gebhart/patrepeval huggingface dataset:
INCREASED GRANZYME B mRNA AFTER ALLOINCOMPATIBLE MYOBLAST TRANSPLANTATION (1995)

GUéRETTE, BENOIT; ROY, RAYNALD; TREMBLAY, MARTINE; ASSELIN, ISABELLE; KINOSHITA, IKUO; PUYMIRAT, JACK; TREMBLAY, JACQUES P. Author Information
Effects of a Kaolin-Based Particle Film on Obliquebanded Leafroller (Lepidoptera: Tortricidae) (2000)

Studies were conducted in 1997 to evaluate the effects of the kaolin-based particle film formulation M96-018 on adults, eggs, and larvae of the obliquebanded leafroller, Choristoneura rosaceana (Harris). Particle film treatments significantly reduced female longevity, mating success, and number of egg masses oviposited compared with moths on untreated apple leaves in sleeve-cage and screen-cage tests. No differences in mating success or oviposition were caused by the application rates and coverage density of M96-018 on foliage. Females avoided ovipositing on particle film-treated leaves in choice tests. Larval hatch was not affected by topical application or residual exposure to M96-018. Larval weight gain and pupal weight were significantly reduced and larval mortality increased in no-choice feeding tests with M96-018. In choice tests, larvae preferred to feed on untreated leaf surfaces. The negative effects on larval development and survivorship on M96-018-treated foliage did not differ across a fourfold difference in spray application rate. A significant reduction in the number of infested shoots was found in orchard trials when M96-018 was applied before bud break in late March compared with untreated trees. No reductions in larval densities were found compared with an untreated control following prebloom and postbloom applications.
Inhibition of skin carcinomas but not papillomas by sphingosine,N‐methylsphingosine, andN‐acetylsphingosine (1998)

The sphingoid base backbones of sphingolipids are highly bioactive compounds that affect cell growth, differentiation, diverse cell behaviors, and programmed cell death. Therefore, the efficacy of sphingosine (SPH) and the analogs N-acetylsphingosine (NAS), N-methylsphingosine (NMS), octylamine (OCT), and sterylamine (STR) in the prevention of skin cancer was assessed in female Sencar mice by measuring effects on the induction of epidermal ornithine decarboxylase (ODC) activity and hyperplasia by 12-O-tetradecanoylphorbol-13-acetate (TPA) and effects on the induction of skin tumors by 7, 12-dimethylbenz[a]anthracene (DMBA) and TPA. ODC was measured in the shaved dorsal skin of mice treated topically with 0.05-20 mumol of these compounds 30 minutes before application of 8.5 nmol of TPA in 0.2 ml of acetone. ODC activity was inhibited by > or = 5 mumol of SPH and STR, > or = 10 mumol of NAS and NMS, and 20 mumol of OCT. In contrast, the induction of hyperplasia was not inhibited by application of these compounds 30 minutes before TPA. Two carcinogenesis studies were conducted with 10 nmol of DMBA as the initiator and 3.2 nmol of TPA (2x/wk for 15 wk) as the promoter. In the first study, NAS, NMS, OCT, and STR (0.05 and 0.5 mumol) were applied before each TPA application. Papilloma incidence and multiplicity were not inhibited, but NAS (0.05 mumol) and NMS (0.05 and 0.50 mumol) increased cancer-free survival. In the second experiment, SPH, NAS, and NMS (0.05 and 0.5 mumol) were applied 30 minutes before each TPA treatment and twice weekly for 10 weeks after the final TPA treatment. Papilloma incidence and multiplicity were not inhibited; however, the proportion of mice without carcinoma was increased by both doses of SPH and by 0.5 mumol of NAS. Thus low doses of sphingolipids that were not effective in inhibiting ODC activity, reducing hyperplasia, or preventing epidermal papilloma development were, nonetheless, effective in inhibiting carcinoma development.
Round‐robin wavelength assignment: a new packet sequence criterion in optical packet switching SCWP networks (2005)

Abstract The WASPNET project proposed a packet sequence criterion to preserve end‐to‐end packet order in optical packet switching (OPS) networks controlled by the scattered wavelength path (SCWP) operational mode. This paper shows that this packet ordering methodology causes performance impairments, related to unbalanced wavelength usage in fibre links. This skewed usage is inherent to the WASPNET sequencing criterion. As a solution, a round‐robin sequence criterion is proposed. The presented technique eliminates non‐uniform wavelength utilisation in fibre links for any traffic pattern, as well as the performance impairments associated. We also propose an optimum scheduling algorithm for OPS output‐buffered switch fabrics, which preserves packet order by following the new sequencing criterion. Copyright © 2005 AEIT.
Characterization of fiber Bragg gratings using spectral interferometry based on minimum-phase functions (2006)

We report a powerful interferometric measurement technique utilizing Spectral Interferometry using Minimum-phase Based Algorithms (SIMBA) to fully characterize the spectrum (either in reflection or transmission) of <i>any</i> fiber Bragg grating (FBG). This complex spectrum information is crucial to recover several important parameters of an FBG, such as its impulse response or refractive index profile. The core of our approach involves sending an unknown short laser pulse, e.g., ~1-50 ps of temporal width, into the FBG of interest, and using an optical spectrum analyzer (OSA) to record the spectrum of the interference between the reflected pulse from the grating and the time-delayed replicas of the original pulse. This measured spectrum, which yields the square of the Fourier transform (FT) magnitude of the pulse sequence's electric field envelope, is then processed to uniquely recover both the phase and amplitude of the FBG spectrum. The underlying principle of our approach is that by design of the experimental set-up, the pulse sequence sent to the OSA is close to a minimum phase function (MPF). Thus, it is possible to recover its FT phase spectrum using only the knowledge of its FT magnitude spectrum. This is an important result since by merely measuring an FT magnitude, with a rather simple set-up the full complex spectrum of the grating can be recovered. This technique has significant advantages over existing techniques, including a higher resolution, a better noise performance, and the ability to use longer laser pulses. It can also conveniently be used to simultaneously characterize more than one FBG, with a single FT magnitude measurement. We demonstrate the validity of our approach with numerical simulations.
Beelines: Motion Prediction Metrics for Self-Driving Safety and Comfort (2021)

The commonly used metrics for motion prediction do not correlate well with a self-driving vehicle&#x2019;s system-level performance. The most common metrics are average displacement error (ADE) and final displacement error (FDE), which omit many features, making them poor self-driving performance indicators. Since high-fidelity simulations and track testing can be resource-intensive, the use of prediction metrics better correlated with full-system behavior allows for swifter iteration cycles. In this paper, we offer a conceptual framework for prediction evaluation highly specific to self-driving. We propose two complementary metrics that quantify the effects of motion prediction on safety (related to recall) and comfort (related to precision). Using a simulator, we demonstrate that our safety metric has a significantly better signal-to-noise ratio than displacement error in identifying unsafe events.
Carnosine Supplementation Improves Serum Resistin Concentrations in Overweight or Obese Otherwise Healthy Adults: A Pilot Randomized Trial (2018)

Adipokines play an important role in the regulation of glucose metabolism. We have previously shown that carnosine supplementation in overweight or obese non-diabetic individuals improves glucose metabolism but does not change adiponectin concentrations. However, its effect on other adipokines has not been investigated. Herein we further determined the effect of carnosine supplementation on serum adipsin, resistin and leptin. Twenty-two overweight or obese otherwise healthy adults were randomly assigned to receive either 2 g of carnosine (<i>n</i> = 13) or identically looking placebo (<i>n</i> = 9) for 12 weeks. Serum adipsin, leptin and resistin were analyzed using a bead-based multiplex assay. Carnosine supplementation decreased serum resistin concentrations compared to placebo (mean change from baseline: -35 ± 83 carnosine vs. 35 ± 55 ng/mL placebo, <i>p</i> = 0.04). There was a trend for a reduction in serum leptin concentrations after carnosine supplementation (-76 ± 165 ng/mL carnosine vs. 20 ± 28 ng/mL placebo, <i>p</i> = 0.06). The changes in leptin and resistin concentrations were inversely related to the change in concentration for urinary carnosine (<i>r</i> = -0.72, <i>p</i> = 0.0002; <i>r</i> = -0.67, <i>p</i> = 0.0009, respectively), carnosine-propanal (<i>r</i> = -0.56, <i>p</i> = 0.005; <i>r</i> = -0.63, <i>p</i> = 0.001, respectively) and carnosine-propanol (<i>r</i> = -0.61, <i>p</i> = 0.002; <i>r</i> = -0.60, <i>p</i> = 0.002, respectively). There were no differences between groups in change in adipsin concentrations. Our findings show carnosine supplementation may normalize some, but not all, of the serum adipokine concentrations involved in glucose metabolism, in overweight and obese individuals. Further clinical trials with larger samples are needed to confirm these results.
Abstract 4497: Distinct structural classes of activating FOXA1 alterations in prostate cancer progression (2019)

Abstract Forkhead box A1 (FOXA1) is a pioneer transcription factor that is essential for the normal development of several endoderm-derived organs, including the prostate gland. FOXA1 is frequently mutated in the hormone-receptor driven prostate, breast, bladder, and salivary gland tumors. In prostate luminal epithelial cells, wild-type FOXA1 delimits tissue-specific enhancers that are transcriptionally activated by AR, and extensively reprograms AR-activity in the transformed prostate epithelia. However, how FOXA1 alterations affect cancer development is unclear, with FOXA1 previously ascribed both tumor suppressive and oncogenic roles. In this study, we assemble an aggregate cohort of 1546 prostate cancers (PCa) and, for the first time, show that FOXA1 alterations fall into three distinct structural classes that diverge in clinical incidence, genetic co-alteration profiles, and oncogenic gain-of-functions. Notably, we find the three classes of FOXA1 alterations to collectively recur at a frequency of 35% in metastatic PCa. Class1 activating mutations originate in early PCa without concurrent ETS or SPOP alterations, selectively recur within the Wing2-region of the DNA-binding Forkhead domain (FKHD), confer enhanced chromatin mobility and binding frequency, and strongly trans-activate a luminal androgen receptor (AR) program of prostate oncogenesis. By contrast, class2 activating mutations are acquired in metastatic PCa, truncate the C-terminal regulatory domain of FOXA1, confer chromatin-binding dominance by increasing DNA affinity, and aberrantly activate the WNT/β-Catenin pathway to enable PCa metastasis. Finally, class3 genomic rearrangements are comprised of tandem duplications and translocations within the highly-syntenic FOXA1 locus. These structural variations amplify or reposition a conserved enhancer element, which we named FOXA1 Mastermind (FOXMIND), to drive overexpression of FOXA1 or other oncogenes, respectively. In summary, our study reaffirms the central role of FOXA1 in mediating AR-driven oncogenesis, and provides mechanistic insights into how different classes of FOXA1 alterations uniquely promote PCa initiation and/or metastatic progression. Furthermore, these results have direct implications in understanding the biology of other hormone-receptor driven cancers where similar FOXA1 alterations are found, and rationalize therapeutic co-targeting of oncogenic FOXA1-activity to extort more potent and durable disease remissions. Citation Format: Abhijit Parolia, Marcin Cieslik, Shih-Chun Chu, Lanbo Xiao, Takahiro Ouchi, Yuping Zhang, Xiaoju Wang, Pankaj Vats, Xuhong Cao, Fengyun Su, Rui Wang, Felix Feng, Yi-Mi Wu, Robert Lonigro, Dan R. Robinson, Arul M. Chinnaiyan. Distinct structural classes of activating FOXA1 alterations in prostate cancer progression [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 4497.
Dopant Selection Strategy for High Quality Factor LSPR from Doped Metal Oxide Nanocrystals (2019)

&lt;div&gt; &lt;div&gt; &lt;p&gt;Thin films of&lt;b&gt; &lt;/b&gt;degenerately doped metal oxides such as those of Sn-doped In&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3 &lt;/sub&gt;(Sn:In&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt;) are commercially significant for their broad utilization as transparent conducting electrodes in optoelectronic devices. Over the last decade, nanocrystals (NCs) of Sn:In&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3 &lt;/sub&gt; and other doped metal oxides have also attracted interest for localized surface plasmon resonance (LSPR) that occurs in the near to mid-infrared region. The suitability of this LSPR for some applications depends on its capacity to concentrate light in small regions of space, known as near-field hot spots. This efficiency to create near-field hot spots can be judged through an LSPR figure-of-merit such as Quality factor, defined as the ratio of LSPR peak energy to its linewidth. The free electron density determines the LSPR peak energy while the extent of electron scattering controls the LSPR linewidth and hence these factors together essentially dictate the value of the Quality factor. An unfortunate tradeoff arises when dopants are introduced since the aliovalent dopants generating the free electrons (increasing LSPR energy) also act as centers of scattering of electrons (increasing LSPR linewidth), thereby decreasing the LSPR Quality factor. Dopant selection is hence of paramount importance to achieve a high value of LSPR Quality factor. Here, we describe the properties of aliovalent cationic dopants that allow both high LSPR energy and low LSPR linewidth and, subsequently, high LSPR Quality factor. In this context, we identify Zr&lt;sup&gt;4+&lt;/sup&gt; as a model aliovalent dopant for high LSPR Quality factor in the In&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt; lattice. The resulting Zr-doped In&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt; NCs exhibit one of the highest LSPR Quality factors reported in the mid-infrared region while also performing equivalently to the recognized materials for either high dopant activation (Sn:In&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3 &lt;/sub&gt;NCs) or low LSPR linewidth (Ce-doped In&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt; NCs), simultaneously. The Zr donor level is positioned well into the conduction band of In&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt; and Zr doping is surface segregated, both minimizing electron scattering. The combination of this low electron scattering and high dopant activation of Zr&lt;sup&gt;4+ &lt;/sup&gt;ions is responsible for the high LSPR Quality factors. These strategies can be used to design a variety of doped metal oxide NC systems exhibiting high LSPR Quality factors. &lt;/p&gt; &lt;/div&gt; &lt;/div&gt; &lt;br&gt;
The glass class (2014)

This course will teach how to design and develop effective interfaces for head mounted wearable computers through the application of user-centered design principles. It will enable existing HCI practitioners to enter the fast growing area of wearable computing. Attendees will gain the knowledge and tools needed to develop prototype applications, and also complete a hands-on design task.
Variants Can Recognize Viral Particles for Hepatitis C Virus Hypervariable Region 1 Monoclonal Antibodies with Broad Specificity (2013)

Alfredo Nicosia and Mario U. MondelliFurione, Sabrina Marciano, Miriam Triyatni, T. Jake Liang, Antonella Cerino, Annalisa Meola, Laura Segagni, Milenahttp://www.jimmunol.org/content/167/7/3878J Immunol€2001; 167:3878-3886; ;Referenceshttp://www.jimmunol.org/content/167/7/3878.full#ref-list-1This article cites 37 articles, 22 of which you can access for free at: Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai.org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at: Erratahttp://www.jimmunol.org/content/168/3/1496.full.pdf or: An erratum has been published regarding this article. Please see next page
Probing the mechanism of ligand exchange by two‐dimensional NMR spectroscopy (1989)

Abstract The application of two‐dimensional chemical exchange NMR spectroscopy to the elucidation of ligand‐exchange mechanisms in inorganic complexes is addressed. Specific examples involving inter‐ and intra‐molecular phosphine exchange in platinum and mercury complexes are given, and the generality of the technique is discussed.
Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM (2021)

In Brief Herein, we evaluated the immunogenicity of several BG505 SOSIP-based HIV Env immunogens in the rhesus macaque animal model using a combination of serology and biophysical approaches. We applied electron cryo-microscopy for high-resolution mapping of elicited polyclonal antibody responses, which provided detailed insights into the binding modes of the most common classes of antibodies elicited by BG505 SOSIP immunogens as well as the critical differences in immunogenicity that can occur as a consequence of engineered stabilizing mutations and partial glycan occupancy at different sites. Summary Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic. Graphical abstract
Supplementary Table S4 from A Phase I/II Trial of HER2 Vaccine–Primed Autologous T-Cell Infusions in Patients with Treatment Refractory HER2–Overexpressing Breast Cancer (2023)

&lt;p&gt;Immunologic parameters between pre-treatment and post T cell infusion in PR+SD and PD patients.&lt;/p&gt;
Unwrapping of MR phase images using a Markov random field model (2005)

Phase unwrapping is an important problem in many magnetic resonance imaging applications, such as field mapping and flow imaging. The challenge in two-dimensional phase unwrapping lies in distinguishing jumps due to phase wrapping from those due to noise and/or abrupt variations in the actual function. This paper addresses this problem using a Markov random field to model the true phase function, whose parameters are determined by maximizing the a posteriori probability. To reduce the computational complexity of the optimization procedure, an efficient algorithm is also proposed for parameter estimation using a series of dynamic programming connected by the iterated conditional modes. The proposed method has been tested with both simulated and experimental data, yielding better results than some of the state-of-the-art method (e.g., the popular least-squares method) in handling noisy phase images with rapid phase variations.
99mTc-MDP scintigraphy vs. 18F NaF PET/CT for detection of skeletal metastases (2014)

599 Objectives 99mTc-MDP bone scanning (BS) is highly sensitive and cost-effective, thus having been for decades the standard method for nuclear imaging of the skeletal system. Owing to the pharmacokinetic properties of 18F-NaF and better resolution of PET/CT, 18F-NaF PET/CT has attracted clinical interest. Several published studies reported the value of 18F-NaF PET/CT for skeletal imaging and indicated that it might be superior over 99mTc-MDP BS in detecting bone metastases. However, 18F-NaF PET/CT did not replace 99mTc-MDP BS in routine clinical practice for a variety of reasons. Here we reviewed our clinical experience with 99mTc-MDP BS and 18F-NaF PET/CT for detection of bone metastases. Methods This is a retrospective study (Sep 2007 - Oct 2015) of 77 patients with proven malignancy (51 prostate cancer, 12 sarcoma, 7 breast cancer, 7 other cancers), who had 99mTc-MDP BS and 18F-NaF PET/CT for evaluation of skeletal metastases. There were 65 men and 12 women, 19-88 year-old (average: 62.8±15.1). 99mTc-MDP BS and 18F-NaF PET/CT were performed within 2-30 days (average: 22±9.7). The lesions detected with each test were tabulated and the results compared. Results Neither scan identified bone metastases in 27/77 patients (27%). Skeletal metastases were detected by 99mTc-MDP BS in 41/77 patients (53%) and by 18F-NaF PET/CT in 50/77 patients (65%). For the group with skeletal metastases on both scans, the extent of disease was greater by 18F NaF-PET/CT over 99mTc-MDP BS in 27/41 patients (66%) and the same in 14/41 patients (34%). 18F-NaF PET/CT showed skeletal metastases not seen on 99mTc-MDP BS in 9/77 patients (12%). Conclusions The evaluation of the extent of skeletal metastases with 18F-NaF PET/CT was superior over 99mTc-MDP BS in our cohort. In addition, 12% of the patients had bone metastases seen only on 18F-NaF PET/CT. However, given the concordance between the results of the two scans, it may be possible to create a clinical workflow to evaluate patients referred for bone scintigraphy with a 99mTc-MDP BS first, followed by 18F-NaF PET/CT only for patients with negative or equivocal 99mTc-MDP BS who continue to have high clinical suspicion for bone metastases.