gebhart/patrepeval huggingface dataset:
Urinary cytology has a poor performance for predicting invasive or high‐grade upper‐tract urothelial carcinoma (2011)

• In this cohort of patients with UTUC treated with radical surgery, urine cytology in isolation lacked performance characteristics to accurately predict muscle-invasive or high-grade disease. • Improved surrogate markers for pathological grade and stage are necessary, particularly when considering endoscopic modalities for UTUC.
A Multidimensional System for Phosphopeptide Analysis Using TiO2Enrichment and Ion-exchange Chromatography with Mass Spectrometry (2012)

Although offline enrichment of phosphorylated peptides is widely used, enrichment for phosphopeptides using <TEX>$TiO_2$</TEX> is often performed manually, which is labor-intensive and can lead to irreproducible results. To address the problems associated with offline enrichment and to improve the effectiveness of phosphopeptide detection, we developed an automated online enrichment system for phosphopeptide analysis. A standard protein mixture comprising BSA, fetuin, crystalline, <TEX>${\alpha}$</TEX>-casein and <TEX>${\beta}$</TEX>-casein, and ovalbumin was assessed using our new system. Our multidimensional system has four main parts: a sample pump, a 20-mm <TEX>$TiO_2$</TEX>-based column, a weak anion-exchange, and a strong cation-exchange (2:1 WAX:SCX) separation column with LC/MS. Phosphorylated peptides were successfully detected using the <TEX>$TiO_2$</TEX>-based online system with little interference from nonphosphorylated peptides. Our results confirmed that our online enrichment system is a simple and efficient method for detecting phosphorylated peptides.
Combination of Autoantibody Signature with PSA Level Enables a Highly Accurate Blood-Based Differentiation of Prostate Cancer Patients from Patients with Benign Prostatic Hyperplasia (2015)

Although an increased level of the prostate-specific antigen can be an indication for prostate cancer, other reasons often lead to a high rate of false positive results. Therefore, an additional serological screening of autoantibodies in patients' sera could improve the detection of prostate cancer. We performed protein macroarray screening with sera from 49 prostate cancer patients, 70 patients with benign prostatic hyperplasia and 28 healthy controls and compared the autoimmune response in those groups. We were able to distinguish prostate cancer patients from normal controls with an accuracy of 83.2%, patients with benign prostatic hyperplasia from normal controls with an accuracy of 86.0% and prostate cancer patients from patients with benign prostatic hyperplasia with an accuracy of 70.3%. Combining seroreactivity pattern with a PSA level of higher than 4.0 ng/ml this classification could be improved to an accuracy of 84.1%. For selected proteins we were able to confirm the differential expression by using luminex on 84 samples. We provide a minimally invasive serological method to reduce false positive results in detection of prostate cancer and according to PSA screening to distinguish men with prostate cancer from men with benign prostatic hyperplasia.
Vertical-cavity surface-emitting lasers: Design, growth, fabrication, characterization (1991)

The authors have designed, fabricated, and tested vertical-cavity surface-emitting lasers (VCSEL) with diameters ranging from 0.5 mu m to>50 mu m. Design issues, molecular beam epitaxial growth, fabrication, and lasing characteristics are discussed. The topics considered in fabrication of VCSELs are microlaser geometries; ion implementation and masks; ion beam etching packaging and arrays, and ultrasmall devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Polyomavirus small t antigen: overproduction in bacteria, purification, and utilization for monoclonal and polyclonal antibody production (1986)

Polyomavirus small t antigen was purified from genetically engineered Escherichia coli and used as the immunogen for the production of polyclonal and monoclonal antibodies. A new series of plasmids for increased expression of polyomavirus T antigens or a T antigen-beta-galactosidase fusion protein was constructed by replacing sequences coding for the ribosome-binding site of previously published plasmids with a chemically synthesized sequence that has a higher degree of complementarity to the 3' end of the 16S rRNA. Cells expressing the fusion protein from the plasmid with the synthetic sequence contained 5- to 10-fold more fusion protein after a 3-h induction than did control cells. Pulse-labeling of cells bearing the new plasmids revealed that the T antigens were synthesized at high levels after induction: 10% of total synthesis for small t; 15% for Py-1387T middle T, a truncated mutant of middle T; and probably 1 to 5% for middle T. Small t and Py-1387T middle T, but not wild-type middle T, were seen as minor bands in total cell protein analyzed on sodium dodecyl sulfate-polyacrylamide gels stained with Coomassie blue. A simple, rapid procedure for purification of bacterial small t from the pellet of sonicated bacteria yielded 1 to 2 mg of small t per liter of bacterial culture at 80 to 90% homogeneity. High-titer polyclonal rabbit antisera raised against purified small t recognized all three T antigens and were suitable for immunoaffinity purification of middle T. Mouse monoclonal antibodies raised against bacterial small t were of four classes, immunoprecipitating either all three polyomavirus T antigens, small t and middle T only, primarily small t, or middle T and large T in preference to small t. One of the latter monoclonal antibodies also immunoprecipitated large T but not small t of simian virus 40, suggesting that the site recognized by this antibody may be functionally important. None of the monoclonal antibodies yielded an immunoprecipitate active in phosphorylating middle T in vitro.
Involvement of Bruton's Tyrosine Kinase in FcεRI-dependent Mast Cell Degranulation and Cytokine Production (1998)

We investigated the role of Bruton's tyrosine kinase (Btk) in FcepsilonRI-dependent activation of mouse mast cells, using xid and btk null mutant mice. Unlike B cell development, mast cell development is apparently normal in these btk mutant mice. However, mast cells derived from these mice exhibited significant abnormalities in FcepsilonRI-dependent function. xid mice primed with anti-dinitrophenyl monoclonal IgE antibody exhibited mildly diminished early-phase and severely blunted late-phase anaphylactic reactions in response to antigen challenge in vivo. Consistent with this finding, cultured mast cells derived from the bone marrow cells of xid or btk null mice exhibited mild impairments in degranulation, and more profound defects in the production of several cytokines, upon FcepsilonRI cross-linking. Moreover, the transcriptional activities of these cytokine genes were severely reduced in FcepsilonRI-stimulated btk mutant mast cells. The specificity of these effects of btk mutations was confirmed by the improvement in the ability of btk mutant mast cells to degranulate and to secrete cytokines after the retroviral transfer of wild-type btk cDNA, but not of vector or kinase-dead btk cDNA. Retroviral transfer of Emt (= Itk/Tsk), Btk's closest relative, also partially improved the ability of btk mutant mast cells to secrete mediators. Taken together, these results demonstrate an important role for Btk in the full expression of FcepsilonRI signal transduction in mast cells.
Polyacrylamide-Based Biocompatible Nanoplatform Enhances the Tumor Uptake, PET/fluorescence Imaging and Anticancer Activity of a Chlorophyll Analog (2014)

In this report we demonstrate the outstanding advantages of multifunctional nanoplatforms for cancer-imaging and therapy. The non-toxic polyacrylamide (PAA) nanoparticles (size:18-25 nm) formulation drastically changed the pharmacokinetic profile of the ¹²⁴I- labeled chlorophyll-a derivative (formulated in 10% ethanol in PBS) with a remarkable enhancement in tumor uptake, and significantly reduced uptake in spleen and liver. Among the various nanoformulations investigated, the ¹²⁴I- labeled photosensitizer (dose: 0.6142 MBq), and the cyanine dye-nanoparticles (CD-NP) conjugate (dose 0.3 μmol/kg) in combination showed great potential for tumor imaging (PET/NIR fluorescence) in BALB/c mice bearing Colon26 tumors. Compared to free non-labeled photosensitizer, the corresponding PAA nanoformulation under similar treatment parameters showed a remarkable enhancement in long-term tumor cure by PDT (photodynamic therapy) and provides an opportunity to develop a single nanoplatform for tumor-imaging (PET/fluorescence) and phototherapy, a practical "See and Treat" approach.
Tolerance and Cross-Tolerance in Chronic Alcoholics: Reduced Membrane Binding of Ethanol and Other Drugs (1981)

Membrane binding of ethanol, anesthetics, and hydrophobic molecules in brain synaptosomes and liver mitochondria from rats is conspicuously reduced after long-term consumption of ethanol. The membranes are resistant to structural disordering by both ethanol and halothane. Tolerance, cross-tolerance, and dependence in chronic alcoholics may in part result from membrane alterations that inhibit the binding of ethanol and other drugs.
Multi-monitor mouse (2005)

Multiple-monitor computer configurations significantly increase the distances that users must traverse with the mouse when interacting with existing applications, resulting in increased time and effort. We introduce the Multi-Monitor Mouse (M3) technique, which virtually simulates having one mouse pointer per monitor when using a single physical mouse device. M3 allows for conventional control of the mouse within each monitor's screen, while permitting immediate warping across monitors when desired to increase mouse traversal speed. We report the results of a user study in which we compared three implementations of M3 and two cursor placement strategies. Our results suggest that using M3 significantly increases interaction speed in a multi-monitor environment. All eight study participants strongly preferred M3 to the regular mouse behavior.
Conversion of syngas into light olefins in one step for process-intensified production of sustainable aviation fuels (2022)

Here, we report on a preliminary investigation for direct conversion of syngas into olefins. This technology combines alcohol(s) production and olefin(s) production into a single unit operation to improve process efficiencies due to the overcoming of equilibrium limitations and also to offer capital savings relative to current synthesis approaches including Fischer-Tropsch synthesis, methanol-to-olefins followed by olefins to gasoline/distillate process and alcohol-to-jet process.
Simplified Rapid Hydrogenation Under Microwave Irradiation: Selective Transformations of β-Lactams1 (1993)

A simplified, easy to conduct, and inexpensive technique for high temperature (at about 130°C) catalytic transfer hydrogenation in a domestic microwave oven is described and examples are provided of selective transformation of ß-lactams using Pd/C or Raney nickel catalyst.
A 23dBm fully digital transmitter using &#x03A3;&#x0394; and pulse-width modulation for LTE and WLAN applications in 45nm CMOS (2014)

This paper presents a 23 dBm fully digital transmitter designed in a standard 45 nm CMOS process. The digital transmitter replaces the entire analog/RF signal chain in a traditional transmitter architecture. It utilizes ΣΔ modulation and pulse-width modulation to turn high resolution baseband I and Q signals into switching signals, thereby allowing efficient Class-D PA stages to be used. In addition, cascaded ΣΔ stages and switched-capacitor combining are incorporated into the architecture to reduced out-of-band quantization noise while maintaining good efficiency. The proposed transmitter achieves peak output power of 23 dBm with 47% power added efficiency (PAE). For a OFDM signal with 8.2 dB peak-to-average power ratio (PAR), the PAE is 23%. The linearity of the digital transmitter meets WiFi spectral mask without any digital predistortion.
Pd-Catalysed Synthesis of 5-Substituted Proline Derivatives from Acetylene-Containing Amino Acids (2003)

Contains fulltext : 306333.pdf (Publisher’s version ) (Open Access)
1331: Expression of Vascular Endothelial Growth Factor A (VEGF-A), VEGF Receptor 1 (VEGFR-1) and VEGFR-2 in Clear Cell and Papillary Renal Cell Carcinoma (RCC): Implications for Therapy (2005)

You have accessJournal of UrologyPodium, Tuesday, May 24, 2005, 1:00 - 3:00 pm1 Apr 20051331: Expression of Vascular Endothelial Growth Factor A (VEGF-A), VEGF Receptor 1 (VEGFR-1) and VEGFR-2 in Clear Cell and Papillary Renal Cell Carcinoma (RCC): Implications for Therapy John T. Leppert, John S. Lam, Hong Yu, David B. Seligson, Jun Dong, Steven Horvath, Allan J. Pantuck, Robert A. Figlin, and Arie S. Belldegrun John T. LeppertJohn T. Leppert More articles by this author , John S. LamJohn S. Lam More articles by this author , Hong YuHong Yu More articles by this author , David B. SeligsonDavid B. Seligson More articles by this author , Jun DongJun Dong More articles by this author , Steven HorvathSteven Horvath More articles by this author , Allan J. PantuckAllan J. Pantuck More articles by this author , Robert A. FiglinRobert A. Figlin More articles by this author , and Arie S. BelldegrunArie S. Belldegrun More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)35476-4AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1331: Expression of Vascular Endothelial Growth Factor A (VEGF-A), VEGF Receptor 1 (VEGFR-1) and VEGFR-2 in Clear Cell and Papillary Renal Cell Carcinoma (RCC): Implications for Therapy." The Journal of Urology, 173(4S), p. 362 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 173Issue 4SApril 2005Page: 362 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information John T. Leppert More articles by this author John S. Lam More articles by this author Hong Yu More articles by this author David B. Seligson More articles by this author Jun Dong More articles by this author Steven Horvath More articles by this author Allan J. Pantuck More articles by this author Robert A. Figlin More articles by this author Arie S. Belldegrun More articles by this author Expand All Advertisement PDF downloadLoading ...
A novel multi-stage subunit vaccine against paratuberculosis induces significant immunity and reduces bacterial burden in tissues (P4304) (2013)

Abstract Effective control of paratuberculosis is hindered by lack of a vaccine preventing infection, transmission and without diagnostic interference with tuberculosis. We have developed a novel multi-stage recombinant subunit vaccine in which a fusion of four early expressed MAP antigens is combined with a MAP protein expressed in latent infection (FET11 vaccine). FET11 vaccine proteins were formulated with CAF01 adjuvant and injected to MAP challenged calves at two different ages. 28 calves divided into two FET11 vaccine groups, a commercial vaccine and a control group were used in the study and followed for a year. The FET11 vaccine induced a significant T cell response against constituent vaccine proteins characterized by a high percentage of CD4+ T cells and participation of polyfunctional CD4+ T cells. Of the two different age groups, late FET11 vaccination conferred protective immunity characterized by a significant containment of bacterial burden in gut tissues compared to non-vaccinated animals. There was no cross-reaction with bovine tuberculosis in vaccinated animals. This novel multi-stage vaccine has the potential to become a marker vaccine for paratuberculosis.
Billboard Saliency Detection in Street Videos for Adults and Elderly (2018)

Detecting salient locations in images and videos that attract human attention is a challenging problem in computer vision. Most of the models developed for this purpose are either based on the bottom-up features of a scene or top-down factors. Observer's age is one of the important top-down factor which influences viewing behavior, some recent studies proposed age-adapted models to predict saliencies for different age groups. However, these studies reported age-impact on eye-gaze distribution for images only and videos still remain unexplored. In this study, we analyze the differences in eye gaze landings between adults and elderly while viewing street videos and develop a novel application of detecting saliency of billboards in the paved area of the street for adult and elderly. Our proposed age-adapted saliency model outperforms the existing video saliency models towards predicting the billboard saliency.
Nucleation period, surface roughness, and oscillations in mass gain per cycle during W atomic layer deposition on Al2O3 (2009)

Nucleation phenomena are critical for the fabrication of W/Al2O3 nanolaminates using atomic layer deposition (ALD) techniques. The nucleation and growth of W ALD on hydroxylated Al2O3 ALD surfaces and Al2O3 ALD on fluorinated W ALD surfaces was studied using in situ quartz crystal microbalance (QCM) and ex situ atomic force microscope (AFM) techniques. The QCM investigations revealed that Al2O3 ALD readily nucleated on the fluorinated W surface and displayed “substrate-enhanced growth.” In contrast, W ALD required 4–10 ALD cycles to nucleate on the hydroxylated Al2O3 surface and displayed “substrate-inhibited growth.” The W ALD nucleation period was shorter for higher Si2H6 and WF6 reactant exposures. The most rapid nucleation of W ALD on the Al2O3 surface occurred with much larger Si2H6 and WF6 exposures on the initial ALD cycle with the WF6 exposure prior to the Si2H6 exposure. By analyzing the individual Si2H6 and WF6 mass gain per cycle (MGPC), three main regions were identified in the W ALD nucleation and growth: initial deposition on Al2O3, W island growth and coalescence, and steady state growth. The root mean square (rms) roughness of the resulting W ALD film was dependent on the Si2H6 exposures and the number of ALD cycles required to nucleate the W ALD. A linear dependence was observed between the rms roughness and the number of ALD cycles required to reach one-half the maximum W MGPC. The W ALD also displayed very periodic oscillations in the W MGPC that were consistent with island nucleation and growth. Four local minima and three local maxima were observed in the W MGPC versus the number of ALD cycles. Comparing the results for W ALD on Al2O3 surfaces with recent simulations of ALD nucleation helps to establish the relationship between the nucleation period and surface roughness with island growth during nucleation.
Explanation of a Selectivity Maximum as a Function of the Material Structure for Organic Gas Separation Membranes (2004)

Many previous studies have examined structure−property relationships of both polymeric and carbon molecular sieve gas separation membranes, which show a widely known tradeoff between permeability and selectivity. This work presents an explanation of a lesser-known trend of a selectivity maximum as a function of the material structure for certain rigid polymers and a variety of carbon molecular sieving materials. Interestingly, this surprising trend of a maximum in selectivity over a range of materials is observed for certain gas pairs and not others over the same range of material structures. First-order modeling efforts, which treat molecular sieving membranes as effective heterogeneous composite materials comprising a distribution of selective entities, are used to explain and understand this trend of a maximum in selectivity. Several composite models are considered, and specific examples are demonstrated using both a parallel model and effective medium theory. The modeling results reflect trends in experimental data and suggest that subtle changes in the distribution of selective entities or the size of gas molecules can result in vastly different overall separation properties.
Supplementary Data 1 from Adoptive Transfer of Autologous T Cells Improves T-cell Repertoire Diversity and Long-term B-cell Function in Pediatric Patients with Neuroblastoma (2023)

&lt;p&gt;PDF file - 405K, Detailed flow cytometric analysis of expanded cells from children and adults&lt;/p&gt;
Biological Earth observation with animal sensors (2022)

Space-based tracking technology using low-cost miniature tags is now delivering data on fine-scale animal movement at near-global scale. Linked with remotely sensed environmental data, this offers a biological lens on habitat integrity and connectivity for conservation and human health; a global network of animal sentinels of environmental change.
Characteristics and Applications of CAAC-IGZO FET with Gate Length of 13nm (2020)

A field-effect transistor (FET) using CAAC-IGZO, a crystalline oxide semiconductor having a c -axis alignment, is considered for application to various circuits. In particular, its extremely low off-state leakage current[1,2] enables design of non-volatile memory and analog memory devices[3], allowing AI tasks to be run in non-von-Neumann architectures. Furthermore, CAAC-IGZO FET can be applied to use cases other than memory, such as RF applications. CAAC-IGZO FET can be integrated in the back-end-of-line processes of CMOS technologies[4], and allows higher power supply voltages than conventional CMOS devices[4]. This may contribute to reduced chip area, which can create smaller packages, which are demanded for IoT endpoints. As there are not many applications that currently use scaled CAAC-IGZO FET, CAAC-IGZO FET is not yet applied to quasi-millimeter-wave applications. In addition, circuit design for high-frequency applications of CAAC-IGZO FETs will require extraction of FET characteristics that will be utilized in this application. Compact models are available for large IGZO FETs [5], but not for scaled CAAC-IGZO FETs. For this work, we have prototyped and evaluated scaled CAAC-IGZO FETs (Fig. 1(a)) that are suitable for high-frequency applications in addition to memory applications. From network measurements, it was found that the CAAC-IGZO FET exhibits a cutoff frequency of 60 GHz (Fig. 1(b)) and a maximum oscillation frequency of 16 GHz, which is promising for quasi-millimeter-wave designs. In addition, we have designed equivalent circuits of the scaled CAAC-IGZO FET using linear devices. This circuit shows not only the characteristics of the scaled CAAC-IGZO FET, but also the potential for circuit designs with the device. This work compiles the characteristics of the scaled CAAC-IGZO FET, and proposes a novel circuit application for the device. Fig. 1 (a) L-direction cross section of the scaled CAAC-IGZO FET. (b) Network measurment result of the scaled CAAC-IGZO FET References [1] N. Kimizuka and S. Yamazaki, “Physics and Technology of Crystalline Oxide Semiconductor CAAC-IGZO FUNDAMENTALS,” WILEY , 2017. [2] S. Yamazaki and M. Fujita, “Physics and Technology of Crystalline Oxide Semiconductor CAAC-IGZO Application to LSI,” WILEY, 2017. [3] Y. Kurokawa et al., JJAP , vol. 59, pp. (SGGB03-1)-(SGGB03-11), 2020. [4] H. Kunitake et al., J-EDS , vol. 7, pp.495-502, 2019. [5] L. J. Giacoletto et al., JSSC , vol. 4, issue 2, pp.80-83, 1969. Figure 1