temperature gradient gel electrophoresis (TGGE) to examine the unfolding of the tertiary structure of P4-P6. In 0.9 mM Mg2+, the global tertiary fold of the molecule has a melting temperature of approximately 40 degreesC and is completely unfolded by 60 degreesC. Calculated thermodynamic parameters for folding of P4-P6 are DeltaH degrees' = -28 +/- 3 kcal/mol and DeltaS degrees' = -91 +/- 8 eu under these conditions. Chemical probing of the P4-P6 tertiary structure using dimethyl sulfate and CMCT confirms that these TGGE experiments monitor the unfolding of the global tertiary fold of the domain and that the secondary structure is largely unaffected over this temperature range. Thus, unlike the entropically driven P1 docking and guanosine binding steps of Tetrahymenagroup I intron self-splicing, which have positive or zero DeltaH terms, P4-P6 tertiary structure formation is stabilized by a negative DeltaH term. This implies that enthalpically favorable hydrogen bond formation, nucleotide base stacking, and/or binding of Mg2+ within the folded structure are responsible for stabilizing the P4-P6 domain.
Heat Transfer and Friction Factors for Flows Inside Circular Tubes With Concavity Surfaces (2003)

Heat transfer and friction coefficients measurements have been obtained for fully developed, turbulent internal flows in circular tubes with six different concavity (dimple) surface array geometries. Two different concavity depths and three different concavity array densities were tested using tube bulk flow Reynolds numbers from 20,000 to 90,000. Liquid-crystal thermography was used to measure the temperature distributions on the outside of the concavity tubes. Using the average heat transfer coefficient for the fully developed region, the overall heat transfer enhancements are compared to baseline smooth tube results. Friction coefficients are also compared to values for a smooth tube. Dimple depths of 0.2–0.4 relative to the dimple surface diameter were used, with surface area densities ranging from 0.3 to 0.7. Dimple arrays were all in-line geometries. The results showed that heat transfer enhancements for dimpled internal surfaces of circular passages can reach factors of 2 or more when the relative dimple depth is greater than 0.3 and the dimple array density is about 0.5 or higher. The associated friction factor multipliers for such configurations are in the range of 4–6. The present study provides a first insight into the heat transfer and friction effects of various concavity arrays for turbulent flows.
Redesign of the Coils for the 60T Controlled-Waveform Magnet at NHMFL (2022)

Driven by the1.4 GW generator, the 60T Controlled Waveform (60 TCW) magnet was the most powerful controlled waveform system in the world and had always been one of most important magnets to the National High Magnetic Field (NHMFL) and high-field research community because of its following unique features: (1) quasi-static field up to 60 T with 100 ms flat-top and total pulse-length of about 2000 ms, (2) variable magnetic field waveforms such as staircase and triangle with flat-top (3) relative large bore (32 mm) and (4) very fast cooling time (20 minutes) between pulses [Boebinger, 2001], [Crooker <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">et al.</i> 2001]. The magnet is composed of nine concentric coils, with each coil consisting of several conductor winding layers reinforced by a high-strength metallic shell. The magnet underwent a catastrophic failure in 2000 and all the coils had to be rebuilt. In late 2014 the second magnet version failed near the mid-plane of coil 7. The simulations afterward that incident indicated that the overall strength of the coil would be increased by replacing a section of the reinforcing shell with Zylon fiber-epoxy composite. This reduces the stress and thus significantly lowers the level of plastic deformation in the windings. The role of the metal and Zylon fiber reinforcing layers in bearing the axial and radial Lorentz forces has been studied to optimize the magnet design. The results of the optimization will be discussed as well as challenges that have been presented in rebuilding the individual coils of the magnet.
Polymer-platform-dependent characteristics of 193-nm photoresists (1999)

The development and refinement of 193 nm single layer photoresist has continued to progress at a quick pace. Published resists efforts have historically been partitioned by polymer family: acrylic, addition cyclic olefin, and alternating cyclic olefin/maleic anhydride. The polymer platforms for 193 nm resists have been a radical departure from 248 nm resists, therefore, publications to date have largely focused on the attributes of each specific variety. Since the physical and chemical properties of the aforementioned polymer platforms are very different, it would follow that, in principal, typical formulation strategies should produce varying results in each platform. This paper investigates the effects of three typical photoacid generators and three model polymers on various aspects of lithographic evaluation.
Formation of low time-bandwidth product, single-sided exponential optical pulses in free-electron laser oscillators (2000)

The detailed shape of picosecond optical pulses from a free-electron laser (FEL) oscillator has been studied for various cavity detunings. For large values of the cavity detuning the optical pulse develops an exponential leading edge, with a time constant proportional to the applied cavity detuning and the quality factor of the resonator. This behavior has been observed at two separate FELs that have completely different resonator layouts and electron beam characteristics, and using different methods of optical pulse length measurement. The optical pulses have a full width at half maximum time-bandwidth product Deltat(FWHM)Deltaf(FWHM) of 0.2-0.3. The results presented here can be used to predict the optical pulse length and corresponding minimum spectral width that can be generated in a FEL pumped by short electron bunches. This is important for the design of new infrared free-electron laser user facilities, which need to make a balanced choice between short pulses for high temporal resolution and narrow bandwidth for linear and nonlinear spectroscopy.
Key Lessons from the ELECTRa Registry in the Modern Era of Transvenous Lead Extraction (2017)

The implantation rate of cardiac electronic devices has grown over the past decades. The number of treated patients has increased in parallel with the complexity of the patient population treated, being older, frailer, having more complex devices (in particular, cardiac resynchronisation therapy) and presenting with a greater comorbidity burden. As a consequence, there is a rising number of related implanted system complications, including malfunction and infection. Thus, the demand for transvenous lead extraction (TLE) has also substantially increased. To identify the indication to TLE by various operators and centres, techniques used to perform TLE, and the safety and efficacy of the current clinical practice of TLE, a large prospective registry has been started in Europe - the European Lead Extraction Controlled (ELECTRa) Registry. The key findings of the ELECTRa Registry are discussed in the present review and placed in the context of previous knowledge. The ELECTRa Registry confirms that the TLE procedure is a safe and effective treatment, with an acceptable risk-benefit ratio that is comparable with other well-known cardiological invasive procedures. Of course, TLE is accompanied by potential life-threatening complications; the vast majority of these can be managed by an experienced multidisciplinary team. Multiple factors predict complications, including patient/lead profile, centre experience and procedure volumes, which may suggest caution when accepting a patient for TLE.
Characterization of SPINK1 in Prostate Cancer (2009)

Abstract : In cancer, specific growth and invasion-promoting proteins are abnormally over-expressed compared to normal cells and these proteins are often the target of therapies designed to inactivate them. The computational methods developed by our lab was used to identify highly over-expressed genes specifically in cancer cells, a method that was instrumental in identifying the first gene fusion in the majority of prostate cancer, TMPRSS-ETS. Utilizing the same method, the gene SPINK1 was later identified as highly over-expressed in prostate cancer, specifically in prostate cancer patients that were negative for the TMPRSS-ETS gene fusions. An antibody that targets the SPINK1 protein was tested in pre-clinical models for its potential as effective therapy to treat TMPRSS-ETS-negative prostate cancer. Here, an antibody against the SPINK1 protein was used to examine its effects on various prostate cancer cell lines. The anti-SPINK1 antibody was able to inhibit the growth of cells that over-expressed SPINK1 but had no effect on cells that harbored other aberrations. Importantly, the anti-SPINK1 antibody also significantly halted the tumor growth in mice that were implanted with SPINK1 over-expressing tumors. These results suggest that a sub-set of TMPRSS-ETS negative prostate cancer patients that over-express SPINK1 can potentially be successfully treated with anti-SPINK1 antibody.
Simple Scheme for Deriving Atomic Force Constants: Application to SiC (1982)

A scheme is presented for deriving atomic force constants that is fairly accurate, yet simple enough to allow determination of the dynamical matrix of bulk solids, relaxed and reconstructed surfaces, defects, etc. For illustrative purposes, the method is applied to bulk SiC to predict the phonon dispersion curves throughout the entire Brillouin zone, and to a carbon vacancy in SiC to study the change of atomic force constants due to atomic relaxations.
The Sixth Annual Translational Stem Cell Research Conference of the New York Stem Cell Foundation (2012)

The New York Stem Cell Foundation's "Sixth Annual Translational Stem Cell Research Conference" convened on October 11-12, 2011 at the Rockefeller University in New York City. Over 450 scientists, patient advocates, and stem cell research supporters from 14 countries registered for the conference. In addition to poster and platform presentations, the conference featured panels entitled "Road to the Clinic" and "The Future of Regenerative Medicine."
Influence of deuterium-induced volume changes on optical transmission in Fe/V (001) and Cr/V (001) superlattices (2022)

The deuterium-induced changes of the optical transmission in Fe/V (001) and Cr/V (001) superlattices are found experimentally to be dominated by the volume changes of the vanadium layers and thus indirectly linked to concentration. The deuterium-induced expansion is 67% larger in Cr/V 2/14 monolayers (ML) as compared to Fe/V 2/14 ML. This large difference can be explained by a difference in the site of deuterium from tetrahedral in Fe/V to octahedral in Cr/V. First-principles calculations based on this assumption give quantitative agreement with both the measured optical transmission and the deuterium-induced expansion coefficient. Placing hydrogen in the middle of the vanadium layers results in total energies at 0 K that favor tetrahedral occupancy at low concentrations, although the energy difference is of the order of the thermal energy available in the experiments. Hence small changes in strain, defect concentration, and/or vibrational spectrum of the superlattices may tip the balance to octahedral occupancy at low concentrations. Given this link to concentration and the linear scaling, optical transmission can, therefore, be used in a straightforward way to obtain pressure-composition isotherms also in thin metal films that do not undergo metal-insulator transitions upon hydrogenation.
Towards low-profile transmitarrays: Multi-objective tradeoffs of inhomogeneous and anisotropic near-field transforming lenses (2017)

Transmitarray antenna performance is limited by the amplitude and phase uniformity of the illumination source. Horns are a common feed-source for transmitarrays, but require large separation distances in order to provide uniform illumination, thus, limiting the ability to realize low-profile horn-fed transmitarray systems. In order to overcome this challenge, transformation optics inspired lenses can be introduced to redistribute the horn's near field and provide uniform phase and magnitude illumination on the transmitarray within a compact space.
Posynomial models of inductors for optimization of power electronic systems by geometric programming (2016)

When optimizing power electronic converters for multiple objectives, such as power density and efficiency, the optimization of the magnetic components is often the most challenging and time-consuming task. In order to perform optimization quickly and efficiently, it would be advantageous to formulate converter optimization as a geometric program, a proven convex optimization method. In order to optimize for losses and volume via a geometric program however, all loss and volume models of the various components must be in the form of posynomials. While some loss models, such as those of semiconductors, are naturally in posynomial form or easily transformed, this is not the case for inductors. This paper presents a derivation of posynomial loss, volume, temperature, and saturation models for families of inductive components, based both on simulation and on adapting familiar analytical models into approximate posynomial form. The terms of the derived posynomial models are the inductor design variables, such as the number of turns, the air gap, and so forth. This allows inductors to be optimized for multiple design objectives as a geometric program.
Loss of DNA methylation affects the recombination landscape in Arabidopsis (2012)

During sexual reproduction, one-half of the genetic material is deposited in gametes, and a complete set of chromosomes is restored upon fertilization. Reduction of the genetic information before gametogenesis occurs in meiosis, when cross-overs (COs) between homologous chromosomes secure an exchange of their genetic information. COs are not evenly distributed along chromosomes and are suppressed in chromosomal regions encompassing compact, hypermethylated centromeric and pericentromeric DNA. Therefore, it was postulated that DNA hypermethylation is inhibitory to COs. Here, when analyzing meiotic recombination in mutant plants with hypomethylated DNA, we observed unexpected and counterintuitive effects of DNA methylation losses on CO distribution. Recombination was further promoted in the hypomethylated chromosome arms while it was inhibited in heterochromatic regions encompassing pericentromeric DNA. Importantly, the total number of COs was not affected, implying that loss of DNA methylation led to a global redistribution of COs along chromosomes. To determine by which mechanisms altered levels of DNA methylation influence recombination--whether directly in cis or indirectly in trans by changing expression of genes encoding recombination components--we analyzed CO distribution in wild-type lines with randomly scattered and well-mapped hypomethylated chromosomal segments. The results of these experiments, supported by expression profiling data, suggest that DNA methylation affects meiotic recombination in cis. Because DNA methylation exhibits significant variation even within a single species, our results imply that it may influence the evolution of plant genomes through the control of meiotic recombination.
Bufalin sensitizes human bladder carcinoma cells to TRAIL-mediated apoptosis (2017)

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), a member of the TNF superfamily, has garnered interest as it is relatively non-toxic to normal cells, but selectively induces apoptotic cell death in multiple types of transformed or malignant cells. Bufalin is the major digoxin-like immunoreactive component of Sum Su, which is obtained from the skin and parotid venom gland of the toad. Bufalin is known to inhibit cell proliferation and induce apoptosis in a variety of cancer cells. The present study investigated whether bufalin promoted TRAIL-induced apoptotic cell death. In the present study, a combined treatment using bufalin and TRAIL significantly increased TRAIL-mediated inhibition of cell viability and increased apoptosis in T24 human bladder cancer cells. The apoptotic effects were associated with the upregulation of death receptor proteins and the downregulation of cellular Fas-associated death domain-like interleukin-1β-converting enzyme inhibitory protein and X-linked inhibitor of apoptosis protein. Furthermore, the data revealed that bufalin and TRAIL activated caspase-3, -8 and -9 and subsequently increased the degradation of poly (ADP-ribose) polymerase. Taken altogether, the nontoxic doses of bufalin and TRAIL sensitized T24 cells to TRAIL-mediated apoptosis. Therefore, bufalin may provide an effective therapeutic strategy for the safe treatment of human bladder cancers that are resistant to TRAIL.
Proceedings of the Seventh Annual Deep Brain Stimulation Think Tank: Advances in Neurophysiology, Adaptive DBS, Virtual Reality, Neuroethics and Technology (2020)

The Seventh Annual Deep Brain Stimulation (DBS) Think Tank held on September 8th of 2019 addressed the most current: (1) use and utility of complex neurophysiological signals for development of adaptive neurostimulation to improve clinical outcomes; (2) Advancements in recent neuromodulation techniques to treat neuropsychiatric disorders; (3) New developments in optogenetics and DBS; (4) The use of augmented Virtual reality (VR) and neuromodulation; (5) commercially available technologies; and (6) ethical issues arising in and from research and use of DBS. These advances serve as both "markers of progress" and challenges and opportunities for ongoing address, engagement, and deliberation as we move to improve the functional capabilities and translational value of DBS. It is in this light that these proceedings are presented to inform the field and initiate ongoing discourse. As consistent with the intent, and spirit of this, and prior DBS Think Tanks, the overarching goal is to continue to develop multidisciplinary collaborations to rapidly advance the field and ultimately improve patient outcomes.