gebhart/patrepeval huggingface dataset:
148 Identification of prostate-restricted epithelial antigens for transgenic T cell adoptive therapy against prostate cancer (2020)

<h3>Background</h3> In advanced prostate cancer (PCa), progression to castration-resistant PCa (CRPC) is inevitable and novel therapies for CRPC are needed. Adoptive transfer of T cells targeting tumor antigens is a promising approach in the cancer field. Unfortunately, identifying antigens expressed exclusively in prostate tumor cells has been challenging. Since the prostate is not an essential organ, we alternatively selected prostate-restricted epithelial antigens (PREAs) expressed in both malignant and normal prostate tissue for transgenic T cell studies. <h3>Methods</h3> RNA-seq data sets identifying genes enriched in PCa were cross-referenced with the NIH Genotype-Expression database to identify PREAs. Using a novel molecular immunology approach, select PREAs and major histocompatibility complex class I (MHC-I) molecules were co-expressed in HEK293F cells, from which MHC–peptide complexes were efficiently isolated. Peptides were eluted and sequenced by mass spectrometry. Peptide–MHC binding was validated with a T2 stabilization assay and peptide immunodominance was determined using an interferon-γ (IFN-γ) ELISpot assay following stimulation of healthy HLA-A2+ peripheral blood mononuclear cells (PBMC) with peptide pools. Following peptide stimulation, CD8+ T cells with peptide-specific T cell receptors (TCR) were enriched by peptide–MHC-I dextramer labeling and fluorescence activated cell sorting for single cell TCR α/β chain sequencing. <h3>Results</h3> We identified 11 A2+ peptides (8 previously unpublished) from prostatic acid phosphatase (ACPP), solute carrier family 45 member 3 (SLC45A3), and NK3 homeobox 1 (NKX3.1) that bound to HLA-A2 with varying affinities. Extended culture stimulation of PBMC with peptide pools from each PREA, compared to the standard overnight culture, revealed a greater number of IFN-γ producing cells overall and a greater breadth of response across all the peptides. Antigen specific CD8+ T cells were detectable at low frequencies in both male and female healthy PBMC for 7 of the 11 peptides. Dextramer-sorted antigen-specific cells were used for single-cell paired TCR αβ sequencing and transgenic T cell development. <h3>Conclusions</h3> Through this work we identified HLA-A2-presented antigenic peptides from the PREAs ACPP, SLC45A3, and NKX3.1 that can induce the expansion of IFN-γ producing CD8+ T cells. Through peptide–MHC-I dextramer labeling, we isolated PREA-specific CD8+ T cells and characterized TCR αβ sequences with potential anti-tumor functionality. Our results highlight a rapid and directed platform for the development of MHC-I-restricted transgenic CD8+ T cells targeting lineage-specific proteins expressed in prostate epithelia for adoptive therapy of advanced PCa.
Supplemental Figure 4 from MCL-1 Is a Key Determinant of Breast Cancer Cell Survival: Validation of MCL-1 Dependency Utilizing a Highly Selective Small Molecule Inhibitor (2023)

&lt;p&gt;Supplemental Figure 4: &lt;i&gt;BCL-X&lt;sub&gt;L&lt;/sub&gt;&lt;/i&gt; but not &lt;i&gt;BCL-2&lt;/i&gt; gene silencing sensitize HCC-1806 cells to A-1210477-induced apoptosis.&lt;/p&gt;
Isolated tibial insert exchange in revision total knee arthroplasty (2021)

After ITIE, the risk and reasons for re-revision correlated with preoperative indications. The best results were for polyethylene wear. For other diagnoses, the re-revision rate was higher and the failure mode was most commonly recurrence of the original indication for the revision TKA. Cite this article: <i>Bone Joint J</i> 2021;103-B(6):1103-1110.
Color and Pulsed Doppler Sonography for Arterial Bleeding Detection (2007)

Our results indicate that both color and pulsed Doppler sonography can be used to accurately localize the site of injury, which may facilitate application of hemorrhage control therapies in battlefield situations.
Editorial (2005)

We are very pleased to present this special thematic issue of the Journal of Mass Spectrometry, which is dedicated to research in the neurosciences that utilizes mass spectrometry. Over the past decades mass spectrometry has increasingly been a very important instrument for studying CNS tissue, especially brain. With increasing focus, this technology has been applied to studies that seek to discover the identities and functions of different neurotransmitters, proteins and neuropeptides as well as drugs and metabolites in biological processes of the brain. The papers included in the present issue of JMS represents different approaches of utilizing mass spectrometry in neuroscience. The number of papers that have been published the last 10 years using mass spectrometry in a neuroscience related research project according to ISI Web of Science has increased dramatically (see Figure 1). We anticipate this just to be the start of the integration of neuroscience and mass spectrometry—from the brains of the small insects to human brain tissue—from small molecules to large proteins. We wish to thank our many colleagues and friends in leading for their contribution to this special issue. We also wish to acknowledge and express our sincere gratitude to the reviewers and others who have labored to make this issue possible. Number of mass spectrometry publications in neuroscience from 1995 to 2004. Search words were mass spectrometry and neuro* at ISI Web of Science http://isi3.newisiknowledge.com.
Auger analysis of ultrathin SiO2 layers on silicon (1979)

The Auger LVV lines of ultrathin SiO2 layers thermally grown on Si are analyzed by comparing the measured lines with lines synthesized from standard SiO2 and Si lines. The synthesized lines were corrected for ion and electron beam effects and charging. The synthesis technique provides quantitative interpretation of the Auger lines in the interfacial region. An apparent thickness-dependent transition region is observed which can be explained as either a graded SiO2-Si region or as an abrupt SiO2-Si transition with a nonuniformly thick oxide. The latter is the more probable.
"Paradoxes" of carrier lifetime measurements in high-voltage SiC diodes (2001)

For Silicon Carbide (SiC) high-voltage rectifier diodes, contradictions appear when the most important parameter of the diodes, the minority carrier lifetime, is measured by different techniques. A qualitative analysis and a computer simulation have been carried out to clarify the origin of these contradictions. For 4H-SiC p/sup +/n diodes with 6 kV blocking capability, data on residual voltage drop at high current densities, switch-on time, reverse current recovery, and post-injection voltage decay are analyzed. It is shown that the whole set of experimental data can be explained by the existence of a thin (l/spl sim/0.1 /spl mu/m) layer near the metallurgical boundary of the p/sup +/n junction with very small carrier lifetime /spl tau//sub l/ that is essentially smaller than the carrier lifetime /spl tau/ across the remaining part of the 50-/spl mu/m n-base. It is emphasized that the existence of such a layer allows, under certain conditions, the combination of a relatively low residual forward voltage drop and very fast reverse recovery. Approaches to minority carrier lifetime measurements are discussed.
[D-Ala1, Leu9-ψ-CH2NH-Leu0]Neuromedin C Antagonizes Neuromedin C-Stimulated Amylase Release by Acini Isolated from the Rat Pancreas (1990)

Two novel neuromedin C analogs [D-Ala1, Leu9-psi-CH2NH-Leu10]neuromedin C and [Leu9-psi-CH2NH-Leu10]neuromedin C, were synthesized by rapid solid phase methods and examined for their abilities to inhibit neuromedin C-stimulated amylase release by isolated rat pancreatic acini. Both analogs significantly inhibited maximally stimulated amylase release by neuromedin C in a dose-dependent manner with maximal inhibition seen at concentrations of 100 and 300 microM of [D-Ala1, Leu9-psi-CH2NH-Leu10]neuromedin C and [Leu9-psi-CH2NH-Leu10]neuromedin C, respectively. The IC50 (concentration required to half-maximally inhibit neuromedin C-stimulated amylase release) was 1.5 microM for [D-Ala1, Leu9-psi-CH2NH-Leu10]neuromedin C compared to a 13.4 microM IC50 for [Leu9-psi-CH2NH-Leu10]neuromedin C. The [D-Ala1, Leu9-psi-CH2NH-Leu10]neuromedin C analog produced a parallel rightward shift in the neuromedin C dose-response curve and Schild plots of the inhibition data gave a slope of 0.969 +/- 0.121 and a pA2 (apparent affinity for the acinar cell receptor in terms of neuromedin C receptor-stimulated amylase release) of 100 nM. While [D-Ala1, Leu9-psi-CH2NH-Leu10]neuromedin C significantly inhibited both neuromedin B- and gastrin releasing peptide-stimulated amylase release, the analog did not inhibit amylase release in response to either cholecystokinin octapeptide, vasoactive intestinal peptide, substance P, carbamylcholine, the Ca2+ ionophore A23187, forskolin, or 8-bromo-cyclic AMP. The results demonstrate that [D-Ala1, Leu9-psi-CH2NH-Leu10]neuromedin C is a potent, specific, and competitive antagonist for neuromedin C and peptides of the gastrin releasing peptide family and may serve as a useful molecule for exploring the physiological role of these peptides.
Synthesis and properties of KTN films by sol-gel deposition and RF-magnetron sputtering (2001)

Abstract Homogeneous KTN (Potassium Tantalate Niobate) solutions were prepared using potassium acetate and metal alkoxides in 2-methoxyethanol by controlled hydrolysis with 1:2 (KTN/H2O) molar ratio. We report on the synthesis of sol-gel KTN for both the fabrication of homogeneous, dense and stoichiometrically correct ceramic discs by hot isostatic pressing and the deposition of spin-on as well as sputtered thin films. The spin-on KTN films on Pt/Si or r-sapphire were polycrystalline and stoichiometric, however, sputtered films on sapphire were fully (100) oriented and polycrystalline on Pt/SiO2/Si substrates with some potassium deficiency. The refractive indices of sputtered, dense KTN films on sapphire were between 2.00 and 2.05.
Role of CeO2-ZrO2Support for Structural, Textural and Functional Properties of Ni-based Catalysts Active in Dry Reforming of Methane (2019)

Positive environmental and technological contexts make dry methane reforming (DMR) an extensively studied reaction. During this process two main greenhouse gases CH 4 and CO 2 can be simultaneously converted into syngas – a mixture of CO and H 2 . Supported-nickel is one of the most frequently applied DMR catalysts. Their activity depends mainly on Ni concentration, kind of its precursor and a deposition method. As DMR is a demanding high-temperature reaction, it requires not only an active but first a very stable catalyst. Structural, textural and functional properties of such support remain thus of crucial efficiency. Main aim of this work was to elucidate how the synthesis of CeO 2 -ZrO 2 support obtained by supercritical fluid method ( i.e. at temperature of 400°C under a pressure of 25 MPa), can influence the properties of Ni-based DMR catalysts. The supports of various compositions (CeO 2 content from 100 to 0 %), subsequently calcined at 800°C for 6h in air have been analyzed. Nickel was deposited from nitrate(V) precursor via classical wet impregnation. The final catalysts have been characterized structurally (XRD, RS), texturally (BET, SEM) and functionally (UV/Vis-DR, XPS). Catalytic tests in dry methane reforming reaction have been performed to determine activity and stability of the synthesized samples.
Electron beam melting of Inconel 718: Effects of processing and post-processing (2018)

This study reports the effect of process temperature on microstructure evolution of electron beam melted Inconel 718. Samples fabricated at 915°C had fine grain boundary δ (∼200 nm) along with coarse intragranular δ spanning through the length of the grains. On the other hand, samples fabricated at 990°C, only had grain boundary δ along with secondary carbides. During hot isostatic pressing, the distribution of carbides governs the grain growth vs. lack of it. The samples fabricated at 990°C having grain boundary carbides had no grain growth owing to the pinning effect of carbides. In contrast, the sample processed at 915°C had significant grain growth owing to dissolution of grain boundary δ phase and absence of grain boundary carbides.
Sensitivity minimization in active networks by port compensation (2017)

This paper extends the notion of sensitivity of feedback systems defined by Bode to interconnected linear multiport active networks. In feedback theory the sensitivity function of the feedback system is a measure of gain and phase as a function of frequency linking variations between closed loop and open loop system. In this paper an analogous sensitivity function is defined for port interconnected networks which is a multiplier between variations in a network’s variable with and without interconnection of compensation at the ports. Like in feedback theory this paper shows that the sensitivity function of the compensated multiport network has an affine parametrization in terms of stable network functions. This opens up a way to optimize the sensitivity function for multiport networks analogous to optimization in feedback theory well known as Hα optimal feedback design. An illustrative sensitivity minimization problem is also demonstrated.
Abstract 1822: Selective inhibition of ZCCHC11/ZCCHC6 TUTases with genetic and pharmacological tools supports a role in glioblastoma cell growth (2022)

Abstract The purpose of the study was to determine if genetic and pharmacological inhibition of terminal uridyltransferases (TUTases) ZCCHC11 and ZCCHC6 could modulate Glioblastoma (GBM) cell growth in vitro. ZCCHC11 (also known as TUT4 and TENT3A) and ZCCHC6 (also known as TUT7 and TENT3B) catalyze uridylation of diverse RNA species. Recent evidence indicates that genetic perturbation of ZCCHC11/6 expression can disrupt cell proliferation of both immortalized and patient-derived primary GBM cell lines (Kim et al., Mol Cell 2020). We confirmed that genetic inhibition of ZCCHC11/6 with siRNA or CRISPR can decrease viability of U-87 MG and A-172 GBM cell lines, and we identified DK-MG as another GBM cell line with sensitivity to ZCCHC11/6 knockdown. Herein, we report the first novel, potent, and selective inhibitor of ZCCHC11/6, TS-1. Biochemically, TS-1 can block ZCCHC11/6-mediated uridylation of an RNA substrate in vitro (IC50 = 0.65 nM for recombinant ZCCHC11 protein; IC50 = 9.6 nM for recombinant ZCCHC6 protein). ZCCHC11/6 inhibitor TS-1 could decrease cell viability in U-87 MG, A-172 and DK-MG cells (cell viability IC50s ranging between 0.7-1.5 μM) and induce apoptosis and cell cycle arrest. A cellular assay detecting uridylation of miR-191 as a marker for ZCCHC11/6 activity was developed and validated. TS-1 strongly decreased uridylation of miR-191 in U-87 MG, A-172 and DK-MG cells (IC50 ranging between 10-40 nM). In contrast, TS-2, a weakly active enantiomer of TS-1 (enzyme IC50 = 0.15 μM and 1.8 μM against ZCCHC11 and ZCCHC6, respectively), had less impact on cell viability, apoptosis, cell cycle and uridylation in cells. In conclusion, we have verified ZCCHC11/6-dependency in a set of GBM cell lines and we have also developed a first-in class potent and selective small molecule that reduces in vitro Glioblastoma cell proliferation through selective inhibition of TUTases activity. Citation Format: Robinson Triboulet, Khikmet Sadykov, Jessica L. Johnson, Andrew R. Snyder, Sarah K. Knutson, Pavan Kumar, Christopher B. Mayo, Dillon Hawley, Andrew Madanjian, Ross L. Stein, David M. Wilson, Darren M. Harvey, Shomir Ghosh, Robert M. Campbell. Selective inhibition of ZCCHC11/ZCCHC6 TUTases with genetic and pharmacological tools supports a role in glioblastoma cell growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1822.
Variance analysis of frequency response function measurements using periodic excitations (2004)

The influence of disturbing noise and non-linear distortions on frequency response function (FRF) measurements using periodic excitations has been studied in detail in the literature. A variance analysis method has been developed that allows to detect and quantify the non-linear distortions and the disturbing noise. In this paper the variance analysis is generalised to detect and quantify the following non-stationary disturbances: (i) non-synchronous periodic signals, for example the 50Hz mains and its harmonics, and (ii) non-stationary behaviour of the device under test, for example phase or frequency modulation.
OPTIMIZATION OF ASSEMBLY LINE LAY-OUT BY COMPUTER-AIDED CHOICE OF ASSEMBLY METHODS AND LINE BALANCING (2023)

This paper presents an integrated method for the design of logical lay-out of assembly lines. It proposes a computer-aided tool to choose the assembly method (manual, hard automated or robotized) for all the assembly operations which have to be performed and assign them to workstations along the line by minimizing the number of stations.<br> After an overview of related works, the paper presents a line balancing method developed on the basis of Grouping Genetic Algorithms (Genetic Algorithms heavily modified to suit grouping problems) to design the logical lay-out of the line.<br> The second part of the paper is devoted to the classification of the main criteria used by the decision-aid tool developed for the choice of the assembly method.<br> The third part of the paper describes the link between the decision-aid tool and the line-balancing software. Finally, conclusions and guidelines for further work are presented.
MScreen: An Integrated Compound Management and High-Throughput Screening Data Storage and Analysis System (2012)

High-throughput screening (HTS) has historically been used by the pharmaceutical industry to rapidly test hundreds of thousands of compounds to identify potential drug candidates. More recently, academic groups have used HTS to identify new chemical probes or small interfering RNA (siRNA) that can serve as experimental tools to examine the biology or physiology of novel proteins, processes, or interactions. HTS presents a significant challenge with the vast and complex nature of data generated. This report describes MScreen, a Web-based, open-source cheminformatics application for chemical library and siRNA plate management, primary HTS and dose-response data handling, structure search, and administrative functions. Each project in MScreen can be secured with passwords or shared in an open-information environment that enables collaborators to easily compare data from many screens, providing a useful means to identify compounds with desired selectivity. Unique features include compound, substance, mixture, and siRNA plate creation and formatting; automated dose-response fitting and quality control (QC); and user, target, and assay method administration. MScreen provides an effective means to facilitate HTS information handling and analysis in the academic setting so that users can efficiently view their screening data and evaluate results for follow-up.
Abstract 1133: Discovery of novel small molecule inhibitors of RNA-binding protein Musashi-1 (2017)

Abstract 1) Background and Objective: Musashi-1(Msi1) is an RNA-binding protein that negatively regulates translation by binding to the 3′-UTRs of target mRNAs including Numb, APC and p21WAF-1, key regulators of Notch, Wnt signaling and cell cycle progression, respectively. We aim to identify small molecule inhibitors of Msi1’s mRNA-binding activity thus blocking the growth of a broad range of cancer cells. 2) Methods: Fluorescence polarization assay was used to screen for small molecules that disrupt the binding of Msi1 to its consensus RNA binding site. Hits were validated by surface plasmon resonance, amplified luminescent proximity homogeneous assay and nuclear magnetic resonance. 3) Results: Among ~2,000 small molecules we screened, we found several clusters of compounds that disrupt the Msi1-numb RNA binding potently, including natural products, herbal extracts and fungal metabolites. One of the clusters is the derivatives of the secondary metabolites from Aspergillus nidulans. The top hit, Aza-9, from this cluster was validated by amplified luminescent proximity homogeneous assay. Further validation by surface plasmon resonance and nuclear magnetic resonance indicate that Aza-9 binds to Msi1 directly, in the RNA binding pocket. 4) Discussion and Conclusions: Our study supports the hypothesis that Msi1 inhibition is a viable and effective anti-cancer strategy. More target validation assays will be carried out for the compounds from other clusters. Citation Format: Lan Lan, Amber Smith, Xiaoqing Wu, Anuradha Roy, Ragul Gowthaman, John Karanicolas, Amber D. Somoza, Clay C.C. Wang, Berl Oakley, Roberto De Guzman, Kristi Neufeld, Liang Xu. Discovery of novel small molecule inhibitors of RNA-binding protein Musashi-1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1133. doi:10.1158/1538-7445.AM2017-1133
Innovating in india: designing for constraint, computing for inclusion (keynote) (2014)

A fundamental tenet of user-centered design is that the needs, wants, limitations, and contexts of end users are central to the process of creating products and services that can be used and understood by the people who will use them. Most of the time these end users aren’t all that different from the people designing the technology. But as the differences increase between designers and the people they’re designing for, understanding and empathizing with users becomes harder and even more important. As we build software for people and communities with vastly diverse backgrounds, cultures, languages, and education, we need to stretch our ideas of what users want and need and how best to serve them.
Identification of the site of interruption in relaxed circles producing during bacteriophage lambda DNA circle replication (1977)

The DNA that accumulates in the lambda infection restricted to the early (circular) stage of replication consists of approximately two-thirds covalently closed circles and one-third relaxed circles bearing a single interruption in either strand of the duplex. The latter molecules are presumed to be a unique class in that the interruption is not repairable by DNA polymerase and ligase. Preferential radioisotopic labeling of the region immediately adjacent to the interruption, followed by hybridization to sheared fragments of the lambda chromosome with varying guanine plus cytosine content, suggested that the nick resides at the position of the mature molecular ends of the lambda chromosome. Digestion of the labeled molecules with restriction enzymes and reconstruction experiments in which Hershey circles were generated by annealing of interrupted strands isolated from the relaxed circles support this interpretation. The results indicate that the relaxed circles consist of a population containing one interruption in either of the two strands of the duplex jointly representing the two "nicks" contained in Hershey circles (in which the cohesive ends are annealed). These molecules could result from the inability of the maturation function to make the required staggered endonucleolytic cuts when the DNA substrate is a monomeric circle rather than a multimeric linear molecule. Alternatively, this interruption could be the result of an endonucleolytic cutting event critical to DNA replication.