gebhart/patrepeval huggingface dataset:
Oncolytic virotherapy induced CSDE1 neo-antigenesis restricts VSV replication but can be targeted by immunotherapy (2021)

In our clinical trials of oncolytic vesicular stomatitis virus expressing interferon beta (VSV-IFNβ), several patients achieved initial responses followed by aggressive relapse. We show here that VSV-IFNβ-escape tumors predictably express a point-mutated CSDE1<sup>P5S</sup> form of the RNA-binding Cold Shock Domain-containing E1 protein, which promotes escape as an inhibitor of VSV replication by disrupting viral transcription. Given time, VSV-IFNβ evolves a compensatory mutation in the P/M Inter-Genic Region which rescues replication in CSDE1<sup>P5S</sup> cells. These data show that CSDE1 is a major cellular co-factor for VSV replication. However, CSDE1<sup>P5S</sup> also generates a neo-epitope recognized by non-tolerized T cells. We exploit this predictable neo-antigenesis to drive, and trap, tumors into an escape phenotype, which can be ambushed by vaccination against CSDE1<sup>P5S</sup>, preventing tumor escape. Combining frontline therapy with escape-targeting immunotherapy will be applicable across multiple therapies which drive tumor mutation/evolution and simultaneously generate novel, targetable immunopeptidomes associated with acquired treatment resistance.
Blockade of Nociceptin/Orphanin FQ Transmission Attenuates Symptoms and Neurodegeneration Associated with Parkinson's Disease (2005)

The opioid-like neuropeptide nociceptin/orphanin FQ (N/OFQ) and its receptor (NOP) are expressed in the substantia nigra (SN), a brain area containing dopamine neurons that degenerate in Parkinson's disease. Endogenous N/OFQ facilitates nigral glutamate release and inhibits nigrostriatal dopamine transmission and motor behavior. Here, we present evidence suggesting that endogenous N/OFQ may contribute to Parkinson's disease. Pharmacological blockade of the SN N/OFQ-NOP receptor system attenuated parkinsonian-like akinesia/hypokinesia in 6-hydroxydopamine hemilesioned or haloperidol-treated rats, whereas deletion of the NOP receptor gene conferred mice partial protection from haloperidol-induced motor depression. The antiparkinsonian action of NOP receptor antagonists was associated with reduction of glutamate release in the SN. In 6-hydroxydopamine hemilesioned rats, enhancement of N/OFQ expression and release was detected in the lesioned compared with the unlesioned SN, indicating that parkinsonism may be associated with overactivation of the N/OFQ-NOP receptor system in the SN. Finally, deletion of the N/OFQ gene conferred mice partial protection against 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced loss of SN dopamine neurons. Based on these data, we propose that NOP receptor antagonists may represent a novel approach for combined (symptomatic and neuroprotective) therapy of Parkinson's disease.
Inhibition of 14q32 microRNA miR-495 reduces lesion formation, intimal hyperplasia and plasma cholesterol levels in experimental restenosis (2017)

GSO-495 administration decreased our primary outcomes, namely intimal hyperplasia, and accelerated atherosclerosis. GSO-495 administration also favourably affected multiple secondary outcomes, including macrophage influx, plaque stability and total plasma cholesterol levels. We conclude that 14q32 microRNA miR-495 is a promising target for prevention of restenosis.
Gettering Mechanism in Carbon-cluster-ion-implanted Epitaxial Silicon Wafers using Atom Probe Tomography (2018)

The difference in agglomerate defects formed by carbon-cluster-ion-implanted Czochralski (CZ)-Si and epitaxial Si has been investigated using atom probe tomography. In the previous work, we reported on the strong gettering capability in implanted epitaxial Si. We found that the distribution of O and C atom concentrations on agglomerates differs between CZ-Si and epitaxial Si. This suggests that a C agglomerate, which grows without including O atoms, results in strong gettering efficiency for Fe.
NMR of Supramolecular Gels (2020)

Recently, supramolecular gel materials have attracted considerable attention in various fields including engineering, medical science, and physical science due to their interesting properties, which are not observed in solid materials, liquid materials, and covalent gel materials. During the design and formation of functional supramolecular gel materials, knowledge of the structures and characteristics of supramolecular gels and their components is crucial. To obtain information, researchers focusing on supramolecular gels have utilized various measurement techniques, including absorption spectroscopy, infrared spectroscopy, rheology, scanning electron microscopy, and X-ray diffraction. Nuclear magnetic resonance (NMR) spectroscopy involves the measurement of the conditions of nuclei affected by their surroundings. NMR is an extensively used and beneficial measurement technique for supramolecular materials as NMR spectra can be recorded under wet and dry conditions. Previously, various NMR measurements have been employed to detect various nuclei and to obtain distance information between nuclei. In this chapter, approaches to examine supramolecular gel materials by NMR measurements with respect to previously reported studies are reviewed.
Supplementary Figures 1-3 from Lithium Treatment Prevents Neurocognitive Deficit Resulting from Cranial Irradiation (2023)

Supplementary Figures 1-3 from Lithium Treatment Prevents Neurocognitive Deficit Resulting from Cranial Irradiation
Comb-calibrated solar spectroscopy through a multiplexed single-mode fiber channel (2015)

We investigate a new scheme for astronomical spectrograph calibration using the laser frequency comb at the Solar Vacuum Tower Telescope on Tenerife. Our concept is based upon a single-mode fiber channel, that simultaneously feeds the spectrograph with comb light and sunlight. This yields nearly perfect spatial mode matching between the two sources. In combination with the absolute calibration provided by the frequency comb, this method enables extremely robust and accurate spectroscopic measurements. The performance of this scheme is compared to a sequence of alternating comb and sunlight, and to absorption lines from Earth's atmosphere. We also show how the method can be used for radial-velocity detection by measuring the well-explored 5 min oscillations averaged over the full solar disk. Our method is currently restricted to solar spectroscopy, but with further evolving fiber-injection techniques it could become an option even for faint astronomical targets.
Experimental Demonstration of Nanosecond Accuracy Wireless Network Synchronization (2014)

Accurate wireless timing synchronization has been an extremely important topic in wireless sensor networks, required in applications ranging from distributed beam forming to precision localization and navigation. However, it is very challenging to realize, in particular when the required accuracy should be better than the runtime between the nodes. This work presents, to our knowledge for the first time, an experimental timing synchronization scheme that achieves a timing accuracy better than 5ns rms in a network with 4 nodes. The experimental hardware is built from commercially available components and based on software defined ultra wideband transceivers. The protocol for establishing the synchronization is based on our recently developed blink protocol that can scale from the small network demonstrated here to larger networks of hundreds or thousands of nodes.
Genetic vasopressin 1b receptor variance in overweight and diabetes mellitus (2016)

Genetic variance of AVPR1B contributes to overweight. Furthermore, our data indicate a link between AVPR1B variance and DM development. Our data point at a relationship between the disturbance of the pharmacologically modifiable AVP system and the body weight regulation.
Wide Timability and Large Mode-Suppression in a Multi-section Semiconductor Laser using Sampled Gratings (1992)

We have recently proposed [1,2] a 4-section semiconductor laser which is capable of tuning over several tens of nanometers. A schematic of this device is shown in Fig. 1, along with the reflection spectra of the two mirrors which form the backbone of this device. These two mirrors consist of "sampled" gratings with mismatched periodic reflection spectra, as indicated in Fig. 1. Lasing in this structure occurs where two reflection maxima are aligned. By inducing index changes in one mirror relative to the other, adjacent reflectivity maxima can be brought into alignment, resulting in wide-range discontinuous tuning with very small index changes. Wavelength coverage between the maxima can be obtained by inducing identical index changes in the two mirrors, and adjusting the phase-shifter appropriately, much like 3-section lasers [3].
Preparation of a tetraphenylporphyrinatocobalt(ii)-poly(3,4-azopyridylene) complex and its oxygen enrichment effect at an oxygen electrode (2004)

The reversible oxygen-binding properties of tetraphenylporphyrinatocobalt(II) (CoTPP) complexed with poly(3,4-azopyridylene) (PAP) were established. The CoTPP complexes functioned as oxygen carriers at the surface of a cathode to enhance the current for the reduction of oxygen. PAP was synthesized by the oxidative polymerization of 3,4-diaminopyridine in a DMF solution at 25 °C using a Cu/pyridine catalyst. The combination of the CoTPP complex and the conventional Pt/C catalyst resulted in a significant increase in the steady-state current for the four-electron reduction of O2, particularly at small overpotentials where typical fuel cells operate, based on the facilitated transport of O2 from the atmosphere to the catalyst at the electrode surface.
Loop-Length-Dependent Folding of G-Quadruplexes (2004)

Guanine-rich DNA sequences can form a large number of structurally diverse quadruplexes. These vary in terms of strand polarity, loop composition, and conformation. We have derived guidelines for understanding the influence of loop length on the structure adopted by intramolecular quadruplex-forming sequences, using a combination of experimental (using CD and UV melting data) and molecular modeling and simulation techniques. We find that a parallel-stranded intramolecular quadruplex structure is the only possible fold when three single residue loops are present. When single thymine loops are present in combination with longer length loops, or when all loops are longer than two residues, both parallel- and antiparallel-folded structures are able to form. Multiple conformations of each structure are likely to coexist in solution, as they were calculated to have very similar free energies.
Deep positive-unlabeled learning for region of interest localization in breast tissue images (2018)

Rapid digitization of whole-slide images (WSIs) with slide scanners, along with the advancements in deep learning strategies has empowered the development of computerized image analysis algorithms for automated diagnosis, prognosis, and prediction of various types of cancers in digital pathology. These analyses can be enhanced and expedited by confining them to relevant tumor region on the large-sized and multi-resolution WSIs. The detection of tumor-region-of-interest (TRoI) on WSIs can facilitate to automatically measure the tumor size as well as to compute the distance to the resection margin. It can also ease the process of identifying high-power-fields (HPFs), which are essential towards the grading of tumor proliferation scores. In practice, pathologists select these regions by visual inspection of WSIs, which is a cumbersome, time-consuming process and affected by inter- and intra- pathologist variability. State-of-the-art deep learning-based methods perform well on the TRoI detection task by using supervised algorithms, however, they require accurate TRoI and non-TRoI annotations to train the algorithms. Acquiring such annotations is a tedious task and incurs observational variability. In this work, we propose a positive and unlabeled learning approach that uses a few examples of HPF regions (positive annotations) to localize the invasive TRoIs on breast cancer WSIs. We use unsupervised deep autoencoders with Gaussian Mixture Model-based clustering to identify the TRoI in a patch-wise manner. The algorithm is developed using 90 HPF-annotated WSIs and is validated on 30 fully-annotated WSIs. It yielded a Dice coefficient of 75.21%, a true positive rate of 78.62% and a true negative rate of 97.48% in terms of pixel-bypixel evaluation compared to the pathologists annotations. Significant correspondence between the results of the proposed algorithm and the state-of-the-art supervised ConvNet indicates the efficacy of the proposed algorithm.
The LDBC Graphalytics Benchmark (2020)

In this document, we describe LDBC Graphalytics, an industrial-grade benchmark for graph analysis platforms. The main goal of Graphalytics is to enable the fair and objective comparison of graph analysis platforms. Due to the diversity of bottlenecks and performance issues such platforms need to address, Graphalytics consists of a set of selected deterministic algorithms for full-graph analysis, standard graph datasets, synthetic dataset generators, and reference output for validation purposes. Its test harness produces deep metrics that quantify multiple kinds of systems scalability, weak and strong, and robustness, such as failures and performance variability. The benchmark also balances comprehensiveness with runtime necessary to obtain the deep metrics. The benchmark comes with open-source software for generating performance data, for validating algorithm results, for monitoring and sharing performance data, and for obtaining the final benchmark result as a standard performance report.
CXCL10 DNA Vaccination Prevents Spontaneous Diabetes through Enhanced β Cell Proliferation in NOD Mice (2005)

CXCL10, a chemokine for Th1 cells, is involved in the pathogenesis of various Th1-dominant autoimmune diseases. Type 1 diabetes is considered to be a Th1-dominant autoimmune disease, and a suppressive effect of CXCL10 neutralization on diabetes development has been reported in a cyclophosphamide-induced accelerated diabetes model through induction of beta cell proliferation. However, intervention in a diabetes model might bring about opposite effects, depending on the timing, amount, or method of treatment. In the present study, we examined the effect of CXCL10 neutralization in a "spontaneous diabetes" model of NOD mice, using CXCL10 DNA vaccination (pCAGGS-CXCL10). pCAGGS-CXCL10 treatment in young NOD mice induced the production of anti-CXCL10 Ab in vivo and suppressed the incidence of spontaneous diabetes, although this treatment did not inhibit insulitis or alter the immunological response. pCAGGS-CXCL10 treatment enhanced the proliferation of pancreatic beta cells, resulting in an increase of beta cell mass in this spontaneous diabetes model as well. Therefore, CXCL10 neutralization is suggested to be useful for maintaining beta cell mass at any stage of autoimmune diabetes.
III-V/Si Photonic Integrated Circuits for the Mid-Infrared (2018)

We review our work on SOI and Ge-on-SOI PICs for the mid-infrared. We demonstrate the integration of III-V semiconductors on the SOI platform for 2–4 μm wavelength range integrated lasers and spectrometers, as well as tunable filters implemented on the Ge-on-SOI platform beyond 4μm.
On the Control of a Solid State Transformer for Multi-MW Utility-Scale PV-Battery Systems (2019)

The utility-scale photovoltaic (PV)-battery systems typically include multiple power converters connected to the grid via traditional line frequency transformers (LFT), which may be considered bulky, and inefficient when compared with the emerging solid state transformers (SST). This paper proposes a SST with power and voltage controls for utility-scale PV-battery systems. The PV system was modeled based on available data from a universal solar facility located in Kentucky, USA. Furthermore, this paper provides detailed controller designs for the proposed utility-scale PV-battery system based on a SST which includes: the PV-side dual-active bridge (DAB) converter tracks the maximum power point, the PV inverter for steady power transformation to the grid, battery-side DAB converter for maintaining stiff dc bus voltage, and the battery inverter for voltage support and balanceing the power mismatch between the grid demand and the PV generation. Moreover, medium frequency transformer (MFT) and Silicon Carbide (SiC) MOSFETs are utilized in the DAB converters and inverters, to improve the efficiency of the PV-battery system. The simulation results based on the data retrieved from an operational PV facility, on one hand, are presented to confirm the benefits of the proposed SiC SST based PV-battery system; on the other hand, provide an alternative analysis on power losses and efficiency for the utilityscale PV farms.
Search for new phenomena in pp collisions in final states with tau leptons, b-jets, and missing transverse momentum with the ATLAS detector (2021)

A search for new phenomena in final states with hadronically decaying tau leptons, $b$-jets, and missing transverse momentum is presented. The analyzed dataset comprises $pp$ collision data at a center-of-mass energy of $\sqrt{s}=13\text{ }\text{ }\mathrm{TeV}$ with an integrated luminosity of $139\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$, delivered by the Large Hadron Collider and recorded with the ATLAS detector from 2015 to 2018. The observed data are compatible with the expected Standard Model background. The results are interpreted in simplified models for two different scenarios. The first model is based on supersymmetry and considers pair production of top squarks, each of which decays into a $b$-quark, a neutrino and a tau slepton. Each tau slepton in turn decays into a tau lepton and a nearly massless gravitino. Within this model, top-squark masses up to 1.4 TeV can be excluded at the 95% confidence level over a wide range of tau-slepton masses. The second model considers pair production of leptoquarks with decays into third-generation leptons and quarks. Depending on the branching fraction into charged leptons, leptoquarks with masses up to around 1.25 TeV can be excluded at the 95% confidence level for the case of scalar leptoquarks and up to 1.8 TeV (1.5 TeV) for vector leptoquarks in a Yang--Mills (minimal-coupling) scenario. In addition, model-independent upper limits are set on the cross section of processes beyond the Standard Model.
S1P1 Modulator-Induced Gi Signaling and β-Arrestin Recruitment Are Both Necessary to Induce Rapid and Efficient Reduction of Blood Lymphocyte Count In Vivo (2017)

S1P<sub>1</sub> (sphingosine-1-phosphate receptor 1) agonists prevent lymphocyte egress from secondary lymphoid organs and cause a reduction in the number of circulating blood lymphocytes. We hypothesized that S1P<sub>1</sub> receptor modulators with pathway-selective signaling properties could help to further elucidate the molecular mechanisms involved in lymphocyte trapping. A proprietary S1P<sub>1</sub> receptor modulator library was screened for compounds with clear potency differences in <i>β</i>-arrestin recruitment and G protein alpha i subunit (G <i><sub>α</sub></i><sub>i</sub>) protein-mediated signaling. We describe here the structure-activity relationships of highly potent S1P<sub>1</sub> modulators with apparent pathway selectivity for <i>β</i>-arrestin recruitment. The most differentiated compound, D3-2, displayed a 180-fold higher potency in the <i>β</i>-arrestin recruitment assay (EC<sub>50</sub> 0.9 nM) compared with the G <i><sub>α</sub></i><sub>i</sub>-activation assay (167 nM), whereas ponesimod, a S1P<sub>1</sub> modulator that is currently in advanced clinical development in multiple sclerosis, was equipotent in both assays (EC<sub>50</sub> 1.5 and 1.1 nM, respectively). Using these novel compounds as pharmacological tools, we showed that although a high potency in <i>β</i>-arrestin recruitment is required to fully internalize S1P<sub>1</sub> receptors, the potency in inducing G <i><sub>α</sub></i><sub>i</sub> signaling determines the rate of receptor internalization in vitro. In contrast to ponesimod, the compound D3-2 did not reduce the number or circulating lymphocytes in rats despite high plasma exposures. Thus, for rapid and maximal S1P<sub>1</sub> receptor internalization a high potency in both G <i><sub>α</sub></i><sub>i</sub> signaling and <i>β</i>-arrestin recruitment is mandatory and this translates into efficient reduction of the number of circulating lymphocytes in vivo.
Using learned optimizers to make models robust to input noise (2019)

State-of-the art vision models can achieve superhuman performance on image classification tasks when testing and training data come from the same distribution. However, when models are tested on corrupted images (e.g. due to scale changes, translations, or shifts in brightness or contrast), performance degrades significantly. Here, we explore the possibility of meta-training a learned optimizer that can train image classification models such that they are robust to common image corruptions. Specifically, we are interested training models that are more robust to noise distributions not present in the training data. We find that a learned optimizer meta-trained to produce models which are robust to Gaussian noise trains models that are more robust to Gaussian noise at other scales compared to traditional optimizers like Adam. The effect of meta-training is more complicated when targeting a more general set of noise distributions, but led to improved performance on half of held-out corruption tasks. Our results suggest that meta-learning provides a novel approach for studying and improving the robustness of deep learning models.
Transfer of specific endothelial cell-binding properties from the procoagulant protein human factor IX into the anticoagulant protein human protein C (1995)

A series of recombinant (r) chimeric mutants of human coagulation protein C (PC) and activated protein C (APC) containing replacements of homologous PC domains by those of human coagulation factor IX (fIX) were generated, with the intention of determining whether the specific bovine aortic endothelial cell (BAEC) receptor-binding characteristics of fIX could be incorporated into the chimeric r-PC while maintaining the essential properties of PC and APC. Using a competitive BAEC displacement assay with [125I]fIX, we found that a chimeric r-PC (r[delta PC1-46/delta fIX1-47]PC), consisting of the entire gamma-carboxyglutamic domain ([GDIX], residues 1-38) and helical stack ([HSIX], residues 38-47) of fIX as replacements for these same domains of PC, provided an IC50 for fIX-related BAEC binding of 13 nM, as compared to 10 nM for that of unlabeled fIX. This showed that all of the BAEC tight binding determinants for fIX existed within the [GDIX/HSIX]. Additionally, this chimera reacted to the same extent as fIX with the Ca(2+)-dependent, [GDIX]-specific monoclonal antibody H5B7 and lost its reactivity to a similar antibody specific for the [GDPC], JTC1. A synthetic peptide containing residues 1-47 of fIX also competed effectively (IC50 = 16 nM) with intact fIX for BAEC binding. Displacement of [125I]fIX from BAEC did not occur with a chimera containing the [HSIX] alone or with another mutant protein possessing a replacement of the two epidermal growth factor (EGF) homology regions of r-PC (residues 47-137) with those same domains of fIX.(ABSTRACT TRUNCATED AT 250 WORDS)
Detecting false signals with automatic gain control (2012)

A component of most GPS receiver front-ends, the automatic gain control (AGC) can flag potential jamming and spoofing attacks. The detection method is simple to implement and accessible to most GPS ...