gebhart/patrepeval huggingface dataset:
One-Pot Synthesis of Dihydroimidazo- and Imidazophenanthridinium Salts (2007)

Two highly efficient and general one-pot annulation reactions are described for the synthesis of dihydroimidazo- and imidazophenanthridinium salts (DIPs(+) and IPs(+)). These two methodologies exploit the difference in reactivity between primary amino-based or ammonia nucleophiles and the dielectrophilic starting material, 2-bromoethylphenanthridinium bromide.
Two-photon fluorescence bioimaging with an all-semiconductor laser picosecond pulse source (2007)

We have demonstrated successful two-photon excitation fluorescence bioimaging using a high-power pulsed all-semiconductor laser. Toward this purpose, we developed a pulsed light source consisting of a mode-locked laser diode and a two-stage diode laser amplifier. This pulsed light source provided optical pulses of 5 ps duration and having a maximum peak power of over 100 W at a wavelength of 800 nm and a repetition frequency of 500 MHz.
Dynamic Action Repetition for Deep Reinforcement Learning (2017)

One of the long standing goals of Artificial Intelligence (AI) is to build cognitive agents which can perform complex tasks from raw sensory inputs without explicit supervision. Recent progress in combining Reinforcement Learning objective functions and Deep Learning architectures has achieved promising results for such tasks. An important aspect of such sequential decision making problems, which has largely been neglected, is for the agent to decide on the duration of time for which to commit to actions. Such action repetition is important for computational efficiency, which is necessary for the agent to respond in real-time to events (in applications such as self-driving cars). Action Repetition arises naturally in real life as well as simulated environments. The time scale of executing an action enables an agent (both humans and AI) to decide the granularity of control during task execution. Current state of the art Deep Reinforcement Learning models, whether they are off-policy or on-policy, consist of a framework with a static action repetition paradigm, wherein the action decided by the agent is repeated for a fixed number of time steps regardless of the contextual state while executing the task. In this paper, we propose a new framework - Dynamic Action Repetition which changes Action Repetition Rate (the time scale of repeating an action) from a hyper-parameter of an algorithm to a dynamically learnable quantity. At every decision-making step, our models allow the agent to commit to an action and the time scale of executing the action. We show empirically that such a dynamic time scale mechanism improves the performance on relatively harder games in the Atari 2600 domain, independent of the underlying Deep Reinforcement Learning algorithm used.
Spherical Compound Micelles with Lamellar Stripes Self‐Assembled from Star Liquid Crystalline Diblock Copolymers in Solution (2017)

Detailed investigations on the self‐assembly of amphiphilic star block copolymers composed of three‐arm poly(ethylene oxide) (PEO) and poly(methacrylate) (PMAAz) with an azobenzene side chain (denoted as 3PEO‐ b ‐PMAAz) into stable spherical aggregates with clear lamellar stripes in solution are demonstrated. Four block copolymers, 3PEO 12 ‐ b ‐PMA(Az) 33 , 3PEO 22 ‐ b ‐PMA(Az) 31 , 3PEO 22 ‐ b ‐PMA(Az) 62 , and linear PEO 68 ‐ b ‐PMA(Az) 31 , are synthesized. The liquid crystalline properties of the block copolymers are studied by differential scanning calorimetry, polarized optical microscopy techniques, and wide‐angle X‐ray diffraction. The morphologies of the compound micelles self‐assembled in tetrahydrofuran (THF)/water mixtures are observed by means of transmission electron microscopy and scanning electron microscopy. The size of the spherical micelles is influenced by the self‐assembly conditions and the lengths of two blocks. The well‐defined three‐arm architecture of the hydrophilic blocks is a key structural element to the formation of stable spherical compound micelles. The micelle surface integrity is affected by the lengths of PEO blocks. The lamellar stripes are clearly observed on these micelles. This work provides a promising strategy to prepare functional stable spherical compound micelles self‐assembled by amphiphilic block copolymers in solution.
Enhancing magnetic resonance imaging tumor detection with fluorescence intensity and lifetime imaging (2010)

Early detection is important for many solid cancers but the images provided by ultrasound, magnetic resonance imaging (MRI), and computed tomography applied alone or together, are often not sufficient for decisive early screening ∕ diagnosis. We demonstrate that MRI augmented with fluorescence intensity (FI) substantially improves detection. Early stage murine pancreatic tumors that could not be identified by blinded, skilled observers using MRI alone, were easily identified with MRI along with FI images acquired with photomultiplier tube detection and offset laser scanning. Moreover, we show that fluorescence lifetime (FLT) imaging enables positive identification of the labeling fluorophore and discriminates it from surrounding tissue autofluorescence. Our data suggest combined-modality imaging with MRI, FI, and FLT can be used to screen and diagnose early tumors.
Quantification of the Free Radical Content of Oilsands Bitumen Fractions (2019)

Electron spin resonance (ESR) spectroscopy was employed to perform quantitative analysis of the free radical content of oilsands bitumen, asphaltenes, deasphalted oil, vacuum residue, and vacuum gas oil fractions, as well as thermally converted product fractions. Calibration standards for ESR were compared, and 2,2-diphenyl-1-picrylhydrazyl was selected. The heaviest fractions, including asphaltenes, had free radical concentrations in the range 1017–1018 spins/g, whereas lighter fractions such as the lighter gas oil fractions had free radical concentrations in the range 1016–1017 spins/g. It was found that the bulk liquid properties affected the measured free radical concentration even after compensating for effects that could affect the spectroscopy. These differences were not analytical artifacts and could be explained with reference to the literature in terms of the “equilibrium” composition resulting from dimerization and decomposition of free radical pairs. Reported free radical concentrations must consequently be interpreted by considering the nature of the bulk liquid that was analyzed. Practically, the results have implications for thermal conversion of bitumen. It appears that the free radical concentration and availability of reactive free radicals can be independently manipulated through temperature and the bulk liquid properties.
Supplementary Table 1 from Loss of E-Cadherin Promotes Metastasis via Multiple Downstream Transcriptional Pathways (2023)

Supplementary Table 1 from Loss of E-Cadherin Promotes Metastasis via Multiple Downstream Transcriptional Pathways
Electrochemical Stability of Thiolate Self-Assembled Monolayers on Au, Pt, and Cu (2023)

Self-assembled monolayers (SAMs) of thiolates have increasingly been used for modification of metal surfaces in electrochemical applications including selective catalysis (e.g., CO<sub>2</sub> reduction, nitrogen reduction) and chemical sensing. Here, the stable electrochemical potential window of thiolate SAMs on Au, Pt, and Cu electrodes is systematically studied for a variety of thiols in aqueous electrolyte systems. For fixed tail-group functionality, the reductive stability of thiolate SAMs is found to follow the trend Au < Pt < Cu; this can be understood by considering the combined influences of the binding strength of sulfur and competitive adsorption of hydrogen. The oxidative stability of thiolate SAMs is found to follow the order: Cu < Pt < Au, consistent with each surface's propensity toward surface oxide formation. The stable reductive and oxidative potential limits are both found to vary linearly with pH, except for reduction above pH ∼10, which is independent of pH for most thiol compositions. The electrochemical stability across different functionalized thiols is then revealed to depend on many different factors including SAM defects (accessible surface metal atom sites decrease stability), intermolecular interactions (hydrophilic groups reduce the stability), and SAM thickness (stability increases with alkanethiol carbon chain length) as well as factors such as SAM-induced surface reconstruction and the ability to directly oxidize or reduce the non-sulfur part of the SAM molecule.
Spontaneous multi-keV electron generation in a low-RF-power axisymmetric mirror machine (2019)

X-ray emission shows the existence of multikilo-electron-volt electrons in low-temperature, low-power, capacitively coupled RF-heated magnetic-mirror plasmas that also contain a warm (300 eV) minority electron population. Though these warm electrons are initially passing particles, we suggest that collisionless scattering—μ nonconservation in the static vacuum field—is responsible for a minority of them to persist in the mirror cell for thousands of transits during which time a fraction is energized to a characteristic temperature of 3 keV, with some electrons reaching energies above 30 keV. A heuristic model of the heating by a Fermi-accelerationlike mechanism is presented, with μ nonconservation in the static vacuum field as an essential feature.
Co<sup>2+</sup> substituted La<sub>2</sub>CuO<sub>4</sub>/LaCoO<sub>3</sub> perovskite nanocomposites: synthesis, properties and heterogeneous catalytic performance (2018)

Cobalt substituted La<sub>2</sub>CuO<sub>4</sub>/LaCoO<sub>3</sub> perovskite nanocomposites were prepared using a microwave combustion method.
Data from Class 1, 2, and 3 &lt;i&gt;BRAF&lt;/i&gt;-Mutated Metastatic Colorectal Cancer: A Detailed Clinical, Pathologic, and Molecular Characterization (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;&lt;i&gt;BRAF&lt;/i&gt; mutations are grouped in activating &lt;i&gt;RAS&lt;/i&gt;-independent signaling as monomers (class 1–V600E) or as dimers (class 2–codons 597/601), and &lt;i&gt;RAS&lt;/i&gt;-dependent with impaired kinase activity (class 3–codons 594/596). Although clinical, pathologic, and molecular features of &lt;i&gt;&lt;sup&gt;V600E&lt;/sup&gt;BRAF&lt;/i&gt;-mutated metastatic colorectal cancer (mCRC) are well known, limited data are available from the two other classes.&lt;/p&gt;Experimental Design:&lt;p&gt;Data from 117 patients with &lt;i&gt;BRAF&lt;/i&gt; (92 class 1, 12 class 2, and 13 class 3)-mutated mCRC were collected. A total of 540 &lt;i&gt;BRAF&lt;/i&gt; wt mCRCs were included as control. IHC profiling was performed to determine the consensus molecular subtypes (CMS), cytokeratin 7/20 profiles, tumor-infiltrating lymphocyte infiltration, and BM1/BM2 categorization. Overall survival (OS) and progression-free survival were evaluated by Kaplan–Meier and log-rank test.&lt;/p&gt;Results:&lt;p&gt;Class 3 &lt;i&gt;BRAF&lt;/i&gt;-mutated mCRC was more frequently left sided (&lt;i&gt;P&lt;/i&gt; = 0.0028), pN0 (&lt;i&gt;P&lt;/i&gt; = 0.0159), and without peritoneal metastases (&lt;i&gt;P&lt;/i&gt; = 0.0176) compared with class 1, whereas class 2 cases were similar to class 1. Hazard ratio for OS, as compared with &lt;i&gt;BRAF&lt;/i&gt; wt, was 2.38 [95% confidence interval (CI), 1.61–3.54] for class 1, 1.90 (95% CI, 0.85–4.26) for class 2, and 0.93 (95% CI, 0.51–1.69) for class 3 (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001). Class 2 and 3 tumors were all assigned to CMS2-3. A higher median CD3/CD8-positive lymphocyte infiltration was observed in &lt;i&gt;BRAF&lt;/i&gt;-mutated class 2 (&lt;i&gt;P&lt;/i&gt; = 0.033) compared with class 3 cases.&lt;/p&gt;Conclusions:&lt;p&gt;For the first time, different clinical and pathologic features and outcome data were reported according to the three &lt;i&gt;BRAF&lt;/i&gt; mutation classes in mCRC. Specific targeted treatment strategies should be identified in the near future for such patients.&lt;/p&gt;&lt;/div&gt;
Supplementary Fig. S3 from ClC-3 expression enhances etoposide resistance by increasing acidification of the late endocytic compartment (2023)

Supplementary Fig. S3 from ClC-3 expression enhances etoposide resistance by increasing acidification of the late endocytic compartment
Intensive 2D SEM model calibration for 45nm and beyond (2006)

Conventional site-base model calibration approaches have worked fine from the 180nm down to the 65nm technology nodes, but with the first 45nm technology nodes rapidly approaching, site-based model calibration techniques may not capture the details contained in these 2D-intensive designs. Due to the compaction of designs, we have slowly progressed from 1D-intensive gates, which were site-based friendly, to very complex and sometimes ornate 2D-gate regions. To compound the problem, these 2D-intensive gate regions are difficult to measure resulting in metrology-induced error when attempting to add these regions to the model calibration data. To achieve the sub-nanometer model accuracy required at this node, a model calibration technique must be able to capture the curvature induced by the process and the design in these gate regions. A new approach in model calibration had been developed in which images from a scanning electron microscope (SEM) are used together with the conventional site-base to calibrate models instead of the traditional single critical dimension (CD) approach. The advantage with the SEM-image model calibration technique is that every pixel in the SEM image contributes as CD information improving model robustness. Now the ornate gate regions could be utilized as calibration features allowing the acquisition of fine curvature in the design. 
This paper documents the issues of the site-base model calibration technique at the 45nm technology node and beyond. It also demonstrates the improvement in model accuracy for critical gate regions over the traditional modeling technique, and it shows the best know methods to achieve the utmost accuracy. Lastly, this paper shows how SEM-based modeling quantifies modeling error in these complex 2D regions.
Factors related to the presentation of patients with thick primary melanomas (1991)

The greatest problem of detecting melanoma at an early (surgically curable) stage appears to be in patients over the age of 50 who have nodular melanoma, particularly in the head and neck.
Abstract 4259: The radiogenomic landscape of cancer (2014)

Abstract Radiotherapy is the mainstay of treatment for many solid malignancies. Despite this, there have not been extensive systematic analyses of the correlation between therapeutic sensitivity and genomic parameters. To accelerate discovery of patient-matched radiotherapy, or precision radiotherapeutics, systematic approaches are needed to identify specific genetic features that confer radiotherapeutic resistance and target these features with small-molecule drugs. We have quantitatively measured the sensitivity of 533 genomically characterized cancer cell lines to radiation, uncovering novel and established genetic, lineage, chromosomal copy number, and gene-expression-based dependencies. We show that small molecules that target genetic alterations driving therapeutic resistance effect genotype selective radiosensitization, establishing a preclinical basis for personalized therapeutic regimens. This dataset is an important resource that can be used to develop novel therapeutic hypotheses and to accelerate discovery of drugs given concurrently with radiation matched to patients by their cancer genotype, thereby enhancing efficacy and limiting toxicity in the context of a new approach of precision radiotherapy. Citation Format: Mohamed Abazeed, Drew Adams, Pablo Tamayo, Matthew Meyerson, Peter Hammerman, Stuart Schreiber. The radiogenomic landscape of cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4259. doi:10.1158/1538-7445.AM2014-4259
Seeing and feeling in robot-assisted surgery (Conference Presentation) (2023)

Haptic devices allow touch-based information transfer between humans and their environment. In minimally invasive surgery, a human teleoperator benefits from both visual and haptic feedback regarding the interaction forces between instruments and tissues. In this talk, I will discuss mechanisms for stable and effective haptic feedback, as well as how surgeons and autonomous systems can use visual feedback in lieu of haptic feedback. For haptic feedback, we focus on skin deformation feedback, which provides compelling information about instrument-tissue interactions with smaller actuators and larger stability margins compared to traditional kinesthetic feedback. For visual feedback, we evaluate the effect of training on human teleoperators’ ability to visually estimate forces through a telesurgical robot. In addition, we design and characterize multimodal deep learning-based methods to estimate interaction forces during tissue manipulation for both automated performance evaluation and delivery of haptics-based training stimuli. Finally, we describe the next generation of soft, flexible surgical instruments and the opportunities and challenges they present for seeing and feeling in robot-assisted surgery.
Self-Attention Capsule Networks for Image Classification. (2019)

We propose a novel architecture for object classification, called Self-Attention Capsule Networks (SACN). SACN is the first model that incorporates the Self-Attention mechanism as an integral layer within the Capsule Network (CapsNet). While the Self-Attention mechanism supplies a long-range dependencies, results in selecting the more dominant image regions to focus on, the CapsNet analyzes the relevant features and their spatial correlations inside these regions only. The features are extracted in the convolutional layer. Then, the Self-Attention layer learns to suppress irrelevant regions based on features analysis and highlights salient features useful for a specific task. The attention map is then fed into the CapsNet primary layer that is followed by a classification layer. The proposed SACN model was designed to solve two main limitations of the baseline CapsNet - analysis of complex data and significant computational load. In this work, we use a shallow CapsNet architecture and compensates for the absence of a deeper network by using the Self-Attention module to significantly improve the results. The proposed Self-Attention CapsNet architecture was extensively evaluated on six different datasets, mainly on three different medical sets, in addition to the natural MNIST, SVHN and CIFAR10. The model was able to classify images and their patches with diverse and complex backgrounds better than the baseline CapsNet. As a result, the proposed Self-Attention CapsNet significantly improved classification performance within and across different datasets and outperformed the baseline CapsNet, ResNet-18 and DenseNet-40 not only in classification accuracy but also in robustness.
In-Situ Measurements of Cirrus Clouds on a Global Scale (2020)

Observations of high-altitude cirrus clouds are reported from measurements made during routine monitoring of cloud properties on commercial aircraft as part of In-Service Aircraft for a Global Observing System. The global scale of the measurements is revealed, with 7 years of in-situ data producing a unique and rapidly growing dataset. We find cloud fractions measured >=10km at aircraft cruise altitude are representative of seasonal trends associated with the mid latitude jet stream in the northern hemisphere, and the relatively higher cloud fractions found in tropical regions such as the Inter-Tropical Convergence Zone and South East Asia. The characteristics of these clouds are discussed and the potential different formation mechanisms in different regions assessed.
THE ROLE OF FIBROBLASTS IN DERMAL VASCULARIZATION AND REMODELING OF RECONSTRUCTED HUMAN SKIN AFTER TRANSPLANTATION ONTO THE NUDE MOUSE (1992)

The vascularization and the dermal remodeling of two different types of human skin reconstructed "in vitro" and grafted onto the nude mouse were studied. They were composed of human keratinocytes grown either on a human acellular deepidermized dermis (DED), or on a lattice composed of human fibroblasts embedded in bovine type I collagen, a living dermal equivalent (LDE). At different stages after grafting, the transplants were harvested and processed for an immunohistological study with species-specific and non-species-specific antibodies. At one month after grafting, the two types of grafted dermis contained blood vessels whose vascular basement membranes were labeled with a mouse-specific anti-type IV collagen antibody. With an antibody specific for human type IV collagen, a constant labeling of the vascular basement membrane was only observed in the LDE containing fibroblasts. In the DED, a constant association of the mouse endothelial cells with human type IV collagen was observed at early stages after grafting. At later stages, the human type IV collagen progressively disappeared. On the other hand, the dermal-epidermal junction underneath the human epidermis contained human type IV collagen in the two types of reconstructed skin. Labeling with the species-specific antibodies directed against human or murine type I collagen showed that the ratio murine type I collagen versus human type I collagen increased with time, suggesting that the DED is progressively invaded by mouse fibroblasts that produce the mouse collagen. On the other hand, in the LDE, the preexisting bovine type I collagen became progressively undetectable while both human type I collagen and elastic fibers were deposited by numerous human fibroblasts. Mouse type I collagen was not detected. Altogether, these observations made by grafting human skin reconstructed "in vitro" onto the nude mouse should be interesting for evaluating the usefulness of grafting a dermal substrate together with the epidermal sheet in the treatment of burns.
IL-15 mediated expansion of rare durable memory T cells following adoptive cellular therapy (2021)

ETC targeting NY-ESO-1 with single-agent cyclophosphamide alone conditioning was well tolerated in patients with SS and those with MRCL. IL-15 can induce proliferation and activity in persisting NY-ESO-1-specific T cells even in patients with disease progression following ACT. These results support future work evaluating whether IL-15 could be incorporated into ACT trials post-infusion or at the time of progression.
SAAST Robotics: An Intensive Three Week Robotics Program for High School Students (2007)

We have designed an intensive, three-week robotics program for high school students that combines theory with hands-on practical experience in cutting edge technologies. Conventional approaches to engineering education are bottom-up. Students are first taught the basics and are then courses that build on the basics. Most students do not take coursework on engineering applications, particularly design and systems engineering, until the end of the curriculum. This has the disadvantage of not exposing students to the excitement in engineering until late in the curriculum. Our goal is to develop a top-down curriculum in which students are introduced first to the applications and systems concepts which then leads to the teaching of fundamentals. This approach has the potential to recruit and retain students in engineering while making the curriculum more relevant and rigorous.
Changes in Color Vision and Contrast Sensitivity After Descemet Membrane Endothelial Keratoplasty for Fuchs Endothelial Dystrophy (2014)

In FED, DMEK may not only be effective for obtaining a higher visual acuity but particularly improving the contrast sensitivity may also lead to better subjective optical performance. Although frequently mentioned spontaneously by patients, an objective change in color vision could not be substantiated. Hence, quantifying contrast sensitivity before surgery may aid in the decision for surgery, and in the evaluation of surgical outcome.