gebhart/patrepeval huggingface dataset:
Expression patterns of fatty acid binding proteins in breast cancer cells. (2005)

We studied the expression levels of fatty acid binding proteins in breast normal and cancer cell lines. Liver fatty acid binding protein (L-FABP) and intestine fatty acid binding proteins were shown to be up-regulated in breast cancer cell lines while adipose- and epidermal-fatty acid binding proteins were down regulated in breast cancer cells compared to normal breast cell lines. We have previously shown that blocking the expression of L-FABP resulted in remarkable effects on apoptosis and cell proliferation of prostate cancer cell lines (Hammamieh et al 2004). To study the mechanism of effect of the liver fatty acid binding protein in breast cancer cells, we designed an antisense oligodeoxynucleotide to block the production of liver-FABP in MCF-7 cells. The antisense was shown to inhibit the expression of L-FABP and to induce apoptosis in MCF-7 cells. This study examines the mechanism by which L-FABP antisense regulates proliferation and apoptosis in breast cancer cell lines. We used human cDNA microarrays to explore differentially expressed genes in MCF-7 breast cancer cells treated with L-FABP antisense oligonucleotide. Some of the genes that were differentially expressed were confirmed using quantitative RT-PCR. Genes related to cell growth, proliferation and angiogenesis showed significant variations. This suggests a possible use of these antisense ODNs as therapeutic agents for breast cancer in future.
Thermoacoustic computed tomography with large planar receivers (2004)

Thermoacoustic imaging is a promising new modality for nondestructive evaluation. So far point measurement data for thermoacoustic imaging are used. In this paper we propose a novel measurement set-up with relatively large piezo foils (planar receivers) and an according real time imaging algorithm based on the Radon transform. We present numerical simulations for simulated and real world data.
Clinical evaluation of long-term epidural monitoring of intracranial pressure. (1979)

Forty-two epidural sensors for measuring intracranial pressure were implanted in 38 patients over the last four years. The sensor is a passive device consisting of an inductance and a pressure sensitive capacitance resonant at about 50 megahertz. The study involved 17 cases of hydrocephalus, nine of pseudotumor cerebri, and the remainder included cases of cranial trauma, brain tumors, and aneurysms. Four of the sensors failed in patients and were removed. Two of these had to be replaced to continue the pressure monitoring. The intracranial pressure is still being monitored in 22 patients, while 15 have been lost to follow-up for various reasons. Fourteen patients have been followed for about a year, and four for two years. The baseline drift rate in most sensors is between 1 and 2 mm H2O per day, with a few having greater rates of drift. Calibration errors were found in some of the sensors after implantation. These errors were corrected by direct measurement of the cerebral spinal fluid pressure via lumbar puncture. The sensors have proven to be a valuable adjunct in the management and diagnosis of neurosurgical patients by simplifying the intermittent and continuous recording of intracranial pressure. This was so despite the presence of calibration errors and a drift which necessitated an occasional lumbar puncture for making corrections.
High performance perovskite solar cells by hybrid chemical vapor deposition (2014)

Organometal halide based perovskites are promising materials for solar cell applications and are rapidly developing with current devices reaching ∼19% efficiency. In this work we introduce a new method of perovskite synthesis by hybrid chemical vapor deposition (HCVD), and demonstrate efficiencies as high as 11.8%. These cells were found to be stable with time, and retained almost the same efficiency after approximately 1100 h storage in dry N2 gas. This method is particularly attractive because of its ability to scale up to industrial levels and the ability to precisely control gas flow rate, temperature, and pressure with high reproducibility. This is the first demonstration of a perovskite solar cell using chemical vapor deposition and there is likely still room for significant optimization in efficiency.
Sequential Decoding of Polar Codes (2014)

The problem of efficient decoding of polar codes is considered. A low-complexity sequential soft decision decoding algorithm is proposed. It is based on the successive cancellation approach, and it employs most likely codeword probability estimates for selection of a path within the code tree to be extended.
Development of flexible dry ECG electrodes based on MWCNT/PDMS composite (2015)

Flexible dry electrode based on multi-walled carbon nanotube (MWCNT)/polydimethylsiloxane (PDMS) composite, for monitoring electrocardiogram (ECG) signals, has been developed. The dry ECG electrode was fabricated by screen printing silver (Ag) ink on flexible polyethylene terephthalate (PET) substrate, followed by bar coating of MWCNT/PDMS composite. The performance of the fabricated device was investigated by measuring ECG signals using printed dry electrodes with radii varying from 8 mm to 16 mm. The results were compared with a traditional wet Ag/AgCl ECG electrode (T716). It was observed that the dry ECG electrode, with the largest area, demonstrated better performance, in terms of signal intensity and correlation, when compared to the traditional wet ECG electrode. The response of the dry ECG electrodes are analyzed and presented in this paper.
Systems Biology and Genomics of Breast Cancer (2010)

It is now accepted that breast cancer is not a single disease, but instead it is composed of a spectrum of tumor subtypes with distinct cellular origins, somatic changes, and etiologies. Gene expression profiling using DNA microarrays has contributed significantly to our understanding of the molecular heterogeneity of breast tumor formation, progression, and recurrence. For example, at least two clinical diagnostic assays exist (i.e., OncotypeDX RS and Mammaprint®) that are able to predict outcome in patients using patterns of gene expression and predetermined mathematical algorithms. In addition, a new molecular taxonomy based upon the inherent, or "intrinsic," biology of breast tumors has been developed; this taxonomy is called the "intrinsic subtypes of breast cancer," which now identifies five distinct tumor types and a normal breast-like group. Importantly, the intrinsic subtypes of breast cancer predict patient relapse, overall survival, and response to endocrine and chemotherapy regimens. Thus, most of the clinical behavior of a breast tumor is already written in its subtype profile. Here, we describe the discovery and basic biology of the intrinsic subtypes of breast cancer, and detail how this interacts with underlying genetic alternations, response to therapy, and the metastatic process.
Selective Extraction of Minor Actinides from Acidic Media Using Symmetric and Asymmetric Dithiophosphinic Acids (2010)

The minor actinides (Am and Cm) and other transplutonium elements represent significant, long-term hazards found in spent nuclear fuel. The selective extraction of the minor actinides from the lanthanides is an important part of advanced reprocessing of spent nuclear fuel. This separation would allow the minor actinides to be fabricated into a target and recycled to a reactor and the lanthanides to be disposed. Due to the similarities in the chemical properties of the trivalent actinides and lanthanides, this separation is difficult to accomplish. The introduction of soft donor groups, such as N or S, into similarly structured ligands increases the differentiation between An(III) and Ln(III) cation coordination. Partly because of limitations imposed by synthetic methodologies, previous studies of dithiophosphinic acid (DPAH) extractants has been restricted to a comparatively small number of symmetrical dialkyl and diaryl derivatives. Research efforts at the Idaho National Laboratory have resulted in the recent development of an innovative synthetic pathway yielding new regiospecific DPAH extractants. The synthesis improves DPAH designs that can address the issues concerning minor actinide separation efficiency and extractant stability. Several new symmetric and asymmetric DPAH extractants have been prepared. The use of these extractants for the separation of minor actinides from lanthanides will be discussed. In addition, the variation in the extent of Am(III) extraction by a related series of DPAH isomers will be presented.
Evaluation of antibodies elicited by immunization with pertussis toxin. (1991)

The monoclonal antibody termed 1B7 neutralizes pertussis toxin in vivo in cell culture systems and can also passively protect mice from a challenge with live Bordetella pertussis (9). It has been suggested that most other independently derived neutralizing monoclonal antibodies recognizing the S1 subunit apparently recognize the same epitope as 1B7, and that the S1 subunit contains only one immunodominant protective epitope (1). These antibodies have been termed Class A antibodies (8) and inhibit the ADP-ribosyltransferase but not the NAD glycohydrolase activity of the toxin (7). We are testing the hypothesis that immunization with inactivated preparations of pertussis toxin that lead to protection are associated with the production of Class A antibodies. If true, then identification of Class A antibodies in sera might provide a serological correlate of protection. If false, then development of assays designed to detect the important protective antibodies are necessary. Our initial results suggest that Class A antibodies are not the predominant neutralizing antibody in mice immunized with vaccines containing formalin-treated pertussis toxin.
Laser Forming for Complex 3D Folding (2017)

Abstract Laser heating to generate plastic strains for controlled bending, known as laser forming, is a promising technique for creating 3D structures based on origami‐inspired principles. Here, for the first time, laser cutting and forming are used to go from flat unpatterned metal sheet to final folded part, including up and down folds, all without manual handling. Folding direction is controlled by adjusting laser travel speed to create either a lateral or a vertical thermal gradient in the workpiece. Numerical modeling followed by experimental verification is used to determine the transition point between bending toward and away from the laser, followed by demonstration of a variety of complex 3D folded parts. Using this approach, laser forming is then used to precisely align two components, demonstrating the positioning of an optical reflector to guide the laser and pattern a portion of the sheeting originally inaccessible on the underside. All work here is done with a commercially available 20 W marking laser without modification.
Effect of Hydrogen Gas Pressure on the Mechanical Properties of Low Alloy Steel for Hydrogen Pressure Vessels (2007)

To provide engineering data useful in design, manufacture and operation of hydrogen storage vessels in hydrogen refueling stations, fatigue test machine equipped with high-pressure hydrogen autoclave was introduced. The effect of steel’s strength level, temperature effect, fracture toughness and pressure effect were evaluated in gaseous hydrogen environment. When steel’s strength level exceeds around 930MPa to 1000MPa, the elongation and notch tensile properties deleteriously degraded. The elongation reduction by the effect of hydrogen increased with lowering the temperature. The same sensitivity to temperature on crack growth behavior was observed. However, it was shown that the gaseous hydrogen environment only affect the slow stable crack growth but did not affect the critical flaw growth of the steel at low temperature, i.e. fast fracture. The pressure dependence of notch tensile strength ranging from 0.1MPa to 75MPa hydrogen pressure shows approximately 1/2 power dependence.
Novel ultrasonic methods of imaging interstitially implanted brachytherapy seeds (2004)

Interstitially implanted radioactive seeds are becoming a popular and effective means of treating a wide range of diseases, primarily cancer. Brachytherapy of prostate cancer, for example, is proving to be as effective, in terms of 5-year survival, as surgery for management of gland-confined disease, and to many, the side effects of brachytherapy are less debilitating than those of surgery. While seeds are implanted under guidance from transrectal ultrasound, gland movement and distortion during implantation may lead to seed misplacement; implanted seeds are difficult to visualize ultrasonically after implantation for a variety of reasons. We are investigating a variety of ultrasonic techniques intended to overcome the limitations of conventional ultrasonic imaging, and the following three methods are showing encouraging promise: resonance/vibration imaging; modified elastography; and two-dimensional correlation. The resonance/vibration method induces natural vibrations in seeds and, using power-Doppler methods, images the movement these vibrations induce in immediately adjacent tissues. The modified-elastography method uses standard elastographic processing with higher-than-normal applied strains so that soft-tissue signals decorrelate while echo signals from rigid seeds retain correlation. The two-dimensional correlation method compares echo signals from tissue with those from a reference seed and shows seed locations by mapping the resulting correlation coefficients.
Supervised Learning of Image Restoration with Convolutional Networks (2007)

Convolutional networks have achieved a great deal of success in high-level vision problems such as object recognition. Here we show that they can also be used as a general method for low-level image processing. As an example of our approach, convolutional networks are trained using gradient learning to solve the problem of restoring noisy or degraded images. For our training data, we have used electron microscopic images of neural circuitry with ground truth restorations provided by human experts. On this dataset, Markov random field (MRF), conditional random field (CRF), and anisotropic diffusion algorithms perform about the same as simple thresholding, but superior performance is obtained with a convolutional network containing over 34,000 adjustable parameters. When restored by this convolutional network, the images are clean enough to be used for segmentation, whereas the other approaches fail in this respect. We do not believe that convolutional networks are fundamentally superior to MRFs as a representation for image processing algorithms. On the contrary, the two approaches are closely related. But in practice, it is possible to train complex convolutional networks, while even simple MRF models are hindered by problems with Bayesian learning and inference procedures. Our results suggest that high model complexity is the single most important factor for good performance, and this is possible with convolutional networks.
Laser-induced fluorescence real-time sensing of trace plastics and dissolved organic compounds in water/seawater (2004)

A dual wavelength (266 nm and 355 nm) laser induced fluorescence system using multipath excitation and emission collection optics has been developed and characterized for the detection of dissolved organic compounds and plastics in water/seawater.
Characterization of a quail suspension cell line for production of a fusogenic oncolytic virus (2023)

The development of efficient processes for the production of oncolytic viruses (OV) plays a crucial role regarding the clinical success of virotherapy. Although many different OV platforms are currently under investigation, manufacturing of such viruses still mainly relies on static adherent cell cultures, which bear many challenges, particularly for fusogenic OVs. Availability of GMP-compliant continuous cell lines is limited, further complicating the development of commercially viable products. BHK21, AGE1. CR and HEK293 cells were previously identified as possible cell substrates for the recombinant vesicular stomatitis virus (rVSV)-based fusogenic OV, rVSV-NDV. Now, another promising cell substrate was identified, the CCX.E10 cell line, developed by Nuvonis Technologies. This suspension cell line is considered non-GMO as no foreign genes or viral sequences were used for its development. The CCX.E10 cells were thus thoroughly investigated as a potential candidate for OV production. Cell growth in the chemically defined medium in suspension resulted in concentrations up to 8.9 × 10<sup>6</sup> cells/mL with a doubling time of 26.6 h in batch mode. Cultivation and production of rVSV-NDV, was demonstrated successfully for various cultivation systems (ambr15, shake flask, stirred tank reactor, and orbitally shaken bioreactor) at vessel scales ranging from 15 mL to 10 L. High infectious virus titers of up to 4.2 × 10<sup>8</sup> TCID<sub>50</sub> /mL were reached in orbitally shaken bioreactors and stirred tank reactors in batch mode, respectively. Our results suggest that CCX.E10 cells are a very promising option for industrial production of OVs, particularly for fusogenic VSV-based constructs.
<title>Optoelectronic closed-loop auto-oscillator for fluorescence lifetime detection: a new fluorimetry technique with applications to chemical/biosensors</title> (2001)

We present a new approach to excited state fluorescence lifetime-based measurements which is inexpensive and highly sensitive. The detection system consists of a closed-loop optoelectronic arrangement containing an intermediate frequency resonance amplifier, a fluorescence excitation light source (for example, a light emitting diode or a semiconductor laser), a fiber optic delay line, and a photodetector. The system exhibits self-oscillations in the vicinity of the frequency (Omega) approximately 1/(tau) (where (tau) is the excited state lifetime) which manifest themselves as modulation of the light. Changes in the excited state lifetime alter the phase delay of the loop, which in turn causes a frequency shift in the modulation signal. The frequency shift can be measured very precisely with a frequency counter. With appropriate averaging, this technique can yield sub-picosecond resolution of shifts in lifetime. This technique is suited for chemical/biological sensing applications, and can be easily duplicated for chemical/biological sensor arrays.
Sterile Protective Immunity to Malaria is Associated with a Panel of Novel P. falciparum Antigens (2011)

The development of an effective malaria vaccine remains a global public health priority. Less than 0.5% of the Plasmodium falciparum genome has been assessed as potential vaccine targets and candidate vaccines have been based almost exclusively on single antigens. It is possible that the failure to develop a malaria vaccine despite decades of effort might be attributed to this historic focus. To advance malaria vaccine development, we have fabricated protein microarrays representing 23% of the entire P. falciparum proteome and have probed these arrays with plasma from subjects with sterile protection or no protection after experimental immunization with radiation attenuated P. falciparum sporozoites. A panel of 19 pre-erythrocytic stage antigens was identified as strongly associated with sporozoite-induced protective immunity; 16 of these antigens were novel and 85% have been independently identified in sporozoite and/or liver stage proteomic or transcriptomic data sets. Reactivity to any individual antigen did not correlate with protection but there was a highly significant difference in the cumulative signal intensity between protected and not protected individuals. Functional annotation indicates that most of these signature proteins are involved in cell cycle/DNA processing and protein synthesis. In addition, 21 novel blood-stage specific antigens were identified. Our data provide the first evidence that sterile protective immunity against malaria is directed against a panel of novel P. falciparum antigens rather than one antigen in isolation. These results have important implications for vaccine development, suggesting that an efficacious malaria vaccine should be multivalent and targeted at a select panel of key antigens, many of which have not been previously characterized.
A new matrix decomposition based on optimum transformation of the singular value decomposition basis sets yields principal features of time-frequency distributions (2002)

The classification of objects or quantities in all fields of science depends on the quality of the features used for classifying them. This includes, for example, classification of phenomena described by nonstationary processes such as electrocardiograms, seismic geophysics signals, submarine transient acoustic signals, and speech signals for recognition. This paper presents a new matrix decomposition that is used to obtain a set of principal features from time-frequency representations for classifying nonstationary time series processes. This new matrix decomposition is based on a transformation of the orthonormal basis from singular value decomposition (SVD). The new basis set yields extrema of the first moment for each vector in the new basis set. These basis sets for time and frequency can then be used to construct features relating to the location and spread of each energy density highlight in the time-frequency plane. This new matrix decomposition is presented in this paper along with a simple example to illustrate its application.
Mini-Me: A min-repro system for database software (2010)

Testing and debugging database software is often challenging and time consuming. A very arduous task for DB testers is finding a min-repro - the ¿simplest possible setup¿ that reproduces the original problem. Currently, a great deal of searching for min-repros is carried out manually using non-database-specific tools, which is both slow and error-prone. We propose to demonstrate a system, called Mini-Me <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> , designed to ease and speed-up the task of finding min-repros in database-related products. Mini-Me employs several effective tools, including: the novel simplification transformations, the high-level language for creating search scripts and automation, the ¿record-and-replay¿ functionality, and the visualization of the search space and results. In addition to the standard application mode, the system can be interacted with in the game mode. The latter can provide an intrinsically motivating environment for developing successful search strategies by DB testers, which can be data-mined and recorded as patterns and used as recommendations for DB testers in the future. Potentially, a system like Mini-Me can save hours of time (for both customers and testers to isolate a problem), which could result in faster fixes and large cost savings to organizations.
Back Cover: Rewiring Translation for Elongation Factor Tu‐Dependent Selenocysteine Incorporation (Angew. Chem. Int. Ed. 5/2013) (2013)

Synthetic tRNA for selenoprotein production is described by D. Söll et al. in their Communication on page 1441 ff. The tRNA is a substrate for three E. coli proteins: seryl-tRNA synthetase (SerRS), selenocysteine synthase (SelA) generating Sec-tRNAUTu, and EF-Tu for Sec-tRNAUTu transport to the ribosome, which allows site-specific Sec insertion into proteins. This system has general utility in protein engineering, molecular biology, and disease research.
Critically coupled resonators in vertical geometry using a planar mirror and a 5 nm thick absorbing film (2006)

A (5.1±0.5) nm thick film of high oscillator strength J-aggregated dye critically couples to a single dielectric mirror, absorbing more than 97% of incident λ=591 nm wavelength light, corresponding to an effective absorption coefficient of (6.9±0.7)×106 cm−1 for (film thickness)/λ<1%.