gebhart/patrepeval huggingface dataset:
Engineered Adipose Tissue from Human Mesenchymal Stem Cells Maintains Predefined Shape and Dimension: Implications in Soft Tissue Augmentation and Reconstruction (2005)

Soft tissue augmentation is a widespread practice in plastic and reconstructive surgery. The objective of the present study was to engineer adipose tissue constructs with predefined shape and dimensions, potentially utilizable in soft tissue augmentation and reconstruction, by encapsulating adult stem cell-derived adipogenic cells in a biocompatible hydrogel system. Bone marrow-derived adult human mesenchymal stem cells (hMSCs) were preconditioned by 1 week of exposure to adipogenic- inducing supplement followed by photoencapsulation in poly(ethylene glycol) diacrylate (PEGDA) hydrogel in predefined shape and dimensions. In two parallel experiments, the resulting hMSC-derived adipogenic cell-polymer constructs were either incubated in vitro in adipogenic medium or implanted in vivo in the dorsum of immunodeficient mice for 4 weeks. Tissue-engineered adipogenic constructs demonstrated positive reaction to oil red O staining both in vitro and in vivo, and expressed PPAR-gamma2 adipogenic gene marker in vivo. By contrast, control PEGDA hydrogel constructs encapsulating undifferentiated hMSCs failed to demonstrate the adipogenic gene marker and were negative for oil red O staining. Recovered in vitro and in vivo constructs maintained their predefined physical shape and dimensions. These data demonstrate that adipose tissue engineered from human mesenchymal stem cells can retain predefined shape and dimensions for soft tissue augmentation and reconstruction.
Adaptive time reversal beamforming in dense multipath communication networks (2008)

In this paper, we study the transmit time reversal beamforming in rich scattering environments in a multi-user wideband communication network. We consider the downlink time reversal transmission where a base station communicates with many users. The base station has multiple antennas and the user has a single antenna. Due to the presence of scatterers, conventional transmit beamforming suffers from crosstalk caused by nearby users. We design a wideband beamformer that focuses on the intended user while minimizing its interference to other users subject to the constraint of the sum rate capacity. We also show that the proposed beamformer is equivalent to time reversal focusing and nulling and yields higher sum data rate than the conventional delay line wideband beamformer. We verify our results using realistic scattering channels simulated by finite-difference time-domain modeling of the scattering environment.
Intratumoral lymphangiogenesis and lymph node metastasis in head and neck cancer. (2002)

How tumors access and spread via the lymphatics is not understood. Although it is clear that dissemination via the blood system involves hemangiogenesis, it is uncertain whether tumors also induce lymphangiogenesis or simply invade existing peritumoral vessels. To address the issue we quantitated tumor lymph vessels in archival specimens of head and neck cancer by immunostaining for the recently described lymphatic endothelial marker LYVE-1, the vascular endothelial marker CD34, and the pKi67 proliferation marker, correlating lymph vessel density and proliferation index with clinical and pathological variables. Discrete "hotspots" of intratumoral small proliferating lymphatics were observed in all carcinomas, and a high intratumoral lymph vessel density was associated with neck node metastases (n = 23; P = 0.027) and an infiltrating margin of tumor invasion (P = 0.046) in the oropharyngeal subgroup. Quantitation of the lymphangiogenic growth factor vascular endothelial growth factor C by real-time PCR and immunohistochemistry revealed higher levels of mRNA in tumor tissue than in normal samples (n = 8; P = 0.017), but no obvious correlation with intratumoral lymphatics. Our results provide new evidence that proliferating lymphatics can occur in human cancers and may in some cases contribute to lymph node metastasis.
3D attention-driven depth acquisition for object identification (2016)

We address the problem of autonomously exploring unknown objects in a scene by consecutive depth acquisitions. The goal is to reconstruct the scene while online identifying the objects from among a large collection of 3D shapes. Fine-grained shape identification demands a meticulous series of observations attending to varying views and parts of the object of interest. Inspired by the recent success of attention-based models for 2D recognition, we develop a 3D Attention Model that selects the best views to scan from, as well as the most informative regions in each view to focus on, to achieve efficient object recognition. The region-level attention leads to focus-driven features which are quite robust against object occlusion. The attention model, trained with the 3D shape collection, encodes the temporal dependencies among consecutive views with deep recurrent networks. This facilitates order-aware view planning accounting for robot movement cost. In achieving instance identification, the shape collection is organized into a hierarchy, associated with pre-trained hierarchical classifiers. The effectiveness of our method is demonstrated on an autonomous robot (PR) that explores a scene and identifies the objects to construct a 3D scene model.
Atypical haemolytic uraemic syndrome (2006)

The haemolytic uraemic syndrome (HUS) is characterized by the triad of thrombocytopenia, microangiopathic haemolytic anaemia and acute renal failure. HUS may be classified as either diarrhoeal-associated or non-diarrhoeal/atypical (aHUS). aHUS has recently been shown to be a disease of complement dysregulation, with 50% of cases involving the complement regulatory genes, factor H (CFH), membrane cofactor protein (MCP; CD46), and factor I (IF). However, incomplete penetrance of mutations in each of these genes is reported. This suggests that a precipitating event or trigger is required to unmask the complement regulatory deficiency. The reported precipitating events predominantly cause endothelial injury. Discovery of these mutations has revealed important genotype-phenotype correlations. MCP-HUS has a better prognosis and a better outcome after transplantation than either CFH-HUS or IF-HUS.
Sitagliptin Treatment After Total Pancreatectomy With Islet Autotransplantation: A Randomized, Placebo-Controlled Study (2016)

Insulin independence after total pancreatectomy and islet autotransplant (TPIAT) for chronic pancreatitis is limited by a high rate of postprocedure beta cell apoptosis. Endogenous glucagon-like peptide-1 and glucose-dependent insulinotropic peptide, which are increased by dipeptidyl peptidase 4 inhibitor therapy (sitagliptin) may protect against beta cell apoptosis. To determine the effect of sitagliptin after TPIAT, 83 adult TPIAT recipients were randomized to receive sitagliptin (n = 54) or placebo (n = 29) for 12 months after TPIAT. At 12 and 18 months after TPIAT, participants were assessed for insulin independence; metabolic testing was performed with mixed meal tolerance testing and frequent sample intravenous glucose tolerance testing. Insulin independence did not differ between the sitagliptin and placebo groups at 12 months (42% vs. 45%, p = 0.82) or 18 months (36% vs. 44%, p = 0.48). At 12 months, insulin dose was 9.0 (standard error 1.7) units/day and 7.9 (2.2) units/day in the sitagliptin and placebo groups, respectively (p = 0.67) and at 18 months 10.3 (1.9) and 7.1 (2.6) units/day, respectively (p = 0.32). Hemoglobin A<sub>1c</sub> levels and insulin secretory measures were similar in the two groups, as were adverse events. In conclusion, sitagliptin could be safely administered but did not improve metabolic outcomes after TPIAT.
Effect of Heat Treatment on Electrical Properties of Amorphous Oxide Semiconductor In–Ga–Zn–O Film as a Function of Oxygen Flow Rate (2009)

The effect of heat treatment on the electrical properties of an amorphous In–Ga–Zn–O (a-IGZO) film deposited by radio frequency (rf) magnetron sputtering at room temperature (RT) was investigated as a function of the oxygen flow rate. All of the films deposited with increasing O2 concentration in the Ar and Ar + O2 atmospheres exhibited insulating behavior in terms of their electrical properties, but their carrier concentration and resistivity were markedly affected after annealing at 400 °C in either a vacuum furnace or an rapid thermal annealing (RTA) system. However, the carrier concentration and resistivity of the films annealed in a normal furnace were not changed, compared with those of the as-deposited films annealed in the vacuum furnace. The difference in the electrical properties as a function of the annealing conditions was attributed to the number of oxygen vacancies. From X-ray photoemission spectroscopy (XPS), we confirmed that the formation of an O-rich surface was reduced by heat treatment under vacuum conditions. The output and transfer characteristics of the thin-film transistors (TFTs) exhibited excellent performance as depletion-mode n-channel field-effect TFTs after being annealed irrespective of the annealing system.
Loss-Sensitive Generative Adversarial Networks on Lipschitz Densities (2017)

In this paper, we present the Lipschitz regularization theory and algorithms for a novel Loss-Sensitive Generative Adversarial Network (LS-GAN). Specifically, it trains a loss function to distinguish between real and fake samples by designated margins, while learning a generator alternately to produce realistic samples by minimizing their losses. The LS-GAN further regularizes its loss function with a Lipschitz regularity condition on the density of real data, yielding a regularized model that can better generalize to produce new data from a reasonable number of training examples than the classic GAN. We will further present a Generalized LS-GAN (GLS-GAN) and show it contains a large family of regularized GAN models, including both LS-GAN and Wasserstein GAN, as its special cases. Compared with the other GAN models, we will conduct experiments to show both LS-GAN and GLS-GAN exhibit competitive ability in generating new images in terms of the Minimum Reconstruction Error (MRE) assessed on a separate test set. We further extend the LS-GAN to a conditional form for supervised and semi-supervised learning problems, and demonstrate its outstanding performance on image classification tasks.
Naturally-occurring cholesterol analogues in lipid nanoparticles induce polymorphic shape and enhance intracellular delivery of mRNA (2020)

Endosomal sequestration of lipid-based nanoparticles (LNPs) remains a formidable barrier to delivery. Herein, structure-activity analysis of cholesterol analogues reveals that incorporation of C-24 alkyl phytosterols into LNPs (eLNPs) enhances gene transfection and the length of alkyl tail, flexibility of sterol ring and polarity due to -OH group is required to maintain high transfection. Cryo-TEM displays a polyhedral shape for eLNPs compared to spherical LNPs, while x-ray scattering shows little disparity in internal structure. eLNPs exhibit higher cellular uptake and retention, potentially leading to a steady release from the endosomes over time. 3D single-particle tracking shows enhanced intracellular diffusivity of eLNPs relative to LNPs, suggesting eLNP traffic to productive pathways for escape. Our findings show the importance of cholesterol in subcellular transport of LNPs carrying mRNA and emphasize the need for greater insights into surface composition and structural properties of nanoparticles, and their subcellular interactions which enable designs to improve endosomal escape.
Original 2-(3-Alkoxy-1H-pyrazol-1-yl)azines Inhibitors of Human Dihydroorotate Dehydrogenase (DHODH) (2015)

Following our discovery of human dihydroorotate dehydrogenase (DHODH) inhibition by 2-(3-alkoxy-1H-pyrazol-1-yl)pyrimidine derivatives as well as 2-(4-benzyl-3-ethoxy-5-methyl-1H-pyrazol-1-yl)-5-methylpyridine, we describe here the syntheses and evaluation of an array of azine-bearing analogues. As in our previous report, the structure-activity study of this series of human DHODH inhibitors was based on a phenotypic assay measuring measles virus replication. Among other inhibitors, this round of syntheses and biological evaluation iteration led to the highly active 5-cyclopropyl-2-(4-(2,6-difluorophenoxy)-3-isopropoxy-5-methyl-1H-pyrazol-1-yl)-3-fluoropyridine. Inhibition of DHODH by this compound was confirmed in an array of in vitro assays, including enzymatic tests and cell-based assays for viral replication and cellular growth. This molecule was found to be more active than the known inhibitors of DHODH, brequinar and teriflunomide, thus opening perspectives for its use as a tool or for the design of an original series of immunosuppressive agent. Moreover, because other series of inhibitors of human DHODH have been found to also affect Plasmodium falciparum DHODH, all the compounds were assayed for their effect on P. falciparum growth. However, the modest in vitro inhibition solely observed for two compounds did not correlate with their inhibition of P. falciparum DHODH.
A Contactless Method for High-Sensitivity Measurement of p-n Junction Leakage (1980)

A contactless p-n junction leakage measurement method is described that uses low-noise vhf oscillator circuitry to examine the dynamic memory-like behavior of the junctions. This method utilizes the eddy current loading effect, via inductive coupling, in order to determine the leakage-dependent decay time of the photoinduced voltage across the diffused p-n junctions. The contactless measurement is made under low forward bias conditions (≤10 mV) such that this measurement is a function of only generation-recombination processes in the junction depletion region. In the low-noise circuitry, sensitivity is enhanced when the oscillatory amplitude is made directly proportional to the figure of merit Q of the coupled oscillator resonant LC tank. This simple oscillator circuit contains only one JFET and a small number of inductors and capacitors, and is supplied by a constant-current source. Junction decay times between 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−4</sup> and 1 s, corresponding to junction leakages between 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−6</sup> and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−10</sup> A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , respectively, have been measured and are in excellent agreement with the derived theory showing the contactless decay time to be inversely proportional to the conventional contacting reverse leakage.
Hypodermin A, a new inhibitor of human complement for the prevention of xenogeneic hyperacute rejection (2003)

These data suggest that transgenic HA could be used to prevent hyperacute xenogeneic rejection.
Simultaneous amplification and compression of continous-wave mode-locked Nd:YAG laser pulses (1986)

Pulses from a cw mode-locked Nd:YAG laser, spectrally broadened and chirped by self-phase modulation in a single-mode optical fiber, have been compressed in a multiple-stage amplifier system to a pulse width of 12 psec without a grating-pair delay line. Single pulses are amplified in pulsed Nd:YAG stages to energies greater than 10 mJ and are synchronous with the cw mode-locked laser source. We find the amplified pulses to be stable, free of satellite pulses, and close to the transform limit.
Reimplementing the Cedar file system using logging and group commit (1987)

The workstation file system for the Cedar programming environment was modified to improve its robustness and performance. Previously, the file system used hardware-provided labels on disk blocks to increase robustness against hardware and software errors. The new system does not require hardware disk labels, yet is more robust than the old system. Recovery is rapid after a crash. The performance of operations on file system metadata, e.g., file creation or open, is greatly improved. The new file system has two features that make it atypical. The system uses a log, as do most database systems, to recover metadata about the file system. To gain performance, it uses group commit, a concept derived from high performance database systems. The design of the system used a simple, yet detailed and accurate, analytical model to choose between several design alternatives in order to provide good disk performance.
Hydrolysis of Cellulose: Mechanisms of Enzymatic and Acid Catalysis (1979)

Destruction of fiber and achievement of large surface areas are goals in the preparation of cellulose for hydrolysis to fermentable sugars. Pretreatments and cellulosic raw materials that are appropriate differ from those employed in fiber-conserving pulping systems. Alternative pretreatments to disrupt the lignin-hemicellulose-cellulose complex, remove extractives, and generate large surface areas are discussed. The Purdue processes yield amorphous cellulose by treatment of the raw material with Cadoxen, ferric tartrate, or sulfuric acid as solvents. The Iotech process employs explosive depressurization to remove lignin and to increase surface area while maintaining cellulose crystallinity. Plants with low lignin and extractives content and cell morphology that facilitates downstream processing are preferred in systems designed to optimize the production of fermentable sugars.
Exploratory 3D geovisual analytics (2008)

In this paper, we extend our generic ldquoGeoAnalyticsrdquo visualization (GAV) component toolkit, based on the principles behind Visual Analytics (VA), to also support time-oriented, geographically referenced and multivariate attribute volumetric data. GAV includes components that support a mixture of technologies from the three data visualization fields: information visualization (InfoVis), geovisualization (GeoVis) and scientific visualization (SciVis). Our research concentrates on visual user interface (VUI) techniques through dynamic and direct data manipulation that permit the visual analytical process to become more interactive and focused. This paper encourages synergies between well-known information- and volume data visualization methods applied in a multiple-linked and coordinated views interface. We address challenges for improved data interaction techniques with volumetric data and the need for immediate response. Varieties of explorative data analysis (EDA) tasks and the possibility to view the information simultaneously from different perspectives and scenarios are discussed. The effectiveness of our geovisual analytics framework is demonstrated in a tailor-made volume data explorer (VDE) application that integrates InfoVis, GeoVis and SciVis visualization methods assembled from GAV components. VDE facilitates dynamic exploration and correlation of temporal ocean space temperature and salinity data supplied in a NetCDF format from NOAA. This real-world phenomenon that corresponds to a huge volumetric data set comprises more than 31 million values for a time period of 12 months in 1994.
Clinical Myocardial Perfusion PET/CT (2007)

The field of nuclear cardiology is witnessing growing interest in the use of cardiac PET for the evaluation of patients with coronary artery disease (CAD). The available evidence suggests that myocardial perfusion PET provides an accurate means for diagnosing obstructive CAD, which appears superior to SPECT especially in the obese and in those undergoing pharmacologic stress. The ability to record changes in left ventricular function from rest to peak stress and to quantify myocardial perfusion (in mL/min/g of tissue) provides an added advantage over SPECT for evaluating multivessel CAD. There is growing and consistent evidence that gated myocardial perfusion PET also provides clinically useful risk stratification. Although the introduction of hybrid PET/CT technology offers the exciting possibility of assessing the extent of anatomic CAD (CT coronary angiography) and its functional consequences (ischemic burden) in the same setting, there are technical challenges in the implementation of CT-based transmission imaging for attenuation correction. Nonetheless, this integrated platform for assessing anatomy and biology offers a great potential for translating advances in molecularly targeted imaging into humans.
A fast and accurate face detector for indexation of face images (2002)

Detecting faces in images with complex backgrounds is a difficult task. Our approach, which obtains state-of-the-art results, is based on a generative neural network model: the constrained generative model (CGM). To detect side-view faces and to decrease the number of false alarms, a conditional mixture of networks is used. To decrease the computational time cost, a fast search algorithm is proposed. The level of performance reached, in terms of detection accuracy and processing time, allows us to apply this detector to a real-world application: the indexation of face images on the WWW.
Expression of co-stimulator 4-1BB molecule in hepatocellular carcinoma and adjacent non-tumor liver tissue, and its possible role in tumor immunity (2004)

Although HCC may escape from immune attack by weak immunogenicity or downregulated expression of MHC-1 molecules on the tumor cell surface, tumor infiltrating T cells can be activated via other costimulatory signal pathways to exert a limited antitumor effect on local microenvironment. The present study also implicates that modulating 4-1BB/4-1BBL costimulatory pathway may be an effective immunotherapy strategy to augment the host response.
Molecular basis of rotavirus virulence: role of gene segment 4 (1986)

Bovine rotavirus NCDV and simian rotavirus SA-11 exhibited markedly different patterns of gastrointestinal tract disease when inoculated orally into newborn mice. A genetic approach was used to define the molecular basis of these differences. The SA-11 strain of rotavirus was more virulent than the NCDV strain when inoculated orally into newborn mice; the dose of SA-11 required to cause diarrhea in 50% of infant mice was 50-fold less than that required for NCDV. Nineteen reassortant viruses were derived by coinfection of MA-104 cells in vitro with the SA-11 and NCDV strains. The parental origin of reassortant virus double-stranded RNA segments was determined by gene segment migration differences in polyacrylamide gels and hybridization with radioactively labeled parental viral transcripts. The neutralization antigen phenotype of reassortant viruses was determined by plaque reduction neutralization. We found that the dose of SA-11 and NCDV rotavirus required to induce gastroenteritis in newborn mice was determined by gene segment 4. The results suggest that rotavirus virulence may be manipulated by modification or reassortment of gene segment 4.
Parallelized Deep Neural Networks for Distributed Intelligent Systems (2013)

Master of Science thesis (2013) on parallelized deep neural networks at the University of Colorado Boulder.
Anthracycline-derived chemotherapeutics in apoptosis and free radical cytotoxicity (Review). (1998)

Anthracycline-derivatives are frequently used chemotherapeutics in treatment of numerous human malignancies. Anthracyclines are known for their complex cytotoxic mechanism involving i) inhibition of enzymes such as topoisomerase II, RNA polymerase, cytochrome c oxidase and others; ii) intercalation into DNA; iii) chelation of iron and generation of reactive oxygen species (ROS); iv) induction of apoptosis. Here, mechanistic aspects for successful cytostasis and for side effects, e.g. cardiomyopathy, are discussed. We emphasize recent developments in anthracycline-mediated apoptosis and focus on a well known representative, doxorubicin (adriamycin, adriblastin). We reflect on the role of oxidative stress and interactions with intracellular signaling pathways.