gebhart/patrepeval huggingface dataset:
SU-E-T-97: Controllable Fluid Flow Using Polymer Compartments within a Dynamic Contrast Enhanced (DCE) Imaging Phantom Design for Quality Assurance (2011)

Purpose: Dynamic contrast enhanced (DCE) imaging, a powerful tool for prognosis and evaluation during cancer treatment, lacks objective validation of derived quantitative metrics for practical clinical application. Existing validation techniques are limited to small animal models, simulation datasets, preserved organs and static phantoms, all of which fail to provide a reliable, re-usable means for repeated studies under known system conditions. This work investigates the use of tissue-like compartments of differential perfusion, which produce distinct signal intensities within a DCE image study. Methods :Using Selective Laser Sintering (SLS, a rapid prototyping technique), three-dimensional computerized vascular trees with modular tissue compartments were manufactured. The last level of bifurcation within the network feeds compartments which house scaffolds. Scaffolds were fabricated using three techniques, each of which achieves a different minimum pore size and structural architecture: salt leaching-solvent casting (SC/SL), SLS and inverted colloidal crystal (ICC). For each scaffold type, perfusion characteristics were examined in order to evaluate the differential flow rate realizable.Results: Vascular networks with four orders of bifurcation were produced. Four terminal vessels connect to a single compartment. Three scaffold techniques were used to generate scaffolds with pore sizes between 100 – 1000 microns. Estimated permeabilities of each technique were: SLS (1.60E-5 - 1.12E-4 m̂4/N·s), SL/SC (1.48E-7 - 1.75E-6 m̂4/N·s) and ICC (9.17E-8 - 3.29E-7 m̂4/N·s). Each scaffold type offered a distinct differential flow Conclusions: The permeability characteristics supporting phantom-based simulation of hepatic parenchyma perfusion are achievable using scaffolds. In the development of a perfusion phantom for quality assurance of DCE imaging and analysis, these compartments of known permeability may be used to validate systems. Current efforts include computing the known volumetric flow rate and performing various DCE post-processing techniques on the phantom.
Reduction in Subventricular Zone-Derived Olfactory Bulb Neurogenesis in a Rat Model of Huntington’s Disease Is Accompanied by Striatal Invasion of Neuroblasts (2015)

Huntington's disease (HD) is an inherited progressive neurodegenerative disorder caused by an expanded CAG repeat in exon 1 of the huntingtin gene (HTT). The primary neuropathology of HD has been attributed to the preferential degeneration of medium spiny neurons (MSN) in the striatum. Reports on striatal neurogenesis have been a subject of debate; nevertheless, it should be considered as an endogenous attempt to repair the brain. The subventricular zone (SVZ) might offer a close-by region to supply the degenerated striatum with new cells. Previously, we have demonstrated that R6/2 mice, a widely used preclinical model representing an early onset HD, showed reduced olfactory bulb (OB) neurogenesis but induced striatal migration of neuroblasts without affecting the proliferation of neural progenitor cell (NPCs) in the SVZ. The present study revisits these findings, using a clinically more relevant transgenic rat model of late onset HD (tgHD rats) carrying the human HTT gene with 51 CAG repeats and mimicking many of the neuropathological features of HD seen in patients. We demonstrate that cell proliferation is reduced in the SVZ and OB of tgHD rats compared to WT rats. In the OB of tgHD rats, although cell survival was reduced, the frequency of neuronal differentiation was not altered in the granule cell layer (GCL) compared to the WT rats. However, an increased frequency of dopamenergic neuronal differentiation was noticed in the glomerular layer (GLOM) of tgHD rats. Besides this, we observed a selective proliferation of neuroblasts in the adjacent striatum of tgHD rats. There was no evidence for neuronal maturation and survival of these striatal neuroblasts. Therefore, the functional role of these invading neuroblasts still needs to be determined, but they might offer an endogenous alternative for stem or neuronal cell transplantation strategies.
Mahalanobis Motion Generation (2004)

Representing motions as linear sums of principal components has become a widely accepted animation technique. While powerful, the simplest version of this approach is not particularly well suited to modeling the specific style of an individual whose motion had not yet been recorded when building the database: It would take an expert to adjust the PCA weights to obtain a motion style that is indistinguishable from his. Consequently, when realism is required, current practice is to perform a full motion capture session each time a new person must be considered. In this paper, we extend the PCA approach so that this requirement can be drastically reduced: For whole classes of motion such as walking or running, it is enough to observe the newcomer moving only once at a particular speed using either an optical motion capture system or a simple pair of synchronized video cameras. This one observation is used to compute a set of principal component weights that best approximates the motion and to extrapolate in real-time realistic animations of the same person walking or running at different speeds.
B-SCST: Bayesian Self-Critical Sequence Training for Image Captioning (2020)

Bayesian deep neural networks (DNNs) can provide a mathematically grounded framework to quantify uncertainty in predictions from image captioning models. We propose a Bayesian variant of policy-gradient based reinforcement learning training technique for image captioning models to directly optimize non-differentiable image captioning quality metrics such as CIDEr-D. We extend the well-known Self-Critical Sequence Training (SCST) approach for image captioning models by incorporating Bayesian inference, and refer to it as B-SCST. The "baseline" for the policy-gradients in B-SCST is generated by averaging predictive quality metrics (CIDEr-D) of the captions drawn from the distribution obtained using a Bayesian DNN model. We infer this predictive distribution using Monte Carlo (MC) dropout approximate variational inference. We show that B-SCST improves CIDEr-D scores on Flickr30k, MS COCO and VizWiz image captioning datasets, compared to the SCST approach. We also provide a study of uncertainty quantification for the predicted captions, and demonstrate that it correlates well with the CIDEr-D scores. To our knowledge, this is the first such analysis, and it can improve the interpretability of image captioning model outputs, which is critical for practical applications.
Origin of Metallic Nature of Na3N (2020)

Among inorganic clathrates, the inner cavity space rarely affects the electronic structure of the framework. We report that the anti-ReO<sub>3</sub>-type compound Na<sub>3</sub>N has a metallic nature irrespective of the stoichiometric chemical composition of simple representative elements and that this unusual nature originates from the collapse of the bandgap owing to the presence of a crystallographic cavity. We synthesized Na<sub>3</sub>N by the plasma-assisted nitridation of alkali metals, and diffuse reflectance measurements indicated a metallic nature. The introduction of nitrogen into the Na metal induced the formation of both the Na<sup>+</sup> ion and the crystallographic cavity. The former increased the density of the lattice of Na<sup>+</sup> ions to form a wide Na 3s conduction band. The latter interacted with the Na 3s band to enhance the bandwidth, resulting in the collapse of the bandgap. Na<sub>3</sub>N is a unique nitride, which possesses an electronically active cavity space.
A Diabetes Treatment Strategy to Reduce the Risk of Cardiovascular Events: Clinical Benefits and Potential of Linagliptin (2013)

Dipeptidyl peptidase-4 (DPP-4) inhibitors suppress degradation of active glucagon-like peptide-1 and promote insulin secretion from pancreatic β cells in a blood glucose-dependent manner to decrease the blood glucose level. They lower the risk of hypoglycemia without causing weight gain and may protect pancreatic β cells; thus, DPP-4 inhibitors may overcome the challenges faced by conventional diabetes treatments. In particular, linagliptin, which has been shown to prevent cardiovascular events in meta-analyses of randomized studies and phase III studies performed, might extend healthy life expectancy, which is the goal of diabetes treatment. Given that one goal of diabetes treatment is prevention of cardiovascular events, glycemic control alone does not suffice; thus, expectations are placed on DPP-4 inhibitors with more potent effects regarding cardiovascular events. In fact, the greatest risk factor for cardiovascular events in patients with diabetes is a high LDL cholesterol level, followed by a high triglyceride level and a low HDL cholesterol level. Thus, future DPP-4 inhibitors must serve to effectively control diabetes and eliminate other risk factors. In addition to its hypoglycemic effect, linagliptin suppresses hepatic steatosis and has beneficial effects on lipid metabolism. Because of these favorable properties, linagliptin may be ascribed as a second-generation DPP-4 inhibitor. Keywords: DPP-4 inhibitor, glycemic control, hepatic steatosis, linagliptin, lipid metabolism, metabolic syndrome, obesity, prevention of cardiovascular events, postprandial hyperglycemia, residual risk, risk factor, treatment goal, type 2 diabetes mellitus.
Decoration of Dibenzofuran Using Cyanocarbazole via 6‐Position as a Molecular Design Approach for High‐Triplet‐Energy Bipolar Host Materials (2018)

In this study, two new dibenzofuran derivatives featuring one or two cyanocarbazole units, 6-(dibenzo[b,d]furan-4-yl)-9-phenyl-9H-carbazole-3-carbonitrile (mBFCzCN) and 6,6'-(dibenzo[b,d]furan-4,6-diyl)bis(9-phenyl-9H-carbazole-3-carbonitrile) (dBFCzCN), were developed as host materials for phosphorescent organic light emitting diodes (PhOLEDs). A new molecular design connecting the cyanocarbazole to the dibenzofuran using the cyanocarbazole 6-position instead of its 9-position was created, and the effects of number of cyanocarbazole units in the dibenzofuran building block on the photophysical and electroluminescence properties were investigated in detail. The mBFCzCN compound revealed high triplet energy (2.78 eV) than that of dBFCzCN (2.68 eV) and good bipolar charge transporting properties. The potential of these materials as hosts for blue and green PhOLEDs was investigated using bis(4,6-(difluorophenyl)pyridinato-N,C<sup>2'</sup> )picolinate iridium(III) (FIrpic) and tris(2-phenylpyridinato)iridium(III) (Ir(ppy)<sub>3</sub> ) dopants, respectively. The results indicated that the mBFCzCN with one cyanocarbazole unit showed better device performance than the dBFCzCN with two cyanocarbazole units in the blue and green devices. High external quantum efficiencies of 19.0 and 21.2 % were demonstrated in the blue and green PhOLEDs with the mBFCzCN host due to its high triplet energy and good bipolar charge transporting characteristics.
Achieving WIPP certification for software: A white paper (1998)

The NMT-1 and NMT-3 organizations within the Chemical and Metallurgical Research (CMR) facility at the Los Alamos National Laboratory (LANL) is working to achieve Waste Isolation Pilot Plant (WIPP) certification to enable them to transport their TRU waste to WIPP. In particular, the NMT-1 management is requesting support from the Idaho National Engineering and Environmental Laboratory (INEEL) to assist them in making the Laboratory Information Management System (LIMS) software WIPP certifiable. Thus, LIMS must be compliant with the recognized software quality assurance (SQA) requirements stated within the QAPD. Since the Idaho National Engineering and Environmental Laboratory (INEEL) has achieved WIPP certification, INEEL personnel can provide valuable assistance to LANL by sharing lessons learned and recommendations. Thus, this white paper delineates the particular software quality assurance requirements required for WIPP certification.
Gram-Scale One-Pot Synthesis of Highly Luminescent Blue Emitting Cd1−xZnxS/ZnS Nanocrystals (2008)

We demonstrated a facile synthesis of highly luminescent blue emitting Cd1−xZnxS/ZnS core/shell structured nanocrystals (NCs) in straightforward and reproducible manner. The alloyed Cd1−xZnxS cores with homogeneity in both size and composition were prepared by introducing S precursors (S dissolved in the noncoordinating solvent (1-octadecene)) into the mixed solution of Cd−Oleate (Cd(OA)2) and Zn−Oleate (Zn(OA)2) at elevated temperature (300 °C). ZnS shells were successively overcoated on the prepared cores by the second injection of S precursors (S powder dissolved in tributylphosphine, TBPS) directly into the reactor with existing alloyed Cd1−xZnxS NC cores without any purification steps. The prepared NCs exhibit strong band edge emission with high photoluminescent quantum yield (PL QY, up to 80%) and narrow spectral bandwidth (fwhm < 25 nm), which is believed to originate from the successful growth of ZnS shell layers on the Cd1−xZnxS cores and the interfacial compatibility between Cd1−xZnxS cores and the ZnS shell layers through the intradiffusion of Zn atoms from the ZnS shells into the Cd1−xZnxS cores during the shell formation reaction. The emission wavelength (PL λmax.) of Cd1−xZnxS/ZnS core/shell NCs was finely tuned from violet (415 nm) to blue (461 nm) by adjusting the amount of S precursors in the first injection (S in 1-octadecene) and thus changing actual Cd content ratio in the alloyed Cd1−xZnxS cores (0.49 ≤ x ≤ 0.76). Furthermore, multigram (3 g) scale production of Cd1−xZnxS/ZnS core/shell NCs with narrow size distribution and spectral bandwidth was also demonstrated.
Macrophage-Derived Tumor Necrosis Factor α, an Early Developmental Signal for Motoneuron Death (2004)

Mechanisms inducing neuronal death at defined times during embryogenesis remain enigmatic. We show in explants that a developmental switch occurs between embryonic day 12 (E12) and E13 in rats that is 72-48 hr before programmed cell death. Half the motoneurons isolated from peripheral tissues at E12 escape programmed cell death, whereas 90% of motoneurons isolated at E13 enter a death program. The surrounding somite commits E12 motoneurons to death. This effect requires macrophage cells, is mimicked by tumor necrosis factor alpha (TNFalpha), and is inhibited by anti-TNFalpha antibodies. In vivo, TNFalpha is detected within somite macrophages, and TNF receptor 1 (TNFR1) is detected within motoneurons precisely between E12 and E13. Although motoneuron cell death occurs normally in TNFalpha-/- mice, this process is significantly reduced in explants from TNFalpha-/- and TNFR1-/- mice. Thus, embryonic motoneurons acquire the competence to die, before the onset of programmed cell death, from extrinsic signals such as macrophage-derived TNFalpha
KEAP1-Dependent Synthetic Lethality Induced by AKT and TXNRD1 Inhibitors in Lung Cancer (2013)

Intrinsic resistance to agents targeting phosphoinositide 3-kinase (PI3K)/AKT pathway is one of the major challenges in cancer treatment with such agents. The objective of this study is to identify the genes or pathways that can be targeted to overcome the resistance of non-small cell lung carcinoma (NSCLC) to the AKT inhibitor MK2206, which is currently being evaluated in phase I and II clinical trials. Using a genome-wide siRNA library screening and biologic characterization, we identified that inhibition of thioredoxin reductase-1 (TXNRD1), one of the key antioxidant enzymes, with siRNAs or its inhibitor, auranofin, sensitized NSCLC cells to MK2206 treatment in vitro and in vivo. We found that simultaneous inhibition of TXNRD1 and AKT pathways induced robust reactive oxygen species production, which was involved in c-jun-NH2-kinase (JNK; MAPK8) activation and cell apoptosis. Furthermore, we found that the synthetic lethality interaction between the TXNRD1 and AKT pathways occurred through the KEAP1/NRF2 cellular antioxidant pathway. Finally, we found that synthetic lethality induced by TXNRD1 and AKT inhibitors relied on wild-type KEAP1 function. Our study indicates that targeting the interaction between AKT and TXNRD1 antioxidant pathways with MK2206 and auranofin, a U.S. Food and Drug Administration-approved drug, is a rational strategy to treat lung cancer and that KEAP1 mutation status may offer a predicative biomarker for such combination approaches.
Keyframe-based tracking for rotoscoping and animation (2004)

We describe a new approach to rotoscoping --- the process of tracking contours in a video sequence --- that combines computer vision with user interaction. In order to track contours in video, the user specifies curves in two or more frames; these curves are used as keyframes by a computer-vision-based tracking algorithm. The user may interactively refine the curves and then restart the tracking algorithm. Combining computer vision with user interaction allows our system to track any sequence with significantly less effort than interpolation-based systems --- and with better reliability than "pure" computer vision systems. Our tracking algorithm is cast as a spacetime optimization problem that solves for time-varying curve shapes based on an input video sequence and user-specified constraints. We demonstrate our system with several rotoscoped examples. Additionally, we show how these rotoscoped contours can be used to help create cartoon animation by attaching user-drawn strokes to the tracked contours.
Intratumoral expression of IL-7 and IL-12 using an oncolytic virus increases systemic sensitivity to immune checkpoint blockade (2020)

The immune status of the tumor microenvironment is a key indicator in determining the antitumor effectiveness of immunotherapies. Data support the role of activation and expansion of tumor-infiltrating lymphocytes (TILs) in increasing the benefit of immunotherapies in patients with solid tumors. We found that intratumoral injection of a tumor-selective oncolytic vaccinia virus encoding interleukin-7 (IL-7) and IL-12 into tumor-bearing immunocompetent mice activated the inflammatory immune status of previously poorly immunogenic tumors and resulted in complete tumor regression, even in distant tumor deposits. Mice achieving complete tumor regression resisted rechallenge with the same tumor cells, suggesting establishment of long-term tumor-specific immune memory. Combining this virotherapy with anti-programmed cell death-1 (PD-1) or anti-cytotoxic T lymphocyte antigen 4 (CTLA4) antibody further increased the antitumor activity as compared to virotherapy alone, in tumor models unresponsive to either of the checkpoint inhibitor monotherapies. These findings suggest that administration of an oncolytic vaccinia virus carrying genes encoding for IL-7 and IL-12 has antitumor activity in both directly injected and distant noninjected tumors through immune status changes rendering tumors sensitive to immune checkpoint blockade. The benefit of intratumoral IL-7 and IL-12 expression was also observed in humanized mice bearing human cancer cells. These data support further investigation in patients with non-inflamed solid tumors.
Abstract 4389: Post-translational modifications of histone demethylase JMJD1A in prostate cancer cells (2019)

Abstract Castration-resistant prostate cancer (CRPC) is the major cause of death for prostate cancer (PCa) patients. Re-activation of androgen receptor (AR) activity during androgen-deprivation therapy is believed to underlie CRPC development. We have found that histone demethylase JMJD1A primarily regulates AR and c-Myc activity and thus plays a key role in promoting PCa cell proliferation or survival. Unfortunately, specific JMJD1A inhibitors are not yet available. Here, we identified several post-translational modifications of JMJD1A by performing the JMJD1A immunoprecipitation and mass spectrometry analysis. These modifications include the canonical ubiquitination that targets JMJD1A for proteasome-dependent degradation, non-canonical ubiquitination that enhances the recruitment of co-activators, as well as those that can regulate these ubiquitination events. We also found that these modifications could be manipulated by commercially available inhibitors, to reduce the JMJD1A protein level and prostate cancer cell growth. Thus, targeting the JMJD1A modifications may serve as an alternative means to inhibit JMJD1A activity for the anti-PCa therapy. Note: This abstract was not presented at the meeting. Citation Format: Songhui Xu, Lingling Fan, Xiaolu Cui, Fengbo Zhang, Arif Hussain, Ladan Fazli, Martin Gleave, Jianfei Qi. Post-translational modifications of histone demethylase JMJD1A in prostate cancer cells [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 4389.
Supplementary Figures from Gain-of-Function <i>RHOA</i> Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer (2023)

&lt;p&gt;Supplementary Figures and Legends&lt;/p&gt;
Mechanism of film formation of latices (1970)

Abstract The following mechanism is proposed for latex film formation. Initially, the latex particles move about freely, with characteristic Brownian motion. As the water evaporates, their motion becomes more restricted, and eventually the water‐air interfacial tension forces them together in a packed array, with their double layers hindering their further mutual approach. The continued evaporation of the water exerts a force to overcome this repulsion, so that the double layers are ‘ruptured’ and a polymer‐polymer contact is formed. This brings the polymer‐water interfacial tension into play, to reinforce and complement the water‐air interfacial tension. If the combined forces are sufficient to deform the polymer spheres, they form a continuous film. This film becomes more homogeneous upon ageing; there occurs a further gradual coalescence, the rate of which depends upon the polymer structure and during which any incompatible substance is exuded to the surface.
LED manufacturing issues concerning gallium nitride-on-silicon (GaN-on-Si) technology and wafer scale up challenges (2013)

We demonstrated the growth of blue LED structures grown on 4-inch and 8-inch Si (111) substrates. GaN layers that have low threading dislocation density (TDD) of 1.6×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> /cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , which is comparable to state of the art in GaN on sapphire, can be obtained on 4-inch Si substrate by using a new TDD reduction technology using a silicon nitride (SiN) interlayer. A dependence of LED device performance on threading dislocation density was studied by using 4-inch Si substrate. A LED manufacturing technology has been developed by using 8-inch Si towards mass production technology. The light output power representing a median performance exceeded 641 mW at 350 mA, which was comparable to state-of-the-art LED.
CD optimization methodology for extending optical lithography (2013)

This paper describes the joint development and optimization of an advanced critical dimension (CD) control methodology at IBM’s 300 mm semiconductor facility. The work is initially based on 22 nm critical level gate CD control, but the methodology is designed to support both the lithography equipment (1.35 NA scanners) and processes for 22, 20, 18, and 14 nm node applications. Specifically, this paper describes the CD uniformity of processes with and without enhanced CD control applied. The control methodology is differentiated from prior approaches<sup>1</sup> by combining independent process tool compensations into an overall CD dose correction signature to be applied by the exposure tool. In addition, initial investigations of product specific focus characterization and correction are also described.