gebhart/patrepeval huggingface dataset:
Glycolytic Metabolic Remodeling by the Truncate of Glioma-Associated Oncogene Homolog 1 in Triple-Negative Breast Cancer Cells (2022)

Hedgehog (Hh) signaling pathway plays an essential role in embryonic development, tissue regeneration, and stem cell renewal. In particular, terminal effectors of the Hh signaling pathway are associated with the regulation of glioma-associated oncogene homolog 1 (GLI1) transcription factors. Overexpression of GLI1 is closely associated with poor prognosis in breast cancer. The Hh-GLI1 signaling pathway is activated and participates in the tumorigenesis and progression of breast cancer, especially in the aggressive subtype of triple-negative breast cancer (TNBC). However, the role of GLI1 in regulating TNBC metabolism remains unclear. This study aimed to explore the functional role of GLI1 in glycolytic metabolism in TNBC. Immunohistochemical analysis of GLI1 expression in a tissue microarray revealed significant correlations between GLI1 expression and advanced tumor stage and grade. GLI1 expression levels were drastically increased in MDA-MB-231 cells compared to those in other cell lines. Inhibition of GLI1 expression using GLI1 small interfering RNA (siRNA) in MDA-MB-231 cells resulted in a significant reduction in cell proliferation and induced cell cycle arrest at the G1 phase. Furthermore, GLI1 downregulation significantly reduced the expression of glycolysis-regulated proteins. GLI1 knockdown resulted in reduced glycolytic rates and extracellular lactate levels. Moreover, metabolic stress after GLI1 knockdown activated the energy sensor, adenosine monophosphate-activated protein kinase, which subsequently resulted in autophagy induction. In conclusion, this study indicates that targeting GLI1 reprograms the tumor glucose metabolism to suppress breast cancer cell growth and proliferation.
Online Videos Provide Poor Information Quality, Reliability, and Accuracy Regarding Rehabilitation and Return to Sport After Anterior Cruciate Ligament Reconstruction (2020)

Current YouTube videos regarding rehabilitation and RTS after ACLR do not meet the necessary quality standards. Physicians should also be able to provide alternative sources of high-quality information.
EEG discrimination of perceptually similar tastes (2018)

Perceptually similar stimuli, despite not being consciously distinguishable, may result in distinct cortical brain activations. Hypothesizing that perceptually similar tastes are discriminable by electroencephalography (EEG), we recorded 22 human participants' response to equally intense sweet-tasting stimuli: caloric sucrose, low-caloric aspartame, and a low-caloric mixture of aspartame and acesulfame K. Time-resolved multivariate pattern analysis of the 128-channel EEG was used to discriminate the taste responses at single-trial level. Supplementing the EEG study, we also performed a behavioral study to assess the participants' perceptual ability to discriminate the taste stimuli by a triangle test of all three taste pair combinations. The three taste stimuli were found to be perceptually similar or identical in the behavioral study, yet discriminable from 0.08 to 0.18 s by EEG analysis. Comparing the participants' responses in the EEG and behavioral study, we found that brain responses to perceptually similar tastes are discriminable, and we also found evidence suggesting that perceptually identical tastes are discriminable by the brain. Moreover, discriminability of brain responses was related to individual participants' perceptual ability to discriminate the tastes. We did not observe a relation between brain response discriminability and calorie content of the taste stimuli. Thus, besides demonstrating discriminability of perceptually similar and identical tastes with EEG, we also provide the first proof of a functional relation between brain response and perception of taste stimuli at individual level.
Under the Umbrella of Clinical Pharmacology: Inflammatory Bowel Disease, Infliximab and Adalimumab, and a Bridge to an Era of Biosimilars (2022)

Monoclonal antibodies (MAbs) have revolutionized the treatment of many chronic inflammatory diseases, including inflammatory bowel disease (IBD). IBD is a term that comprises two quite similar, yet distinctive, disorders-Crohn's disease (CD) and ulcerative colitis (UC). Two blockbuster MAbs, infliximab (IFX) and adalimumab (ADL), transformed the pharmacological approach of treating CD and UC. However, due to the complex interplay of pharmacology and immunology, MAbs face challenges related to their immunogenicity, effectiveness, and safety. To ease the burden of IBD and other severe diseases, biosimilars have emerged as a cost-effective alternative to an originator product. According to the current knowledge, biosimilars of IFX and ADL in IBD patients are shown to be as safe and effective as their originators. The future of biosimilars, in general, is promising due to the potential of making the health care system more sustainable. However, their use is accompanied by misconceptions regarding their effectiveness and safety, as well as by controversy regarding their interchangeability. Hence, until a scientific consensus is achieved, scientific data on the long-term effectiveness and safety of biosimilars are needed.
Vasomotor Dysfunction Early after Exposure of Normal Rabbit Arteries to an Adenoviral Vector (1997)

We aimed to investigate whether infection of normal rabbit arteries with a recombinant adenovirus vector would result per se in alterations in contractile and endothelial functions. In one group of rabbits, right or left femoral and ear artery segments were injected in vivo with a replication-deficient adenoviral vector expressing a beta-galactosidase (beta-Gal) reporter gene (4 x 10(10) pfu/ml) to demonstrate efficient gene transfer. Contralateral arteries were injected with the same concentration of a recombinant adenoviral vector carrying no transgene (Ad.MLPnull). In another group of animals, Ad.MLPnull was injected into the lumen of femoral and ear artery segments. The contralateral arteries were used as controls with the injection of vehicle alone. Histochemical assessment of gene transfer using beta-Gal activity (group 1) or in vitro contractility and endothelial function (group 2) was performed 3 days after adenoviral infection. Gene transfer was efficient and reproducible in the endothelium and was associated with the presence of inflammatory cells in the media. In Ad.MLPnull-injected arteries, in vitro contractile response of femoral artery rings to either KCl 60 mM or phenylephrine (10 microM) was reduced to 10.5 +/- 2.3% (n = 14; p < 0.001) and 8.8 +/- 2.0% (n = 7; p < 0.001) of the control values, respectively. Furthermore, in arteries injected with Ad.MLPnull, the endothelium-dependent relaxation produced by acetylcholine (10 microM) was virtually abolished. Similarly, the relaxant effects of the alpha 2-adrenoreceptor agonist UK14304 (1 microM) or the Ca2+ ionophore A23187 (1 microM) were also abolished. By contrast, sodium nitroprusside (10 microM) was still able to relax adenovirus-infected arteries. We conclude that infection with a recombinant adenoviral vector can induce early severe vasomotor alterations in both contractile function and endothelium-mediated relaxation of normal rabbit arteries.
&lt;p&gt;Epithelial–mesenchymal transition is driven by transcriptional and post transcriptional modulations in COPD: implications for disease progression and new therapeutics&lt;/p&gt; (2019)

COPD is a common and highly destructive disease with huge impacts on people and health services throughout the world. It is mainly caused by cigarette smoking though environmental pollution is also significant. There are no current treatments that affect the overall course of COPD; current drugs focus on symptomatic relief and to some extent reducing exacerbation rates. There is an urgent need for in-depth studies of the fundamental pathogenic mechanisms that underpin COPD. This is vital, given the fact that nearly 40%-60% of the small airway and alveolar damage occurs in COPD well before the first measurable changes in lung function are detected. These individuals are also at a high risk of lung cancer. Current COPD research is mostly centered around late disease and/or innate immune activation within the airway lumen, but the actual damage to the airway wall has early onset. COPD is the end result of complex mechanisms, possibly triggered through initial epithelial activation. To change the disease trajectory, it is crucial to understand the mechanisms in the epithelium that are switched on early in smokers. One such mechanism we believe is the process of epithelial to mesenchymal transition. This article highlights the importance of this profound epithelial cell plasticity in COPD and also its regulation. We consider that understanding early changes in COPD will open new windows for therapy.
The Future of Illumination Design (2007)

Many modern problems in illumination design require the use of free-form optics -a concept that is relatively new in the history of optical science. More and more, optical designers and manufacturers are applying the concepts of non-imaging optics to avoid restrictions on surface geometry and create simpler designs with better performance.
PET imaging of PD-L1 using anti-PD-L1-B11 antibody in breast cancer tumor model (2021)

1486 Introduction: Immunotherapy targeting PD-1/PD-L1 immune checkpoint inhibition (ICI) has been found to be efficacious in numerous solid & hematologic malignancies. However, its response rate to therapy is only 15-35%. In order to optimize ICI therapies, a reliable assessment of PD-L1 expression is needed for selecting patients for ICI treatment & to assess potential alteration of PD-L1 expression during & post-therapy conferring resistance. Immunohistochemistry quantification of PD-L1 following biopsy is severely limited by random tissue sampling & inherent heterogeneity of PD-L1 expression within & among metastatic lesions. A non-invasive imaging based assessment of PD-L1 expression is critically needed. Although radiolabeled PET probes based on PD-L1 targeted therapeutic antibodies, like Atezolizumab have shown encouraging results, slow blood clearance (half-life = 27 days for therapeutic Atezolizumab) complicates the use of [89Zr]Zr-Atezolizumab as imaging probe. Therefore, alternate PD-L1 imaging probes based on antibodies with faster blood clearance could be advantageous.
 Methods: In this study, we radiolabeled antibody against PD-L1-clone B11 (anti-PD-L1-B11) with zirconium-89 (89Zr) and tested it as a PET probe to detect PD-L1 expressing breast cancer MDA-MB-231 subcutaneous tumor in NOD-SCID mice. Micro-PET imaging was performed at day 3 & at day 5 post-injection using a small animal PET/X-RAY system. The uptake of our novel PET probe [89Zr]Zr-anti-PD-L1-B11 was compared with the known [89Zr]Zr-Atezolizumab. The tumor: background (tumor: blood and tumor: muscle) SUV ratios were also calculated at both time points from PET scans using. Both the PET probes were also evaluated for an ex-vivo biodistribution performed at day 5 post-injection.
Results: We successfully radiolabeled anti-PD-L1-B11 with zirconium-89 (89Zr) to produce an immunoPET probe, [89Zr]Zr-anti-PD-L1-B11 with radiolabeling yield of ~89-96% (n=2) with a specific activity of 0.024-0.032MBq/μg. The biodistribution profiles of [89Zr]Zr-anti-PD-L1-B11 and [89Zr]Zr-Atezolizumab were found to be different, [89Zr]Zr-anti-PD-L1-B11 showed higher uptake in tumor, liver and spleen compared to [89Zr]Zr-Atezolizumab. In addition to, [89Zr]Zr-anti-PD-L1-B11 also showed 5 fold higher tumor:blood SUV and 2-fold higher tumor:muscle SUV ratio as compared to [89Zr]Zr-Atezolizumab at both the time points day 3 and day 5, post-injection (Figure 1).
Conclusion: In summary, our preliminary data demonstrates that [89Zr]Zr-anti-PD-L1-B11 is a superior PET probe and could potentially be useful as a better imaging probe for a non-invasive assessment of PD-L1 expression in tumors for the therapy management.
 Acknowledgements: This study was financially supported by Mayo Clinic’s Center for Clinical and Translational Science (CCaTS), Office of Translation to Practice (OTP), the Erivan K. and Helga Haub Family Fund and the Department of Radiology, Mayo Clinic, Rochester MN. The authors would also like to thank Dr. Jeff R. Anderson and Dr. Bharath Wootla for their support in project management.
3d spatial layout and geometric constraints for scene understanding (2011)

An image is nothing but a projection of the physical world around us, where objects do not occur randomly but follow certain spatial rules. Many existing computer vision approaches tend to ignore this aspect of understanding images. In this work, we build representations and propose strategies for exploiting such constraints towards extracting a 3D understanding of a scene from its single image. 
We model a scene in terms of its spatial layout abstracted as a box, object cuboids, camera viewpoint, and interactions between them. We take a supervised approach towards estimation, and learn models from training data that is fully annotated with the 3D spatial extent of objects, walls, and floor. We assume the world is populated with axis aligned objects and surfaces, and exploit constrained appearance models which use geometric cues from the scene. Our methods are tailored towards indoor scenes that are highly structured and require careful spatial reasoning. 
We show that our box layout representation is able to capture the full spatial extent of a 3D scene, which we can successfully estimate even for heavily cluttered rooms. Similarly, by exploiting the geometric constraints offered by the scene, we can approximate the extent of the objects as cuboids in 3D. The box layout provides rich contextual information for detecting objects. We show that modeling the 3D interactions between object cuboids and scene layout improves object detection. Finally, we show how to use our 3D spatial layout models together with object cuboid models to predict the free space in the scene.
Direct and indirect photoluminescence excitation and ultraviolet emission from Tm-doped AlxGa1−xN (2009)

We provide experimental evidence for direct and indirect excitations of photoluminescence (PL) from Tm-doped AlxGa1−xN of varying Al content. Direct excitation of Tm3+ ions is observed primarily at 85K through transitions H63→I61, P03, P13, and P23 when these levels are below the absorption edge of the AlxGa1−xN for a given Al content. Strong ultraviolet emission at 298nm (I61→H63), 355nm (I61→F43), and 371nm (D21→H63), as well as the familiar blue emission at 463nm (D21→F43), and 479nm (G41→H63), is found to depend sensitively on the Al content, excitation wavelength (i.e., direct or indirect), excitation type (continuous wave versus pulsed), and upper state of the transition. PL excitation spectroscopy and time-integrated and time-resolved PL spectra are compared to elucidate the complex energy transfer pathways.
Development of Monogenic and Digenic Rice Lines for Blast Resistance Genes <i>Pi‐ta</i>, <i>Pi‐k<sup>h</sup></i>/<i>Pi‐k<sup>s</sup></i> (2010)

The major blast resistance ( R ) genes Pi‐ta , Pi‐k s , Pi‐k h have been effectively deployed in rice ( Oryza sativa L.) in the southern USA for preventing disease caused by the predominant U.S. races of Magnaporthe oryzae Cav. [= Magnaporthe grisea (Herbert) Barr.]. In the present study, the codominant single nucleotide length polymorphism DNA marker for the Pi‐ta gene, and the simple sequence repeat markers, RM144 and RM224, that cosegregate with two alleles of the Pi‐k gene, Pi‐k s and Pi‐k h , were used for R identification in a F 10 recombinant inbred line population. This population (Reg. no. MP‐3, NSL 452303) was derived from the cross RU9101001/‘Katy’. This population composed of 235 individual lines was jointly released on 24 Apr. 2009 by the USDA–ARS and the University of Arkansas Division of Agriculture Arkansas Agriculture Experiment Station. R gene containing RIL lines were verified with standard pathogenicity assays by means of a set of differential races of M. oryzae in the USA. One hundred eighty‐two pure lines were identified from the population with the Pi‐ta, Pi‐k s , and Pi‐k h genes. A total of 56 had Pi‐ta and Pi‐k s , 51 lines had Pi‐k s , 27 had Pi‐k h , and 48 lines had Pi‐k h and Pi‐ta . These monogenic and digenic rice lines with the major blast R genes are expected to be useful for studying effects of each R gene singly and in combination for their epistatic interaction with yield and for introducing blast resistance with marker assisted selection.
A data version of the Gauss-Markov theorem and its application to adaptive subspace splitting (2002)

How does one adaptively split a measurement subspace into signal and orthogonal subspaces of reduced rank so that detectors, estimators, and quantizers may be adaptively designed from experimental data? The authors provide some answers to this question by decomposing experimental correlations into their Wishart distributed Schur complements and showing how these distributions may be used to identify subspaces.
Negative Photoconductive Effects in Uncooled InAs Nanowire Photodetectors (2021)

One-dimensional, direct, and narrow band gap indium arsenide (InAs) nanowires (NWs) have been emerging with great potentials for the next-generation wide-spectrum photodetectors. In this study, metal–semiconductor–metal (MSM) structure InAs NW-based photodetectors were fabricated by transferring MBE-grown NWs onto a sapphire substrate via a mechanical stamping method. These NW detectors exhibit strong negative photoconductive (NPC) effects, which are likely caused by the carrier dynamics in the “core-shell” structure of the NWs. Specifically, under the irradiation of a 405 nm violet laser, the maximum I dark / I light ratio reaches ∼10 2 and the NPC gain reaches 10 5 at a low bias voltage of 0.2 V. At room temperature, the rise and decay times of InAs NW devices are 0.005 and 2.645 s, respectively. These InAs NW devices with a high I dark / I light ratio and NPC gain can be potentially used in the field of vis/near-IR light communication in the future.
Robinson's landmark synthesis of tropinone (2013)

The 1917 total synthesis of tropinone by Sir Robert Robinson represents a landmark achievement in organic synthesis. Decades ahead of its time in terms of its retrosynthetic logic and biomimetic approach, the elegant combination of these two elements in this synthesis continues to serve as an inspiration for the development of new and efficient strategies for complex molecule synthesis.
Relational Learning with Gaussian Processes (2007)

Correlation between instances is often modelled via a kernel function using input attributes of the instances.Relational knowledge can further reveal additional pairwise correlations between variables of interest.In this paper, we develop a class of models which incorporates both reciprocal relational information and input attributes using Gaussian process techniques.This approach provides a novel non-parametric Bayesian framework with a data-dependent covariance function for supervised learning tasks.We also apply this framework to semi-supervised learning.Experimental results on several real world data sets verify the usefulness of this algorithm.
Generation of anatomically realistic numerical phantoms for optoacoustic breast imaging (2016)

Because optoacoustic tomography (OAT) can provide functional information based on hemoglobin contrast, it is a promising imaging modality for breast cancer diagnosis. Developing an effective OAT breast imaging system requires balancing multiple design constraints, which can be expensive and time-consuming. Therefore, computer- simulation studies are often conducted to facilitate this task. However, most existing computer-simulation studies of OAT breast imaging employ simple phantoms such as spheres or cylinders that over-simplify the complex anatomical structures in breasts, thus limiting the value of these studies in guiding real-world system design. In this work, we propose a method to generate realistic numerical breast phantoms for OAT research based on clinical magnetic resonance imaging (MRI) data. The phantoms include a skin layer that defines breast-air boundary, major vessel branches that affect light absorption in the breast, and fatty tissue and fibroglandular tissue whose acoustical heterogeneity perturbs acoustic wave propagation. By assigning realistic optical and acoustic parameters to different tissue types, we establish both optic and acoustic breast phantoms, which will be exported into standard data formats for cross-platform usage.
Syntesis, antifungal and antiviral activity of hydrophosphoryl derivatives of lucensomycin (2012)

A reaction of polyene macrolide antibiotic, lucensomycin, with aromatic aldehydes and hypophosphorous acid results in formation of its hydrophosphoryl derivatives. Physicochemical and biomedical properties of the synthesized lucensomycin derivatives were studied. Biological examination showed that hydrophosphoryl lucensomycin derivatives were less toxic medicines than original antibiotic and they are of higher antifungal and antiviral activity.
Towards a greener synthesis of (S)-3-aminobutanoic acid: process development and environmental assessment (2010)

An improved, greener process for the enantioselective chemoenzymatic synthesis of (S)-3-aminobutanoic acid has been developed. Reaction steps comprise an initial aza-Michael addition starting from cheap prochiral compounds, subsequent enzymatic resolution via aminolysis using commercially available Candida antarctica lipase B in a solvent-free one-pot process, hydrolysis of the resulting ester and removal of the N-benzyl moiety via hydrogenation. After isolation, the desired (S)-3-aminobutanoic acid was obtained in an overall yield of 28% and with an excellent enantiomeric excess of 99% ee. Notably, this reaction sequence does not require column chromatography with organic solvents and only one purification step of an intermediate is needed. The environmental impact of this optimized process has been evaluated and an E-factor of 41 has been calculated for the overall process. A comparative assessment with the previous process was done via mass balancing using the E-factor, the selectivity index S−1 as well as an SHE assessment.
Effects of morphology and geometry of inclusions on two-point correlation statistics in two phase composites (2014)

A spectral form of the two-point correlation functions for two-phase composites is presented and the effects of secondary phase morphology, geometry and volume fraction on the coefficients of the corresponding series are studied. Initially, a principal component analysis is performed on the coefficients of the series and then, the effects of different morphological and geometrical parameters of the second phase inclusions on two-point correlation functions are examined. A direct linkage between the principal components of the coefficients with the morphological features (inclusion shape, aspect ratio and size) is established and the influence of preferred orientation of the anisotropic inclusions is also investigated. Finally a composite hull is constructed using the principal components of the coefficients in a three-dimensional space, which helps in determining the interrelation of properties and microstructures of any composite containing these types of inclusions.