gebhart/patrepeval huggingface dataset:
3,5-Diarylisoxazoles: Individualized Three-Step Synthesis and Isomer Determination Using 13C NMR or Mass Spectroscopy (2006)

As a multistep synthetic project for the second-semester organic laboratory, the three-step synthesis and definitive characterization of a 3,5-diarylisoxazole via the chalcone and the chalcone dibromide is described. As each student prepares a differently substituted chalcone, and thus isoxazole, the project is individualized with regard to compound purification, characterization, and literature searches. To determine which isoxazole isomer was obtained from the synthesis, students compare their experimental 13C NMR data for C4 of the isoxazole to that predicted for each isomer. The predicted values are calculated using a formula that utilizes Hammett constants for estimating substituent NMR-shift effects on C4. Isomer determination can also be accomplished through interpretation of the fragmentation pattern observed in the mass spectrum.
Temperature Dependence of Sensitivity of 2DEG-Based Hall-Effect Sensors (2019)

The magnetic sensitivity of Hall-effect sensors made of InAlN/GaN and AlGaN/GaN heterostructures was measured between room temperature and 576°C. Both devices showed decreasing voltage-scaled magnetic sensitivity at high temperature, declining from 53 to 8.3 mV/V/T for the InAlN/GaN sample and from 89 to 8.5 mV/V/T for the AlGaN/GaN sample, corresponding to the decreasing electron mobility due to scattering effects at elevated temperatures. Alternatively, current-scaled sensitivities remained stable over the temperature range, only varying by 13.1% from the mean of 26.3 V/A/T and 10.5% from the mean of 60.2 V/A/T for the InAlN/GaN and AlGaN/GaN samples respectively. This is due to the minimal temperature dependence of the electron sheet density on the 2-dimensional electron gas (2DEG). Both devices showed consistency in their voltage- and current-scaled sensitivity over multiple temperature cycles as well as nearly full recovery when returned to room temperature after thermal cycling. Additionally, an AlGaN/GaN sample held at 576°C for 12 hours also showed nearly full recovery at room temperature, further suggesting that GaN-based Hall-effect sensors are a good candidate for use in high temperature applications.
Molecular dynamics evidence for nonthermal effects of electric fields on pectin methylesterase activity (2021)

Experimental studies relevant to the nonthermal effects of electric fields on biological systems are emerging. However, these effects are poorly understood at the molecular level. The present study investigates pectin methylesterase, a cell wall modifying enzyme in plants, exposed to various electric field strengths. Molecular dynamics (MD) of the enzyme were studied with and without (thermal-only) electric field applications. The measurements were interpreted on the basis of equivalent energy input to gain insights into the effect of electric field treatment time at a constant temperature (50 °C). Results reveal that electric fields exert nonthermal effects on both local and global protein structure. In 1 μs simulations, the results show significant (P ≤ 0.05) shrinkage of the catalytic domain and shortening of enzyme-water hydrogen bond lifetime by a 50 V cm-1 electric field. Unwinding of the helical segments, altered intra- and intermolecular hydrogen bond patterns, and increased hydration are also caused by the 50 V cm-1 electric field. This study serves to understand the electric field influence on the functional role of proteins.
Immunosuppression Decreases Inflammation and Increases AAV6-hSERCA2a-Mediated SERCA2a Expression (2012)

The calcium pump SERCA2a (sarcoplasmic reticulum calcium ATPase 2a), which plays a central role in cardiac contraction, shows decreased expression in heart failure (HF). Increasing SERCA2a expression in HF models improves cardiac function. We used direct cardiac delivery of adeno-associated virus encoding human SERCA2a (AAV6-hSERCA2a) in HF and normal canine models to study safety, efficacy, and the effects of immunosuppression. Tachycardic-paced dogs received left ventricle (LV) wall injection of AAV6-hSERCA2a or solvent. Pacing continued postinjection for 2 or 6 weeks, until euthanasia. Tissue/serum samples were analyzed for hSERCA2a expression (Western blot) and immune responses (histology and AAV6-neutralizing antibodies). Nonpaced dogs received AAV6-hSERCA2a and were analyzed at 12 weeks; a parallel cohort received AAV-hSERCA2a and immunosuppression. AAV-mediated cardiac expression of hSERCA2a peaked at 2 weeks and then declined (to ~50%; p<0.03, 6 vs. 2 weeks). LV end diastolic and end systolic diameters decreased in 6-week dogs treated with AAV6-hSERCA2a (p<0.05) whereas LV diameters increased in control dogs. Dogs receiving AAV6-hSERCA2a developed neutralizing antibodies (titer ≥1:120) and cardiac cellular infiltration. Immunosuppression dramatically reduced immune responses (reduced inflammation and neutralizing antibody titers <1:20), and maintained hSERCA2a expression. Thus cardiac injection of AAV6-hSERCA2a promotes local hSERCA2a expression and improves cardiac function. However, the hSERCA2a protein level is reduced by host immune responses. Immunosuppression alleviates immune responses and sustains transgene expression, and may be an important adjuvant for clinical gene therapy trials.
Intermolecular Alignment in Beta 2-Microglobulin Amyloid Fibrils (2010)

The deposition of amyloid-like fibrils, composed primarily of the 99-residue protein β2-microglobulin (β2m), is one of the characteristic symptoms of dialysis-related amyloidosis. Fibrils formed in vitro at low pH and low salt concentration share many properties with the disease related fibrils and have been extensively studied by a number of biochemical and biophysical methods. These fibrils contain a significant β-sheet core and have a complex cryoEM electron density profile. Here, we investigate the intrasheet arrangement of the fibrils by means of [superscript 15]N−[superscript 13]C MAS NMR correlation spectroscopy. We utilize a fibril sample grown from a 50:50 mixture of [superscript 15]N,[superscript 12]C- and [superscript 14]N,[superscript 13]C-labeled β2m monomers, the latter prepared using 2-[superscript 13]C glycerol as the carbon source. Together with the use of ZF-TEDOR mixing, this sample allowed us to observe intermolecular [superscript 15]N−[superscript 13]C backbone-to-backbone contacts with excellent resolution and good sensitivity. The results are consistent with a parallel, in-register arrangement of the protein subunits in the fibrils and suggest that a significant structural reorganization occurs from the native to the fibril state.
A novel recurrent network for signal processing (2002)

A new recurrent network is developed for the signal processing applications of spectral estimation, direction of arrival estimation, and pattern classification. For the development of the network, the above problems are posed as linear inverse problems with sparseness constraints. The results are provided to support the usefulness of the network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ettingshausen Effect around a Landau Level Filling Factorν=3Studied by Dynamic Nuclear Polarization (2007)

A spin current perpendicular to the electric current is investigated around a Landau level filling factor nu=3 in a GaAs/AlGaAs two-dimensional electron system. Measurements of dynamic nuclear polarization in the vicinity of the edge of a specially designed Hall bar sample indicate that the direction of the spin current with respect to the Hall electric field reverses its polarity at nu=3, where the dissipative current carried by holes in the spin up Landau level is replaced with that by electrons in the spin down Landau level.
Solid state synthesis of carbon-encapsulated iron carbide nanoparticles and their interaction with living cells (2014)

Superparamagnetic carbon-encapsulated iron carbide nanoparticles (NPs), Fe<sub>7</sub>C<sub>3</sub>@C, with unique properties, were produced from pure ferrocene by high pressure-high temperature synthesis. These NPs combine the merits of nanodiamonds and SPIONs but lack their shortcomings which limit their use for biomedical applications. Investigation of these NPs by X-ray diffraction, electron microscopy techniques, X-ray spectroscopic and magnetic measurement methods has demonstrated that this method of synthesis yields NPs with perfectly controllable physical properties. Using magnetic and subsequent fractional separation of magnetic NPs from residual carbon, the aqueous suspensions of Fe<sub>7</sub>C<sub>3</sub>@C NPs with an average particle size of ∼25 nm were prepared. The suspensions were used for in vitro studies of the interaction of Fe<sub>7</sub>C<sub>3</sub>@C NPs with cultured mammalian cells. The dynamics of interaction of the living cells with Fe<sub>7</sub>C<sub>3</sub>@C was studied by optical microscopy using time-lapse video recording and also by transmission electron microscopy. Using novel highly sensitive cytotoxicity tests based on the cell proliferation assay and long-term live cell observations it was shown that the internalization of Fe<sub>7</sub>C<sub>3</sub>@C NPs has no cytotoxic effect on cultured cells and does not interfere with the process of their mitotic division, a fundamental property that ensures the existence of living organisms. The influence of NPs on the proliferative activity of cultured cells was not detected as well. These results indicate that the carbon capsules of Fe<sub>7</sub>C<sub>3</sub>@C NPs are air-tight which could offer great opportunities for future use of these superparamagnetic NPs in biology and medicine.
Preparation and characterization of nanopigment‐poly(styrene‐co‐n‐butyl acrylate‐co‐methacrylic acid) composite particles by high speed homogenization‐assisted suspension polymerization (2008)

Abstract Composite particles of nanoblue pigment‐poly(styrene‐ co ‐ n ‐butyl acrylate‐ co ‐methacrylic acid) of controllable size were successfully prepared using high‐speed homogenization‐assisted suspension polymerization. This composite has potential application as a toner for high‐resolution printing. A nanosized hybrid blue pigment, with a monodispersed and uniform spherical shape, was employed for the production of composite particles. The effects of agitation speed, pigment concentration, and anionic surfactant concentration on the properties of the prepared composite particles were investigated. Agitation speed plays an important role in controlling particle size. The prepared composite particles have geometric mean diameters in the range of 4.4–7.4 μm with the geometric standard deviation ranging from 1.23 to 1.33. High‐speed homogenization during droplet formation is useful for a reduction in the size of the prepared composite particles. In addition, the appropriate surfactant concentration has a significant effect on the particles' morphology. However, the concentration of the nanopigment did not significantly change either particle morphology or particle size. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Discovery and Development of RSV604 (2011)

This chapter contains sections titled: Introduction Discovery Synthesis Preclinical Pharmacokinetic and Toxicology Phase I-III Safety and Efficacy Future Directions References
Modulation of macrophage-mediated tumoricidal activity by neuropeptides and neurohormones. (1985)

Recent evidence has suggested that stress may suppress the immune system and increase the frequency and severity of viral and neoplastic disease. The mechanisms for stress-induced modulation of immune function are unclear, but several neuropeptides are thought to be involved. Because macrophages play an important role in the host defense against infection and neoplasia, several stress-related neuropeptides were screened in efforts to determine whether these substances affect macrophage-mediated tumoricidal activity. Adrenocorticotropin and noradrenaline each completely blocked the capacity of mouse recombinant interferon-gamma (INF-gamma) to activate murine peritoneal macrophages to a tumoricidal state as measured by the lysis of 125I-UdR-labeled melanoma target cells. Vasoactive intestinal peptide significantly potentiated the suppressive effects of noradrenaline. In contrast, neurotensin markedly enhanced the cytolytic capability of peritoneal macrophages activated with INF-gamma. Several other neuropeptides, including substance P, alpha-endorphin, beta-endorphin, Leu-enkephalin, and Met-enkephalin, had no effect on macrophage activation. These findings demonstrate that selected stress-related neuropeptides and neurohormones significantly modulate the capacity of macrophages to attain a tumoricidal state and suggest that alteration of macrophage function by neuropeptides may be a prominent feature of stress-induced enhancement of neoplastic disease.
Effect of Surface Wettability on Frictional Conditions of PVA Roll Brushes (2013)

In order to gain insight into the mechanisms of polyvinyl acetal (PVA) roll brush cleaning in semiconductor device fabrication, we measure the coefficient of friction (COF) between the PVA brush and a substrate. In particular, we focus on the brush rotation speed and the surface wettability. The COF is found to decrease and approach 0.5 as the brush rotation speed increases. For the case of low rotation speeds, the COF of hydrophobic surfaces has a large value, almost 1.0, while that of hydrophilic surfaces is small. These results imply that the brush and the surface directly contact and the real contact area of the PVA brush increases over the duration of the contact time.
Filtered-X Least Mean Fourth (FXLMF) and Leaky FXLMF adaptive algorithms (2016)

Adaptive filtering algorithms promise an improvement of the active noise control (ANC) problem encountered in many scenarios. Just to name a few, the Filtered-X Least Mean Square (FXLMS) algorithm, the Leaky FXLMS (LFXLMS) algorithm, and other modified LMS-based algorithms have been developed and utilized to combat the ANC problem. All of these algorithms enjoy great performance when the signal-to-noise ratio (SNR) is high. On the other hand, when the SNR is low, which is a known trend in ANC scenarios, the performance of these algorithms is not attractive. The performance of the Least Mean Fourth (LMF) algorithm has never been tested on any ANC scenario under low or high SNR. Therefore, in this work, reflecting the development in the LMS family on the LMF, we are proposing two new adaptive filtering algorithms, which are the Filtered-X Least Mean Fourth (FXLMF) algorithm and the Leakage-based variant (LFXLMF) of the FXLMF algorithm. The main target of this work is to derive the FXLMF and LFXLMF adaptive algorithms, study their convergence behaviors, examine their tracking and transient conduct, and analyze their performance for different noise environments. Moreover, a convex combination filter utilizing the proposed algorithm and algorithm robustness test is carried out. Finally, several simulation results are obtained to validate the theoretical findings and show the effectiveness of the proposed algorithms over other adaptive algorithms.
Development of Fuel/Engine Systems—The Way Forward to Sustainable Transport (2019)

The global demand for transport energy is large, growing, and primarily met by petroleum-derived liquid fuels powering internal combustion engines (ICEs). Moreover, the demand for jet fuel and diesel is projected to grow faster than the demand for gasoline in the future, and is likely to result in low-octane gasoline components becoming more readily available. Significant initiatives with varying motivations are taking place to develop the battery electric vehicle (BEV) and the fuel cell as alternatives to ICE vehicles, and to establish fuels such as biofuels and natural gas as alternatives to conventional liquid fuels. However, each of these alternatives starts from a very low base and faces significant barriers to fast and unrestrained growth; thus, transport—and particularly commercial transport—will continue to be largely powered by ICEs running on petroleum-based liquid fuels for decades to come. Hence, the sustainability of transport in terms of affordability, energy security, and impact on greenhouse gas (GHG) emissions and air quality can only be ensured by improving ICEs. Indeed, ICEs will continue to improve while using current market fuels, through improvements in combustion, control, and after-treatment systems, assisted by partial electrification in the form of hybridization. However, there is even more scope for improvement through the development of fuel/engine systems that can additionally leverage benefits in fuels manufacture and use components that may be readily available. Gasoline compression ignition (GCI), which uses low-octane gasoline in a compression ignition engine, is one such example. GCI would enable diesel-like efficiencies while making it easier to control nitrogen oxides (NOx) and particulates at a lower cost compared with modern diesel engines. Octane on demand (OOD) also helps to ensure optimum use of available fuel anti-knock quality, and thus improves the overall efficiency of the system.
Reformulation of the covering and quantizer problems as ground states of interacting particles (2010)

It is known that the sphere-packing problem and the number-variance problem (closely related to an optimization problem in number theory) can be posed as energy minimizations associated with an infinite number of point particles in d-dimensional Euclidean space R(d) interacting via certain repulsive pair potentials. We reformulate the covering and quantizer problems as the determination of the ground states of interacting particles in R(d) that generally involve single-body, two-body, three-body, and higher-body interactions. This is done by linking the covering and quantizer problems to certain optimization problems involving the "void" nearest-neighbor functions that arise in the theory of random media and statistical mechanics. These reformulations, which again exemplify the deep interplay between geometry and physics, allow one now to employ theoretical and numerical optimization techniques to analyze and solve these energy minimization problems. The covering and quantizer problems have relevance in numerous applications, including wireless communication network layouts, the search of high-dimensional data parameter spaces, stereotactic radiation therapy, data compression, digital communications, meshing of space for numerical analysis, and coding and cryptography, among other examples. In the first three space dimensions, the best known solutions of the sphere-packing and number-variance problems (or their "dual" solutions) are directly related to those of the covering and quantizer problems, but such relationships may or may not exist for d≥4 , depending on the peculiarities of the dimensions involved. Our reformulation sheds light on the reasons for these similarities and differences. We also show that disordered saturated sphere packings provide relatively thin (economical) coverings and may yield thinner coverings than the best known lattice coverings in sufficiently large dimensions. In the case of the quantizer problem, we derive improved upper bounds on the quantizer error using sphere-packing solutions, which are generally substantially sharper than an existing upper bound in low to moderately large dimensions. We also demonstrate that disordered saturated sphere packings yield relatively good quantizers. Finally, we remark on possible applications of our results for the detection of gravitational waves.
A pH-driven ring translocation switch against cancer cells (2018)

A molecular switch built with cucurbit[7]uril and a 3-station viologen-phenylene-imidazole compound exhibited pH actuated ring translocation with high fatigue resistance (up to 102 cycles). The switch movement was harnessed toward selectively masking the toxicity of the viologen fragment at neutral pH near non-cancerous cells, while exposing it at acid pH near cancer cells.
Ethylene/butadiene copolymers, catalytic system and process for the synthesis thereof (2006)

US Patent 7,094,854
Prognostic factors and molecular markers for renal cell carcinoma (2001)

Renal cell carcinoma is the most common cancer in the kidney, affecting nearly 30,000 Americans every year and is associated with over 12,000 deaths annually. If detected early, renal cell carcinomas can be cured surgically. However, once metastatic disease develops the prognosis for long-term survival is poor. Unfortunately, one-third of patients have metastatic disease at the time of diagnosis and approximately 50% of the patients undergoing surgical resection for less advanced disease eventually relapse. This review examines the clinical and molecular prognostic tools currently available or under investigation for kidney cancer.
Texture Evolution in Hydroentangled Nonwovens (2003)

We recently reported on a co-occurrence-based method for texture analysis. This paper uses this texture analysis method to examine the development of the texture during hydroentangling as a function process conditions. We report on the development of texture as a function of hydroentangling energy. Energy was varied by controlling the pressure and number of passes. All fabrics were produced using the same web on the same forming belt substrate. Our preliminary data indicate that the degree of texture definition increases as a function of pressure up to a point and then begins to deteriorate.
Bisphosphonates inactivate human EGFRs to exert antitumor actions (2014)

Bisphosphonates are the most commonly prescribed medicines for osteoporosis and skeletal metastases. The drugs have also been shown to reduce cancer progression, but only in certain patient subgroups, suggesting that there is a molecular entity that mediates bisphosphonate action on tumor cells. Using connectivity mapping, we identified human epidermal growth factor receptors (human EGFR or HER) as a potential new molecular entity for bisphosphonate action. Protein thermal shift and cell-free kinase assays, together with computational modeling, demonstrated that N-containing bisphosphonates directly bind to the kinase domain of HER1/2 to cause a global reduction in downstream signaling. By doing so, the drugs kill lung, breast, and colon cancer cells that are driven by activating mutations or overexpression of HER1. Knocking down HER isoforms thus abrogates cell killing by bisphosphonates, establishing complete HER dependence and ruling out a significant role for other receptor tyrosine kinases or the enzyme farnesyl pyrophosphate synthase. Consistent with this finding, colon cancer cells expressing low levels of HER do not respond to bisphosphonates. The results suggest that bisphosphonates can potentially be repurposed for the prevention and therapy of HER family-driven cancers.