gebhart/patrepeval huggingface dataset:
Identification of diagnostic and therapeutic targets of pancreatic cancer using proteomic approaches (2009)

Pancreatic cancer remains one of the most lethal of all the solid malignancies. Using a quantitative proteomic strategy, we have carried out profiling studies to identify novel biomarkers and therapeutic targets in pancreatic cancer. Phosphotyrosine profiling revealed aberrant activation of epidermal growth factor receptor (EGFR) in a subset of pancreatic cancers. This correlated with phospho‐EGFR staining and response to the EGFR inhibitor, erlotinib, in mice carrying pancreatic cancer xenografts demonstrating the utility of activated EGFR as a biomarker that could be used to guide therapeutic decisions. Proteomic profiling of membrane fractions identified several proteins that are differentially expressed in pancreatic cancers. Immunohistochemical validation of one of the candidate markers, myeloid associated differentiation marker (MYADM), confirmed overexpression of this molecule in greater than 80% of pancreatic adenocarcinomas. Our studies emphasize the utility of advanced proteomic approaches in identifying novel biomarkers and therapeutic targets. This work was supported by Sol Goldman Trust for Pancreatic Cancer Research.
A direct role for c-fos in AP-1-dependent gene transcription. (1990)

Transcription factor activator protein 1 (AP-1) is a protein fraction that contains c-fos, c-jun, and several other related proteins. Although this protein fraction can stimulate transcription in vitro, the relative contributions of c-fos and c-jun to the transcriptional effect of AP-1 are not clear. In order to approach this question, we have overexpressed both proteins using a baculovirus-mediated expression system and defined their DNA-binding and transcriptional enhancement activities in vitro. Gel mobility-shift and DNase 1 footprinting assays showed that c-jun protein specifically binds to DNA through an AP-1 binding site. Under the same conditions, no detectable binding of c-fos protein was observed. However, when the DNA binding assays were performed in the presence of both c-jun and c-fos, a marked increase in the affinity of c-jun for the AP-1 site was observed. An AP-1-dependent transcription assay was used to test the capability of both proteins to stimulate correctly initiated RNA synthesis in vitro. Under our conditions, c-jun protein was capable of stimulating specific RNA transcription in an AP-1 site-dependent manner. In contrast, c-fos protein showed no detectable transcriptional activation by itself. However, a transcription assay carried out in the presence of both c-fos and c-jun proteins showed that the c-fos/c-jun complex was more active as a transcriptional regulator than c-jun protein alone. These experimental results indicate that c-fos and c-jun proteins are required to reconstitute full AP-1-dependent transcriptional activation and directly demonstrate that c-fos is a regulator of gene expression.
Imaging budgets for EUV optics: ready for 22-nm node and beyond (2009)

We derive an imaging budget from the performance of EUV optics with NA = 0.32, and demonstrate that the 22nm node requirements are met. Based on aerial image simulations, we analyze the impact of all relevant contributors, ranging from conventional quantities, like straylight or aberrations, to EUV-specific topics, namely influence of 3D mask effects and facetted illumination pupils. As test structures we consider dense to isolated lines, contact holes, and 2D elbows. We classify the contributions in a hierarchical order according to their weight in the CDU budget and identify the main drivers. The underlying physical mechanisms causing different contributions to be critical or less significant are clarified. Finally, we give an outlook for the 16nm and 11nm nodes. Future developments in optics manufacturing will keep the budgets controlled, thereby paving the way to enable printing of these upcoming nodes.
Application of Neural Networks to Population Pharmacokinetic Data Analysis (1997)

This research examined the applicability of using a neural network approach to analyze population pharmacokinetic data. Such data were collected retrospectively from pediatric patients who had received tobramycin for the treatment of bacterial infection. The information collected included patient-related demographic variables (age, weight, gender, and other underlying illness), the individual's dosing regimens (dose and dosing interval), time of blood drawn, and the resulting tobramycin concentration. Neural networks were trained with this information to capture the relationships between the plasma tobramycin levels and the following factors: patient-related demographic factors, dosing regimens, and time of blood drawn. The data were also analyzed using a standard population pharmacokinetic modeling program, NON-MEM. The observed vs predicted concentration relationships obtained from the neural network approach were similar to those from NONMEM. The residuals of the predictions from neural network analyses showed a positive correlation with that from NONMEM. Average absolute errors were 33.9 and 37.3% for neural networks and 39.9% for NONMEM. Average prediction errors were found to be 2.59 and -5.01% for neural networks and 17.7% for NONMEM. We concluded that neural networks were capable of capturing the relationships between plasma drug levels and patient-related prognostic factors from routinely collected sparse within-patient pharmacokinetic data. Neural networks can therefore be considered to have potential to become a useful analytical tool for population pharmacokinetic data analysis.
Evaluation of Mental Stress in Automated Following Driving (2018)

Automatic driving and auxiliary driving functions are expected to improve safety and efficiency, and reduce the burden on drivers. These driving assist functions change the task of the driver not to control the vehicle but to monitor the driving operation, which could lead to new kind of stress. In this research, the driver stress during automated follow-up driving is evaluated based on subjective evaluation in a driving simulator environment. We confirmed that the subjective anxiety change due to acceleration / deceleration intensity varies depending on the distance between vehicles.
A New Design of a Broadband Microwave Test Fixture for Odd Mode Excitation in Monolithic Coplanar Coupled Strips (1990)

In this paper, we present the design and performances of a precision microwave test fixture suitable for odd mode excitation in both monolithic and coplanar coupled strips (CPS). The proposed test fixture is based on a new type of a broadband coaxial-to-CPS transition. The test fixture was used to measure the Sij parameters of a GaAs monolithic CPS in the 2-18 GHz frequency range. Some time domain reflectometry results are presented.
Synthesis of O-Phosphotyrosine-Containing Peptides. II. Solution-Phase Synthesis of Asn-Glu-PTyr-Thr-Ala Through Methyl Phosphate Protection (1989)

The PTyr (O-phosphotyrosine) pentapeptide H-Asn-Glu-Tyr(PO3H2)-Thr-Ala-OH.HO2CCF3, which is a naturally occurring sequence from the autophosphorylated Rous sarcoma virus pp60V-SrC, was prepared in high yield by the use of Boc-Tyr(PO3Me2)-OH in the Boc mode of solution-phase peptide synthesis. The protected pentapeptide, Z-Asn-Glu(OBzl)-Tyr(PO3Me2)-Thr(Bzl)-Ala-OBzl, was deprotected by a two-stage procedure which involved initial palladium-catalysed hydrogenolysis followed by the removal of the phosphate methyl groups by the use of one of the following treatments: (A) 10% bromotrimethylsilane/acetonitrile, (B) 1 M bromotrimethylsilane/thioanisole in trifluoroacetic acid, or (C) trifluoromethanesulfonic acid/trifluoroacetic acid/dimethyl sulfide/ m -cresol.
Abstract 5310: Positron emission tomography imaging of endometrial cancer using an anti-EMP2 minibody (2011)

Abstract Endometrial cancer is increasingly affecting pre-menopausal women, prompting a need to develop fertility-sparing therapy, and monitor response to treatment by quantitative non-invasive strategies. Epithelial membrane protein 2 (EMP2) is a tetraspan protein associated with surface localization and function of cancer-relevant integrin isoforms, and EMP2 expression in endometrial cancer correlates with increasing cancer stage and poor prognosis. As EMP2 is highly expressed in endometrial cancer, this pre-clinical study tested the feasibility of non-invasive detection of human endometrial tumor xenografts using a radiolabeled anti-EMP2 diabody and positron emission tomography (PET). EMP2 biodistribution in murine organ was determined by western blot and immunohistochemistry. Anti-EMP2 minibody (MB83) fragment was designed and transfected into CHO-K1 cells. Purified minibody was DOTA conjugated and the binding activity was tested by flow cytometry using endometrial cancer cell line, Hec-1A/EMP2 cells. Then conjugated minibody was chelated with Cu-64. In vivo biodistribution of Cu-64 labeled MB83 in Balb/c nu/nu mice were determined by microPET imaging and AMIDE sofeware. MB83 location was determined by microPET in mice bearing Hec1a/EMP2 xenograft. EMP2 expression was detectable in the lung but not other organs by either western or immunohistochemistry. The absence of detectable EMP2 protein in the organs reflects that the target tumor with high EMP2 protein could uptake anti-EMP2 antibody which could be observed by microPET. The specific uptake of MB83 minibody within the Hec1a/EMP2 tumor can be seen both visually and quantitatively. Selective tumor uptake became more specific over time. In contrast, 2-deoxy-2-[18F]fluoro-D- glucose (FDG) microPET uptake by HEC-1A/EMP2 was minimal, reflecting the poor detection of gynecologic cancer cell types by conventional FDG-PET imaging. These findings demonstrate the feasibility of imaging endometrial and other gynecological cancers which have upregulated EMP2 expression using recombinant anti-EMP2 antibodies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5310. doi:10.1158/1538-7445.AM2011-5310
Metis: a thin-client application framework (1997)

Abstract This paper introduces a thin-client programming model and then presents an objectoriented framework for developing applications using the model. The programming model and the framework have evolved from interactions with developers and users of commercial applications. The key aspects of the thin-client programming model are that the client downloads application front ends from the network; that these applications rely only on services found on network servers; that the services are bound as late as possible; and that the applications interact with each other within the con nes of a workspace. We implemented the framework using Java Beans and JDK 1.1, and developed several sample applications using the framework. 1
Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry (2014)

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).
Comment lePlasmodiumse glisse dans un globule rouge (2004)

> Les rythrocytes sont incapables d'endocytose. Comment donc les parasites du genre Plasmodium, dont une partie importante du cycle parasitaire se droule l'intrieur des globules rouges, russissent-ils pntrer dans ces cellules ? C'est l la question fondamentale que se sont pos les auteurs d'un article rcent du groupe de K. Haldar [1]. Avant de discuter les travaux dcrits dans cet article, il est important de rappeler que, dans le globule rouge dans lequel il a pntr, le parasite ne sjourne pas directement au contact du cytoplasme rythrocytaire, mais lintrieur d'une vacuole dite vacuole parasitophore (VP). Des tudes ultrastructurales et biochimiques suggrent que la VP rsulte d'une invagination de la membrane plasmique des rythrocytes. Le groupe de K. Haldar avait montr antrieurement [2] que la VP contient certaines protines retenues la membrane par une liaison glycosyl phospatidyl inositol (GPI). Ces protines sont localises dans les fractions enrichies en radeaux rsistants aux dtergents (DRM, detergent-resistant membrane), alors que d'autres protines de la membrane plasmique rythrocytaire, qui ne sont pas associes ces radeaux, sont exclues de la VP. Une observation qui a retenu l'attention des auteurs tait l'inclusion dans la VP de certains membres de la famille des protines G htrotrimriques, comme la sous-unit Gs, alors que d'autres (par exemple Gq) en sont exclues. Les protines G htrotrimriques forment une famille de molcules membranaires, bien conserve chez les eucaryotes suprieurs, capables de lier le GTP, et dont le
Cone density at 1- degree and 3-degree retinal eccentricity. (2015)

&lt;p&gt;***: &lt;i&gt;P&lt;/i&gt; &lt;0.001, Wilcoxon’s signed rank test.&lt;/p&gt;&lt;p&gt;Cone density at 1- degree and 3-degree retinal eccentricity.&lt;/p&gt;
Data from Genetic Heterogeneity and Tissue-specific Patterns of Tumors with Multiple <i>PIK3CA</i> Mutations (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;To comprehensively characterize tissue-specific and molecular subclasses of multiple &lt;i&gt;PIK3CA&lt;/i&gt; (multi-&lt;i&gt;PIK3CA&lt;/i&gt;) mutations and assess their impact on potential therapeutic outcomes.&lt;/p&gt;Experimental Design:&lt;p&gt;We profiled a pan-cancer cohort comprised of 352,392 samples across 66 tumor types using a targeted hybrid capture-based next-generation sequencing panel covering at least 324 cancer-related genes. Molecularly defined subgroups, allelic configuration, clonality, and mutational signatures were identified and tested for association with PI3K inhibitor therapeutic response.&lt;/p&gt;Results:&lt;p&gt;Multi-&lt;i&gt;PIK3CA&lt;/i&gt; mutations are found in 11% of all &lt;i&gt;PIK3CA&lt;/i&gt;-mutant tumors, including 9% of low tumor mutational burden (TMB) &lt;i&gt;PIK3CA&lt;/i&gt;-mutant tumors, and are enriched in breast and gynecologic cancers. Multi-&lt;i&gt;PIK3CA&lt;/i&gt; mutations are frequently clonal and in &lt;i&gt;cis&lt;/i&gt; on the same allele and occur at characteristic positions across tumor types. These mutations tend to be mutually exclusive of mutations in other driver genes, and of genes in the PI3K pathway. Among &lt;i&gt;PIK3CA&lt;/i&gt;-mutant tumors with a high TMB, 18% are multi-&lt;i&gt;PIK3CA&lt;/i&gt; mutant and often harbor an apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) mutational signature. Despite large differences in specific allele combinations comprising multi-&lt;i&gt;PIK3CA&lt;/i&gt; mutant tumors, especially across cancer types, patients with different classes of multi-&lt;i&gt;PIK3CA&lt;/i&gt; mutant estrogen receptor–positive, HER2-negative breast cancers respond similarly to PI3K inhibition.&lt;/p&gt;Conclusions:&lt;p&gt;Our pan-tumor study provides biological insights into the genetic heterogeneity and tissue specificities of multi-&lt;i&gt;PIK3CA&lt;/i&gt; mutations, with potential clinical utility to guide PI3K inhibition strategies.&lt;/p&gt;&lt;/div&gt;
Synthesis, Electronic Structure, and Charge Transport Characteristics of Naphthalenediimide‐Based Co‐Polymers with Different Oligothiophene Donor Units (2013)

Naphthalenediimide (NDI)‐based polymers co‐polymerized with thienyl units are an interesting class of polymer semiconductors because of their good electron mobilities and unique film microstructure. Despite these properties, understanding how the extension of the thienyl co‐monomer affects charge transport properties remains unclear. With this goal in mind, we have synthesized a series of NDI derivatives of the parent poly{[ N,N ′‐bis(2‐octyldodecyl)‐naphthalene‐1,4,5,8‐bis(dicarboximide)‐2,6‐diyl]‐alt‐5,5′‐(2,2′‐bithiophene) (P(NDI2OD‐T2)), which exhibited excellent electron mobility. The strategy comprises both the extension of the donor o‐conjugation length and the heteroatomic fusion of the thiophene rings. These newly synthesized compounds are characterized experimentally and theoretically vis‐à‐vis with P(NDI2OD‐T2) as the reference. UV‐vis data and cyclic‐voltammetry are adopted to assess the effect of the donor modification on the frontier energy levels and on the bandgap. Intra‐molecular polaronic effects are accounted for by computing the internal reorganization energy with density functional theory (DFT) calculations. Finally electrons and holes transport is experimentally investigated in field‐effect transistors (FETs), by measuring current‐voltage characteristics at variable temperatures. Overall we have identified a regime where inter‐molecular effects, such as the wavefunction overlap and the degree of energetic disorder, induced by the different donor group prevail over polaronic effects and are the leading factors in determining electrons mobility.
CLA og andre stoffer i mælk relateret til den humane sundhed - hvordan kan primærproducenten påvirke indholdet (2005)

Mælkens indhold af CLA er interessant ud fra en human ernæringssynsvinklen, idet flere undersøgelser har vist en positiv sammenhæng mellem indtag af CLA og risikoen for cancer. Der blev fundet en betydelig variation mellem bedrifter i mælkens indhold af CLA, og ikke noget entydigt billede af niveauet i konventionel og økologisk mælk. Resultater viser desuden at foderrationens sammensætning påvirker niveauet, men også at der synes at være en forskel mellem de enkelte køer.&#13;\n&#13;\n&#13;\n
In‐flight calibration and performance of the Mars Exploration Rover Panoramic Camera (Pancam) instruments (2006)

The Mars Exploration Rover Panoramic Camera (MER/Pancam) instruments have acquired more than 60,000 high‐resolution, multispectral, stereoscopic images of soil, rocks, and sky at the Gusev crater and Meridiani Planum landing sites since January 2004. These images, combined with other MER data sets, have enabled new discoveries about the composition, mineralogy, and geologic/geochemical evolution of both sites. One key to the success of Pancam in contributing to the overall success of MER has been the development of a calibration pipeline that can quickly remove instrumental artifacts and generate both absolute radiance and relative reflectance images with high accuracy and precision in order to influence tactical rover driving and in situ sampling decisions. This paper describes in detail the methods, assumptions, and models/algorithms in the calibration pipeline developed for Pancam images, based on new measurements and refinements performed primarily from flight data acquired on Mars. Major calibration steps include modeling and removal of detector bias signal, active and readout region dark current, electronic “shutter smear,” and pixel‐to‐pixel responsivity (flatfield) variations. Pancam images are calibrated to radiance (W/m 2 /nm/sr) using refined preflight‐derived calibration coefficients, or radiance factor (I/F) using near‐in‐time measurements of the Pancam calibration target and a model of aeolian dust deposition on the target as a function of time. We are able to verify that the absolute radiance calibration of most Pancam images is accurate to within about 10% or less and that the filter‐to‐filter and pixel‐to‐pixel precision of the calibrated relative reflectance data (both based on measurements of the Pancam calibration target) are typically about 3% and 1% or less, respectively. Examples are also presented of scientific applications made possible by the high fidelity of the calibrated Pancam data. These include 11‐color visible to near‐IR spectral analysis, calculation of “true color” and chromaticity values, and generation of “super resolution” image data products. This work represents a follow‐on and enhancement to the Pancam preflight calibration process described by Bell et al. (2003).
Enhancing Favorable Propagation in Cell-Free Massive MIMO Through Spatial User Grouping (2018)

Cell-Free (CF) Massive multiple-input multiple-output (MIMO) is a distributed antenna system, wherein a large number of back-haul linked access points randomly distributed over a coverage area serve simultaneously a smaller number of users. CF Massive MIMO inherits favorable propagation of Massive MIMO systems. However, the level of favorable propagation which highly depends on the network topology and environment may be hindered by user' spatial correlation. In this paper, we investigate the impact of the network configuration on the level of favorable propagation for a CF Massive MIMO network. We formulate a user grouping and scheduling optimization problem that leverages users' spatial diversity. The formulated design optimization problem is proved to be NP-hard in general. To circumvent the prohibitively high computational cost, we adopt the semidefinite relaxation method to find a sub-optimal solution. The effectiveness of the proposed strategies is then verified through numerical results which demonstrate a non-negligible improvement in the performance of the studied scenario.
Optoelectronic properties and depth profile of charge transport in nanocrystal films (2017)

We investigate the charge transport in nanocrystal (NC) films using field effect transistors (FETs) of silicon NCs. By studying films with various thicknesses in the dark and under illumination with photons with different penetration depths (UV and red light), we are able to predictably change the spatial distribution of charge carriers across the films' profile. The experimental data are compared with photoinduced charge carrier generation rates computed using finite-difference time-domain (FDTD) simulations complemented with optical measurements. This enables us to understand the optoelectronic properties of NC films and the depth profile dependence of the charge transport properties. From electrical measurements, we extract the total (bulk) photoinduced charge carrier densities (${n}_{\text{photo}}$) and the photoinduced charge carrier densities in the FETs channel (${n}_{\text{photo}}^{*}$). We observe that the values of ${n}_{\text{photo}}$ and their dependence on film thickness are similar for UV and red light illumination, whereas a significant difference is observed for the values of ${n}_{\text{photo}}^{*}$. The dependencies of ${n}_{\text{photo}}$ and ${n}_{\text{photo}}^{*}$ on film thickness and illumination wavelength are compared with data from FDTD simulations. Combining experimental data and simulation results, we find that charge carriers in the top rough surface of the films cannot contribute to the macroscopic charge transport. Moreover, we conclude that below the top rough surface of NC films, the efficiency of charge transport, including the charge carrier mobility, is homogeneous across the film thickness. Our work shows that the use of NC films as photoactive layers in applications requiring harvesting of strongly absorbed photons such as photodetectors and photovoltaics demands a very rigorous control over the films' roughness.