gebhart/patrepeval huggingface dataset:
Faculty Opinions recommendation of The brain as an immune privileged site: dendritic cells of the central nervous system inhibit T cell activation. (2003)

Dendritic cells (DC) are unique in their ability to prime naive T cells and initiate adaptive immunity. In recent years, DC were identified in the inflamed central nervous system (CNS), but their role in the initiation or regulation of the tissue specific immune response is unknown. As shown here, DC isolated from mice with experimental autoimmune encephalomyelitis (EAE) exhibit a maturational phenotype similar to immature bone marrow-derived DC or splenic DC as characterized by intermediate surface MHC class II and low expression of the costimulatory molecule CD80. However, they are unable to prime naive T cells. Moreover, they inhibit T cell proliferation stimulated by mature bone marrow-derived DC. TGFbeta, IL-10 and TRAIL were found to significantly contribute to the CNS-DC-mediated inhibition of allo-T cell proliferation. Thus CNS-DC may be the key responsibles for maintaining immune privilege within the inflamed CNS. PMID: 14579268
3 Million Volt Electron Microscope (1972)

A 3 MV electron microscope has been developed. The high voltage is generated by a 30-stage symmetrical Cockcroft-Walton circuit which is driven by a fully electronic ac supply. The Cockcroft-Walton circuit and the accelerating tube are enclosed in a single tank which is filled with freon gas for electrical insulation. The drift and the ripple of high voltage are less than 1×10−5/min and 1×10−6 respectively. The calculated resolving power of this electron microscope is 2Å. The electron microscope column consists of a double condenser lens and a 4-stage image forming lens. The objective lens is excited with 45,000 ampere-turns at 3 MV. The height and weight of this electron microscope are 11 meters and 67 tons respectively. Special attentions are paid on vibration-proof of the electron microscope and protection of leakage X-ray. The latter is kept less than 0.1 mr/hr at the operator position.
ChemInform Abstract: Oxygen‐17 NMR Spectroscopy: Applications in Organic Chemistry (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Robust multi-qubit quantum network node with integrated error detection (2022)

Long-distance quantum communication and networking require quantum memory nodes with efficient optical interfaces and long memory times. We report the realization of an integrated two-qubit network node based on silicon-vacancy centers (SiVs) in diamond nanophotonic cavities. Our qubit register consists of the SiV electron spin acting as a communication qubit and the strongly coupled silicon-29 nuclear spin acting as a memory qubit with a quantum memory time exceeding 2 seconds. By using a highly strained SiV, we realize electron-photon entangling gates at temperatures up to 1.5 kelvin and nucleus-photon entangling gates up to 4.3 kelvin. We also demonstrate efficient error detection in nuclear spin-photon gates by using the electron spin as a flag qubit, making this platform a promising candidate for scalable quantum repeaters.
Association of HLA Genotype and Fulminant Type 1 Diabetes in Koreans (2015)

Fulminant type 1 diabetes (T1DM) is a distinct subtype of T1DM that is characterized by rapid onset hyperglycemia, ketoacidosis, absolute insulin deficiency, and near normal levels of glycated hemoglobin at initial presentation. Although it has been reported that class II human leukocyte antigen (HLA) genotype is associated with fulminant T1DM, the genetic predisposition is not fully understood. In this study we investigated the HLA genotype and haplotype in 11 Korean cases of fulminant T1DM using imputation of whole exome sequencing data and compared its frequencies with 413 participants of the Korean Reference Panel. The HLA-DRB1*04:05-HLA-DQB1*04:01 haplotype was significantly associated with increased risk of fulminant T1DM in Fisher's exact test (odds ratio [OR], 4.11; 95% confidence interval [CI], 1.56 to 10.86; p = 0.009). A histidine residue at HLA-DRβ1 position 13 was marginally associated with increased risk of fulminant T1DM (OR, 2.45; 95% CI ,1.01 to 5.94; p = 0.054). Although we had limited statistical power, we provide evidence that HLA haplotype and amino acid change can be a genetic risk factor of fulminant T1DM in Koreans. Further large-scale research is required to confirm these findings.
Abstract 5156: Biochemical characterization of recombinant woodchuck vascular endothelium growth factor (wVEGF) (2011)

Abstract Vascular endothelial growth factor (VEGF) is one of the most potent and predominant angiogeneic signals. It binds receptors on blood vessels and stimulates proliferation, migration, survival and permeability of endothelial cells that form new vasculature for malignant tumors. Human hepatocellular carcinoma (HCC) is a highly VEGF-driven tumor and frequently occurs in the context of chronic hepatitis B or C virus infection. The woodchuck is a well characterized model of hepatitis B virus related HCC as it develops acute and chronic infection after neonatal infection with sera containing woodchuck hepatitis virus. This is a valuable model for translational studies of novel VEGF targeted agents as results may have great clinical relevance. We cloned a VEGF cDNA (wVEGF) from woodchuck liver tissue and transiently expressed it in COS-1 cells. A variety of parameters were measured to functionally characterize the wVEGF. Woodchuck cell lines, namely WCH17, WHK44 (woodchuck HCC), WC3 (woodchuck hepatocyte) and HepG2 cells were also characterized. The wVEGF peptide sequence was 94% identical to the human VEGFA. Two protein bands were detected in the supernatant (secreted) with molecular weights of approximately 25 and 17kDa, and a single band of 25kDa in the cell lysates. The major band observed in the cell lines was 25kD. The amount of wVEGF protein in the supernatant was 14-fold higher than in the lysate. The mRNA level in the cell lysate was significantly higher than was present in either the COS cells transfected with empty vector and also in the woodchuck and HepG2 cell lines. After 72 hours of stimulation with supernatant wVEGF, COS cells exhibited approximately 34% higher growth compared to cells in absence of wVEGF. The antiproliferative property of sunitinib, (a VEGF receptor tyrosine kinase inhibitor) on COS cells overexpressing wVEGF showed similar IC50 values for MTS assay 7.6±1.4 µM and for cell death (cell counts), 6.4±1.5 µM. In the cell lines, sensitivity to sunitinib ranked from WHK44 (4.5±1.2 µM) &amp;gt; WC3 (4.8±1.3 µM) &amp;gt;HepG2 (9.5±1.4 µM) &amp;gt;WCH17 (17.9±1.4 µM). In summary, the wVEGF was 94% identical in amino acid sequence to the human VEGF 189. It produced two protein bands that were associated with the supernatant after overexpressing the wVEGF in COS cells, one protein band was associated with the cell lysate. The wVEGF protein stimulated cell growth and exhibited sensitivity to the sunitinib with reduction in cell proliferation. (Support:American Cancer Society MRSG-08-096-01-CCE, Roswell Park Alliance Grant, PI Iyer) 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 5156. doi:10.1158/1538-7445.AM2011-5156
I M Avatar: Implicit Morphable Head Avatars from Videos (2022)

Traditional 3D morphable face models (3DMMs) provide fine-grained control over expression but cannot easily capture geometric and appearance details. Neural volumetric representations approach photorealism but are hard to animate and do not generalize well to unseen expressions. To tackle this problem, we propose IMavatar (Implicit Morphable avatar), a novel method for learning implicit head avatars from monocular videos. Inspired by the fine-grained control mechanisms afforded by conventional 3DMMs, we represent the expression- and pose-related deformations via learned blendshapes and skinning fields. These attributes are pose-independent and can be used to morph the canonical geometry and texture fields given novel expression and pose parameters. We employ ray marching and iterative root-finding to locate the canonical surface intersection for each pixel. A key contribution is our novel analytical gradient formulation that enables end-to-end training of IMavatars from videos. We show quantitatively and qualitatively that our method improves geometry and covers a more complete expression space compared to state-of-the-art methods. Code and data can be found at https://ait.ethz.ch/projects/2022/IMavatar/.
Supplementary Figure 3 from Fhit Modulates the DNA Damage Checkpoint Response (2023)

Supplementary Figure 3 from Fhit Modulates the DNA Damage Checkpoint Response
Organic Electrochemical Transistors Based on the Conjugated Polyelectrolyte PCPDTBT‐SO3K (CPE‐K) (2020)

PCPDTBT-SO<sub>3</sub> K (CPE-K), a conjugated polyelectrolyte, is presented as a mixed conductor material that can be used to fabricate high transconductance accumulation mode organic electrochemical transistors (OECTs). OECTs are utilized in a wide range of applications such as analyte detection, neural interfacing, impedance sensing, and neuromorphic computing. The use of interdigitated contacts to enable high transconductance in a relatively small device area in comparison to standard contacts is demonstrated. Such characteristics are highly desired in applications such as neural-activity sensing, where the device area must be minimized to reduce invasiveness. The physical and electrical properties of CPE-K are fully characterized to allow a direct comparison to other top performing OECT materials. CPE-K demonstrates an electrical performance that is among the best reported in the literature for OECT materials. In addition, CPE-K OECTs operate in the accumulation mode, which allows for much lower energy consumption in comparison to commonly used depletion mode devices.
Abstract B77: CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma (2016)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a very aggressive disease with poor prognosis. Treatment with gemcitabine, the FOLFIRINOX scheme or nab-paclitaxel offer only a modest increase in overall survival. For a number of other carcinomas, tumor subtypes have been uncovered that allow the use of targeted therapies. Although subtypes of PDAC were described, this malignancy is clinically still treated as a single disease. We established patient-derived models representing the full spectrum of previously identified quasi-mesenchymal (QM-PDA), classical and exocrine-like PDAC subtypes, and identified two markers—HNF1A and KRT81—that enable stratification of tumors into different subtypes by immunohistochemistry. Patients bearing tumors of these subtypes show significant differences in overall survival and their tumors differ in drug sensitivity, with the exocrine-like subtype being resistant to tyrosine kinase inhibitors and paclitaxel. The xenobiotic enzyme, cytochrome P450 3A5 (CYP3A5), metabolizes these compounds in tumors of the exocrine-like subtype, and pharmacological or short hairpin RNA (shRNA)-mediated CYP3A5 inhibition sensitizes tumor cells to these drugs. Additionally, retrospective analysis of a large patient cohort confirmed that CYP3A5 is predominantly found in those patient tumors classified as exocrine-like. Whereas the hepatocyte nuclear factor 4, alpha (HNF4A) controls basal expression of CYP3A5, drug-induced CYP3A5 upregulation is mediated by the nuclear receptor NR1I2. Interfering with these regulatory mechanisms may provide an alternative approach to suppress the CYP3A5 pathway. CYP3A5 also contributes to acquired drug resistance in QM-PDA and classical PDAC, and is highly expressed in several additional malignancies. These findings designate CYP3A5 as predictor of therapy response and as a tumor cell-autonomous detoxification mechanism that must be overcome to prevent drug resistance. Citation Format: Elisa M. Noll, Christian Eisen, Albrecht Stenzinger, Elisa Espinet, Alexander Muckenhuber, Corinna Klein, Vanessa Vogel, Bernd Klaus, Wiebke Nadler, Christoph Rösli, Christian Lutz, Michael Kulke, Jan Engelhardt, Franziska Zickgraf, Octavio Espinosa, Matthias Schlesner, Xiaoqi Jiang, Annette Kopp-Schneider, Peter Neuhaus, Marcus Bahra, Bruno V. Sinn, Roland Eils, Nathalia A. Giese, Thilo Hackert, Oliver Strobel, Jens Werner, Markus W. Büchler, Wilko Weichert, Andreas Trumpp, Martin R. Sprick.{Authors}. CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr B77.
Robust Repetitive Control System With On-Line Identification of the Period of Periodic Disturbances (2004)

Repetitive control system is a servo system that achieves zero steady-state tracking error for any periodic desired outputs and any periodic disturbance inputs with a known period. This paper deals with a repetitive control problem for the case where the plant has a norm-bounded uncertainty and the period of periodic disturbances is unknown but is within known lower and upper bounds. A new robust repetitive controller is proposed not only to guarantee the robust stability against the uncertainty but also to estimate the unknown period and to reject any periodic disturbances with the period. It is shown that the design problem is reduced to a simple and feasible l1 norm minimization problem. The controller can be obtained easily by solving a simple linear programming problem. Simulation results show the effectiveness of the proposed controller for rejection of periodic disturbances with uncertain periods.
Total Variation Iterative Linear Expansion of Thresholds with Applications in CT (2018)

The iterative linear expansion of threshold framework, or iLET, offers a new approach for solving image restoration problems under sparsity assumptions. Instead of estimating the reconstructed image directly, the iLET paradigm parametrizes the reconstruction process as a linear combination of elementary thresholding functions and optimizes over their coefficients. Here, we rely on the fast and accurate convergence of iLET, and propose an extension of this framework, under the assumption that the reconstructed object is approximately piece-wise constant. This assumption leads to a new total-variation framework of iLET. We demonstrate the applicability of our technique to bio-medical imaging problems, such as computerized tomography reconstruction. Our technique surpasses state-of-the-art reconstructions in terms of PSNR and SSIM, while offering an automatic way for tuning its regularization parameter.
Affine Invariant Information Embedment for Accurate Camera-Based Character Recognition (2006)

Recognizing characters in a scene image taken by a digital camera has been studied for decades. However, it is still a challenging problem to achieve high accuracy. In this paper, we propose a method of embedding information in a character pattern so that the class of the character can be identified. The information should be robust against geometric distortions since an image taken by a digital camera is usually geometrically distorted. In the proposed method, a character pattern is designed in two colors so that the information is embedded as the area ratio of regions of two colors. Since the area ratio is affine invariant, it is expected that the area ratio is correctly extracted even if a character image is affine-transformed. We generate character patterns with the embedded information and discuss the effectiveness of the proposed method
Synthesis of power efficient systems-on-silicon (2002)

We developed a new modular synthesis approach for design of low-power core-based data-intensive application-specific systems on silicon. The power optimization is conducted in three steps: minimization of instruction cache misses, placement of frequently executed sequential basic blocks of code in consecutive Gray code addressed memory locations, and processor and cache application-driven selection for low power. In order to bridge the gap between the profiling and modeling tools from the two traditionally disjoint synthesis domains (architecture and CAD), we developed a new synthesis and evaluation platform. The platform integrates the existing modeling, profiling, and simulation tools with the developed system-level synthesis tools. The effectiveness of the approach is demonstrated on a variety of modern industrial-strength multimedia and communication applications.
SiliFuzz: Fuzzing CPUs by proxy (2021)

CPUs are becoming more complex with every generation, at both the logical and the physical levels. This potentially leads to more logic bugs and electrical defects in CPUs being overlooked during testing, which causes data corruption or other undesirable effects when these CPUs are used in production. These ever-present problems may also have simply become more evident as more CPUs are operated and monitored by large cloud providers. If the RTL ("source code") of a CPU were available, we could apply greybox fuzzing to the CPU model almost as we do to any other software [arXiv:2102.02308]. However our targets are general purpose x86_64 CPUs produced by third parties, where we do not have the RTL design, so in our case CPU implementations are opaque. Moreover, we are more interested in electrical defects as opposed to logic bugs. We present SiliFuzz, a work-in-progress system that finds CPU defects by fuzzing software proxies, like CPU simulators or disassemblers, and then executing the accumulated test inputs (known as the corpus) on actual CPUs on a large scale. The major difference between this work and traditional software fuzzing is that a software bug fixed once will be fixed for all installations of the software, while for CPU defects we have to test every individual core repeatedly over its lifetime due to wear and tear. In this paper we also analyze four groups of CPU defects that SiliFuzz has uncovered and describe patterns shared by other SiliFuzz findings.
DNA vaccine encoding heat shock protein 90 protects from murine lupus (2020)

The beneficial effects of DNA vaccination with HSP90 in murine SLE support the possibility of HSP90-based therapeutic modalities of intervention in SLE.
Search for new phenomena in final states with two opposite-charge, same-flavor leptons, jets, and missing transverse momentum in pp collisions at s = 13 $$ \sqrt{s}=13 $$ TeV (2018)

Search results are presented for physics beyond the standard model in final states with two opposite-charge, same-flavor leptons, jets, and missing transverse momentum. The data sample corresponds to an integrated luminosity of 35.9 fb -1 of protonproton collisions at s = 13 TeV collected with the CMS detector at the LHC in 2016.
Preparation and Characterization of Amphiphilic Triblock Terpolymer-Based Nanofibers as Antifouling Biomaterials (2012)

Antifouling surfaces are critical for the good performance of functional materials in various applications including water filtration, medical implants, and biosensors. In this study, we synthesized amphiphilic triblock terpolymers (tri-BCPs, coded as KB) and fabricated amphiphilic nanofibers by electrospinning of solutions prepared by mixing the KB with poly(lactic acid) (PLA) polymer. The resulting fibers with amphiphilic polymer groups exhibited superior antifouling performance to the fibers without such groups. The adsorption of bovine serum albumin (BSA) on the amphiphilic fibers was about 10-fold less than that on the control surfaces from PLA and PET fibers. With the increase of the KB content in the amphiphilic fibers, the resistance to adsorption of BSA was increased. BSA was released more easily from the surface of the amphiphilic fibers than from the surface of hydrophobic PLA or PET fibers. We have also investigated the structural conformation of KB in fibers before and after annealing by contact angle measurements, transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDX), and coarse-grained molecular dynamics (CGMD) simulation to probe the effect of amphiphilic chain conformation on antifouling. The results reveal that the amphiphilic KB was evenly distributed within as-spun hybrid fibers, while migrated toward the core from the fiber surface during thermal treatment, leading to the reduction in antifouling. This suggests that the antifouling effect of the amphiphilic fibers is greatly influenced by the arrangement of amphiphilic groups in the fibers.
Test structures to quantify contact placement-impacted drain current variations (2010)

The difference in the number of contacts across different transistors and standard cells results in current variations across the channel. In this work, we present test structures to target this effect and characterize and quantify the impact on 45 nm SOI silicon. After comparing the impact of contact resistance between 65 nm and 45 nm silicon, we provide and analyze our 45 nm test structure results and provide a means to extract mean contact resistance from our test structures. We observe that impact due to contact resistance can be up to 10% for 45 nm, while it could have been of less importance (less than 4%) for 65 nm technology. Such test structures and methodology help us provide intrinsic device models in 45 nm without inaccuracies or resistive double counting that may be introduced due to placement-impacted contact resistance variations.
Polymeric Cups for Cavitation-mediated Delivery of Oncolytic Vaccinia Virus (2016)

Oncolytic viruses (OV) could become the most powerful and selective cancer therapies. However, the limited transport of OV into and throughout tumors following intravenous injection means their clinical administration is often restricted to direct intratumoral dosing. Application of physical stimuli, such as focused ultrasound, offers a means of achieving enhanced mass transport. In particular, shockwaves and microstreaming resulting from the instigation of an ultrasound-induced event known as inertial cavitation can propel OV hundreds of microns. We have recently developed a polymeric cup formulation which, when delivered intravenously, provides the nuclei for instigation of sustained inertial cavitation events within tumors. Here we report that exposure of tumors to focused ultrasound after intravenous coinjection of cups and oncolytic vaccinia virus , leads to substantial and significant increases in activity. When cavitation was instigated within SKOV-3 or HepG2 xenografts, reporter gene expression from vaccinia virus was enhanced 1,000-fold (P < 0.0001) or 10,000-fold (P < 0.001), respectively. Similar increases in the number of vaccinia virus genomes recovered from tumors were also observed. In survival studies, the application of cup mediated cavitation to a vaccinia virus expressing a prodrug converting enzyme provided significant (P < 0.05) retardation of tumor growth. This technology could improve the clinical utility of all biological therapeutics including OV.