gebhart/patrepeval huggingface dataset:
Abstract 530: Circulating γδ T cells are activated and depleted during progression of high-grade gliomas: Implications for γδ T cells therapy of GBM (2012)

Abstract Glioblastoma multiforme (GBM) remains frustratingly impervious to any existing therapy. We have previously shown that GBM is sensitive to recognition and lysis by ex vivo activated γδ T cells, a minor subset of lymphocytes that innately recognize autologous stress-associated target antigens via the T cell receptor and/or NKG2D. However, circulating γδ T cell counts and function are significantly reduced in patients with GBM. We sought to determine the role of γδ T cells in the immune response to high-grade gliomas in C57BL/6 mice bearing GL261 cell line-derived intracranial gliomas. Examination of mice 15 days after intracranial tumor placement and prior to development of neurologic symptoms revealed small infiltrating high-grade gliomas near the injection site. Concurrently, the peripheral blood γδ T cell count was significantly increased when compared to control mice that received only the methylcellulose vehicle (p=0.0003). T cell expansion was confined to the γδ T cell compartment, and a substantial proportion of γδ T cells in tumor-bearing mice expressed Annexin-V (20%-45%) indicating progression to apoptosis. Annexin-V expression in control mice was confined to 2-5% of γδ T cells, significantly less than tumor-bearing mice (p&amp;lt;0.0001). GL261-derived tumors expressed γδ T cell target stress-associated NKG2D ligands H60, MULT-1 and RAE-1, yet γδ T cells did not infiltrate the intracranial tumors. In a separate experiment, we found no survival advantage between wild-type (WT) mice over γδ T cell-deficient (C57BL/6α-/−) tumor-bearing mice. Based on this observation that activated γδ T cells did not invade the tumor, we treated mice with a stereotactic intracranial injection of 1.5 x 106 ex vivo expanded/activated γδ T cells approximately 15 minutes following placement of 5 x 106 GL261 glioma cells. Mice that received intracranial γδ T cells were protected from tumor development at site of injection, although distant tumors did eventually form. These data suggest that γδ T cells are stimulated in glioma-bearing mice and that depletion in γδ T cells observed in mouse glioma models and human GBM are likely due to activation-induced cell death in response to the tumor. Activated γδ T cells do not traffic to the tumor parenchyma; however, an antitumor effect can be achieved by direct placement of ex vivo activated γδ T cells in the vicinity of microscopic disease, suggesting a potential post-resection strategy for treatment of minimal residual GBM. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 530. doi:1538-7445.AM2012-530
Automating embedded analysis capabilities and managing software\n complexity in multiphysics simulation part II: application to partial\n differential equations (2012)

A template-based generic programming approach was presented in a previous\npaper that separates the development effort of programming a physical model\nfrom that of computing additional quantities, such as derivatives, needed for\nembedded analysis algorithms. In this paper, we describe the implementation\ndetails for using the template-based generic programming approach for\nsimulation and analysis of partial differential equations (PDEs). We detail\nseveral of the hurdles that we have encountered, and some of the software\ninfrastructure developed to overcome them. We end with a demonstration where we\npresent shape optimization and uncertainty quantification results for a 3D PDE\napplication.\n
Monolithic Optoelectronic Implementation of Neural Planes (1992)

Abstract : The implementation of a neural computing system, whose structure and function is motivated by natural intelligence, will provide a unique way to solve problems that are typically too difficult for the conventional electronic computers to tackle. Interest in this type of computer has emerged largely because it is hoped that by building a computer that share some of the characteristics of the biological systems, we will be able to address problems such as image recognition which animals do exceedingly well but current computer do not. There had been considerable progress on the theoretical research in neural network to justify the optimism of future applications. This has resulted in a focused attention on the hardware realization of neural architectures. The computational power of neural computer arises from matching the computer architecture and the physical properties of the devices used in the implementation to the requirements of the problem. In other words, a neural computer is highly specialized and it is therefore very difficult to derive its full advantages on a general purpose computer. This provides a strong impetus for advancing the technologies for the physical realization of neural computers in parallel and interactively with the development of theoretical neural network models.
Nano-Gap Piezoelectric Resonators for Mechanical RF Magnetic Field Modulation (2005)

Novel piezoelectric MEMS resonators with magnetic shielding have been developed to mechanically generate RF magnetic fields in the MHz frequency range from static magnetic fields. Thermally evaporated thin film nickel iron (NiFe) (10 to 20 nm) was deposited with a saturation flux density of 0.5 T, coercivity of 500 A/m and a high relative permeability of 3.7 × 103. Aluminum nitride (AlN) resonators developed for high frequency operation, resonate in a contour mode to increase and decrease a gap surrounding the resonator. This gap, 200 to 350 nm, is formed using a silicon sidewall deposition as a sacrificial spacer. Resonators with frequencies up to 60 MHz have been fabricated and tested.
Monolithic Spiral Transformers: A Design Methodology (2007)

A method to design spiral transformers is outlined. It utilizes simple inductance estimates in order to initially design the dimensions for the desired transformer, after which an EM simulation is used to extract s-parameters of the structure; a compact model is then extracted from the s-parameter results. A wideband compact model is proposed that is accurate up to the self-resonance frequency (SRF) of the structure. A 3-to-1 transformer is designed and its measured performance verified in a 0.18 μm RF CMOS process.
Toward Developing an Approach for Alerting Drivers to the Direction of a Crash Threat (2007)

These findings should facilitate developing a multimodality integrated crash alert approach for vehicles equipped with multiple crash avoidance systems.
Nonlinear metamaterial surfaces for absorption of high power microwave surface currents (2013)

Surface currents due to high power microwaves can damage or interfere with sensitive antennas and electronic devices. Absorbers tend to be thick and heavy, and reactive coatings such as high impedance surfaces alter the scattering properties of a surface, thereby affecting the radiation pattern of nearly antennas. In this paper, a novel metamaterial surface with nonlinear properties is introduced, and we numerically demonstrate how this structure overcomes the limitations of conventional absorbers or reactive surfaces, and how it works as an absorbing structure for high power microwave surface currents without affecting the behavior of the surface of low power levels.
Supplementary Methods from Fc Optimization of Therapeutic Antibodies Enhances Their Ability to Kill Tumor Cells &lt;i&gt;In vitro&lt;/i&gt; and Controls Tumor Expansion &lt;i&gt;In vivo&lt;/i&gt; via Low-Affinity Activating Fcγ Receptors (2023)

Supplementary Methods from Fc Optimization of Therapeutic Antibodies Enhances Their Ability to Kill Tumor Cells &lt;i&gt;In vitro&lt;/i&gt; and Controls Tumor Expansion &lt;i&gt;In vivo&lt;/i&gt; via Low-Affinity Activating Fcγ Receptors
Supplementary Data from Identification of a Synthetic Lethal Relationship between Nucleotide Excision Repair Deficiency and Irofulven Sensitivity in Urothelial Cancer (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
Structure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity (2020)

Dipeptidase 3 (DPEP3) is one of three glycosylphosphatidylinositol-anchored metallopeptidases potentially involved in the hydrolytic metabolism of dipeptides. While its exact biological function is not clear, DPEP3 expression is normally limited to testis, but can be elevated in ovarian cancer. Antibody drug conjugates targeting DPEP3 have shown efficacy in preclinical models with a pyrrolobenzodiazepine conjugate, SC-003, dosed in a phase I clinical trial (NCT02539719). Here we reveal the novel atomic structure of DPEP3 alone and in complex with the SC-003 Fab fragment at 1.8 and 2.8 Å, respectively. The structure of DPEP3/SC-003 Fab complex reveals an eighteen-residue epitope across the DPEP3 dimerization interface distinct from the enzymatic active site. DPEP1 and DPEP3 extracellular domains share a conserved, dimeric TIM (β/α)8-barrel fold, consistent with 49% sequence identity. However, DPEP3 diverges from DPEP1 and DPEP2 in key positions of its active site: a histidine to tyrosine variation at position 269 reduces affinity for the β zinc and may cause substrate steric hindrance, whereas an aspartate to asparagine change at position 359 abolishes activation of the nucleophilic water/hydroxide, resulting in no in vitro activity against a variety of dipeptides and biological substrates (imipenem, leukotriene D4 and cystinyl-bis-glycine). Hence DPEP3, unlike DPEP1 and DPEP2, may require an activating co-factor in vivo or may remain an inactive, degenerate enzyme. This report sheds light on the structural discriminants between active and inactive membrane dipeptidases and provides a benchmark to characterize current and future DPEP3-targeted therapeutic approaches.
Synthesisand Dual-Mode Electrochromism of AnisotropicMonoclinic Nb12O29 Colloidal Nanoplatelets (2020)

Transition
metal oxide nanocrystals with dual-mode electrochromism
hold promise for smart windows enabling spectrally selective solar
modulation. We have developed the colloidal synthesis of anisotropic
monoclinic Nb12O29 nanoplatelets (NPLs) to investigate
the dual-mode electrochromism of niobium oxide nanocrystals. The precursor
for synthesizing NPLs was prepared by mixing NbCl5 and
oleic acid to form a complex that was subsequently heated to form
an oxide-like structure capped by oleic acid, denoted as niobium oxo
cluster. By initiating the synthesis using niobium oxo clusters, preferred
growth of NPLs over other polymorphs was observed. The structure of
the synthesized NPLs was examined by X-ray diffraction in conjunction
with simulations, revealing that the NPLs are monolayer monoclinic
Nb12O29, thin in the [100] direction and extended
along the b and c directions. Besides
having monolayer thickness, NPLs show decreased intensity of Raman
signal from Nb–O bonds with higher bond order when compared
to bulk monoclinic Nb12O29, as interpreted by
calculations. Progressive electrochemical reduction of NPL films led
to absorbance in the near-infrared region (stage 1) followed by absorbance
in both the visible and near-infrared regions (stage 2), thus exhibiting
dual-mode electrochromism. The mechanisms underlying these two processes
were distinguished electrochemically by cyclic voltammetry to determine
the extent to which ion intercalation limits the kinetics, and by
verifying the presence of localized electrons following ion intercalation
using X-ray photoelectron spectroscopy. Both results support that
the near-infrared absorption results from capacitive charging, and
the onset of visible absorption in the second stage is caused by ion
intercalation.
Notice of Removal: Forward-looking IVUS transducer with front-end ASIC for 3D imaging (2017)

Removed.
Composite surface for blocking bacterial adsorption on protein biochips (2002)

The design and fabrication of protein biochips requires characterization of blocking agents that minimize nonspecific binding of proteins or organisms. Nonspecific adsorption of Escherichia coli, Listeria innocua, and Listeria monocytogenes is prevented by bovine serum albumin (BSA) or biotinylated BSA adsorbed on SiO(2) surfaces of a biochip that had been modified with a C(18) coating. Biotinylated BSA forms a protein-based surface that in turn binds streptavidin. Because streptavidin has multiple binding sites for biotin, it in turn anchors other biotinylated proteins, including antibodies. Hence, biotinylated BSA simultaneously serves as a blocking agent and a foundation for binding an interfacing protein, avidin or streptavidin, which in turns anchors biotinylated antibody. In our case, the antibody is C11E9, an IgG-type antibody that binds Listeria spp. Nonspecific adsorption of another bacterium, Escherichia coli, is also minimized due to the blocking action of the BSA. The blocking characteristics of BSA adsorbed on C(18)-derivatized SiO(2) surfaces for construction of a protein biochip for electronic detection of pathogenic organisms is investigated.
HBV messenger RNA (mRNA) is a strong predictive marker for HBeAg and HBsAg loss during antiviral treatment with nucleoside/nucleotide analogues (NUCs) in patients with chronic hepatitis B virus (HBV) infection (2012)

Aims: Treatment with NUCs can completely suppress HBV DNA levels in most patients, however there are few markers for the prediction of long term response. We studied the association of HBeAg and HBsAg loss with serum levels of circulating full-length (fl) and truncated (tr)HBV mRNA before and during NUC treatment. Methods: For specific detection and quantification of fl and trRNA species, two step real-time reverse transcription PCRs were developed (detection limit 450 and 600 copies/mL, respectively). 67 patients (45 HBeAg positive, mean HBV DNA level 7.6±8[9–2.8] log10copies/mL) receiving either tenofovir (TDF) 300mg/day (n=34) or lamivudine (LAM) 100mg/day (n=33) for ≥ 24 months were retrospectively analyzed. Levels of flRNA and trRNA were compared to levels of HBV DNA and HBsAg derived from frozen serum samples representing months 0, 3, 6, 9, and 12. Results: At treatment months 0 and 24 the mean fl and trRNA levels were 6.7±7.3 [8–2.6] and 5.9±6.5 [7.2–2.6], and 7.1±7.7 [8.5–2.7] and 5.1±5.5 [6.2–2.7] (p=n.s.), while mean HBV DNA levels decreased from 7.6±8.2 [9–3.9] to 2.9±1.6 [3.1–1.5] log10copies/mL, respectively. Patients receiving TDF showed a significantly stronger decrease in HBV DNA levels compared to patients receiving LAM (p=0.02), however there were no differences in fl, trRNA or HBsAg levels. However, in patients remaining HBeAg positive (n=30) flRNA levels remained unchanged until month 12, while in patients who achieved HBeAg loss (n=15) flRNA and tr RNA levels were already lower at baseline (p=0.02) and showed a significant decrease at months 3, 6 and 12 (p<0.001). HBV DNA and HBsAg levels were not predictive for HBeAg loss (p=n.s.). In all 4 patients achieving HBsAg loss between month 7–24, fl and trRNA levels already became undetectable until month 5. Conclusion: HBV RNA levels represent a strong predictor of HBeAg and HBsAg loss during treatment with NUCs which shloud be evaluated in further studies.
Mutation in DHP receptor alpha 1 subunit (CACLN1A3) gene in a Dutch family with hypokalaemic periodic paralysis. (1995)

Hypokalaemic periodic paralysis (HypoPP) is characterised by transient attacks of muscle weakness of varying duration and severity accompanied by a drop in serum potassium concentration during the attacks. The largest known HypoPP family is of Dutch origin and consists of 277 members in the last five generations, 55 of whom have HypoPP inherited in an autosomal dominant pattern. Forty-eight persons including 28 patients with a proven diagnosis of HypoPP were used for linkage analysis. Microsatellite markers were used to exclude 45 to 50% of the genome and linkage to chromosome 1q31-32 was found. No recombinants were found between HypoPP and D1S412 and a microsatellite contained within the DHP receptor alpha 1 subunit (CACLN1A3) gene. A previously reported G to A mutation causing an arginine to histidine substitution at residue 528 in the transmembrane segment IIS4 of the CACLN1A3 gene was shown in patients by restriction analysis of genomic PCR products.
Therapeutic Targeting of CD47 to Modulate Tissue Responses to Ischemia and Radiation (2011)

CD47 is a widely expressed cell surface receptor that serves as a counter-receptor for signal regulatory protein-α and as a receptor for the secreted matricellular protein thrombospondin-1. Thrombospondin-1 signaling through CD47 regulates cellular signaling pathways that control cell survival, growth, motility, mitochondrial biogenesis, arterial vasoactive responses to physiologic vasodilators and blood flow, and responsiveness to growth factors. Studies employing mice lacking either thrombospondin-1 or CD47 have revealed an important role for this receptor-ligand interaction in tissue responses to injury and stress. These null mice show enhanced recovery from soft tissue fixed ischemic injuries, ischemia reperfusion injuries, and radiation injuries. These studies have led to development of antisense strategies to locally or globally suppress CD47 gene expression. A translation-blocking CD47 morpholino improves tissue survival in skin flap and hindlimb fixed ischemia models, full thickness skin grafts, and a liver ischemia/reperfusion model of organ transplantation in mice. Furthermore, the benefits of morpholino treatment extend to aged mice and mice with dysregulated fat metabolism that characteristically exhibit impaired recovery from ischemic injuries. Activity of the morpholino was also demonstrated for treatment of ischemic injury in miniature pigs. Treatment with the CD47 morpholino protects mice from major effects of ionizing radiation including alopecia, deterioration of muscle function, soft tissue and cutaneous fibrosis, and loss of hematopoietic stem cells in bone marrow. Remarkably, the same treatment does not protect tumors but instead enhances their ablation by irradiation. We discuss prospects for further development of CD47 antisense therapeutics for clinical applications including reconstructive surgery, organ transplantation, angioplasty, and cancer.
An Effective Method Based on Time Reversal and Optimization Techniques for Locating Faults on Power Grids (2020)

Electromagnetic time reversal (EMTR) has recently emerged as a promising technique applied for locating faults in power networks. It directly transposes the idea of focusing energy back to its source introduced in original time-reversal (TR) methods. Accordingly, we present in this paper, FasTR, a method based on the tenets of TR, that estimates the fault location by employing optimization based algorithms for fetching the highest peak amplitude with maximum coherence in space and time. However, it uses an alternative approach for executing the cumbersome TR post-processing, thanks to a simplified analytical model capable of evaluating the voltage (or current) at any position and any instant of the tested network resulting from the back-injection of the recorded time-revered signals. FasTR is shown to accurately locate a fault in a complex network with just a basic knowledge of its topology in no more than a couple tens of seconds. More importantly is its ability to locate multiple faults in non-homogeneous networks. The performance of the proposed method is validated by numerical simulations as well as an experimental setup by making reference to a reduced-scale coaxial cable network where real faults are hardware-emulated.
Figure S5 from Endothelial Activation and Blood–Brain Barrier Disruption in Neurotoxicity after Adoptive Immunotherapy with CD19 CAR-T Cells (2023)

&lt;p&gt;Supplementary Figure 5. Immunohistochemistry of brain in a patient with fatal neurotoxicity&lt;/p&gt;
Kinetics Model for Initiation and Promotion for Describing Tumor Prevalence From HZE Radiation (2003)

A kinetics model for cellular repair and misrepair for multiple radiation-induced lesions (mutation-inactivation) is coupled to a two-mutation model of initiation and promotion in tissue to provide a parametric description of tumor prevalence in the Harderian gland in a mouse. Dose-response curves are described for gamma-rays and relativistic ions. The effects of nuclear fragmentation are also considered for high-energy proton and alpha-particle exposures. The model described provides a parametric description of age-dependent cancer induction for a wide range of radiation fields. We also consider the two hypotheses that radiation acts either solely as an initiator or as both initiator and promoter and make model calculations for fractionation exposures from gamma-rays and relativistic Fe ions. For fractionated Fe exposures, an inverse dose-rate effect is provided by a promotion hypothesis using a mutation rate for promotion typical of single-gene mutations.
Common Capacitor Multiphase LLC Converter With Passive Current Sharing Ability (2017)

In high-power applications, parallel operation is required to improve both efficiency and reliability. In an LLC converter, it is difficult to achieve parallel operation due to the gain sensitivity to component tolerance. This paper proposes a new structure of a common resonant capacitor for a multiphase LLC converter, which can achieve very good current-sharing performance with no additional components or control. To evaluate the current-sharing performance, a new first harmonic approximation (FHA) model is built in this paper to analyze the LLC converter with coupled resonant tanks. Both FHA analysis and powersim (PSIM) simulation results demonstrate the load-sharing improvement of the proposed common capacitor LLC resonant converter over the conventional two-phase LLC converter. The current-sharing performance from the FHA analysis and the PSIM simulation are compared, and the error of the FHA analysis is evaluated and explained. A 600 W two-phase LLC converter prototype based on the proposed method is also built to verify the feasibility. Excellent current-sharing performance (6% resonant current sharing error at a wide load range) has been achieved.
Mode Selection and Mode-Dependency Modeling for Power-Aware Embedded Systems (2002)

Among the techniques for system-level power management, it is not currently possible to guarantee timing constraints and have a comprehensive system model supporting multiple components at the same time. We propose a new method for modeling and selecting the power modes for the optimal system-power management of embedded systems under timing and power constraints. First, we not only model the modes and the transitions overhead at the component level, but we also capture the application-imposed relationships among the components by introducing a mode dependency graph at the system level. Second, we propose a mode selection technique, which determines when and how to change mode in these components such that the whole system can meet all power and timing constraints. Our constraint-driven approach is a critical feature for exploring power/performance tradeoffs in power-aware embedded systems. We demonstrate the application of our techniques to a low-power sensor and an autonomous rover example.