gebhart/patrepeval huggingface dataset:
Novel evaluation of targeted receptor internalization as a predictive tool for HER2/EGFR antibody-based therapeutics (2004)

3157 Background: Receptor-tyrosine kinase (RTK) internalization is a key event in signaling and a requisite event for certain RTK-targeted therapeutics. Endocytosis is the hallmark of trastuzumab and immunoliposomes (ILs) efficacy. To provide a biomarker of ErbB internalization, we developed a quantitative assay of HER2 and EGFR endocytosis triggered by specific probes. Methods: scFv against HER2 (F5) or EGFR (C10) were linked to nickel-containing and fluorescence-labeled liposomes to generate ErbB-targeted immunoliposome probes (ILs-fluor). After incubation with ILs-fluor (2h, 37C), tumor cells were washed +/-EDTA to dissociate scFv from liposomes; this allows FACS-based quantitation of internalized ILs-fluor (EDTA-insensitive fraction) vs. cell-surface bound scFv (EDTA-sensitive). Results: Assay was validated against a panel of cell lines, and was highly specific (HER2- or EGFR-specific vs. irrelevant MAb) and sensitive (internalization measurable at very low HER2/EGFR content). In trastuzumab-sensitive BT474, SKBr3, AU565, HER2 was efficiently internalized by anti-HER2 ILs-fluor: mean total uptake=1713 fluorescence units, internalized=957 (55%). HER2-overexpressing but trastuzumab-resistant SKOV3 cells showed only 35% internalization. Low HER2-expressing cells (MCF7, MB468) showed minimal uptake (105) and internalization (5%). Internalization of anti-EGFR ILs-fluor in EGFR-overexpressing MB468 cells was 92%, with only 19% in control cells. FACS analysis of cell suspensions of xenografts (BT474, MB468) and primary breast tumors showed high ErB uptake of ILs-fluor in ErB/EpCAM (+) epithelial cells, while minimal internalization was seen in ErB/EpCAM (-) stromal cells. Conclusions: This novel assay allows quantitative assessment of HER2/EGFR internalization in complex cell populations, and may predict response to ErbB-targeted therapies. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Hermes Hermes Hermes
<title>Focused ion beam direct micromachining of DOEs</title> (2000)

We discuss here the capability of direct manufacture of various high- resolution diffractive optics, in particular regarding micromachining of DOEs in 3D. Preliminary demonstrations were made in 2-D using an automated FIB system operated at 30 KeV with a Gallium liquid metal ion source and equipped with a gas injection system (GIS). Gratings with a 20 nm line width and zone plates with 32 nm outer ring were milled in a reactive atmosphere (iodine) directly through 3.5 (mu) m and 800 nm of gold respectively. Plans for combining FIB and X-ray lithography to make diffractive optical elements (DOEs) for JPL are also mentioned.
Supplementary Figure 2 from Analysis of Mitosis and Antimitotic Drug Responses in Tumors by <i>In Vivo</i> Microscopy and Single-Cell Pharmacodynamics (2023)

Supplementary Figure 2 from Analysis of Mitosis and Antimitotic Drug Responses in Tumors by &lt;i&gt;In Vivo&lt;/i&gt; Microscopy and Single-Cell Pharmacodynamics
Success Criteria Tool in EMC Tests for Interferometric Radiometers (2008)

The Microwave Imaging Radiometer using Aperture Synthesis (MIRAS) is the single payload of the SMOS (Soil Moisture and Ocean Salinity) mission by the European Space Agency (ESA) to be launched by spring 2009. This work presents the success criteria tool that has been designed to easily assess the impact of any perturbation on the payload system performance. The tool is illustrated by showing some of the main results obtained during the MIRAS system performance tests by the prime contractor, EADS-CASA Espacio, Spain, at ESA premises in ESTEC, The Netherlands, and after payload integration with the Proteus platform at Thales Alenia Space in Cannes, France.
Chemoprevention of Colorectal Cancer: Ready for Routine Use? (2005)

In the third millennium preventive medicine is becoming a corner stone in our concept of health. Colorectal cancer (CRC) prevention, in particular, has become an important goal for health providers, physicians and the general public. CRC fits the criteria of a disease suitable for chemopreventive interventions. It is a prevalent disease that is associated with considerable mortality and morbidity rates, with more than 1,000,000 new cases and 500,000 deaths expected, worldwide, in 2004. CRC has a natural history of transition from precursor to malignant lesion that spans, on average, 15-20 years, providing a window of opportunity for effective interventions and prevention. A pre-malignant precursor lesion (i.e., adenoma) usually precedes cancer, and helps to identify a subset of the population that is at increased risk of harbouring and developing cancer. Science and technology have evolved to a point where we are able to use our knowledge of cancer biology to identify individuals at risk and interrupt the process of malignant transformation at the level of the pre-cancerous lesion. Recent progress in molecular biology and pharmacology enhances the likelihood that cancer prevention will increasingly rely on chemoprevention. Chemoprevention, a new emerging science, means the use of agents to inhibit, delay or reverse carcinogenesis. Recent observations suggest a number of potential targets for chemoprevention. Many agents have potential benefit, but only modest chemopreventive efficacy in clinical trials. There is much evidence suggesting an inverse relationship between aspirin or NSAIDs consumption and CRC incidence and mortality. However, NSAID consumption is not problem-free, as 1997 data showed 107,000 hospitalisations and 16,500 deaths due to NSAIDs consumption in the US alone. Therefore, although chemoprevention of CRC is already possible, drugs that have more acceptable side-effect profiles than the currently available NSAIDs are required. COX-2-specific inhibitors, which have an improved safety profile, as compared to traditional NSAIDs that inhibit both the COX-1 and COX-2 enzymes, seem to be well suited drug candidates for CRC prevention. The inhibition of the growth of pre-cancerous and cancerous cells without affecting normal cells is the ultimate aim of cancer treatment and is of particular importance in chemoprevention studies, which may be long term in nature, involve healthy subjects and minimal toxicity. Cancer prevention is certain to be a significant focus of research and intervention in the coming years, propelled by the realization that we will be able to identify both individuals susceptible to specific cancers as well as the molecular targets that can alter or stop the carcinogenesis process. Pharmacology and genetics are collaborating to develop new chemoprevention agents designed to affect molecular targets linked to specific pre-malignant or predisposing conditions.
The Architectural Evolution of a High-Performance Graphics Terminal (1984)

This case study of the design of the Tektronix 4115B details the design constraints, shows how the architecture evolved from the Tektronix 4113, and shows how performance was gained by adding a microcoded picture processor and some special-purpose hardware.
Heavy Oil Production with Energy Effective Steam-Assisted Gravity Drainage (2016)

In reservoirs with extra heavy oil and bitumen, thermal methods are used to reduce the viscosity, in order to extract the oil. Steam-assisted gravity drainage (SAGD) is a thermal method where continuous steam injection is used. In this method, two horizontal wells are placed in parallel. The upper well injects steam and the lower well produces oil and condensed water. The continuous steam injection creates a chamber with uniform temperature. Heavy oil and bitumen reserves in Western Canada, which exceed 175 billion barrels, are becoming increasingly important petroleum sources due to the technical success of the SAGD processes. This study includes Computational fluid dynamics (CFD) modelling and simulations of a horizontal oil well with SAGD. The simulations are performed with inflow control devices (ICD) and autonomous inflow control valves (AICV) completion. In the SAGD processes, it is important that the residence time for steam in the reservoir is high enough to ensure that all the injected steam condenses in the reservoir to reduce the amount of steam injection and thereby making the SAGD process more energy effective. The simulations are carried out with ICD completion to delay the steam breakthrough and with AICV completion to prevent breakthrough of steam and water to the well. The numerical results showed that a most of the steam was produced together with the oil when ICD completion was used. AICV was able to close for steam and water, and the steam was thereby forced to condense in the reservoir, resulting in better utilization of the condensation energy.
Solder-Free Pressure Contact Micro-Springs in High-Density Flip-Chip Packages (2005)

This work investigates electrical pressure contacts based on a micro-spring with orders of magnitude smaller pitch and force than conventional pressure contacts. Flip-chip packages were assembled with hundreds of micro-springs at 20 mum pad-pitch, 40 mum spring-pitch, and an operating force of 0.01 gram on gold pads. These packages are shown to have stable resistance values during both in-situ thermocycle (0 degC to 125 degC) and humidity testing (60 degC at 95% RH). High-speed glitch measurements are performed to confirm the pressure contact does not have intermittent opens during thermocycling. These results suggest that a low-force solder-free pressure spring contact is a viable technology for next generation flip-chip packaging
Visible Diffraction from Graphene and Its Application in Holograms (2013)

A fundamental study of visible diffraction effects from patterned graphene layers is presented. By patterning graphene into optical gratings, visible diffraction from graphene is experimentally measured as a function of the number of layers and visible wavelengths. A practical application of these effects is also presented, by demonstrating an optical hologram based on graphene. A high resolution (pixel size 400 nm) intensity hologram is fabricated which, in response to incident laser light, generates a visible image. These findings suggest that visible diffraction in graphene can find practical application in holograms and should also be considered during the design and characterisation of graphene‐based optical applications.
Cell‐free media of mixed lymphocyte cultures augmenting sensitization in vitro of mouse T lymphocytes against allogeneic fibroblasts (1975)

Using an in vitro mouse lymphocyte anti-fibroblast reaction (AFR), we recently reported that the addition of allogeneic stimulator lymphocytes to the sensitization phase of the AFR enhanced sensitization to fibroblast antigens as evidenced by a marked increase in the cytolytic activity of the sensitized lymphocyte population. In the present report we studied the mechanism of this helper effect by testing the capacity of cell-free media derived from 48-h mixed spleen cultures to enhance anti-fibroblast sensitization. We found that such cell-free media could produce a marked helper effect when applied to the sensitization phase of the AFR, but not when added to the cytolytic effector phase. The stimulator cells in the mixed lymphocyte culture (MLC) did not have to be syngeneic with the sensitizing fibroblasts in the AFR in order for the helper effect to be demonstrated. Lymphocytes sensitized to fibroblast antigens in the presence of MLC medium retained their specificity of the effector phase. Our data suggest that the MLC medium acts by enhancing differentiation processes of antigen-triggered lymphocytes. Generation of helper activity by the MLC was abolished by 1000 r irradiation of the responder cells. By using nu/nu and normal spleens, both from two different strains, as cell sources for the MLC, we found that the generation of helper activity depended on T cells capable of proliferation. Furthermore, stimulator lymphocytes differing from responder lymphocytes by non-H-2 alloantigens as well as by point mutation with the H-2 complex were capable of eliciting helper factor(s). Thus, soluble factor(s) produced in a MLC, which are dependent on T lymphocyte proliferation, have the capacity to enhance the sensitization of mouse lymphocytes against antigens present on allogeneic fibroblasts.
Plaque-Associated Overexpression of Insulin-Degrading Enzyme in the Cerebral Cortex of Aged Transgenic Tg2576 Mice With Alzheimer Pathology (2006)

It was proposed that insulin-degrading enzyme (IDE) participates in the clearance of amyloid beta (Abeta) in the brain, and its low expression or activity may be relevant for the progression of Alzheimer disease. We performed a longitudinal study of brain level, activity, and distribution of IDE in transgenic mice (Tg2576) expressing the Swedish mutation in human Abeta precursor protein. At 16 months of age, Tg2576 showed a significant 2-fold increment in IDE protein level as compared with 4.5- and 11-month-old animals. The peak of IDE was in synchrony with the sharp accumulation of sodium dodecyl sulfate-soluble Abeta and massive Abeta deposition into plaques. At this stage, IDE appeared surrounding Abeta fibrillar deposits within glial fibrillar acidic protein-positive astrocytes, suggesting that it was locally overexpressed during the Abeta-mediated inflammation process. When primary astrocytes were exposed to fibrillar Abeta in vitro, IDE protein level increased as compared with control, and this effect was reduced by the addition of U0126, a specific inhibitor of the ERK1/2 mitogen-activated protein kinase cascade. We propose that in Tg2576 mice and in contrast to its behavior in Alzheimer brains, active IDE increases with age around plaques as a component of astrocyte activation as a result of Abeta-triggered inflammation.
Computer-assisted karyotyping with human interaction. (1977)

A system for machine assisted karyotyping and chromosome analysis has been developed. The system uses a drum- or TV-scanner as input device, runs provisionally in 32 K memory, and also allows human interaction on several stages. The accuracy with which banded chromosomes are karyotyped depends strongly on the type of classifier and varies from 40 up to 80%. The accuracy of the human assisted classifier (98%) comes close to that of a skilled technician (99.5%) using manual chromosomal analysis. Due to technical and memory limitations, the time necessary for the karyotyping of one cell is too long and depends on the interaction time; however karyotyping within 5 min, including human interaction, will be possible in the near future.
The Plasmodesmal Protein PDLP1 Localises to Haustoria-Associated Membranes during Downy Mildew Infection and Regulates Callose Deposition (2014)

The downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) is a filamentous oomycete that invades plant cells via sophisticated but poorly understood structures called haustoria. Haustoria are separated from the host cell cytoplasm and surrounded by an extrahaustorial membrane (EHM) of unknown origin. In some interactions, including Hpa-Arabidopsis, haustoria are progressively encased by host-derived, callose-rich materials but the molecular mechanisms by which callose accumulates around haustoria remain unclear. Here, we report that PLASMODESMATA-LOCATED PROTEIN 1 (PDLP1) is expressed at high levels in Hpa infected cells. Unlike other plasma membrane proteins, which are often excluded from the EHM, PDLP1 is located at the EHM in Hpa-infected cells prior to encasement. The transmembrane domain and cytoplasmic tail of PDLP1 are sufficient to convey this localization. PDLP1 also associates with the developing encasement but this association is lost when encasements are fully mature. We found that the pdlp1,2,3 triple mutant is more susceptible to Hpa while overexpression of PDLP1 enhances plant resistance, suggesting that PDLPs enhance basal immunity against Hpa. Haustorial encasements are depleted in callose in pdlp1,2,3 mutant plants whereas PDLP1 over-expression elevates callose deposition around haustoria and across the cell surface. These data indicate that PDLPs contribute to callose encasement of Hpa haustoria and suggests that the deposition of callose at haustoria may involve similar mechanisms to callose deposition at plasmodesmata.
Neural Stem Cell Transplant Survival in Brains of Mice: Assessing the Effect of Immunity and Ischemia by using Real-time Bioluminescent Imaging (2006)

Immune status and host immunity can have an influence on NPC graft survival, and these changes can be noninvasively assessed with bioluminescent imaging in this experimental model.
Abstract 555: Platelet Volume Indices as Markers of Platelet Reactivity in Atherosclerotic Coronary Artery Disease (2019)

Background: Platelet volume indices (PVIs) - mean platelet volume (MPV), platelet distribution width (PDW) and platelet-large cell ratio (P-LCR) - are measures of platelet size. Larger platelets with more granules have been shown to have higher thrombotic potential. Therefore, PVIs may be useful to gauge platelet reactivity and as markers of thrombotic risk. Objectives: To determine whether there is a significant difference in PVIs of patients with acute coronary syndrome (ACS) when compared to stable angina patients and matched controls without known atherosclerotic disease. Methods: This was an observational cross-sectional study involving 180 patients (60 each with ACS and stable angina, 60 controls without known atherosclerotic disease). PVIs were measured on venous blood samples using an automated hematology analyzer. Data was analyzed using SPSS. Results: Baseline characteristics and traditional risk factors were similar between the ACS patients, stable angina patients and controls as shown in table 1. ACS patients were found to have significantly higher PVIs (MPV 10.85 ± 1.28 femtoliters [fL], PDW 12.93 ± 1.78 fL, P-LCR 32.34 ± 5.00 %) compared to stable angina patients (MPV 9.92 ± 1.09 fL, PDW 11.82 ± 1.47 fL, P-LCR 26.03 ± 4.93 %) and controls (MPV 9.36 ± 1.01 fL, PDW 11.11 ± 1.32 fL, P-LCR 23.01 ± 4.36 %), as shown in figure 1, p&lt;0.001 for all. Conclusion: ACS patients have higher platelet volume and PVIs compared to stable angina patients and those without known atherosclerotic disease. PVIs may thus be useful markers of platelet reactivity and thrombotic risk in atherosclerotic coronary artery disease. Their exact role in risk stratification needs to be explored further.
Mind the Backbone: Minimizing Backbone Distortion for Robust Object Detection (2023)

Building object detectors that are robust to domain shifts is critical for real-world applications. Prior approaches fine-tune a pre-trained backbone and risk overfitting it to in-distribution (ID) data and distorting features useful for out-of-distribution (OOD) generalization. We propose to use Relative Gradient Norm (RGN) as a way to measure the vulnerability of a backbone to feature distortion, and show that high RGN is indeed correlated with lower OOD performance. Our analysis of RGN yields interesting findings: some backbones lose OOD robustness during fine-tuning, but others gain robustness because their architecture prevents the parameters from changing too much from the initial model. Given these findings, we present recipes to boost OOD robustness for both types of backbones. Specifically, we investigate regularization and architectural choices for minimizing gradient updates so as to prevent the tuned backbone from losing generalizable features. Our proposed techniques complement each other and show substantial improvements over baselines on diverse architectures and datasets. Code is available at https://github.com/VisionLearningGroup/mind_back.
Error correction scheme for uncompressed HD video over wireless (2009)

Digital transmission of uncompressed high-definition video is challenging because of its high data rate and its extreme sensitivity to bit errors. In this paper we propose a simple error correction scheme to reduce the bit error effects in the video at the receiver end of a wireless channel. Our scheme uses the large amount of spatial redundancy already present in uncompressed HD video data to provide an extra layer of protection in addition to that provided by channel coding. Thus, our method requires no change to the video signal being transmitted and is compatible with any existing solution for HD video transmission. Using simulations over a range of byte error rates, we show that our scheme effectively reduces the number of visible artifacts because of uncorrected channel errors, and provides approximately 7 dB improvement in peak signal to noise ratio.
Super absorbers from renewable feedstock by catalytic oxidation (2008)

An improved, environmentally sound three-component system, MTO/H2O2/LiBr, used to prepare biodegradable oxidized starch super absorbers is reported. In contrast to previous systems (ref. 1: W. A. Herrmann, J. P. Zoller and R. W. Fischer, J. Organomet. Chem., 1999, 579, 404), a highly acidic reaction media is avoided, thus limiting product depolymerisation to a low level. This paper presents an optimized catalytic approach to make carboxy starch, which reduces overall reaction cost, and produces less harmful waste.
SUMOylation Is an Inhibitory Constraint that Regulates the Prion-like Aggregation and Activity of CPEB3 (2015)

Protein synthesis is crucial for the maintenance of long-term-memory-related synaptic plasticity. The prion-like cytoplasmic polyadenylation element-binding protein 3 (CPEB3) regulates the translation of several mRNAs important for long-term synaptic plasticity in the hippocampus. Here, we provide evidence that the prion-like aggregation and activity of CPEB3 is controlled by SUMOylation. In the basal state, CPEB3 is a repressor and is soluble. Under these circumstances, CPEB3 is SUMOylated in hippocampal neurons both in vitro and in vivo. Following neuronal stimulation, CPEB3 is converted into an active form that promotes the translation of target mRNAs, and this is associated with a decrease of SUMOylation and an increase of aggregation. A chimeric CPEB3 protein fused to SUMO cannot form aggregates and cannot activate the translation of target mRNAs. These findings suggest a model whereby SUMO regulates translation of mRNAs and structural synaptic plasticity by modulating the aggregation of the prion-like protein CPEB3.