gebhart/patrepeval huggingface dataset:
Nano-enabled pancreas cancer immunotherapy using immunogenic cell death and reversing immunosuppression (2017)

While chemotherapy delivery by nanocarriers has modestly improved the survival prospects of pancreatic ductal adenocarcinoma (PDAC), additional engagement of the immune response could be game changing. We demonstrate a nano-enabled approach for accomplishing robust anti-PDAC immunity in syngeneic mice through the induction of immunogenic cell death (ICD) as well as interfering in the immunosuppressive indoleamine 2,3-dioxygenase (IDO) pathway. This is accomplished by conjugating the IDO inhibitor, indoximod (IND), to a phospholipid that allows prodrug self-assembly into nanovesicles or incorporation into a lipid bilayer that encapsulates mesoporous silica nanoparticles (MSNP). The porous MSNP interior allows contemporaneous delivery of the ICD-inducing chemotherapeutic agent, oxaliplatin (OX). The nanovesicles plus free OX or OX/IND-MSNP induce effective innate and adaptive anti-PDAC immunity when used in a vaccination approach, direct tumor injection or intravenous biodistribution to an orthotopic PDAC site. Significant tumor reduction or eradication is accomplishable by recruiting cytotoxic T lymphocytes, concomitant with downregulation of Foxp3<sup>+</sup> T cells.
Efficient collection of Raman-scattered light (1982)

The design and implementation of a device used for Raman-scattering experiments are reported. This device, namely an optically reflecting bulb, has been found to serve as an efficient collector of light scattered by a sample located at its center. It can be constructed easily and inexpensively and can be used for both room- and low-temperature experiments. A second device which makes use of maximum reflecting surface area and a light pipe is also described.
Analysis of Narrow Depressed-Cladding Fibers for Minimization of Cladding and Radiation Mode Losses in Fiber Bragg Gratings (1997)

Undesirable losses in highly reflective fiber Bragg gratings due to coupling to bound cladding modes or lossy radiation modes are well documented 1 - 5 . Several approaches have been proposed for reducing this coupling, including high LP 01 mode confinement fibers (high numerical aperture single-mode fibers 6 and two-mode fibers 7 ), fibers with equally photosensitive core and cladding regions 8 , and, recently, fibers with wide depressed cladding regions 5 . However, the solution detailed by Komukai, et al. 6 is undesirable due to mode-field mismatch losses when splicing to conventional single-mode telecommunication fibers operated at 1550 nm (e.g, Corning SMF-28) and the solution of Okude, et al. 7 requires advanced fabrication techniques. Additionally, while the solutions detailed by Dong, et al. 5 and Delevaque, et al. 8 reduce cladding mode losses for gratings with no variation of the photoinduced index transverse to the fiber axis, it is well known that strong asymmetries in the transverse photoinduced index profile can occur in Type I 9 and Type II 10 gratings due to the sidewriting process. In fact, elaborate writing schemes have been proposed to reduce this asymmetry 11 - 12 . Additionally, in practice, small tilts of the grating fringe planes can be introduced during fabrication due to mask-fiber misalignment. It is demonstrated in this paper that the solutions detailed by Dong, et al. 5 and Delevaque, et al. 8 are not optimum for azimuthally asymmetric transverse photoinduced index distributions, and a new narrow depressed cladding fiber design that has superior loss suppression characteristics for moderate grating asymmetries is presented.
Passivation of Germanium by Graphene (2017)

The oxidation of Ge covered with graphene that is either grown on or transferred to the surface is investigated by X-ray photoelectron spectroscopy, Raman spectroscopy, and transmission electron microscopy. Graphene properly grown by chemical vapor deposition on Ge(100), (111), or (110) effectively inhibits room-temperature oxidation of the surface. When graphene is transferred to the Ge surface, oxidation is reduced relative to that on uncovered Ge but has the same power law dependence. We conclude that access to the graphene/Ge interface must occur via defects in the graphene. The excellent passivation provided by graphene grown on Ge should enhance applications of Ge in the electronic-device industry.
Stokes-parameter photopolarimeter using an optically or mechanically rotatable two-detector assembly (1990)

A two-detector photopolarimeter for measuring the four Stokes parameters of a monochromatic or quasi-monochromatic light beam in an arbitrary state of partial elliptical polarization is described. Each detector is partially specularly reflecting at oblique incidence, and the plane of incidence is rotated (by other than 90 degrees ) between the two successive reflections. The two-detector assembly is itself rotated manually or with a stepping motor solidly as one unit around the axis of the incident beam. Mechanical rotation may be eliminated by using a Faraday rotator in front of a stationary arrangement of two detectors. Conditions under which singularities may occur (which lead to an incomplete measurement of polarization) are discussed. Optimum geometry and detector-surface characteristics are identified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
260. AAV Ancestral Reconstruction Library Enables Selection of Broadly Infectious Viral Variants (2015)

Adeno-associated virus (AAV) vectors have demonstrated clinical efficacy in treating several diseases. Improved vectors may extend these landmark successes to other indications, and protein engineering approaches are enhancing the gene delivery properties of AAV vectors to address such unmet medical needs. To access new viral sequences with potentially enhanced infectious properties, and to gain insights into AAV's evolutionary history, we computationally designed and experimentally characterized an ancestral reconstruction of the AAV capsid. To this end, we first generated a phylogenetic tree of AAV sequences through Bayesian Markov chain Monte Carlo simulations, then selected a node for reconstruction based on its relative confidence value and proximity to AAV serotypes of clinical interest. We next used HandAlign, a Markov chain Monte Carlo alignment sampler, to predict the ancestral sequence of the most likely alignment at the selected node. This generated a reconstruction where most amino acids were predicted with high confidence, while 32 of the positions were predicted with low confidence. In order to address uncertainty in these positions, we synthesized the inferred ancestral capsid as a large combinatorial library incorporating degenerate residues at the 32 variable amino acid sites. We then characterized the evolutionary flexibility of these residues, the majority of which have not been previously studied, by subjecting the library to six rounds of selection on a panel of representative cell lines. The resulting variants exhibited transduction efficiencies comparable to the most efficient extant serotypes, and in general the selected ancestral libraries were broadly infectious across the cell line panel, indicating that they favor promiscuity over specificity. Unlike many current serotypes, these ancestral AAVs do not utilize sialic acids, galactose, or heparan sulfate proteoglycans for cellular entry. Additionally, ancestral libraries were found to be as susceptible to neutralizing antibodies as extant serotypes, suggesting that such ancestral variant candidates exhibit immunogenic properties similar to modern descendants. Interestingly, ancestral AAVs retained infectivity at temperatures that completely ablated infectivity of modern serotypes; this higher thermostability may have supported increased evolvability through mutational tolerance. Finally, selected variants mediated 19-31 fold higher gene expression in muscle compared to AAV1, a serotype clinically utilized for muscle delivery, highlighting their potential promise for gene therapy.
Identification of CD163 as an antiinflammatory receptor for HMGB1-haptoglobin complexes (2018)

Secreted by activated cells or passively released by damaged cells, extracellular HMGB1 functions as a pro-inflammatory mediator of infection or injury. It was previously unknown whether HMGB1 can be partner with other endogenous proteins to tilt the balance towards anti-inflammatory activities. Here we demonstrated that an acute phase protein, haptoglobin, effectively binds HMGB1, and triggers anti-inflammatory programs in a CD163-dependent fashion. Specifically, the HMGB1 and haptoglobin complexes elicit the production of anti-inflammatory enzymes (heme oxygenase-1) and cytokines (e.g., IL-10) in wild type, but not in CD163-deficient macrophages. Genetic disruption of haptoglobin or CD163 expression renders animals more susceptible to lethal sepsis, whereas administration of haptoglobin to wild type or to haptoglobin-gene deficient animals confers significant protection. These findings reveal a novel mechanism by which an acute phase protein modulates extracellular HMGB1 activities, and provides a novel strategy for treatment of HMGB1-dependent inflammatory diseases.
Bayesian graph convolutional neural networks for semi-supervised classification (2018)

Recently, techniques for applying convolutional neural networks to graph-structured data have emerged. Graph convolutional neural networks (GCNNs) have been used to address node and graph classification and matrix completion. Although the performance has been impressive, the current implementations have limited capability to incorporate uncertainty in the graph structure. Almost all GCNNs process a graph as though it is a ground-truth depiction of the relationship between nodes, but often the graphs employed in applications are themselves derived from noisy data or modelling assumptions. Spurious edges may be included; other edges may be missing between nodes that have very strong relationships. In this paper we adopt a Bayesian approach, viewing the observed graph as a realization from a parametric family of random graphs. We then target inference of the joint posterior of the random graph parameters and the node (or graph) labels. We present the Bayesian GCNN framework and develop an iterative learning procedure for the case of assortative mixed-membership stochastic block models. We present the results of experiments that demonstrate that the Bayesian formulation can provide better performance when there are very few labels available during the training process.
Reconfigurable fault-tolerant multielectrode array for dependable monitoring of the human brain (2011)

We introduce a fault-tolerant strategy to improve the dependability of a multi-electrode array (MEA), an issue of considerable concern. We propose an interstitial redundancy approach with local reconfiguration. Here spare modules are placed at interstitial sites and can replace neighboring primary modules when they develop faults. We evaluate the performance of such a system under different faults to characterize MEA dependability as a function of redundancy. The results demonstrate that a considerable improvement in MEA dependability can be achieved with a well designed increase in redundancy.
Fluorogenic Selective and Differential Medium for Isolation of <i>Enterobacter sakazakii</i> (2004)

4-Methylumbelliferyl-alpha-D-glucoside, the fluorogenic substrate of alpha-glucosidase, was used as a selective marker to develop a differential medium for Enterobacter sakazakii. This bacterium showed strong fluorogenic characteristics clearly distinguishable from other microorganisms. On the basis of reducing background noise, an optimum basal medium and nitrogen source were selected. Incubation conditions were optimized.
An investigation of the effect of graded layers and tunneling on the performance of AlGaAs/GaAs heterojunction bipolar transistors (1984)

We present the results of theoretical and experimental studies of the heterojunction bipolar transistor. Our calculations are based on a new thermionic field-diffusion model which takes into account the dependence of the emitter efficiency on the height of the interface conduction band spike and tunneling across the spike. Based on this theory we derive analytical expressions for the current-voltage characteristics and relate the short-circuit common emitter current gain to the material parameters, doping levels, grading length, and device temperature. We demonstrate that the thermoemission transport across the interface spike limits the rate of increase in the collector current with the emitter-base voltage and, as a consequence, the maximum common emitter current gain. Tunneling also plays an important role, especially for abrupt heterojunctions. Our calculations reveal an important role played by grading of the composition of the emitter region in the vicinity of the heterointerface. Such grading decreases the barrier height at the interface and greatly enhances the emitter injection efficiency.
948. Rapid Production of Specific Artificial Meganucleases for Gene Correction in Patients with Inherited Disease (2006)

Meganucleases are sequence-specific endonucleases recognizing large (>14 bp) sequences. Because of this unusual specificity, meganuclease have emerged as powerful tools for genome engineering: creation of double-strand breaks by meganucleases at specific loci can be used to enhance homologous gene targeting by several orders of magnitude in mammalian and plant cells. Recently, such proteins could be used to induce gene repair in mouse hepatocytes, paving the way for a novel strategy for inherited diseases therapy based on gene correction instead of complementation.
Leakage current behavior of SrBi2Ta2O9 ferroelectric thin films on different bottom electrodes (2002)

SrBi 2 Ta 2 O 9 thin films on various bottom electrodes/substrates such as Pt/TiO2/SiO2/Si (Pt) and LaNiO3/Pt/TiO2/SiO2/Si (LNO) were grown using the pulsed laser deposition technique. X-ray diffraction studies revealed that as-grown (at 500 °C) films were crystallized in the layered structure after annealing at 800 °C. Films grown on platinized silicon exhibited maximum value of remanent polarization (2Pr∼21.5 μC/cm2) with coercive field (Ec) of ∼67 kV/cm. The dielectric constant and dissipation factor also decreased with the introduction of a 50 nm conducting LaNiO3 oxide electrode at the interface of Pt and SBT thin films, which might be contributed by the high resistive oxide electrode layers. The dc leakage characteristics of the films were studied at elevated temperatures and the data were fitted with the Schottky emission model. The barrier heights of the films grown on Pt and LNO substrates were estimated to be 1.27 and 1.12 eV with optical dielectric constants of 6.3 and 17, respectively. The reduction in barrier height was attributed to the lower work function of the LNO electrode.
A Small Molecule Inhibitor of the MITF Molecular Pathway (2014)

Micropthalmia-associated transcription factor (MITF) is a lineage restricted basic helix-loop-helix leucine zipper transcription factor that is essential for melanocyte development, function and survival. 15% of human melanomas have MITF gene amplification (1). In addition, a vast majority of melanomas are dependent upon MITF for survival. We set out to identify small molecule inhibitors of MITF activity that would allow for better molecular characterization of MITF's role in melanoma. Using an MITF-dependent melanoma cell line, SK-MEL-5, in a cell-based luminescence assay, we measured the promoter activity of a MITF target gene, melastatin (TRPM-1), in a high throughput screen (HTS). 331,578 compounds from the NIH MLPCN compound library were screened. Of these, 3,206 compounds were active (a hit rate of 0.96%). A chloronaphthoquinone (CID 1716436/SID 22416871) was identified in the primary HTS as an inhibitor of TRPM-1 promoter activity. It had potent activity upon retesting in the primary assay, as did several closely related analogs. Structure activity relationship (SAR) studies were performed to improve potency and to minimize deleterious properties. These efforts generated a probe (CID 12387471/ML329) with improved chemical properties and selectivity. In particular, ML329 was not prone to nucleophilic glutathione addition, whereas the initial hit underwent adduct formation. ML329 was tested in two MITF-dependent melanoma cell viability assays, SK-MEL-5 and MALME-3M plus a MITF-independent cell line, A375. ML329 showed specific activity against the MITF-dependent cells, primary melanocytes but no effect on the viability in A375 cells. ML329 reduced the expression of multiple MITF target genes, including pigment-related genes and the cell cycle regulator CDK2. As a tool compound, ML329 will be useful in elucidating the role of MITF in melanocyte lineage development and in melanoma disease progression.
Effect of grape seed extract on postprandial oxidative status and metabolic responses in men and women with the metabolic syndrome - randomized, cross-over, placebo-controlled study (2013)

Objective: This investigation was undertaken to determine whether a grape seed extract (GSE) that is rich in mono-, oligo- and poly- meric polyphenols would modify postprandial oxidative stress and inflammation in individuals with the metabolic syndrome (MetS).Background: MetS is known to be associated with impaired glucose tolerance and poor glycemic control. Consumption of a meal high in readily available carbohydrates and fat causes postprandial increases in glycemia and lipidemia and markers of oxidative stress, inflammation and insulin resistance.Materials/methods: After an overnight fast, twelve subjects with MetS (5 men and 7 women) consumed a breakfast meal high in fat and carbohydrate in a cross-over design. A GSE (300 mg) or placebo capsule was administrated 1 hr before the meal (-1 hr). Changes in plasma insulin, glucose, oxidative stress and inflammatory markers were measured hourly for 6 hr. Results: Plasma hydrophilic oxygen radical absorbance capacity (ORAC) measured as the positive incremental area under the curve (-1 to 5 hr) was significantly increased when the meal was preceded by GSE compared with placebo (P<0.05). Meal-induced increases in oxidized LDL were attenuated with GSE (P<0.05). Plasma glucose concentrations (area under the curve from -1 to 5 hr) were also significantly lower when the meal was preceded by GSE (P<0.05) while the insulin concentrations remained unchanged (P>0.05). No changes in inflammatory markers were evident. Conclusion: These data suggest that GSE enhances postprandial plasma antioxidant status and reduces the glycemic response to a meal, high in fat and carbohydrate in subjects with the MetS. Key words: Polyphenols, Oxidative stress, Inflammation, ORAC, Oxidized LDL
Improved Orthogonal Code Hopping Multiplexing Using Both Division and Hopping (2008)

We previously proposed an Orthogonal Code Hopping Multiplexing (OCHM) scheme for statistical multiplexing on a synchronous downlink. OCHM enables a large number of users to share a limited number of code channels through statistical multiplexing. We here improve the performance of OCHM by prioritizing encoded symbols according to their importance using both the conventional code division and the previously proposed code hopping multiplexing schemes. Prioritization is useful for channel coding schemes with different levels of importance for encoded symbols such as turbo-codes. Scheme performance is evaluated by simulation in terms of the required Eb/N0 for a 1% block error rate.
Abstract 182: Mimetic peptide overcomes dysregulated L-Type Calcium Channel density and recovers myocardial function (2014)

Voltage dependent L-Type calcium-channels (LTCCs) are located on the cardiomyocyte membrane and regulate cardiac contraction and rhythmicity. In human pathologies, such as heart failure (HF), decreased inward calcium current (I Ca ) is frequently observed. Here, we generated a mimetic peptide (MP) that targets LTCCs and restores impaired intracellular calcium homeostasis through a novel mechanism. Effective delivery of MP, fused with a cell penetrating peptide, was found to correct Ca2+ alterations in a mouse model of HF, in human cardiomyocytes derived from induced pluripotent stem-cells. These data provide a proof-of-concept supporting a therapeutic role for MP to treat human diseases related to LTCC abnormalities. Category: heart failure biology
Finding Critical Traffic Matrices (2005)

A traffic matrix represents the amount of traffic between origin and destination in a network. It has tremendous potential utility for many IP network engineering applications, such as network survivability analysis, traffic engineering, and capacity planning. Recent advances in traffic matrix estimation have enabled ISPs to measure traffic matrices continuously. Yet a major challenge remains towards achieving the full potential of traffic matrices. In practical networking applications, it is often inconvenient (if not infeasible) to deal with hundreds or thousands of measured traffic matrices. So it is highly desirable to be able to extract a small number of "critical" traffic matrices. Unfortunately, we are not aware of any good existing solutions to this problem (other than a few ad hoc heuristics). This seriously limits the applicability of traffic matrices. To bridge the gap between the measurement and the actual application of traffic matrices, we study the critical traffic matrices selection (CritMat) problem in this paper. We developed a mathematical problem formalization after identifying the key requirements and properties of CritMat in the context of network design and analysis. Our complexity analysis showed that CritMat is NP-hard. We then developed several clustering-based approximation algorithms to CritMat. We evaluated these algorithms using a large collection of real traffic matrices collected in AT&T's North American backbone network. Our results demonstrated that these algorithms are very effective and that a small number (e.g., 12) of critical traffic matrices suffice to yield satisfactory performance.
Working within the Current System—Cryptology and Private Communication (2013)

This chapter considers a potential privacy solution for cellular networks, one which assumes the continued existence of a centralized cellular architecture that uses a spectrum licensed to a small number of service providers. The solution involves the use of key cryptography to separate user identity from user equipment. This separation is created through a cryptographic overlay for existing cellular systems. The overlay proposed here assumes that availability of Public Key Infrastructure (PKI)—the same technology used to protect e-commerce transactions. The PKI provides the network and all subscribers with a public encryption key and a private decryption key. The chapter includes a brief overview of cryptography.
Eigenvalue calibration method for dual rotating-compensator Mueller matrix polarimetry (2021)

Dual rotating-compensator Mueller matrix polarimetry (DRC-MMP) has achieved wide spread applications in material characterization, nano-scale measurement, and biomedical diagnostics. However, the traditional calibration method for DRC-MMP relies on establishing an accurate system model, making its implementation cumbersome, especially in the presence of polarizing components that are to complex to be modeled. We propose a novel, to the best of our knowledge, eigenvalue calibration method for DRC-MMP without system modeling. Two specific basis vectors are introduced in order to transform the continuously modulated light intensity in DRC-MMP into a 5×5 projection matrix. Eigenvalue analysis is then performed based on the light intensity projection matrix to obtain the modulation matrix and the analysis matrix associated with the polarization state generator and the polarization state analyzer, respectively. The method is applied for DRC-MMP in both single-pass and double-pass setups. The experimental results have verified the proposed calibration method.