gebhart/patrepeval huggingface dataset:
The Pancreas Secreting Insulin for Decades after Onset of Type I Diabetes — Implications for Care and Management (2015)

Up until recently, the prevailing dogma was that insulin secretion ceased within a couple of years after the diagnosis of type I diabetes, a clinical time period called the honeymoon. But a series of recent studies have established that release of C-peptide, which is the best measure of endogenous insulin production, can commonly persist for decades after disease onset. The release of C-peptide, even at low levels, is shown to have functional and clinical significance. For example, C-peptide levels &gt;10 pmol/l are associated with fewer diabetes complications, i.e., nephropathy, neuropathy, foot ulcers, and retinopathy. The diabetic population may also be heterogeneous in risk for fall in C-peptide, with early age of diabetes onset a risk factor for more rapid C-peptide decline. The persistence of insulin release for decades and its functional and clinical significance suggest that assays for C-peptide should be a regular part of diabetes management. Furthermore, patients with established diabetes should be eligible to participate in clinical trials of immune therapies since preservation of these low levels appears clinically important to prevent complications.
Bioorthogonal Labeling of Human Prostate Cancer Tissue Slice Cultures for Glycoproteomics (2017)

Abstract Sialylated glycans are found at elevated levels in many types of cancer and have been implicated in disease progression. However, the specific glycoproteins that contribute to the cancer cell‐surface sialylation are not well characterized, specifically in bona fide human disease tissue. Metabolic and bioorthogonal labeling methods have previously enabled the enrichment and identification of sialoglycoproteins from cultured cells and model organisms. Herein, we report the first application of this glycoproteomic platform to human tissues cultured ex vivo. Both normal and cancerous prostate tissues were sliced and cultured in the presence of the azide‐functionalized sialic acid biosynthetic precursor Ac 4 ManNAz. The compound was metabolized to the azidosialic acid and incorporated into cell surface and secreted sialoglycoproteins. Chemical biotinylation followed by enrichment and mass spectrometry led to the identification of glycoproteins that were found at elevated levels or uniquely in cancerous prostate tissue. This work therefore extends the use of bioorthogonal labeling strategies to problems of clinical relevance.
Entropic Control of HD Exchange Rates over Dilute Pd-in-Au Alloy Nanoparticle Catalysts (2021)

Dilute Pd-in-Au alloy catalysts are promising materials for selective hydrogenation catalysis. Extensive surface science studies have contributed mechanistic insight on the energetic aspect of hydrogen dissociation, migration, and recombination on dilute alloy systems. Yet, translating these fundamental concepts to the kinetics and free energy of hydrogen dissociation on nanoparticle catalysts operating at ambient pressures and temperatures remains challenging. Here, the effect of the Pd concentration and Pd ensemble size on the catalytic activity, apparent activation energy, and rate-limiting process is addressed by combining experiment and theory. Experiments in a flow reactor show that a compositional change from 4 to 8 atm% Pd of the Pd-in-Au alloy catalyst leads to a strong increase in activity, even exceeding the activity per Pd atom of monometallic Pd under the same conditions, albeit with an increase in apparent activation energy. First-principles calculations show that the rate and apparent activation enthalpy for HD exchange increase when increasing the Pd ensemble size from single Pd atoms to Pd trimers in a Au surface, suggesting that the ensemble size distribution shifts from mainly single Pd atoms on the 4 atm% Pd alloy to larger Pd ensembles of at least three atoms for the 8 atm% Pd/Au catalyst. The DFT studies also indicated that the rate-controlling process is different: H2 (D2) dissociation determines the rate for single atoms, whereas recombination of adsorbed H and D determines the rate on Pd trimers, similar to bulk Pd. Both experiment and theory suggest that the increased reaction rate with increasing Pd content and ensemble size stems from an entropic driving force. Finally, our results support hydrogen migration between Pd sites via Au and indicate that the dilute alloy design prevents the formation of subsurface hydrogen, which is crucial in achieving high selectivity in hydrogenation catalysis.
Exploring Real Time Multimedia Content Creation in Video Games (2007)

Video games represent a class of media applications for which creating video content is as important as displaying it. In this paper, we compare video games running on an Apple Macintosh G5 to DVD playback and the QuickTime media player. We use performance monitor counters to find the IPC, the L1 data cache miss rate and the AGP and processor memory bandwidth. We find the frame-oriented nature of all of these applications reflected in many of the metrics used in this study. Video game applications exhibit significantly less idle time between updates to the screen than DVD playback and QuickTime. The results also show that adding computer controlled characters to a video game further reduces the idle time, and causes a decrease in the L2 cache pressure, spreading the access misses over a longer time period. 1.
Theoretical lateral and axial sensitivity limits and choices of molecular reporters for Cherenkov-excited luminescence in tissue during x-ray beam scanning (2020)

Models of thin x-ray and electron sources were compared with experimental measurements, showing similar trends in energy and source type. Surface detection of Cherenkov-excited luminescence appears to be limited by the mean free path of the luminescence emission, where for the given simulation only 2% of the inclusion emissions reached the surface from a depth of 7 mm in a multilayer tissue model.
A Multi-stage 19.2-dBm, 30.4%-PAE D-band Power Amplifier in a 250-nm InP HBT Process (2023)

In this paper, we demonstrate results for 2 and 3-stage power amplifiers in 250-nm InP HBT technology that offer the highest combination of peak power added efficiency (PAE) and saturated output power (Psat) published to date. The 2- and 3-stage designs achieve a PAE of 30.4% and 23.8% and Psat of 19.2 dBm and 17.1 dBm, respectively. Both designs offer high gain with up to 14.7 dB of gain for the 2-stage and 18.5 dB for the 3-stage as well as compact area for high-density applications such as phased arrays.
CMOS Integrated Nanophotonics for Future Computing Systems (2011)

CMOS Integrated Nanophotonics allows ultra‐dense monolithic single‐chip integration of optical and electrical functions. This technology can enable future Exaflops supercomputers by connecting racks, modules, and chips together with ultra‐low power massively parallel optical interconnects. I will describe the progress this field witnessed during last several years starting from explorations of fundamental optical phenomena at the nanoscale through development of advanced nanophotonics devices to demonstration of advanced optoelectronic systems integrated into a single CMOS die.
The Presence of a vpu Gene and the Lack of Nef-Mediated Downmodulation of T Cell Receptor-CD3 Are Not Always Linked in Primate Lentiviruses (2010)

Nef is an accessory protein critical for the ability of human and simian immunodeficiency viruses (HIV and SIV) to replicate efficiently in their respective hosts. Previous analyses of members of 15 different primate lentivirus lineages revealed a link between Nef function and the presence of a vpu gene. In particular, Nef proteins of all vpu-containing viruses had lost their ability to downmodulate the T cell (TCR-CD3) receptor. Here we examined Nef proteins from eight additional SIV lineages, including SIVgor, SIVwrc, SIVolc, SIVgri, SIVdrl, SIVlho, SIVden, and SIVasc, from western lowland gorillas, western red colobus monkeys, olive colobus monkeys, grivet monkeys, drills, L'Hoest's monkeys, Dent's mona monkeys, and red-tailed monkeys, respectively. We found that except for the nef gene of SIVdrl, all of them were efficiently expressed and modulated CD4, major histocompatibility complex class I (MHC-I), CD28, CXCR4, and Ii cell surface expression and/or enhanced viral infectivity and replication. Furthermore, the Nef proteins of SIVgri, SIVlho, SIVwrc, SIVolc, and SIVgor antagonized tetherin. As expected, the Nef protein of SIVgor, which carries vpu, failed to downmodulate CD3, whereas those of SIVwrc, SIVgri, SIVlho, and SIVasc, which lack vpu, were capable of performing this function. Surprisingly, however, the Nef protein of the vpu-containing SIVden strain retained the ability to downmodulate TCR-CD3, whereas that of SIVolc, which does not contain vpu, was unable to perform this function. Although the SIVden Vpu is about 20 amino acids shorter than other Vpu proteins, it degrades CD4 and antagonizes tetherin. Our data show that there are exceptions to the link between the presence of a vpu gene and nef alleles deficient in CD3 modulation, indicating that host properties also affect the selective pressure for Nef-mediated disruption of TCR-CD3 signaling. Our results are also further evidence that tetherin antagonism is a common function of primate lentivirus Nef proteins and that the resistance of human tetherin to Nef represents a relevant barrier to cross-species transmission of SIVs to humans.
Surface modification of polyamide-6: graft copolymerization of vinyl monomers onto polyamide-6 and thermal analysis of the graft copolymers (1998)

Graft copolymerization of vinyl monomers onto polyamide-6 using radical initiation has been investigated. Two monomers were used: methacrylic acid and acrylic acid. The initiators selected included hydrogen peroxide, benzoyl peroxide and azobisisobutyronitrile. The extent of graft copolymerization depends on the concentrations and identity of the initiator and monomer and the time and temperature of the reaction. The graft copolymers were not soluble in solvents that will dissolve the starting material; definitive proof for the formation of the graft copolymers was obtained from infrared spectroscopy. Thermogravimetric analysis was performed on the graft copolymers and it was found that the presence of the acid invariably accelerated the degradation of the polyamide. © 1998 John Wiley & Sons, Ltd.
Suppression of inelastic deformation of nanocoated thin film microstructures (2004)

We study the suppression of time-dependent inelastic deformation due to creep, stress relaxation, and microstructural evolution in multilayer thin film microstructures by the use of alumina nanocoatings realized by atomic layer deposition (ALD). Gold (0.5 μm thick)/polysilicon (1.5 or 3.5 μm thick) beam and plate microstructures were fabricated using surface micromachining. The microstructures were then coated on each side with a 40-nm-thick amorphous Al2O3 layer by ALD. The beam and plate microstructures were initially thermal cycled between room temperature and 190 °C to partially stabilize the gold microstructure. After the initial thermal cycles, the microstructures were cooled from 190 to 120 °C and held at 120 °C for about 700 h (4 weeks). We measured, using an interferometric microscope with a custom-built temperature chamber, full-field deformed shapes (and from these determined the average curvatures in the x and y directions) of the microstructures during the initial thermal cycles, during the cooling process from 190 to 120 °C, and during the isothermal hold. Measurements were made on both coated and uncoated microstructures to assess the influence of the coating. We find that while the 40-nm-thick coating has a small effect on the thermoelastic response of the microstructure, it significantly reduces the extent of inelastic deformation during the isothermal hold. We modeled the curvature evolution with time assuming the inelastic deformation mechanism can be described by power-law creep in the gold, ε̇=Aσn, and that the polysilicon and alumina deform elastically. The simple model describes the observed behavior reasonably well for the uncoated microstructures (when the power-law parameters are fit using the measured curvature), however, for the coated microstructures, the model predicts a decrease in the inelastic deformation, but nowhere near the magnitude observed. This suggests not only an alternation of the stress state in the gold film by the nanoscale coating, but also a change in the fundamental inelastic deformation mechanisms.
Challenges of the Integration of Millimeter Wave Power Amplifier Using Nanometer Silicon Technologies (2014)

International audience
Abstract ES12-2: Single cell analysis of circulating tumor cells (2022)

Abstract Epithelial to mesenchymal plasticity (EMP), an embryonic process, is reinstated in cancer and has been implicated in tumor metastasis and drug resistance. Tumor cells circulating in the blood of breast cancer patients show extensive EMP with dynamic shifts from one state to another. Comparison of the molecular characteristics of epithelial and mesenchymal circulating tumor cell (CTC) populations shows that epithelial CTCs compared with mesenchymal CTCs express multiple structural ribosomal proteins and exhibit enrichment of translational signatures; these epithelial CTCs are more proliferative and their presence in the blood correlates with poor clinical outcome. Mechanistically, overexpression of a single structural ribosomal protein, RPL15, which encodes a component of the large ribosomal subunit, increased the expression of multiple structural ribosomal proteins, global translation and cell proliferation coinciding with increased metastatic growth in multiple organs. Tumors overexpressing RPL15 were more sensitive to translational inhibitors suggesting that therapies targeting translation in this aggressive subset of epithelial CTCs may serve as potential suppressors of metastatic progression of breast cancer. Citation Format: S Maheswaran, R Ebright, D Micalizzi, D , M Toner, D Haber. Single cell analysis of circulating tumor cells [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr ES12-2.
Detection of Metadata Tampering Through Discrepancy Between Image Content and Metadata Using Multi-task Deep Learning (2017)

Image content or metadata editing software availability and ease of use has resulted in a high demand for automatic image tamper detection algorithms. Most previous work has focused on detection of tampered image content, whereas we develop techniques to detect metadata tampering in outdoor images using sun altitude angle and other meteorological information like temperature, humidity and weather, which can be observed in most outdoor image scenes. To train and evaluate our technique, we create a large dataset of outdoor images labeled with sun altitude angle and other meteorological data (AMOS+M2), which to our knowledge, is the largest publicly available dataset of its kind. Using this dataset, we train separate regression models for sun altitude angle, temperature and humidity and a classification model for weather to detect any discrepancy between image content and its metadata. Finally, a joint multi-task network for these four features shows a relative improvement of 15.5% compared to each of them individually. We include a detailed analysis for using these networks to detect various types of modification to location and time information in image metadata.
Endothelial actin depolymerization mediates NADPH oxidase-superoxide production during flow reversal (2014)

Slow moving blood flow and changes in flow direction, e.g., negative wall shear stress, can cause increased superoxide (O2·−) production in vascular endothelial cells. The mechanism by which shear ...
OBTENÇÃO DE CÁPSULAS DE ALGINATO CONTENDO Trichoderma asperellum T356 (2018)

RESUMO -O controle biolgico constitui uma estratgia de grande importncia para a reduo do uso de pesticidas qumicos no controle de fitopatgenos. Neste sentido, um microrganismo amplamente utilizado neste mtodo o fungo Trichoderma. O presente trabalho teve por objetivo avaliar a viabilidade de condios submersos e microesclerdios (MS) de Trichoderma asperellum T356 em cpsulas de alginato ntegras e liofilizadas. O fungo foi produzido por fermentao submersa em frascos agitados e, aps a recuperao dos propgulos por filtrao, estes foram encapsulados em matriz de alginato pelo mtodo de extruso. Foi avaliada a cintica de produo de MS, enquanto a viabilidade das cpsulas ntegras e liofilizadas foi monitorada ao longo de 120 dias de
Data from An Integrated View of Copy Number and Allelic Alterations in the Cancer Genome Using Single Nucleotide Polymorphism Arrays (2023)

&lt;div&gt;Abstract&lt;p&gt;Changes in DNA copy number contribute to cancer pathogenesis. We now show that high-density single nucleotide polymorphism (SNP) arrays can detect copy number alterations. By hybridizing genomic representations of breast and lung carcinoma cell line and lung tumor DNA to SNP arrays, and measuring locus-specific hybridization intensity, we detected both known and novel genomic amplifications and homozygous deletions in these cancer samples. Moreover, by combining genotyping with SNP quantitation, we could distinguish loss of heterozygosity events caused by hemizygous deletion from those that occur by copy-neutral events. The simultaneous measurement of DNA copy number changes and loss of heterozygosity events by SNP arrays should strengthen our ability to discover cancer-causing genes and to refine cancer diagnosis.&lt;/p&gt;&lt;/div&gt;
Displacement analysis of diagnostic ultrasound backscatter: A methodology for characterizing, modeling, and monitoring high intensity focused ultrasound therapy (2010)

Accurate monitoring of high intensity focused ultrasound (HIFU) therapy is critical for widespread clinical use. Pulse-echo diagnostic ultrasound (DU) is known to exhibit temperature sensitivity through relative changes in time-of-flight between two sets of radio frequency (RF) backscatter measurements, one acquired before and one after therapy. These relative displacements, combined with knowledge of the exposure protocol, material properties, heat transfer, and measurement noise statistics, provide a natural framework for estimating the administered heating, and thereby therapy. The proposed method, termed displacement analysis, identifies the relative displacements using linearly independent displacement patterns, or modes, each induced by a particular time-varying heating applied during the exposure interval. These heating modes are themselves linearly independent. This relationship implies that a linear combination of displacement modes aligning the DU measurements is the response to an identical linear combination of heating modes, providing the heating estimate. Furthermore, the accuracy of coefficient estimates in this approximation is determined a priori, characterizing heating, thermal dose, and temperature estimates for any given protocol. Predicted performance is validated using simulations and experiments in alginate gel phantoms. Evidence for a spatially distributed interaction between temperature and time-of-flight changes is presented.
A cognition-based framework for the development of visualization literacy (2009)

Data visualizations are prevalent in scientific simulation, medicine, physical therapy, product design, manufacturing, weather predictions, simulations, and engineering. They are also used in information and scientific visualization for WWW exploration, document searching, and education. This pervasiveness makes it important to understand how we comprehend these visualizations, what comprehension difficulties can be expected in diverse populations, and which visual properties increase comprehension difficulty. This will enable us to create training methods that help people gain basic comprehension strategies and analytic skills for visualizations.The goal of this dissertation is to define an approach that can be used to determine the factors that make a visualization difficult to comprehend by certain individuals. This information is then used to test if training using this information helps individuals develop new and workable strategies for visualization analysis. In this dissertation we present an approach that is designed as a series of steps designed (1) to determine what cognitive abilities are correlated with comprehension of the visualization, (2) to identify visual properties that make a basic visualization difficult to comprehend and (3) to measure the effect of basic incremental training using these visual properties.
Supplementary Figure 4 from Adoptive Transfer of MART-1 T-Cell Receptor Transgenic Lymphocytes and Dendritic Cell Vaccination in Patients with Metastatic Melanoma (2023)

&lt;p&gt;PDF file - 278KB, Pre- and post-treatment PET scans showing evidence of major tumor response and MART-1-specific TCR transgenic cell levels in patient F5-10.&lt;/p&gt;
Evaluation of Additively Manufactured Parts in Disruptive Manner as Deformation Elements for Structural Integrated Force Sensors (2022)

Laser-based powder bed fusion (LPBF) as an additive manufacturing (AM) process allows the integration of sensors at any location within the manufactured part. This allows for manufacturing smart parts that can be integrated into complex structures for monitoring applications, as they can perform in situ measurements. Especially, monitoring of force and torque is gaining increasing interest. However, a proper strain transmission from the mechanically loaded part to the embedded strain sensing element must be ensured, as the performance of such sensors is strongly dependent on it. In this work, we present an approach for additively manufactured deformation elements in a disruptive manner with integrated strain gauges using a steel plate as a measuring element carrier. To evaluate the strain transmission, and, thus, the performance of the additively manufactured deformation elements, we compare them to a conventionally manufactured deformation element with identical geometry. The strain gauges are applied after manufacturing at locations with a proper strain, which are determined by finite-element analysis (FEA). Loading these additively and conventionally manufactured prototypes with 15N results in only 0.1% linearity and 0.2% hysteresis error. Furthermore, a nearly linear temperature behavior of manufactured prototypes with a TK 0 of up to 0.3%/10K and a TK C of up to 0.6%/10K is achieved. These results confirm that a proper strain transmission is ensured within the additively manufactured deformation elements, making them competitive with conventionally manufactured deformation elements. Thus, the disruptive manufacturing process introduced is suitable for fabricating structurally integrated force sensors based on strain gauges.
Incremental Flip Angle Snapshot FLASH MRI of Hepatic Lesions (1992)

Incremental flip angle (IFA) snapshot fast low angle shot (FLASH) is a new modification of inversion recovery snapshot FLASH MR imaging. The method changes the flip angle incrementally from low to high during data acquisition and was applied in the evaluation of 16 focal hepatic lesions in 10 patients. Sequence comparisons were performed with a fixed flip angle inversion recovery snapshot FLASH sequence (standard), a T1− and T2-weighted spin-echo (SE) sequence, and a T1-weighted breath-hold FLASH sequence. Whereas snapshot FLASH images in both pulse sequences were free from physiological motion artifacts, SE and FLASH images at low hepatic and low lesion signal revealed both superior lesion-liver signal-differences-to-noise ratio (SD/N) and superior contrast compared with standard snapshot FLASH without additional artifacts. Unless motion artifacts were evident, SE and FLASH images showed a higher anatomic resolution but lower SD/N and lower contrast than IFA snapshot images. Because of its superior SD/N and contrast, IFA snapshot FLASH will likely widen the application of fast MR imaging techniques.