gebhart/patrepeval huggingface dataset:
Development of large area nanostructured AR coatings for EO/IR sensor applications (2013)

Electro-optical/infrared nanosensors are being developed for a variety of defense and commercial systems applications. One of the critical technologies that will enhance EO/IR sensor performance is the development of advanced antireflection coatings with both broadband and omnidirectional characteristics. In this paper, we review our latest work on high quality nanostructure-based antireflection structures, including recent efforts to deposit nanostructured antireflection coatings on large area substrates. Nanostructured antireflection coatings fabricated via oblique angle deposition are shown to enhance the optical transmission through transparent windows by minimizing broadband reflection losses to less than one percent, a substantial improvement over conventional thin-film antireflection coating technologies. Step-graded antireflection structures also exhibit excellent omnidirectional performance, and have recently been demonstrated on 6-inch diameter substrates.
System and methods for hardware-software cooperative pipeline error detection (2023)

An error reporting system utilizes a parity checker to receive data results from execution of an original instruction and a parity bit for the data. A decoder receives an error correcting code (ECC) for data resulting from execution of a shadow instruction of the original instruction, and data error correction is initiated on the original instruction result on condition of a mismatch between the parity bit and the original instruction result, and the decoder asserting a correctable error in the original instruction result.
Abstract 4118: Molecular cytometry for immunotherapy trials (2019)

Abstract The ability to simultaneously query both protein and mRNA expression on tens of thousands of single cells has emerged only recently, with the development of CITE-seq, REAP-seq, and Ab-seq platforms. Each technology relies on antibodies conjugated to oligonucleotide tags, followed by capture of antibody-stained cells for single cell RNA-sequencing. The technologies have important advantages over flow cytometry, chiefly in that they allow study of a limitless number of parameters, and single cell RNA sequencing, which cannot identify cell populations with as much verity as protein/antibody-based analysis. We characterized the newest molecular cytometry technique (Ab-seq, BD Biosciences) by titrating nearly 100 antibodies (in a single staining experiment and sequencing run), and demonstrated that oligonucleotide antibodies exhibit the same staining characteristics and patterns as flow cytometry antibodies. We also comprehensively examined cells discordant for protein and mRNA expression, in order to discriminate true features of immune cell biology from artifacts caused by drop-out in sequencing assays. Importantly, we also found that mRNA expression could guide the discrimination of cells expressing a protein versus those lacking expression, and define a remarkably low limit of detection for the technology: 1-5 molecules. This remarkable sensitivity will allow detection of cells expressing even the lowest levels of immune exhaustion and checkpoint molecules in cancer immunotherapy trials, and could enable better biomarker discovery than existing technologies. Moreover, this approach allows more detailed characterization of the tumor microenvironment and periphery than ever before. Indeed, in a lymphoma patient, we show that cells expressing both PD1 and CTLA4 carry a unique and specific signature that includes markers never revealed by flow cytometry or other technologies, which might represent new targets for immunotherapy. In sum, this presentation will characterize this new technology and demonstrate the power and promise of new molecular cytometry tools. Citation Format: Woodrow E. Lomas, Aidan F. Winters, Jason Alexandre, Jody Martin, Nidhanjali Bansal, Margaret Nakamoto, Brent Gaylord, Suraj Saksena, Pratip K. Chattopadhyay. Molecular cytometry for immunotherapy trials [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4118.
Data from <i>TMPRSS2-ERG</i> Status Is Not Prognostic Following Prostate Cancer Radiotherapy: Implications for Fusion Status and DSB Repair (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Preclinical data suggest that &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; gene fusions, present in about 50% of prostate cancers, may be a surrogate for DNA repair status and therefore a biomarker for DNA-damaging agents. To test this hypothesis, we examined whether &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; status was associated with biochemical failure after clinical induction of DNA damage following image-guided radiotherapy (IGRT).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; Pretreatment biopsies from two cohorts of patients with intermediate-risk prostate cancer [T1/T2, Gleason score (GS) &lt; 8, prostate-specific antigen (PSA) &lt; 20 ng/mL; &gt;7 years follow-up] were analyzed: (i) 126 patients [comparative genomic hybridization (CGH) cohort] with DNA samples assayed by array CGH (aCGH) for the &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; fusion; and (ii) 118 patients [immunohistochemical (IHC) cohort] whose biopsy samples were scored within a defined tissue microarray (TMA) immunostained for ERG overexpression (known surrogate for &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; fusion). Patients were treated with IGRT with a median dose of 76 Gy. The potential role of &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; status as a prognostic factor for biochemical relapse-free rate (bRFR; nadir + 2 ng/mL) was evaluated in the context of clinical prognostic factors in multivariate analyses using a Cox proportional hazards model.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt;&lt;i&gt;TMPRSS2-ERG&lt;/i&gt; fusion by aCGH was identified in 27 (21%) of the cases in the CGH cohort, and ERG overexpression was found in 59 (50%) patients in the IHC cohort. In both cohorts, &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; status was not associated with bRFR on univariate or multivariate analysis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; In two similarly treated IGRT cohorts, &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; status was not prognostic for bRFR, in disagreement with the hypothesis that these prostate cancers have DNA repair defects that render them clinically more radiosensitive. &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; is therefore unlikely to be a predictive factor for IGRT response. &lt;i&gt;Clin Cancer Res; 19(18); 5202–9. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Trajectory generation for continuous leg forces during double support and heel-to-toe shift based on divergent component of motion (2014)

This paper works with the concept of Divergent Component of Motion (DCM), also called `(instantaneous) Capture Point'. We present two real-time DCM trajectory generators for uneven (three-dimensional) ground surfaces, which lead to continuous leg (and corresponding ground reaction) force profiles and facilitate the use of toe-off motion during double support. Thus, the resulting DCM trajectories are well suited for real-world robots and allow for increased step length and step height. The performance of the proposed methods was tested in numerous simulations and experiments on IHMC's Atlas robot and DLR's humanoid robot TORO.
Efficacy of a Replikin Peptide Vaccine Against Low-Pathogenicity Avian Influenza H5 Virus (2009)

In this study, the sequence of the H5 and PB1 genes of the low-pathogenic avian influenza virus (LPAI) A/Black Duck/NC/674-964/06 isolate were determined for replikin peptides and used to design and chemically synthesize a vaccine. The vaccine was used to immunize specific-pathogen-free (SPF) leghorn chickens held in Horsfall isolation units, by the upper respiratory route, at 1, 7, and 14 days of age. The birds were challenged at 28 days of age with 1 x 10(6) 50% embryo infective dose of the LPAI Black Duck/NC/674-964/06 H5N1 virus per bird. Oropharyngeal and cloacal swabs were collected at 2, 4, and 7 days postinoculation (PI) for virus detection by real-time RT-PCR. Serum was collected at 7, 14, and 21 days PI and examined for antibodies against avian influenza virus by the enzyme-linked immunosorbent assay and hemagglutination inhibition (HI) tests. Tissue samples for histopathology were collected from three birds per group at 3 days PI. The experimental design consisted of a negative control group (not vaccinated and not challenged) and a vaccinated group, a vaccinated and challenged group, and a positive control group (challenged only). None of the nonchallenged birds, the vaccinated birds, or the vaccinated and challenged birds showed overt clinical signs of disease during the study. A slight depression was observed in the nonvaccinated challenged birds on day 2 postchallenge. Although the numbers of birds per group are small, no shedding of the challenge virus was detected in the vaccinated and challenged birds, whereas oropharyngeal and cloacal shedding was detected in the nonvaccinated and challenged birds. HI antibodies were detected in the vaccinated and nonchallenged group as well as in the vaccinated and challenged group, but rising antibody titers, indicating infection with the LPAI challenge virus, were not detected. Rising HI titers were observed in the nonvaccinated and challenged group. In addition, no antibodies were detected in the nonchallenged birds. Noteworthy microscopic lesions were not observed in the vaccinated and challenged birds, whereas nonvaccinated-challenged birds had microscopic lesions consistent with infection with LPAI viruses. Taken together, these data indicate that a replikin peptide vaccine, specifically made against the H5N1 Black Duck/NC/674-964/06 isolate, and administered three times to the upper respiratory tract, was capable of protecting chickens from infection and from shedding of the homologous virus, which is extremely important because reduced virus shedding and transmission decreases the potential for H5 LPAI viruses to become HPAI viruses. The study is also important because it shows that the vaccine can be effectively mass-delivered to the upper respiratory tract.
Data from Exploiting Natural Killer Cell Engagers to Control Pediatric B-cell Precursor Acute Lymphoblastic Leukemia (2023)

&lt;div&gt;Abstract&lt;p&gt;Natural killer (NK) cells represent a promising cell type in antitumor immunotherapy for efficacy and safety, particularly in the treatment of hematologic malignancies. NK cells have been shown to exert antileukemia activity in the context of haploidentical hematopoietic stem cell transplantation (haplo-HSCT). Products have been developed to boost the activation of NK cells only when cross-linked by tumor cells, avoiding any off-target effect. Here, we tested the &lt;i&gt;in vitro&lt;/i&gt; effect of different NK-cell engagers (NKCE), which trigger either NKp46 or NKp30 together with CD16A, and target either CD19 or CD20 to induce killing of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Target cells were NALM-16 and MHH-CALL-4 cell lines and four primary leukemias, while effector cells were resting NK cells derived from healthy donors and pediatric patients with leukemia after αβT/B-depleted haplo-HSCT. The NK cell–resistant MHH-CALL-4 was efficiently killed using all NKCEs. Boosting of NK activity against MHH-CALL-4 was also evident by degranulation and IFNγ production. Because of the lack of CD20 and high expression of CD19 on primary BCP-ALL, we focused on NKCEs targeting CD19. NKp46- and NKp30-based NKCEs displayed similar potency at inducing NK-cell activity, even when challenged with primary BCP-ALL blasts. Their efficacy was shown also using NK cells derived from transplanted patients. NKCE-induced activation against BCP-ALL can override HLA-specific inhibitory interactions, although the strongest response was observed by the alloreactive NK-cell subset. These data support the therapeutic use of NKp46/CD16A/CD19-NKCE to fight refractory/relapsed leukemia in pretransplantation or posttransplantation settings.&lt;/p&gt;&lt;/div&gt;
Narrowband MIMO Channel Modeling for LOS Indoor Scenarios (2002)

Herein, a line-of-sight (LOS) multiple input multiple output (MIMO) channel model is presented based on 5.2 GHz indoor MIMO channel measurements. The signal from the dominant direction is estimated and removed from the channel data. The residual part is shown to be Rayleigh distributed and its covariance matrix can be well approximated by the Kronecker product of the covariance matrices seen from the transmitter and receiver respectively. Therefore we model the whole narrowband LOS indoor MIMO channel as a static rank one matrix plus a statistical model based on Rayleigh distribution with a multiplicative covariance structure. 1
Automated design of network security metrics (2018)

Many abstract security measurements are based on characteristics of a graph that represents the network. These are typically simple and quick to compute but are often of little practical use in making real-world predictions. Practical network security is often measured using simulation or real-world exercises. These approaches better represent realistic outcomes but can be costly and time-consuming. This work aims to combine the strengths of these two approaches, developing efficient heuristics that accurately predict attack success. Hyper-heuristic machine learning techniques, trained on network attack simulation training data, are used to produce novel graph-based security metrics. These low-cost metrics serve as an approximation for simulation when measuring network security in real time. The approach is tested and verified using a simulation based on activity from an actual large enterprise network. The results demonstrate the potential of using hyper-heuristic techniques to rapidly evolve and react to emerging cybersecurity threats.
Dispatching packets on a global combining network of a parallel computer (2023)

Methods, apparatus, and products are disclosed for dispatching packets on a global combining network of a parallel computer comprising a plurality of nodes connected for data communications using the network capable of performing collective operations and point to point operations that include: receiving, by an origin system messaging module on an origin node from an origin application messaging module on the origin node, a storage identifier and an operation identifier, the storage identifier specifying storage containing an application message for transmission to a target node, and the operation identifier specifying a message passing operation; packetizing, by the origin system messaging module, the application message into network packets for transmission to the target node, each network packet specifying the operation identifier and an operation type for the message passing operation specified by the operation identifier; and transmitting, by the origin system messaging module, the network packets to the target node.
Type 2 innate lymphoid cells in the induction and resolution of tissue inflammation (2018)

Type 2 immunity against pathogens is tightly regulated to ensure appropriate inflammatory responses that clear infection and prevent excessive tissue damage. Recent research has shown that type 2 innate lymphoid cells (ILC2s) contribute to steady-state tissue integrity and exert tissue-specific functions. However, upon exposure to inflammatory stimuli, they also initiate and amplify type 2 inflammation by inducing mucus production, eosinophilia, and Th2 differentiation. In this review, we discuss the regulation of ILC2 activation by transcription factors and metabolic pathways, as well as by extrinsic signals such as cytokines, lipid mediators, hormones, and neuropeptides. We also review recent discoveries about ILC2 plasticity and heterogeneity in different tissues, as revealed partly through single-cell RNA sequencing of transcriptional responses to various stimuli. Understanding the tissue-specific pathways that regulate ILC2 diversity and function is a critical step in the development of potential therapies for allergic diseases.
Analytical modeling of vertical interconnect in single-ended applications (2015)

Despite the shorter physical length and superior electrical properties of the vertical interconnects, the arrangement of corresponding grounding pins drastically affects the characteristic impedance, resulting in impedance mismatch during the propagation of signals, which leads to signal reflection. Therefore, to potentially overcome this disadvantage, this paper endeavors to establish the analytical model of the vertical interconnects for improving the impedance matching in single-ended configurations. The key approach is to use the method of image charges for analyzing the capacitance between the signal pin and grounding pins of the vertical interconnect. The established models are capable of predicting the changes in the capacitance of various grounding pin arrangements in the vertical interconnect, and based on the prediction results the optimal impedance-matching design can be found.
Gene expression and tissue microarray analysis of interleukin-2 complete responders in patients with metastatic renal cell carcinoma (2005)

4535 Background: Although some aspects of the molecular genetics of RCC are beginning to be understood, little is known about the genes that dictate treatment response. We hoped to characterize IL-2 Complete Responders by gene expression profile and tissue array analysis. Methods: Total RNA was extracted from fresh frozen tissue, purified, reverse transcribed to cDNA, and hybridized to Affymetrix UI33a gene chips. To reveal global gene differences, we used unsupervised and supervised learning analyses. Tumors were clustered based on a combination of fold change and absolute difference in gene expression. A p value of 0.05 was considered significant. Genes of interest identified by gene arrays having available antibodies suitable for immunohistochemistry (IHC) were evaluated in a RCC tissue array containing 109 patients treated by nephrectomy and immunotherapy. Results: Statistically significant global gene differences between CR and NR groups included genes involved in apoptosis, G protein signaling, the ubiquitin-proteasome proteolytic system, chemokines, intermediate filaments and actin associated proteins heat shock proteins, MHC antigens, and the MAP kinase pathway. A set of 73 genes was able to distinguish Complete from Non Responders. Genes of particular interest included the PTEN tumor suppressor and Carbonic Anhydrase IX (CAIX), both expressed greater in the CR group. Antibodies for CAIX, CAXII, PTEN, Vimentin, Gelsolin, EpCAM, p53, and Ki67 were analyzed by IHC. Univariate predictors of immunotherapy response included CAIX>85% (p=0.027), PTEN (p=0.012), EpCAM (p=0.05), and Vimentin (p=0.02). CAIX and PTEN were the only two markers retained as independent predictors in multivariate models. Conclusions: IL-2 Complete Responders have a signature gene expression pattern that can be differentiated from Non-Responders, and these differences translate into corresponding differences in protein expression. CAIX, PTEN, CXCR4, and other genes may play important roles in dictating IL-2 treatment response in RCC or as possible therapeutic targets. If prospectively validated, gene expression analysis may aid clinicians in selecting appropriate treatment options. No significant financial relationships to disclose.
SDS-Polyacrylamide Gel Electrophoresis of Peptides (2003)

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) has proven to be among the most useful tools yet developed in the area of molecular biology. The discontinuous buffer system, first described by Laemmli (1), has made it possible to separate, visualize, and compare readily the component parts of complex mixtures of molecules (e.g., tissues, cells). SDS-PAGE separation of proteins and peptides makes it possible to quantify the amount of a particular protein/peptide in a sample, obtain fairly reliable molecular mass information, and, by combining SDSPAGE with immunoelectroblotting, evaluate the antigenicity of proteins and peptides. SDS-PAGE is both a powerful separation system and a reliable preparative purification technique (2; and see Chapter 11 ).
Supplementary Figure S5 from Shifting the Balance of Activating and Inhibitory Natural Killer Receptor Ligands on <i>BRAF</i><sup>V600E</sup> Melanoma Lines with Vemurafenib (2023)

&lt;p&gt;Effect of Vemurafenib on BRAF non mutated melanoma cell lines&lt;/p&gt;
Antinociceptive effects of α 2 /α 3 ‐selective GABA A receptor positive allosteric modulators on opioid‐induced hyperalgesia (2022)

Opioids have been increasingly prescribed to treat chronic pain since the 1980s, despite evidence that long‐term use of opioids may lead to tolerance and pain sensitization called opioid‐induced hyperalgesia (OIH). OIH has been demonstrated in both preclinical models and healthy human volunteers, but is understudied and there is need for novel analgesics capable of mitigating OIH. α 2 /α 3 ‐selective GABA A receptor positive allosteric modulators (PAMs) act specifically at subunits of the GABA A receptor found to mediate analgesia, and have demonstrated antinociceptive effects in models of chronic inflammatory and neuropathic pain. However, the efficacy of these compounds at relieving opioid‐induced pain hypersensitivity have not yet been investigated. This study systematically examined the antinociceptive effects of α 2 /α 3 ‐selective GABA A receptor PAMs alone and in combination with acetaminophen in an OIH rat model wherein repeated treatment with the opioid fentanyl induces mechanical hyperalgesia. The von Frey test was used to measure mechanical nociception. Duration of actions of α 2 /α 3 ‐selective GABA A receptor PAMs (KRM‐II‐81, NS16085, HZ‐166) alone were studied, and combinations of KRM‐II‐81 and acetaminophen were also studied at fixed ratios (1:1, 1:3, 3:1). Dose‐addition analysis was used to assess the antinociceptive interactions between KRM‐II‐81 and acetaminophen. α 2 /α 3 ‐selective GABA A receptor PAMs were able to fully reverse mechanical sensitivity caused by OIH. Furthermore, KRM‐II‐81/acetaminophen combinations produced additive to supra‐additive interactions depending on the drug mixture ratios. These findings support the idea that α 2 /α 3 ‐selective GABA A receptor PAMs could serve as novel analgesics for treating OIH, and may interact favorably with other non‐opioid analgesics.
Focus measurement using SEM image analysis of circuit pattern (2016)

We have developed a new focus measurement method based on analyzing SEM images that can help to control a scanner. In advanced semiconductor fabrication, rigorous focus control of the scanner has been required because focus error causes a defect. Therefore, it is essential to ensure focus error are detected at wafer fabrication. In the past, the focus has been measured using test patterns made outside of the chip by optical metrology system. Thus, present focus metrology system can’t measure the focus of an arbitrary point in the chip. The new method enables a highly precise focus measurement of the arbitrary point of the chip based on a focus plane of a reference scanner. The method estimates the focus amount by analyzing side wall shapes of circuit patterns of SEM images. Side wall shapes are quantified using multisliced contours extracted from SEM-images high accuracy. By using this method, it is possible to measure the focus of the arbitrary circuit pattern area of the chip without a test pattern. We believe the method can contribute to control the scanner and to detect hot spots which appear by focus error. This new method and the evaluation results will be presented in detail in this paper.