gebhart/patrepeval huggingface dataset:
Data from Demonstration of a Genetic Therapeutic Index for Tumors Expressing Oncogenic <i>BRAF</i> by the Kinase Inhibitor SB-590885 (2023)

&lt;div&gt;Abstract&lt;p&gt;Oncogenic &lt;i&gt;BRAF&lt;/i&gt; alleles are both necessary and sufficient for cellular transformation, suggesting that chemical inhibition of the activated mutant protein kinase may reverse the tumor phenotype. Here, we report the characterization of SB-590885, a novel triarylimidazole that selectively inhibits Raf kinases with more potency towards B-Raf than c-Raf. Crystallographic analysis revealed that SB-590885 stabilizes the oncogenic B-Raf kinase domain in an active configuration, which is distinct from the previously reported mechanism of action of the multi-kinase inhibitor, BAY43-9006. Malignant cells expressing oncogenic B-Raf show selective inhibition of mitogen-activated protein kinase activation, proliferation, transformation, and tumorigenicity when exposed to SB-590885, whereas other cancer cell lines and normal cells display variable sensitivities or resistance to similar treatment. These studies support the validation of oncogenic B-Raf as a target for cancer therapy and provide the first evidence of a correlation between the expression of oncogenic &lt;i&gt;BRAF&lt;/i&gt; alleles and a positive response to a selective B-Raf inhibitor. (Cancer Res 2006; 66(23): 11100-5)&lt;/p&gt;&lt;/div&gt;
(Invited) Axial Silicon-Germanium Nanowires: Properties and Device Applications (2020)

Dense nanowire films can be considered as quasi-porous structures with a high surface-to-volume ratio. From this perspective, structural, optical and electrical properties of axial Si-Ge nanowire heterojunctions produced by the vapor-liquid-solid growth method using Au nanoclusters as catalysts are analyzed. The lattice mismatch induced strain is partially relieved due to spontaneous SiGe intermixing at the heterointerface and lateral expansion of the Ge segment of the nanowire. The mismatch in Ge and Si coefficients of thermal expansion and low thermal conductivity of Si-Ge nanowire heterojunctions are found to be responsible for the thermally induced stress detected under intense laser radiation in photoluminescence and Raman scattering measurements. In electrical measurements, the observed non-linear current-voltage characteristics, strong flicker noise, and damped current oscillations with frequencies of 20-30 MHz are explained using a proposed Si-Ge nanowire heterojunction energy band diagram that includes energy states associated with structural imperfections at the nanowire surface. It is also shown that the nanowire surface states act as shunt resistors and considerably degrade the Si-Ge nanowire device characteristics.
Optical add/drop multiplexers based on X-crossing vertical coupler filters (2002)

A simple OADM based on X-crossing InGaAsP-InP vertical coupler filters is demonstrated. Laterally separated input and output waveguides is achieved using a wafer bonding technique and double side wafer processing. Sidelobe level of /spl sim/26 dB and coupling efficiency of 97% are achieved for OADM with X-crossing angle of 0.25.
Early stages of simian immunodeficiency virus infection in lymph nodes. Evidence for high viral load and successive populations of target cells. (1994)

Lymph nodes obtained from 14 macaques sacrificed at early time points following experimental inoculation with simian immunodeficiency virus were analyzed by in situ hybridization for virus load and virus cellular tropism. The lymph nodes presented a remarkably high viral load during the early phase of infection, as viral RNA was detected in as many as 2% of lymph node cells 1 week after inoculation. At this stage, macrophages and T4 lymphocytes were identified by combined immunohistochemistry and in situ hybridization as the target cells of the virus. Simian immunodeficiency virus-positive macrophages concentrated in the subcapsular sinuses, suggesting an entry of infected cells via the afferent lymphatics. A shift in the pattern of viral infection was observed at 2 weeks after inoculation, with a concentration of viral RNA in the germinal centers of the developing lymphoid follicles. Follicular dendritic cells were found to be the major target of the virus at this stage. Follicular dendritic cells were associated with high levels of viral RNA but little or no detectable viral DNA, suggesting that the virus was present mostly in the form of viral particles trapped at the cell surface. Follicular dendritic cell-associated virus persisted at high levels for 2 months before subsiding, indicating that follicular dendritic cells constituted a major reservoir of the virus during the early stages of simian immunodeficiency virus infection.
The validity of retiming sequential circuits (1995)

Retiming has been proposed as an optimization step for sequential circuits represented at the net-list level. Retiming moves the latches across the logic gates and in doing so changes the number of latches and the longest path delay between the latches. In this paper we show by example that retiming a design may lead to differing simulation results when the retimed design replaces the original design. We also show, by example, that retiming may not preserve the testability of a sequential test sequence for a given stuck-at fault as measured by a simulator. We identify the cause of the problem as forward retiming moves across multiple-fanout points in the circuit. The primary contribution of this paper is to show that, while an accurate logic simulation may distinguish the retimed circuit from the original circuit, a conservative three-valued simulator cannot do so. Hence, retiming is a safe operation when used in a design methodology based on conservative three-valued simulation starting each latch with the unknown value.
Artículos originales seleccionados y analizados por expertos (2009)

En los ultimos anos, el tratamiento mediante sistemas de infusion continua de insulina (ISCI) ha adquirido un protagonismo cre-ciente en el campo de la diabetes, al igual que los sistemas de mo-nitorizacion continua de glucemia (MCG), de forma que todo pro-fesional implicado en la atencion al paciente con diabetes tipo 1 debe estar familiarizado con estas tecnicas. La comercializacion en 2006 del sistema MiniMed Paradigm
Targeted resequencing identifies genes with recurrent variation in cerebral palsy (2019)

A growing body of evidence points to a considerable and heterogeneous genetic aetiology of cerebral palsy (CP). To identify recurrently variant CP genes, we designed a custom gene panel of 112 candidate genes. We tested 366 clinically unselected singleton cases with CP, including 271 cases not previously examined using next-generation sequencing technologies. Overall, 5.2% of the naïve cases (14/271) harboured a genetic variant of clinical significance in a known disease gene, with a further 4.8% of individuals (13/271) having a variant in a candidate gene classified as intolerant to variation. In the aggregate cohort of individuals from this study and our previous genomic investigations, six recurrently hit genes contributed at least 4% of disease burden to CP: <i>COL4A1</i>, <i>TUBA1A, AGAP1</i>, <i>L1CAM</i>, <i>MAOB</i> and <i>KIF1A</i>. Significance of Rare VAriants (SORVA) burden analysis identified four genes with a genome-wide significant burden of variants, <i>AGAP1</i>, <i>ERLIN1</i>, <i>ZDHHC9</i> and <i>PROC</i>, of which we functionally assessed <i>AGAP1</i> using a zebrafish model. Our investigations reinforce that CP is a heterogeneous neurodevelopmental disorder with known as well as novel genetic determinants.
Chronic hyperammonemia in vivo impairs long‐term potentiation in hippocampus by altering activation of cyclic GMP‐dependent‐protein kinase and of phosphodiesterase 5 (2005)

Long-term potentiation (LTP) is impaired in the CA1 area of hippocampal slices from rats with chronic moderate hyperammonemia. We studied the mechanisms by which hyperammonemia in vivo impairs LTP. This process requires sequential activation of soluble guanylate cyclase, cyclic GMP-dependent protein kinase (PKG) and cyclic GMP-degrading phosphodiesterase. Application of the tetanus induced a rapid increase of cyclic GMP in slices from control or hyperammonemic rats, which is followed in control slices by a sustained decrease in cyclic GMP due to sustained activation of cyclic GMP-degrading phosphodiesterase, which in turn is due to sustained activation of PKG. In slices from rats with chronic hyperammonemia tetanus-induced decrease in cyclic GMP was delayed and transient due to lower and transient activation of PKG and of the phosphodiesterase. Hyperammonemia-induced impairment of LTP may be involved in the alterations of cognitive function in patients with hepatic encephalopathy.
Figure S2 from Paternally Expressed Gene 10 (PEG10) Promotes Growth, Invasion, and Survival of Bladder Cancer (2023)

&lt;p&gt;PEG10 levels are elevated in chemotherapy-resistant cells.&lt;/p&gt;
Cloning of a Carboxyl-terminal Isoform of the Prostanoid FP Receptor (1997)

An FP prostanoid receptor isoform, which appears to arise from alternative mRNA splicing, has been cloned from a mid-cycle ovine large cell corpus luteum library. The isoform, named the FP(B) receptor, is identical to the original isoform, the FP(A), throughout the seven transmembrane domains, but diverges nine amino acids into the carboxyl terminus. In contrast to FP(A), whose carboxyl terminus continues for another 46 amino acids beyond the nine shared residues, the FP(B) terminates after only one amino acid. The FP(A) isoform appears to arise by the failure to utilize a potential splice site, while a 3.2-kilobase pair intron is spliced out from the FP gene to generate the FP(B) isoform mRNA. The two isoforms have indistinguishable radioligand binding properties, but seem to differ in functional coupling to phosphatidylinositol hydrolysis. Thus, in COS-7 cells transiently transfected with either the FP(A) or the FP(B) receptor cDNAs, prostaglandin F(2alpha) stimulates inositol phosphate accumulation to the same absolute maximum, but the basal level of inositol phosphate accumulation is approximately 1.3-fold higher in cells transfected with the FP(B) as compared with cells transfected with the FP(A) isoform. Using the polymerase chain reaction, mRNA encoding the FP(B) isoform was identified in the ovine corpus luteum.
A novel immunoassay to quantify paclitaxel in plasma using monoclonal antibody–coated nanoparticles. (2011)

e11544 Background: Paclitaxel (PTX) is used in first line treatment of patients having a variety of solid tumors including breast, ovarian, and NSCL carcinomas. Paclitaxel has substantial variability in PK parameters, with up to 10-fold inter-patient differences in Cmax and/or AUC. This variability has critical clinical consequences for severe toxicities at high concentrations and decreased efficacy at low concentrations. The time above a critical paclitaxel plasma concentration of 0.05 µmol/L (Tc>0.05, 42 ng/mL) is correlated to toxicity and efficacy in many clinical studies. The current chromatographic methods for measuring paclitaxel blood levels are time-consuming and expensive. A new nanoparticle-based automated assay provides a rapid, simple and cost-effective measurement of PTX levels in patients undergoing treatment to allow timely personalized dose adjustment. Methods: A prototype automated homogenous immunoassay to quantify PTX, requiring less than 10μL plasma, was developed for use on the Beckman Coulter AU400 clinical analyzer. Total imprecision and linearity of the assay were evaluated using normal human plasma (NHP) pools spiked with PTX. Background of assay was determined by measuring >200 NHP samples. Selectivity was characterized by testing metabolites and degradation products of PTX for cross-reactivity at relevant concentrations. Results: With a quantitation range from 20 to 320 ng/mL, and instrument auto-dilution, plasma PTX levels can be measured up to 12,000 ng/mL. Time-to-first result was < 9 minutes and 400 samples per hour could be measured using a stored calibration curve. The total imprecision of spiked NHP was < 5% CV and the assay was linear from 15 to 300 ng/mL. The background of the assay was < 8 ng/mL. Cross-reactivities to 6α- and 3’-p-hydroxypaclitaxel, the major metabolites of PTX, were 16% and 7%, respectively, and <1% for the major degradation product, baccatin III. Conclusions: This immunoassay is suitable for routine measurement of plasma PTX concentrations with the advantages of speed, small sample size, no sample pretreatment, and application on automated instrumentation, and may provide a tool for optimization of PTX blood levels with PK-guided dosing.
Massive-MIMO and Digital mm-Wave Arrays on RF-SoCs using FDM for M-Fold Increase in Antennas per ADC/DAC (2021)

Communication systems of the future will require hundreds of independent spatial channels achieved through dense antenna arrays connected to digital signal processing software defined radios. The cost and complexity of data converters are a significant concern with systems having hundreds of antennas. This paper explores frequency division multiplexing as an approach for augmenting the baseband signals of multiple antenna channels such that a single ADC can sample a multitude of antennas in an array. The approach is equally applicable to both massive MIMO and mm-wave digital wireless arrays. An example design based on Xilinx RF SoC for combining 4 antenna channels at 28 GHz into a single ADC is provided.
Millimeter‐Wave Channels (2021)

This article provides an overview of measurements and models of millimeter‐wave (mmWave) propagation channels. After a review of the frequency dependence of propagation phenomena and the definition of parameters of interest, we then discuss the different methods for measuring mmWave channels both indoors and outdoors. Then follows an overview of the key measurement results, surveying again the literature of indoor channels, outdoor channels, and the impact of moving people. A survey of different types of channel models, including 3GPP type, geometry‐based stochastic channel models, and map‐based models elucidates the aspects of those models that are particularly relevant for mmWave frequencies. A discussion of the interaction of channels and mmWave systems and an outlook and discussion of future research topics round off this article.
Specifying subtypes in SCJ programs (2011)

Modular reasoning about programs that use subtypes requires that an overriding method in a subtype obeys the specifications of all methods that it overrides. For example, if method m is specified in a supertype T to take at most 42 nanoseconds to execute, then m cannot take more than 42 nanoseconds to execute in any subtype of T. Subtyping is an important aid to maintenance of programs, since it allows one to write polymorphic code (reducing code size and increasing reuse), and allows for convenient extension and enhancement of programs, all of which could be very useful in real-time programming. In this paper we show how to specify timing constraints for subtypes in a way that: permits modular reasoning about timing constraints, supports subtype polymorphism and object-oriented design patterns, and still permits precise reasoning about execution times. This technique supports object-oriented coding and design patterns based on subtype polymorphism, with all their maintenance advantages, to be used in real-time software.
Awareness and identification of athletes with sickle cell disorders at historically black colleges and universities. (1996)

We suggest that there is a likelihood for athletic trainers to encounter athletes with sickle cell disorders. Further education regarding sickle cell disorders may be needed.
Triple-A syndrome with prominent ophthalmic features and a novel mutation in the AAASgene: a case report (2004)

In addition to known ophthalmic manifestations, triple-A syndrome can present with accommodative dysregulation and ocular signs of autonomic dysfunction.
Antroquinonol D, Isolated from Antrodia camphorata, with DNA Demethylation and Anticancer Potential (2014)

DNA methyltransferase 1 (DNMT1) catalyzes DNA methylation and is overexpressed in various human diseases, including cancer. A rational approach to preventing tumorigenesis involves the use of pharmacologic inhibitors of DNA methylation; these inhibitors should reactivate tumor suppressor genes (TSGs) in tumor cells and restore tumor suppressor pathways. Antroquinonol D (3-demethoxyl antroquinonol), a new DNMT1 inhibitor, was isolated from Antrodia camphorata and identified using nuclear magnetic resonance. Antroquinonol D inhibited the growth of MCF7, T47D, and MDA-MB-231 breast cancer cells without harming normal MCF10A and IMR-90 cells. The SRB assay showed that the 50% growth inhibition (GI50) in MCF7, T47D, and MDA-MB-231 breast cancer cells following treatment with antroquinonol D was 8.01, 3.57, and 25.08 μM, respectively. d-Antroquinonol also inhibited the migratory ability of MDA-MB-231 breast cancer cells in wound healing and Transwell assays. In addition, antroquinonol D inhibited DNMT1 activity, as assessed by the DNMT1 methyltransferase activity assay. As the cofactor SAM level increased, the inhibitory effects of d-antroquinonol on DNMT1 gradually decreased. An enzyme activity assay and molecular modeling revealed that antroquinonol D is bound to the catalytic domain of DNMT1 and competes for the same binding pocket in the DNMT1 enzyme as the cofactor SAM, but does not compete for the binding pocket in the DNMT3B enzyme. An Illumina Methylation 450 K array-based assay and real-time PCR assay revealed that antroquinonol D decreased the methylation status and reactivated the expression of multiple TSGs in MDA-MB-231 breast cancer cells. In conclusion, we showed that antroquinonol D induces DNA demethylation and the recovery of multiple tumor suppressor genes, while inhibiting breast cancer growth and migration potential.
Contact wetting angle as a characterization technique for processing CdTe/CdS solar cells (2006)

Abstract The feasibility of measuring contact wetting angles to characterize processing induced changes to thin film semiconductors in CdTe/CdS solar cells is evaluated. The contact angles of water and formamide are used to determine the polar and dispersive surface energies of the thin films using two analysis methods. Changes in surface energies resulting from processing are correlated to changes in surface chemistry and structure detected by glancing incidence X‐ray diffraction (GIXRD), X‐ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). Surface energies are evaluated for sputtered In 2 O 3 :SnO 2 , chemical surface‐deposited CdS, and physical vapor‐deposited (PVD) CdTe thin films under as‐deposited and treated conditions. Treatments include thermal anneal in air, argon, and CdCl 2 ambient as well as surface etching. Indium tin oxide (ITO) and CdS films exhibit increased polar surface energy corresponding to enhanced crystallization of surfaces resulting from processing and increasing CdS growth temperature. Native oxidation of PVD CdTe (111)‐oriented film surfaces occurs rapidly and is readily detected by changes in contact angle. Surface energies of PVD (111)‐oriented CdTe stored under various humidities prior to processing are energetically similar due to native oxidation. The polar energy of CdTe surfaces is affected by the addition or removal of crystalline surface oxides during film processing. Copyright © 2006 John Wiley &amp; Sons, Ltd.
Shortest path bridging: Efficient control of larger ethernet networks (2010)

This article provides an overview of IEEE 802.1aq shortest path bridging and outlines some application scenarios that will benefit from the new capabilities SPB offers. SPB is built on the IEEE 802.1 standards, and inherits unaltered the existing OAM and data plane scalability enhancements, such as the MAC-in-MAC forwarding paradigm. SPB introduces link state control for bridge networks, thus improving control plane scalability, network bandwidth utilization, and control of the forwarding paths. Furthermore, SPB minimizes latency by forwarding frames on the shortest path. Network-wide load balancing is also supported by spreading the traffic on multiple equal cost paths in a user controllable manner. Thus, SPB provides enhanced control for Ethernet networks in metro, RAN backhaul, or data center environments.
Design and development of caffeic acid conjugated with Bombyx mori derived peptide biomaterials for anti-aging skin care applications (2017)

This study examined the significant features of caffeic acid conjugated with peptide (APPPKK) to determine if it meets the requirements for a cosmetic anti-aging biomolecule.
Fungal Origins of the Bicyclo[2.2.2]diazaoctane Ring System of Prenylated Indole Alkaloids (2012)

Over eight different families of natural products consisting of nearly 70 secondary metabolites that contain the bicyclo[2.2.2]diazaoctane ring system have been isolated from various Aspergillus, Penicillium, and Malbranchea species. Since 1968, these secondary metabolites have been the focus of numerous biogenetic, synthetic, taxonomic, and biological studies and, as such, have made a lasting impact across multiple scientific disciplines. This review covers the isolation, biosynthesis, and biological activity of these unique secondary metabolites containing the bridging bicyclo[2.2.2]diazaoctane ring system. Furthermore, the diverse fungal origin of these natural products is closely examined and, in many cases, updated to reflect the currently accepted fungal taxonomy.
Highly efficient catalytic production of oximes from ketones using in situ–generated H 2 O 2 (2022)

The ammoximation of cyclohexanone using preformed hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) is currently applied commercially to produce cyclohexanone oxime, an important feedstock in nylon-6 production. We demonstrate that by using supported gold-palladium (AuPd) alloyed nanoparticles in conjunction with a titanium silicate-1 (TS-1) catalyst, H<sub>2</sub>O<sub>2</sub> can be generated in situ as needed, producing cyclohexanone oxime with >95% selectivity, comparable to the current industrial route. The ammoximation of several additional simple ketones is also demonstrated. Our approach eliminates the need to transport and store highly concentrated, stabilized H<sub>2</sub>O<sub>2</sub>, potentially achieving substantial environmental and economic savings. This approach could form the basis of an alternative route to numerous chemical transformations that are currently dependent on a combination of preformed H<sub>2</sub>O<sub>2</sub> and TS-1, while allowing for considerable process intensification.
Optimization of energy state transition trajectory supports the development of executive function during youth (2020)

Executive function develops during adolescence, yet it remains unknown how structural brain networks mature to facilitate activation of the fronto-parietal system, which is critical for executive function. In a sample of 946 human youths (ages 8-23y) who completed diffusion imaging, we capitalized upon recent advances in linear dynamical network control theory to calculate the energetic cost necessary to activate the fronto-parietal system through the control of multiple brain regions given existing structural network topology. We found that the energy required to activate the fronto-parietal system declined with development, and the pattern of regional energetic cost predicts unseen individuals' brain maturity. Finally, energetic requirements of the cingulate cortex were negatively correlated with executive performance, and partially mediated the development of executive performance with age. Our results reveal a mechanism by which structural networks develop during adolescence to reduce the theoretical energetic costs of transitions to activation states necessary for executive function.