gebhart/patrepeval huggingface dataset:
Tissue Engineering Using Transfected Growth-Factor Genes (2005)

A method of growing bioengineered tissues includes, as a major component, the use of mammalian cells that have been transfected with genes for secretion of regulator and growth-factor substances. In a typical application, one either seeds the cells onto an artificial matrix made of a synthetic or natural biocompatible material, or else one cultures the cells until they secrete a desired amount of an extracellular matrix. If such a bioengineered tissue construct is to be used for surgical replacement of injured tissue, then the cells should preferably be the patient s own cells or, if not, at least cells matched to the patient s cells according to a human-leucocyteantigen (HLA) test. The bioengineered tissue construct is typically implanted in the patient's injured natural tissue, wherein the growth-factor genes enhance metabolic functions that promote the in vitro development of functional tissue constructs and their integration with native tissues. If the matrix is biodegradable, then one of the results of metabolism could be absorption of the matrix and replacement of the matrix with tissue formed at least partly by the transfected cells. The method was developed for articular chondrocytes but can (at least in principle) be extended to a variety of cell types and biocompatible matrix materials, including ones that have been exploited in prior tissue-engineering methods. Examples of cell types include chondrocytes, hepatocytes, islet cells, nerve cells, muscle cells, other organ cells, bone- and cartilage-forming cells, epithelial and endothelial cells, connective- tissue stem cells, mesodermal stem cells, and cells of the liver and the pancreas. Cells can be obtained from cell-line cultures, biopsies, and tissue banks. Genes, molecules, or nucleic acids that secrete factors that influence the growth of cells, the production of extracellular matrix material, and other cell functions can be inserted in cells by any of a variety of standard transfection techniques.
Genes Associated with Prostate Cancer Are Differentially Expressed in African American and European American Men (2013)

The results support the notion that therapeutic benefits will be realized when targeted treatments are designed to acknowledge and address a greater spectrum of PCa subtypes and molecular distinctions.
Polarization-Induced pn Diodes in Wide-Band-Gap Nanowires with Ultraviolet Electroluminescence (2012)

Almost all electronic devices utilize a pn junction formed by random doping of donor and acceptor impurity atoms. We developed a fundamentally new type of pn junction not formed by impurity-doping, but rather by grading the composition of a semiconductor nanowire resulting in alternating p and n conducting regions due to polarization charge. By linearly grading AlGaN nanowires from 0% to 100% and back to 0% Al, we show the formation of a polarization-induced pn junction even in the absence of any impurity doping. Since electrons and holes are injected from AlN barriers into quantum disk active regions, graded nanowires allow deep ultraviolet LEDs across the AlGaN band-gap range with electroluminescence observed from 3.4 to 5 eV. Polarization-induced p-type conductivity in nanowires is shown to be possible even without supplemental acceptor doping, demonstrating the advantage of polarization engineering in nanowires compared with planar films and providing a strategy for improving conductivity in wide-band-gap semiconductors. As polarization charge is uniform within each unit cell, polarization-induced conductivity without impurity doping provides a solution to the problem of conductivity uniformity in nanowires and nanoelectronics and opens a new field of polarization engineering in nanostructures that may be applied to other polar semiconductors.
Catching a Viral Video (2010)

The sharing and re-sharing of videos on social sites, blogs e-mail, and other means has given rise to the phenomenon of viral videos - videos that become popular through internet sharing. In this paper we seek to better understand viral videos on You Tube by analyzing sharing and its relationship to video popularity using 1.5 million You Tube videos. The social ness of a video is quantified by classifying the referrer sources for video views as social (e.g. an emailed link) or non-social (e.g. a link from related videos). By segmenting videos according to their fraction of social views, we find that highly social videos behave differently than less social videos. For example, the highly social videos rise to, and fall from, their peak popularity more quickly than less social videos. We also find that not all highly social videos become popular, and not all popular videos are highly social. And, despite their ability to generate large volumes of views over a short period of time, only 21% of the most popular videos (in terms of 30-day views) can be classified as viral. The observations made here lay the ground work for future work related to the creation of classification and predictive models for online videos.
A frequency-weighted post-filtering transform for compensation of the over-smoothing effect in HMM-based speech synthesis (2014)

Over-smoothing is one of the major sources of quality degradation in statistical parametric speech synthesis. Many methods have been proposed to compensate over-smoothing with the speech parameter generation algorithm considering Global Variance (GV) being one of the most successfull. This paper models over-smoothing as a radial relocation of poles and zeros of the spectral envelope towards the origin of the z-plane and uses radial scaling to enhance spectral peaks and to deepen spectral valeys. The radial scaling technique is improved by introducing over-emphasis, spectral-tilt compensation and frequency weighting. Listening test results indicate that the proposed method is 11%-13% more preferable than GV while it has less algorithmic delay (only 5 ms) and computational complexity.
Subwavelength resolution imaging by ultra-thin meta-lens (2016)

We demonstrate high numerical aperture (NA=0.8) transmissive metasurface-based lenses with efficiencies as high as 86% in the visible spectrum. Meta-lenses allow diffraction-limited focusing at red (λ=660 nm), green (λ=532 nm), and blue (λ=405 nm) wavelengths. They can resolve nanoscale features with sub-wavelength gaps.
Desalination with a cascade of cross‐flow hollow fiber membrane distillation devices integrated with a heat exchanger (2010)

Abstract Cost‐efficient desalination technology was developed successfully by integrating a countercurrent cascade of the novel cross‐flow direct contact membrane distillation (DCMD) devices and solid polymeric hollow fiber‐based heat exchange devices. Simulations have been carried out for the whole DCMD cascade to project values of gained output ratio (GOR) as a function of the number of DCMD stages as well as other important factors in the cascade vis‐à‐vis the temperatures and flow rates of the incoming hot brine and cold distillate streams. The simulation results were verified with experimental results from cascades consisting of two to eight stages. The numerical simulator predicts a GOR of 12 when unequal flow rates of the incoming brine and distillate streams are used. An artificial sea water was concentrated eight times successfully when a countercurrent cascade composed of four stages of the DCMD modules and a heat exchanger was used during the DCMD process. © 2010 American Institute of Chemical Engineers AIChE J, 2011
Computer-aided septal defect diagnosis and detection (2007)

To facilitate the clinical diagnosis, surgical planning and after operation follow-up, a computer aided septal defect diagnosis and detection framework is proposed. The framework is consisted of four steps: image registration, flow balance measurement, heart wall tracking and septal defects detection. First, a global smooth constrained localized registration method is employed to register the image; Then, flow balance measurement is employed to determine the unbalance of in and out blood flow, which usually indicate the septal defects in the heart; After that, the wall of the heart is tracked using the same framework used in the registration to improve the efficiency and accuracy; Defects along septal are detected using a Bayesian based information fusion to analyze the profile lines from registered image, difference image and original grey image for the whole sequence (3D+T). The proposed method is tested using gated cardiac MRI, which is a well-established clinical diagnosis method for septal defect detection. Experimental results show that the proposed framework is able to successfully detect the septal defects and provide the visual assistance to the radiologist for further diagnosis. The proposed detection can be widely used in both clinical practice, surgical planning and after operation follow-up. To the best of our knowledge, the work is first such an effort.
A New Actinomycin Complex Produced by a <i>Micromonospora</i> Species: Fermentation, Isolation, and Characterization (1976)

A species of Micromonospora, Micromonospora floridensis NRRL 8020, has been found to produce an actinomycin complex consisting of at least 25 active components. After solvent extraction of the complex, separation of the individual components was carried out by preparative thin-layer chromatography. Hydrolysis and subsequent electrophoretic and chromatographic identification of the amino acid content of each of the isolated components have shown differences from known actinomycins, and the probability exists that these contain a number of amino or imino acids not previously found in other members of this group of antibiotics.
3D virtual colonoscopy (2002)

The authors present here a method called 3D virtual colonoscopy, which is an alternative method to existing procedures of imaging the mucosal surface of the colon. Using 3D reconstruction of helical CT data and volume visualization techniques, the authors generate images of the inner surface of the colon as if the viewer's eyes were inside the colon. They also create interactive flythroughs and off-line automatically-produced animations through the inside of the colon. The visualization is accomplished with VolVis, which is a comprehensive system for interactive volume visualization. The authors are specifically interested in visualizing colonic polyps larger than one cm since these have a high probability of containing carcinoma. The authors present testing results of their method as applied to two plastic pipe simulations and to the Visible Human data set.
A passive acoustic monitor of treatment effectiveness during extracorporeal lithotripsy (2011)

Although extracorporeal shockwave lithotripsy (ESWL) has now been in the clinic for at least three decades, there has been little advance in efforts (i) to estimate the efficacy of the treatment whilst it is in progress, or (ii) to determine the end-point of a treatment session in terms of the degree of stone fragmentation achieved. Previous in vitro experimentation and clinical trials have shown that a passive acoustic monitor has the potential to provide evidence of the effectiveness and end-point of lithotripsy. The system exploits secondary emissions generated during shock-tissue interaction, whose features depend on the quality of tissue at the beam focus. This prototype was developed into the first commercially available clinical ESWL treatment monitor (Precision Acoustic Ltd, Dorchester, UK), and a unit has been acquired and tested in the clinical routine by urologists at Guy's and St Thomas NHS Trust in March 2009. This paper critically assesses the performance of the new system for the first 25 treatments monitored. The ESWL monitor correctly predicted the treatment outcome of 15 of the 18 treatments that were followed-up clinically. In addition, it was noted that the measure of treatment effectiveness provided by the monitor after 500 shocks was predictive of the final treatment outcome (p &lt; 0.001). This suggests that the system could be used in pre-assessment; indicating if the stone is susceptible to ESWL or if the patient should be sent for surgery
New Approaches to Enzymatic Oligosaccharide Synthesis: Glycosynthases and Thioglycoligases (2003)

An overview of the applications of engineered glycosynthases and thioglycoligases for the enzymatic synthesis of O- and S-glycosidic linkages in oligosaccharides is presented. Glycosynthases lack the catalytic nucleophile of retaining glycosidases and use glycosyl fluorides with inverted anomeric stereochemistry as glycosyl donors. To date, nine enzymes from seven different glycosyl hydrolase families have been engineered to perform the glycosynthase reaction. Thioglycoligases lack the catalytic acid/base residue of retaining glycosidases and use dinitrophenyl glycosides as donors and deoxy-thiosugars as acceptors. The regioselectivity of the transglycosylation reaction is entirely controlled by the position of the thiol in the acceptor. To date, two retaining exo glycosidases and one endo glycanase, all from different glycosyl hydrolase families, have been engineered in this fashion.
8D-THERMO CAM: Combination of Geometry with Physiological Information for Face Recognition (2005)

Biometrics-based technologies in the area of identity management are gaining increasing importance, as a means of establishing non-falsifiable credentials for end users. However, in the three-way tug-of-war between convenient, unobtrusive data collection (required for user acceptance), accuracy in results (required for justifying deployment), and speed (required for widespread use in practice), no single biometric to date has managed to hold the middle ground that would allow for its ready adoption. The overall goal of our project is to develop the theoretical framework and computational tools that will lead to the development of a practical, unobtrusive, and accurate face recognition system for convenient and effective access control. This framework encompasses 8D characteristics of the face (3D geometry+2D visible texture+2D infrared texture, over time). In this paper, we present a novel multi-modal facial recognition approach that employs data from both visible spectrum and thermal infrared sensors. From the fitted parametric model we extract two images corresponding to the subject's face and process these images to extract biometric signatures. Specifically, the deformation image is compressed using a wavelet transform and the vasculature graph is extracted from the parametric thermal image.
Preparation and thermal analysis of cotton–clay nanocomposites (2004)

Abstract Nanocomposites were produced from cotton with montmorillonite clay used as the nanofiller material. Three exfoliation and intercalation methods with different solvents and clay pretreatment techniques were tested for the production of these organic–inorganic hybrids. The method that resulted in superior clay–cotton nanocomposites used a clay pretreatment with 4‐methylmorpholine‐ N ‐oxide as the cotton solvent. The nanocomposites showed significant improvements in the thermal properties in comparison with unbleached cotton and cotton processed under the conditions for nanocomposite preparation. The degradation temperature of the nanocomposites increased by 45°C, and the char yields for some compositions were twice those of unbleached cotton. The crystalline melt of the materials decreased by 15°C. Future research will include the development of textiles based on these cotton–clay materials and testing for flame‐retardant properties and product strength. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 92: 2125–2131, 2004
Immunogenicity of a Trivalent Human Papillomavirus L1 DNA-Encapsidated, Non-Replicable Baculovirus Nanovaccine (2014)

Previously, we developed a non-replicating recombinant baculovirus coated with human endogenous retrovirus envelope protein (AcHERV) for enhanced cellular delivery of human papillomavirus (HPV) 16L1 DNA. Here, we report the immunogenicity of an AcHERV-based multivalent HPV nanovaccine in which the L1 segments of HPV 16, 18, and 58 genes were inserted into a single baculovirus genome of AcHERV. To test whether gene expression levels were affected by the order of HPV L1 gene insertion, we compared the efficacy of bivalent AcHERV vaccines with the HPV 16L1 gene inserted ahead of the 18L1 gene (AcHERV-HP16/18L1) with that of AcHERV with the HPV 18L1 gene inserted ahead of the 16L1 gene (AcHERV-HP18/16L1). Regardless of the order, the bivalent AcHERV DNA vaccines retained the immunogenicity of monovalent AcHERV-HP16L1 and AcHERV-HP18L1 DNA vaccines. Moreover, the immunogenicity of bivalent AcHERV-HP16/18L1 was not significantly different from that of AcHERV-HP18/16L1. In challenge tests, both bivalent vaccines provided complete protection against HPV 16 and 18 pseudotype viruses. Extending these results, we found that a trivalent AcHERV nanovaccine encoding HPV 16L1, 18L1, and 58L1 genes (AcHERV-HP16/18/58L1) provided high levels of humoral and cellular immunogenicity against all three subtypes. Moreover, mice immunized with the trivalent AcHERV-based nanovaccine were protected from challenge with HPV 16, 18, and 58 pseudotype viruses. These results suggest that trivalent AcHERV-HPV16/18/58L1 could serve as a potential prophylactic baculoviral nanovaccine against concurrent infection with HPV 16, 18, and 58.
3D reconstruction of the human jaw from a sequence of images (2002)

A novel approach is proposed to obtain a record of the patient's occlusion using computer vision. Data acquisition is obtained using intra-oral video cameras. The technique utilizes shape from shading to extract 3D information from 2D views of the jaw, and a novel technique for 3D data registration using genetic algorithms. The resulting 3D model can be used for diagnosis, treatment planning, and implant purposes. The overall purpose of this research is to develop a model-based vision system for orthodontics to replace traditional approaches. This system will be flexible, accurate, and will reduce the cost of orthodontic treatments.
The VDAC1 N-terminus is essential both for apoptosis and the protective effect of anti-apoptotic proteins (2009)

The release of mitochondrial-intermembrane-space pro-apoptotic proteins, such as cytochrome c, is a key step in initiating apoptosis. Our study addresses two major questions in apoptosis: how are mitochondrial pro-apoptotic proteins released and how is this process regulated? Accumulating evidence indicates that the voltage-dependent anion channel (VDAC) plays a central role in mitochondria-mediated apoptosis. Here, we demonstrate that the N-terminal domain of VDAC1 controls the release of cytochrome c, apoptosis and the regulation of apoptosis by anti-apoptotic proteins such as hexokinase and Bcl2. Cells expressing N-terminal truncated VDAC1 do not release cytochrome c and are resistant to apoptosis, induced by various stimuli. Employing a variety of experimental approaches, we show that hexokinase and Bcl2 confer protection against apoptosis through interaction with the VDAC1 N-terminal region. We also demonstrate that apoptosis induction is associated with VDAC oligomerization. These results show VDAC1 to be a component of the apoptosis machinery and offer new insight into the mechanism of cytochrome c release and how anti-apoptotic proteins regulate apoptosis and promote tumor cell survival.
Speech reinforcement system for car cabin communications (2005)

A speech reinforcement system is presented to improve communication between the front and the rear passengers in large motor vehicles. This type of communication can be difficult due to a number of factors, including distance between speakers, noise and lack of visual contact. The system described makes use of a set of microphones to pick up the speech of each passenger, then it amplifies these signals and plays them back to the cabin through the car audio loudspeaker system. The two main problems are noise amplification and electro-acoustic coupling between loudspeakers and microphones. To overcome these problems the system uses a set of acoustic echo cancellers, echo suppression filters and noise reduction stages. In this paper, the stability of a speech reinforcement system is studied. We propose a solution based on echo cancellers and residual echo suppression filters. The spectral estimation method for the power spectral density of the residual echo existing after the echo canceller is presented along with the derivation of the optimal residual echo suppression filter. Some results about the performance of the proposed system are also provided.
Learning to invert: Signal recovery via Deep Convolutional Networks (2017)

The promise of compressive sensing (CS) has been offset by two significant challenges. First, real-world data is not exactly sparse in a fixed basis. Second, current high-performance recovery algorithms are slow to converge, which limits CS to either non-real-time applications or scenarios where massive back-end computing is available. In this paper, we attack both of these challenges head-on by developing a new signal recovery framework we call DeepInverse that learns the inverse transformation from measurement vectors to signals using a deep convolutional network. When trained on a set of representative images, the network learns both a representation for the signals (addressing challenge one) and an inverse map approximating a greedy or convex recovery algorithm (addressing challenge two). Our experiments indicate that the DeepInverse network closely approximates the solution produced by state-of-the-art CS recovery algorithms yet is hundreds of times faster in run time. The tradeoff for the ultrafast run time is a computationally intensive, off-line training procedure typical to deep networks. However, the training needs to be completed only once, which makes the approach attractive for a host of sparse recovery problems.
Advanced Distributed Fiber Optic Sensors for Monitoring Poor Zonal Isolation with Hydrocarbon Migration in Cemented Annuli (2016)

Abstract The cement annulus between a wellbore and a casing string should provide reliable zonal isolation throughout the life of a well. However, zonal isolation may be negatively affected by several factors which can compromise cement integrity and lead to the development of channels that provide migration paths for hydrocarbons. This paper is dedicated to monitoring the unwanted presence and migration of hydrocarbons in cemented annuli using a sophisticated fiber optic sensing system. The system is comprised of a distributed temperature and strain sensing (DTSS) data acquisition unit and a newly designed fiber optic cable that is capable of detecting hydrocarbons in cemented annuli. The DTSS system is based on Brillouin and Rayleigh backscattering mechanisms, which are sensitive to both strain and temperature changes. The cable consists of a single-mode optical fiber packaged with a hydrocarbon-sensitive polymer. This combination was tested extensively and successfully for its ability to identify cement integrity issues through detection of hydrocarbons in the cement. The presence of hydrocarbons causes the polymer around the fiber to swell, leading to changes in strain distribution on the fiber. These strain variations were detected using the DTSS monitoring system. The observed strain variations were found to be dependent on the type of fluids, which indicates that the proposed system has selective sensitivity to certain hydrocarbons. For example, synthetic-based mud had little effect on strain, while kerosene showed a significant response. In conclusion, the new fiber optic sensing system can be beneficial in verifying zonal isolation by detecting and monitoring any unwanted hydrocarbon migration in cemented annuli, identifying zones from which hydrocarbons are originating, and providing other essential information to identify the need for well intervention such as remedial cementing.