gebhart/patrepeval huggingface dataset:
Formation of low resistivity alpha Ta by ion beam sputtering (2003)

The properties of tantalum thin film prepared by ion beam sputtering with Xe ions (0.6–1.5 KV) have been investigated. β-Ta thin films with high resistivity (170 μΩ cm) on Si substrate were obtained without Cr underlayer. With Cr underlayer, however, a body-centered-cubic phase (bcc) α-Ta thin film with low resistivity (20 μΩ cm) has been successfully obtained at room temperature. The experimental results indicate that the Cr underlayer plays an important role in α-Ta formation and that the critical thickness of Cr is 20 Å. Properties of α-Ta are also influenced by Ta thickness and ion beam deposition process conditions. α-Ta with lower resistivity was achieved by using approximate beam energy of 1000 eV and beam current of 150 mA. X-ray diffraction analysis indicates that changes in resistivity can be attributed to changes in microstructure that is influenced by the ion beam conditions.
First SAR Study for Overriding NRAS Mutant Driven Acute Myeloid Leukemia (2018)

GNF-7, a multitargeted kinase inhibitor, served as a dual kinase inhibitor of ACK1 and GCK, which provided a novel therapeutic strategy for overriding AML expressing NRAS mutation. This SAR study with GNF-7 derivatives, designed to target NRAS mutant-driven AML, led to identification of the extremely potent inhibitors, 10d, 10g, and 11i, which possess single-digit nanomolar inhibitory activity against both ACK1 and GCK. These substances strongly suppress proliferation of mutant NRAS expressing AML cells via apoptosis and AKT/mTOR signaling blockade. Compound 11i is superior to GNF-7 in terms of kinase inhibitory activity, cellular activity, and differential cytotoxicity. Moreover, 10k possessing a favorable mouse pharmacokinetic profile prolonged life-span of Ba/F3-NRAS-G12D injected mice and significantly delayed tumor growth of OCI-AML3 xenograft model without causing the prominent level of toxicity found with GNF-7. Taken together, this study provides insight into the design of novel ACK1 and GCK dual inhibitors for overriding NRAS mutant-driven AML.
Fundamentals of Organic Chemistry as Applicable to the Biotransformation of Foreign Compounds (2014)

Organic chemistry plays a central role in drug discovery not only in the design and synthesis of biologically active compounds but also in the areas of drug metabolism and toxicology. Within the metabolism domain, possessing a fundamental understanding of organic chemistry principles is extremely valuable in understanding/rationalizing biotransformation fates of structurally diverse xenobiotics, including drugs. It is a valuable attribute to be able to glance at the structure of a drug and be able to predict with a degree of certainty the metabolic fate of the molecule. To make the overall contents of this book more accessible to a nonchemistry audience, we have reviewed some of the key mechanistic chemistry concepts (e.g., electronegativity, valence electrons, acidity, basicity, resonance, nucleophilicity, electrophilicity, and leaving group effects) that are required to fully appreciate the individual molecular peculiarity that usually accompanies biotransformation reactions. Using these basic principles, we have explored the mechanistic basis for several nonintuitive xenobiotic and drug biotransformation reactions that occur in nature.
Carotid Stents and Embolic Protection Devices (2008)

he Cleveland Clinic hosted the fourth StentSummit from August 30 through September 1,2007. The purposes of this meeting were to discussrecent research and development involving carotidartery stenting (CAS) with embolic protection and thoracicaortic aneurysm (TAA) endovascular grafting and to identi-fy potential pathways to improving the design and evalua-tion of these devices. This interdisciplinary meeting includedkeynote presentations and open discussions involving repre-sentatives from the entire endovascular community, includ-ing clinicians, engineers, and regulatory officials.In the April 2008 issue of
A Method of Monitoring Partial Discharge in Switchgear Based on Ozone Concentration (2018)

We accurately established an air discharge simulation experiment system to obtain the variation of ozone concentration in air discharge process, which includes pin-to-plate discharge, air-gap discharge, creeping discharge as well as metal particle discharge model, consisting of voltage console, transformer, and discharge device, gas absorption cell, spectrometer, and computer. Through online monitoring, the ozone concentration in a relatively closed container to simulate internal partial discharges for an hour with the voltage increases from 3 to 0.2 kV increment, we obtained four basic models with discharge inception voltage grade of 4.0, 4.5, 4.7, and 4.1. Besides, we applied the method of Fourier transform-differential absorption spectroscopy to process and analyze the experimental data, and obtained the ozone concentration curve. The ozone concentration increases with the increasing voltage loading time, and it tends to be stable and reaches an equilibrium state under a certain voltage.
Nonlinear Structural Vector Autoregressive Models With Application to Directed Brain Networks (2019)

Structural equation models (SEMs) and vector autoregressive models (VARMs) are two broad families of approaches that have been shown useful in effective brain connectivity studies. While VARMs postulate that a given region of interest in the brain is directionally connected to another one by virtue of time-lagged influences, SEMs assert that directed dependencies arise due to instantaneous effects, and may even be adopted when nodal measurements are not necessarily multivariate time series. To unify these complementary perspectives, linear structural vector autoregressive models (SVARMs) that leverage both instantaneous and time-lagged nodal data have recently been put forth. Albeit simple and tractable, linear SVARMs are quite limited since they are incapable of modeling nonlinear dependencies between neuronal time series. To this end, the overarching goal of the present paper is to considerably broaden the span of linear SVARMs by capturing nonlinearities through kernels, which have recently emerged as a powerful nonlinear modeling framework in canonical machine learning tasks, e.g., regression, classification, and dimensionality reduction. The merits of kernel-based methods are extended here to the task of learning the effective brain connectivity, and an efficient regularized estimator is put forth to leverage the edge sparsity inherent to real-world complex networks. Judicious kernel choice from a preselected dictionary of kernels is also addressed using a data-driven approach. Numerical tests on ECoG data captured through a study on epileptic seizures demonstrate that it is possible to unveil previously unknown directed links between brain regions of interest.
A feasibility study of the 3D fluorescent image reconstruction for the simultaneous PET and fluorescent CT imaging system using depth of interaction PET detector (2008)

The simultaneous imaging system of PET and Fluorescent CT is being developed in the National Institute of Radiological Science in Japan. For the simultaneous system, we are considering using the DOI-PET detectors as simultaneous detectors of the gamma ray for PET and NIR light for fluorescence by changing the upper reflectors to the dichroic mirrors. Here, DOI-PET detector has very low spatial resolution to the NIR light compared to basically used CCD cameras. However, since the NIR light is scattered by biological tissues, it can be possible to reconstruct valuable image from the data which acquired from low resolution devices. In this study, we show feasibility for the Fluorescent CT imaging using the DOI-PET detector by computer simulations. In the simulations, we used a cubic phantom and square shaped detector geometry and a diffusion equation to approximate the light propagation. The system matrices of the Fluorescent CT geometries having different detector resolutions are calculated and we evaluated the singular values of the matrices. Using the system matrices, we simulated the image reconstruction from observed data which is generated by simulation and noise added. As a result, it is confirmed the reconstructed image from low resolution detectors is as same level as one from higher resolution detectors.
Regulation of SREBPs by Sphingomyelin in Adipocytes via a Caveolin and Ras-ERK-MAPK-CREB Signaling Pathway (2015)

Sterol response element binding protein (SREBP) is a key transcription factor in insulin and glucose metabolism. We previously demonstrated that elevated levels of membrane sphingomyelin (SM) were related to peroxisome proliferator-activated receptor-γ (PPARγ), which is a known target gene of SREBP-1 in adipocytes. However, the role of SM in SREBP expression in adipocytes remains unknown. In human abdominal adipose tissue from obese women with various concentrations of fasting plasma insulin, SREBP-1 proteins decreased in parallel with increases in membrane SM levels. An inverse correlation was found between the membrane SM content and the levels of SREBP-1c/ERK/Ras/PPARγ/CREB proteins. For the first time, we demonstrate the effects of SM and its signaling pathway in 3T3-F442A adipocytes. These cells were enriched or unenriched with SM in a range of concentrations similar to those observed in obese subjects by adding exogenous natural SMs (having different acyl chain lengths) or by inhibiting neutral sphingomyelinase. SM accumulated in caveolae of the plasma membrane within 24 h and then in the intracellular space. SM enrichment decreased SREBP-1 through the inhibition of extracellular signal-regulated protein kinase (ERK) but not JNK or p38 mitogen-activated protein kinase (MAPK). Ras/Raf-1/MEK1/2 and KSR proteins, which are upstream mediators of ERK, were down-regulated, whereas SREBP-2/caveolin and cholesterol were up-regulated. In SM-unmodulated adipocytes treated with DL-1-Phenyl-2-Palmitoylamino-3-morpholino-1-propanol (PPMP), where the ceramide level increased, the expression levels of SREBPs and ERK were modulated in an opposite direction relative to the SM-enriched cells. SM inhibited the insulin-induced expression of SREBP-1. Rosiglitazone, which is an anti-diabetic agent and potent activator of PPARγ, reversed the effects of SM on SREBP-1, PPARγ and CREB. Taken together, these findings provide novel insights indicating that excess membrane SM might be critical for regulating SREBPs in adipocytes via a MAPK-dependent pathway.
Photoelectrochemical and Electrochemical Conversion of Carbon Dioxide to Methanol and Higher Order Products Mediated by Pyridinium Based Electrocatalysts (2008)

Abstract not Available.
Supplementary Tables 1-3 from The Novel Tryptamine Derivative JNJ-26854165 Induces Wild-Type p53- and E2F1-Mediated Apoptosis in Acute Myeloid and Lymphoid Leukemias (2023)

Supplementary Tables 1-3 from The Novel Tryptamine Derivative JNJ-26854165 Induces Wild-Type p53- and E2F1-Mediated Apoptosis in Acute Myeloid and Lymphoid Leukemias
Simulatable auditing (2005)

Given a data set consisting of private information about individuals, we consider the online query auditing problem: given a sequence of queries that have already been posed about the data, their corresponding answers -- where each answer is either the true answer or denied (in the event that revealing the answer compromises privacy) -- and given a new query, deny the answer if privacy may be breached or give the true answer otherwise. A related problem is the offline auditing problem where one is given a sequence of queries and all of their true answers and the goal is to determine if a privacy breach has already occurred.We uncover the fundamental issue that solutions to the offline auditing problem cannot be directly used to solve the online auditing problem since query denials may leak information. Consequently, we introduce a new model called simulatable auditing where query denials provably do not leak information. We demonstrate that max queries may be audited in this simulatable paradigm under the classical definition of privacy where a breach occurs if a sensitive value is fully compromised. We also introduce a probabilistic notion of (partial) compromise. Our privacy definition requires that the a-priori probability that a sensitive value lies within some small interval is not that different from the posterior probability (given the query answers). We demonstrate that sum queries can be audited in a simulatable fashion under this privacy definition.
Structural and Functional Characterization of the JH2 Pseudokinase Domain of JAK Family Tyrosine Kinase 2 (TYK2) (2015)

JAK (Janus family of cytoplasmic tyrosine kinases) family tyrosine kinase 2 (TYK2) participates in signaling through cytokine receptors involved in immune responses and inflammation. JAKs are characterized by dual kinase domain: a tyrosine kinase domain (JH1) that is preceded by a pseudokinase domain (JH2). The majority of disease-associated mutations in JAKs map to JH2, demonstrating its central regulatory function. JH2s were considered catalytically inactive, but JAK2 JH2 was found to have low autoregulatory catalytic activity. Whether the other JAK JH2s share ATP binding and enzymatic activity has been unclear. Here we report the crystal structure of TYK2 JH2 in complex with adenosine 5'-O-(thiotriphosphate) (ATP-γS) and characterize its nucleotide binding by biochemical and biophysical methods. TYK2 JH2 did not show phosphotransfer activity, but it binds ATP and the nucleotide binding stabilizes the protein without inducing major conformational changes. Mutation of the JH2 ATP-binding pocket increased basal TYK2 phosphorylation and downstream signaling. The overall structural characteristics of TYK2 JH2 resemble JAK2 JH2, but distinct stabilizing molecular interactions around helix αAL in the activation loop provide a structural basis for differences in substrate access and catalytic activities among JAK family JH2s. The structural and biochemical data suggest that ATP binding is functionally important for both TYK2 and JAK2 JH2s, whereas the regulatory phosphorylation appears to be a unique property of JAK2. Finally, the co-crystal structure of TYK2 JH2 complexed with a small molecule inhibitor demonstrates that JH2 is accessible to ATP-competitive compounds, which offers novel approaches for targeting cytokine signaling as well as potential therapeutic applications.
A phase II clinical trial of adoptive immunotherapy for advanced renal cell carcinoma using mitogen-activated autologous leukocytes and continuous infusion interleukin-2. (1989)

Forty patients with metastatic, recurrent, or unresectable renal cell carcinoma were entered into a study of the therapeutic efficacy of adoptive immunotherapy using periodate (IO4-) and interleukin-2 (IL2)-activated autologous leukocytes and continuous infusion low-dose IL2. Patient survival was also examined. The first 15 consecutive patients were enrolled in protocol A without an IL2 priming phase and the following 25 patients were entered in protocol B where a 5-day priming phase was initiated before leukapheresis. A maintenance regimen consisted of either 3 x 10(6) units of recombinant interferon-alpha (rIFN-alpha), three times per week only or together with leukapheresis and infusion of IO4-/IL2-activated cells and 2 days of continuous infusion IL2 per month. Thirty-four patients completed the protocol treatment. Four patients were removed from the study owing to rapid tumor progression and two patients died while receiving treatment. The clinical response rate was 22%: two patients had a complete response and five patients had a partial response. Among the 25 patients who had no clinical response, 11 patients had either a mixed response or stabilization. Neither response, response duration, nor site response correlated with the total dose of IL2 administered or the number of activated killer cells infused. Patients who received maintenance therapy had longer survival times than patients who did not receive such therapy. All toxicity and side effects associated with IL2 treatment were transient and resolved after discontinuation of the drug. Patients on maintenance therapy tolerated both rIFN-alpha and monthly infusions of activated killer cells and IL2 well. This study confirms the concept of adoptive immunotherapy as a new treatment approach for advanced renal cell carcinoma and suggests that maintenance therapy may prolong survival time.
Chemical investigation and antimicrobial properties of mastic water and its major constituents (2009)

A phytochemical and antimicrobial study of mastic water was carried out for the first time. Mastic water, which is obtained together with mastic essential oil (MEO) during the distillation of mastic gum (the resin of Pistacia lentiscus L. var. Chia), was passed through XAD4 resin and the adsorbed organic compounds were eluted with diethylether, affording the mastic water extract (MWE). The extract was analysed with chiral GCMS and the major compounds identified were verbenone (12.90%), α-terpineol (12.09%), linalool (7.29%) and trans-pinocarveol (5.97%).
Genome Sequence of Lactobacillus rhamnosus Strain CNCM I-3698 (2015)

Lactobacillus rhamnosus CNCM I-3698 is a commercially available probiotic that is used in animal feed as an additive. Here, we announce the draft genome sequence for this strain, consisting of 71 contigs corresponding to 2,966,480 bp and a G+C content of 46.69%.
Cushing's Syndrome Secondary to Isolated Micronodular Adrenocotrical Disease (iMAD) associated with Rapid Onset Weight Gain and Negative Abdominal MRI Findings in a 3 year old Male (2010)

Cushing's syndrome (CS) is uncommon in childhood. CS may be either dependent or independent of adrenocorticotrophic hormone (ACTH). ACTH independent micronodular adrenocortical (MAD) disease may present in the second to third decade of life or between ages 2-3 years. It may occur in isolation, or as a part of the Carney complex and it represents an elusive entity to diagnose. We present a 3 year 7 month old boy with isolated MAD (iMAD). Abdominal CT revealed prominent mildly lobulated anteromedial margin of adrenals with nodular appearance. Cardiac echo, thyroid and testicular ultrasounds performed as a work up for Carney complex were normal. Bilateral adrenalectomy confirmed MAD as the cause of CS.We present the history and identification of a unique case of iMAD.
Fluorescence imaging of viscous materials in the ultraviolet-visible wavelength range (2014)

This paper presents an approach of an innovative measurement principle for the quality control of viscous materials during a manufacturing process based on fluorescence imaging. The main contribution to the state of the art provided by this measurement system is that three equal fluorescence images of a static or moving viscous object are available in different optical paths. The independent images are obtained by two beam splitters which are connected in series. Based on these images, it is possible to evaluate each image separately. In our case, three optical bandpass filters with different center wavelengths of 405 nm, 420 nm, and 440 nm were used to filter the separate fluorescence images. The developed system is useable for the detection of impurities in the micrometer range. Further, incorrect mixing ratios of particular components and wrong single components in the viscous materials can be detected with the setup. Moreover, it is possible to realize static and dynamic measurements. In this case the maximum speed of the objects was 0.2 m/s for the dynamic measurements. Advantages of this measurement setup are the universality due to the use of optical standard components, the small dimension and the opportunity to integrate it easily into ongoing processes. In addition, the measurement system works on a non-contact basis. Thus, the expense for maintenance is at a very low level compared to currently available measurement setups for the investigated application. Furthermore, the setup provides for the first time a simultaneous analysis of more than one component and the detection of impurities concerning their nature and size in a manufacturing process.
ChemInform Abstract: Traveling Reaction Zone Method for Preparation of Textured Ceramic Superconductor Thick Films. (1991)

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.
HIV Type 1 Molecular Clones Able to Use the Bonzo/STRL-33 Coreceptor for Virus Entry (2001)

We describe the cloning of env genes from the mother-infant HIV-1 isolate pair P6-v3 and M6-v3. These viruses are unusual in that they can use the coreceptor Bonzo/STRL33 as well as CCR5 and, in the case of M6, CXCR4, to enter transfected cell lines in vitro. The phenotype of the parental isolates is generally reflected by the properties of the cloned env genes, when these are used in an Env-complementation assay of virus entry. Chimeric viruses were also made that contain the env genes of P6-v3 and M6-v3 inserted into the background of the infectious molecular clone, HIV-1 NL4-3. Some of the chimeric viruses derived from HIV1 P6-v3 were able to use Bonzo for entry into transfected cell lines, albeit to a lesser extent than they could use CCR5. There are some indications that one of these chimeric viruses, P6-v3-22-1, can use a coreceptor other than CCR5, perhaps Bonzo, to enter mitogen-stimulated PBMC, although only weakly. However, formal proof that this virus can use Bonzo in primary cells has not been obtained. The P6-v3-22-1 chimeric virus was unable to infect CD4-negative, placental cell lines, in the presence or absence of soluble CD4. Env sequence analysis revealed several differences among viruses with different tropisms, most notably a four amino acid deletion in the central region of the V3 loop that distinguishes the R5 virus P6-v3-25-4 from the R5, Bonzo virus P6-v3-22-1.
Multipath delay measurement using parallel processing (2003)

An efficient model has been developed to estimate the parameters of a slowly fading multipath channel. A spread-spectrum direct sequence signal is used to resolve the path delays and despread the noise. The multipath parameters, including number of paths, path delays, and fading factors, are estimated by finding the approximated eigenvalues of the covariance matrix of the received signal. The multipath estimator is fully implemented by a parallel processing scheme and two fast and high-resolution algorithms, HSNR and LSNR, are developed for this scheme. The computer simulation results show that reliable multipath estimation can be achieved even when multipath time delays are very close in low signal-to-noise ratio. The resolution of multipath time delays can be improved by using a long direct sequence, and the estimation accuracy of fading factors can be achieved by a long-term observation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Exploring Digital Logic Design Using Ballistic Deflection Transistors Through Monte Carlo Simulations (2011)

We present exploratory studies of digital circuit design using the recently proposed ballistic deflection transistor (BDT) devices. We demonstrate a variety of possible logic functions through simple reconfiguration of two drain-connected BDTs. We further propose the creation of a three-BDT logic cell to yield differential versions of each logic function, improving overall flexibility of BDT circuit design. Each of the proposed gate configurations has been verified through extensive numerical calculations using an in-house Monte Carlo simulator. Simulation results show that the proposed gate arrangements are capable of achieving 400-GHz operating frequencies at room temperature. A compact fit-based analytical model to aid circuit design using BDTs is also introduced.