gebhart/patrepeval huggingface dataset:
Abstract LB-B10: Chemical Proteomic Analysis of BTK and PI3K Using Chloroalkane-Derivatized Small Molecule Inhibitors (2015)

Abstract Chemical proteomics is a rapidly evolving technology that allows for drug target identification for small molecule inhibitors. Here we present an approach utilizing a chloroalkane (CA) moiety capture handle, which can be chemically attached to small molecules and used to pull-down protein binding partners using the HaloTag technology. CA-modified compounds are cell permeable and have minimal impact on potency, allowing for phenotypic assays of the derivatized compound to be recapitulated. Here we present a study looking at the targets of two compounds - a Brutons Tyrosine Kinase (BTK) small molecule inhibitor and a Phospho-inositol 3 Kinase (PI3K) small molecule inhibitor. BTK is a non-receptor tyrosine kinase expressed in most hematopoietic cells except T cells, it is essential for B cell receptor (BCR) signaling in B cells and as such is the therapeutic focus in many autoimmune diseases, including rheumatoid arthritis (RA) and lupus. Upon binding to growth factor receptor, PI3K is activated which initiates a signaling cascade involving AKT and mTOR that promotes cell cycle progression and cell proliferation. Mutations of the catalytic subunit of PI3KA are observed in several types of cancers. Inhibition of PI3K is therefore an important therapeutic focus. Taselisib, a selective inhibitor of PIK3CA, and G02599124, an inhibitor of BTK, were derivitized with the CA linker. Phenotypic screens compared to the parental compound showed comparable IC50 values. Both CA-compounds showed good binding to HaloTag and were cell permeable in a U2OS stable cell line. Control and test experiments were performed with BTK-CA compound using Jurkat (T cells) and Ramos (B cells) cell lines. Taselib-CA was studied after 1h and 8h treatment in the HCC1954 cell line. Cells were lysed and the CA compounds, together with the bound targets, were rapidly captured onto magnetic resin coated with HaloTag. Unmodified compound was used to competitively elute interacting proteins. Eluted proteins were processed using SDS-PAGE and in-gel digestion. Peptides were analyzed using nanoscale LC-MS/MS coupled with an Orbitrap Velos Pro mass spectrometer. Using this approach we were able to specifically isolate BTK when compared to control experiments in T cells. In the Taselib-CA experiment, we were able to specifically isolate the PIK3CA catalytic subunit and PIK3R1 and PIK3R2 regulatory subunits. Observation of the wild type and mutant forms of PI3KCA will be discussed. Citation Format: Victoria Pham, James Crawford, Steve Saben, Michael Ford, Richard Jones, Danette Daniels, Thomas Kirkland, Marjeta Urh, Jennie Lill. Chemical Proteomic Analysis of BTK and PI3K Using Chloroalkane-Derivatized Small Molecule Inhibitors. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-B10.
Supplementary Data from Ubiquitinated PCNA Drives USP1 Synthetic Lethality in Cancer (2023)

&lt;p&gt;Supplementary methods&lt;/p&gt;
Tilted Paraboloidal Reflective Lens for Far Infrared Sensor Fabricated by Mask with Rectangular Openings (2009)

A tilted paraboloidal reflective lens for focusing far infrared (FIR) rays has been devised. Tilted paraboloids with smooth surface and vertical walls were fabricated by two-step etching using microloading effect with a mask which had rectangular openings of various sizes. FIR light was focused by a 30-degree-tilted paraboloid lens. The size of a real image of an FIR source was 110 mum, which agrees with a lens formula.
Sudden Cardiac Arrest: ECG Repolarization After Resuscitation (2010)

In the context of cardiac resuscitation, an ECG with ST elevation favors acute myocardial infarction, whereas the presence of ERep is a marker of a nonischemic event and future ERep syndrome.
Plasmid DNA–Based Vaccines Protect Mice and Ferrets against Lethal Challenge with A/Vietnam/1203/04 (H5N1) Influenza Virus (2008)

Plasmid DNA (pDNA) vaccines represent an alternative to conventional inactivated influenza vaccines that are likely to experience supply constraints during a pandemic. Several Vaxfectin-formulated pDNA vaccines were tested in mice and ferrets for efficacy against a lethal challenge with the highly pathogenic A/Vietnam/1203/04 (H5N1) influenza virus strain; the vaccines encoded influenza A virus hemagglutinin (HA), and/or nucleoprotein (NP), and M2 protein. Complete protection from death and disease was achieved in mice and ferrets with 2 doses of a Vaxfectin-formulated vaccine containing H5 HA, NP, and M2 plasmids and in ferrets with only 1 dose. A Vaxfectin-formulated vaccine containing NP and M2 pDNA provided significant protection against death in mice and provided some benefit in ferrets (i.e., 17% survival, delayed time to illness and death, and significant reduction in viral load compared with that in negative control animals). These experiments support the clinical testing of pDNA vaccine candidates that may ultimately increase global vaccine supply options during pandemics.
The effect of horizontal array orientation on MIMO channel capacity (2004)

In multiple-input multiple-output (MIMO) systems the horizontal orientation of a linear array has, in some situations a large influence on the available channel capacity. In this paper, we investigate the effect of horizontal array orientation on channel capacity, eigenvalue distribution and antenna complex correlation coefficient in such systems. We present channel measurements in an office corridor environment for a 6/spl times/6 MIMO system and compare the capacity results to those of a physical and non-physical model based on the measurements. The results show that under LOS conditions the channel capacity can vary significantly depending on the receiver array orientation in the horizontal plane.
Profitability-based power allocation for speculative multithreaded systems (2010)

With the shrinking of transistors continuing to follow Moore's Law and the non-scalability of conventional out-of-order processors, multi-core systems are becoming the design choice for industry. Performance extraction is thus largely alleviated from the hardware and placed on the pro-gr ammer/compiler camp, who now have to expose Thread Level Parallelism (TLP) to the underlying system in the form of explicitly parallel applications. Unfortunately, parallel programming is hard and error-prone. The programmer has to parallelize the work, perform the data placement, and deal with thread synchronization. Systems that support speculative multithreaded execution like Thread Level Speculation (TLS), offer an interesting alternative since they relieve the programmer from the burden of parallelizing applications and correctly synchronizing them. Since systems that support speculative multithreading usually treat all threads equally, they are energy-inefficient. This inefficiency stems from the fact that speculation occasionally fails and, thus, power is spent on threads that will have to be discarded. In this paper we propose a power allocation scheme for TLS systems, based on Dynamic Voltage and Frequency Scaling (DVFS), that tries to remedy this inefficiency. More specifically, we propose a profitability-based power allocation scheme, where we ¿steal¿ power fro m non-profitable threads and use it to speed up more useful ones. We evaluate our techniques for a state-of-the-art TLS system and show that, with minimal hardware support, they lead to improvements in ED of up to 39.6% with an average of 21.2%, for a subset of the SPEC 2000 Integer benchmark suite.
Flexible gradient driver system for a multi-coil shim setup: design considerations and implementation (2017)

Purpose/Introduction: Recent studies have demonstrated the high potential of local, multi-coil shim setups to mitigate B0 field inhomogeneities through dynamic and global shimming[1][2]. For this approach, each coil needs an individually controllable current driver. The drivers must be able to supply a stable and reproducible current with a minimal power dissipation. Here, we demonstrate a 32-channel, low-cost, modular current driver that can source/sink up to 5A per channel and 120A in total to drive a wide range of inductive loads. Subjects and Methods: The amplifier core is mostly designed based on the Howland current source[3]. The circuit (Fig. 1a) is programmable during runtime by the user, which makes it adaptable for different inductive loads. Each channel comprises a pair of OPA549 high-current op-amps to push and pull the current to the load. A current sense resistor of 0.1X is series with the output to make simultaneous current feedback control and real-time monitoring possible. The power supply for each amplifier can be adjusted through a custom-made GUI. The user can also set an offset for each channel output to compensate for any current drift. The input for the amplifier is generated by a PXIe–6738 unit, a high-density analog output module, and first passes through a PID controller. The parameters of the PID controller are adjustable through the GUI to obtain the best performance for different loads. We packed two drivers into one module (Fig. 1b) that can be readily mounted/dismounted in an amplifier rack. Results: We used our amplifier to drive a home-built 16-channel multi-coil shim setup [1] inside a 9.4 T MR scanner. We applied a range of currents from -2A to +2A and in reverse order with a step size of 0.25A and acquired a B0 map to evaluate the drivers’ output characteristics. The drivers’ output linearity and hysteresis (Table 1) were evaluated by fitting a linear model to the measured B0 maps. After adjusting the PID parameters, a rise time of 50us was achieved by measuring the step response with a load of 128lH (Fig. 2a) while the coil was in the scanner’s bore. Enabling the driver and running a gradient-echo sequence resulted in a maximum current disturbance of 40 mA (Fig. 2b). No artifacts could be detected in the acquired images when the drivers were connected to the coil. Figure 2 Driver performance test; a) a rise time of 50us was achieved with a load of 200 lH; b) maximum current disturbance of 40 mA resulted when running GRE sequence Discussion/Conclusion: A 32-channel flexible modular multi-coil driver was constructed and evaluated successfully. Several safety regulations (thermal, current limit, voltage limit, etc.) are considered in design with adjustable margins.
703 Fabrication of ADC12 Porous Aluminum /A1050 Pipe Composite Materials by Friction Welding (2013)

Porous aluminum (Al) is a lightweight with high energy absorption properties and expected as structural materials In this study, porous Al core filled m Al pipe composite materials was fabricated by friction welding Precursor of porous Al was fabricated by mixing the Al plates and blowing agent powder by friction stir welding route Obtained precursor was put into the Al pipe, and rotating tool was pressed into the precursor Then, bonding Al precursor to Al pipe can be conducted by mean of plastic flow Porous Al core filled in Al pipe composite materials with metal bonding was successfully fabricated by heating the precursor By using X-ray CT, pore structure of inside porous Al was observed
Pilot signal generation scheme using frequency dependent cyclic shift sequence for inter-cell interference mitigation (2009)

Cyclic Shifted Zadoff-Chu (CS-ZC) sequences are adopted as a uplink pilot signal in Evolved Universal Terrestrial Radio Access (E-UTRA). In a Single Carrier Frequency Division Multiplexing Access (SC-FDMA) based cellular system, the Resource Blocks (RBs) are normally assigned independently among the cells. So, the assigned RBs to user equipment (UE) in different cells may partially overlap. These causes deteriorate the orthogonality between CS-ZC sequences. The deterioration of the orthogonality results in significant loss of channel estimation accuracy. The reason of the deterioration is that the different spectrum element of CS-ZC sequence is assigned at overlapped sub-carriers between cells. Therefore, we propose a frequency dependent cyclic shift sequence, which assigns the same spectrum element of CS-ZC sequence at overlapped sub-carriers between cells. Simulation results show that the proposed scheme can improve the BLER performance by 4dB with keeping the low Peak-to-Average power ratio (PAPR) property compared to the conventional scheme.
Fluoride-selective optical sensor based on the dipyrrolyl-tetrathiafulvalene chromophore (2011)

A chemosensor bearing dipyrrolyl motifs as recognition sites and a tetrathiafulvalene redox tag has been evaluated as an optical and redox sensor for a series of anions (F(-), Cl(-), Br(-), HSO(4)(-), CH(3)COO(-), and H(2)PO(4)(-)) in DCM solution. The receptor shows specific optical signaling for fluoride but little electrochemical effect in solution. The solid-state performance of the sensor leads to measurable changes in water. Design implications towards better systems based on these results and other examples are discussed.
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells (2010)

Our results reveal that an SVM approach can be useful for prioritizing genes for functional validation experiments and complement the analyses of high-throughput profiling experimental data in stem cell research.
ChemInform Abstract: Synthesis of Zymosterol, Fecosterol, and Related Biosynthetic Sterol Intermediates. (1989)

Abstract The dienes (IV) serve as common intermediates in the synthesis of zymosterol (VIIa), fecosterol (VIII) and the related compounds (V) and (VIIb).
Effect of crystallinity on the recovery rate of superhydrophobicity in plasma-nanostructured polymers (2020)

This study explored the optimum conditions to achieve superhydrophobicity in polyethylene terephthalate (PET) in terms of crystallinity and microstructure. Surface superhydrophobicity was achieved by nanostructures induced by oxygen plasma etching and the recovery process of low surface energy through thermal aging of various PETs; semi-crystalline biaxial PET (B-PET) film, amorphous PET (A-PET) film, and semi-crystalline PET (F-PET) fabric. Under the anisotropic plasma etching, the nanostructures on the B-PET film were the longest, followed by the F-PET fabric, which developed a hierarchical micro/nanostructure, then the A-PET film. During thermal aging at 80 °C near <i>T</i> <sub>g</sub>, the plasma-treated A-PET film recovered its superhydrophobicity within 3 h, while the plasma-treated B-PET film did not exhibit superhydrophobicity. At 130 °C, higher than <i>T</i> <sub>g</sub>, the plasma-treated B-PET film recovered its superhydrophobicity within 1 h, but the plasma-treated A-PET film became opaque as its nanostructures deformed, decreasing its superhydrophobicity. The plasma-treated F-PET fabric exhibited faster recovery and greater superhydrophobicity than the plasma-treated B-PET film, due to its hierarchical micro/nanostructure. In addition, hydrophobic recovery during thermal aging was proved with a decrease in surface polar groups, lowering the surface energy using XPS analysis. Therefore, by designing the ratio of crystal to amorphous regions and surface micro/nanostructures, one can rapidly fabricate superhydrophobic PETs without additional surface finishing.
Inhibiting Glycolysis and ATP Production Attenuates IL-33-Mediated Mast Cell Function and Peritonitis (2018)

Cellular metabolism and energy sensing pathways are closely linked to inflammation, but there is little understanding of how these pathways affect mast cell function. Mast cells are major effectors of allergy and asthma, and can be activated by the alarmin IL-33, which is linked to allergic disease. Therefore, we investigated the metabolic requirements for IL-33-induced mast cell function, to identify targets for controlling inflammation. We found that IL-33 increases glycolysis, glycolytic protein expression, and oxidative phosphorylation (OX PHOS). Inhibiting OX PHOS had little effect on cytokine production, but antagonizing glycolysis with 2-deoxyglucose or oxamate suppressed inflammatory cytokine production <i>in vitro</i> and <i>in vivo</i>. ATP reversed this suppression. Glycolytic blockade suppressed IL-33 signaling, including ERK phosphorylation, NFκB transcription, and ROS production <i>in vitro</i>, and suppressed IL-33-induced neutrophil recruitment <i>in vivo</i>. To test a clinically relevant way to modulate these pathways, we examined the effects of the FDA-approved drug metformin on IL-33 activation. Metformin activates AMPK, which suppresses glycolysis in immune cells. We found that metformin suppressed cytokine production <i>in vitro</i> and <i>in vivo</i>, effects that were reversed by ATP, mimicking the actions of the glycolytic inhibitors we tested. These data suggest that glycolytic ATP production is important for IL-33-induced mast cell activation, and that targeting this pathway may be useful in allergic disease.
Extreme Coverage Extension in 6G: Cooperative Non-terrestrial Network Architecture Integrating Terrestrial Networks (2022)

Because communications in the future will be as commonplace as the air around us and as important a lifeline as power and water or even more so, the Fifth Generation (5G) Evolution and Sixth Generation (6G) mobile communications systems aim ultimately to expand coverage so that mobile services are available ubiquitously. Towards that goal, we present a new architecture for 5G Evolution and 6G that integrates non-terrestrial networks (NTNs) with terrestrial networks (TNs). The proposed cooperative NTN and TN architecture is promising as a means for expanding coverage in the future because it enables improved cost efficiency by sharing equipment and conservation of frequency resources through shared frequencies. In addition, by making full use of wireless technologies such as handover, carrier aggregation, and dual connectivity between NTNs and TNs, users can connect to 5G Evolution and 6G networks anywhere without being aware of the connection destination. In this paper, we propose a cooperative architecture that focuses on the link between NTNs and TNs, and a cooperative configuration with a particular focus on high-altitude platform stations (HAPSs). Furthermore, we present a HAPS performance evaluation using a 6G system-level simulator developed as a stepping stone for actualizing HAPS technology.
Using Chromatin Immunoprecipitation to Map Cotranscriptional mRNA Processing in <I>Saccharomyces cerevisiae</I> (2004)

The chromatin immunoprecipitation (ChIP) technique has been used to determine where and under what conditions DNA binding proteins associate with specific DNA sequences. Proteins are crosslinked in vivo with formaldehyde, and chromatin is then isolated and sheared. The protein of interest is then immunoprecipitated and the associated DNA sequences identified via PCR. Although this technique was originally designed to assay DNA binding proteins, it can also be used to monitor mRNA processing factors associated with transcription complexes.
Exploiting named entity taggers in a second language (2005)

In this work we present a method for Named Entity Recognition (NER). Our method does not rely on complex linguistic resources, and apart from a hand coded system, we do not use any language-dependent tools. The only information we use is automatically extracted from the documents, without human intervention. Moreover, the method performs well even without the use of the hand coded system. The experimental results are very encouraging. Our approach even outperformed the hand coded system on NER in Spanish, and it achieved high accuracies in Portuguese.
Low CC16 mRNA Expression Levels in Bronchial Epithelial Cells Are Associated with Asthma Severity (2022)

Abstract Rationale CC16 is a protein mainly produced by nonciliated bronchial epithelial cells (BECs) that participates in host defense. Reduced CC16 protein concentrations in BAL and serum are associated with asthma susceptibility. Objectives Few studies have investigated the relationship between CC16 and asthma progression, and none has focused on BECs. In this study, we sought to determine if CC16 mRNA expression levels in BECs are associated with asthma severity. Methods Association analyses between CC16 mRNA expression levels in BECs (242 asthmatics and 69 control subjects) and asthma-related phenotypes in Severe Asthma Research Program were performed using a generalized linear model. Measurements and Main Results Low CC16 mRNA expression levels in BECs were significantly associated with asthma susceptibility and asthma severity, high systemic corticosteroids use, high retrospective and prospective asthma exacerbations, and low pulmonary function. Low CC16 mRNA expression levels were significantly associated with high T2 inflammation biomarkers (fractional exhaled nitric oxide and sputum eosinophils). CC16 mRNA expression levels were negatively correlated with expression levels of Th2 genes (IL1RL1, POSTN, SERPINB2, CLCA1, NOS2, and MUC5AC) and positively correlated with expression levels of Th1 and inflammation genes (IL12A and MUC5B). A combination of two nontraditional T2 biomarkers (CC16 and IL-6) revealed four asthma endotypes with different characteristics of T2 inflammation, obesity, and asthma severity. Conclusions Our findings indicate that low CC16 mRNA expression levels in BECs are associated with asthma susceptibility, severity, and exacerbations, partially through immunomodulation of T2 inflammation. CC16 is a potential nontraditional T2 biomarker for asthma development and progression.
Nitrogen sources affect productivity, desiccation tolerance and storage stability ofBeauveria bassianablastospores (2018)

Nitrogen is the most expensive nutrient in liquid media composition, but this study underscores the feasibility of using low-cost nitrogen compounds composed mainly of agro-industrial by-products for rapid production of desiccation-tolerant B. bassiana blastospores by liquid culture fermentation.
Heterogeneous expression of the adhesion receptor CD226 on murine NK and T cells and its function in NK-mediated killing of immature dendritic cells (2009)

The adhesion receptor CD226 (DNAM-1) is a member of the Ig superfamily possessing two extracellular V-like domains. In humans, CD226 was shown to be expressed by NK as well as T cells. During T cell priming, CD226-mediated costimulatory signals may skew the subsequent differentiation into the Th1 pathway. In addition, CD226 expressed on NK and cytotoxic T cells is engaged by its counter-receptor CD155, present on target cells, thereby triggering their elimination. We established mAb specifically recognizing mCD226, demonstrating that CD226 is expressed by precursor and mature but not developing T cells. In contrast, NK cells are distinguished by a rather heterogeneous CD226 expression profile. In addition, expression of CD226 appears coupled to that of other NK cell receptors, as high expression of CD226 was found to correlate with decreased proportions of Ly49D and H positive NK cells. Upon injection into mice, the anti-CD226 antibodies caused selective depletion of CD8(+) T cells. Moreover, these antibodies as well as a naturally occurring CD226 splice variant lacking the outermost V-like domain were instrumental in determining that CD226 adheres to CD155 via its first domain. In addition, antibodies were identified as capable of blocking the CD226/CD155 interaction and to prevent NK-driven killing of immature DC. CD226 is thus the first mNK receptor identified to be essential for the elimination of this particular cell type.