gebhart/patrepeval huggingface dataset:
FreeRider (2017)

We introduce the design and implementation of FreeRider, the first system that enables backscatter communication with multiple commodity radios, such as 802.11g/n WiFi, ZigBee, and Bluetooth, while these radios are simultaneously used for productive data communication. Furthermore, we are, to our knowledge, the first to implement and evaluate a multi-tag system. The key technique used by FreeRider is codeword translation, where a tag can transform a codeword present in the original excitation signal into another valid codeword from the same codebook during backscattering. In other words, the backscattered signal is still a valid WiFi, ZigBee, or Bluetooth signal. Therefore, commodity radios decode the backscattered signal and extract the tag's embedded information. More importantly, FreeRider does codeword translation regardless of the data transmitted by these radios. Therefore, these radios can still do productive data communication. FreeRider accomplishes codeword translation by modifying one or more of the three dimensions of a wireless signal --- amplitude, phase and frequency. A tag ensures that the modified signal is still comprised of valid codewords that come the same codebook as the original excitation signal. We built a hardware prototype of FreeRider, and our empirical evaluations show a data rate of ~60kbps in single tag mode, 15kbps in multi-tag mode, and a backscatter communication distance up to 42m when operating on 802.11g/n WiFi.
Increased radiation sensitivity of head and neck squamous cell carcinoma with sphingosine kinase 1 inhibition (2010)

SphK1 is upregulated in HNSCC, and inhibition of SphK1 sensitizes HNSCC to radiation-induced cytotoxicity.
Non-contact fluorescence optical tomography with scanning patterned illumination (2006)

This article describes a novel non-contact fluorescence optical tomography scheme which utilizes multiple area illumination patterns, to reduce the ill-posedness of the inverse problem involved in recovering interior fluorescence yield distributions in biological tissue from boundary fluorescence measurements. The image reconstruction is posed as an optimization problem which seeks a tissue optical property distribution minimizing, for all illumination patterns simultaneously, a regularized difference between the observed boundary measurements of light distribution, and the boundary measurements predicted from a physical model. Multiple excitation source illumination patterns are described by line and Gaussian sources scanning the simulated tissue phantom surface and by employing diffractive optics-generated patterns. Multiple measurement data sets generated by scanning excitation sources are processed simultaneously to generate the interior fluorescence distribution in tissue by implementing the fluorescence tomography algorithm in a parallel framework suitable for multiprocessor computers. Image reconstructions for single and multiple fluorescent targets (5mm diameter) embedded in a 512ml simulated tissue phantom are demonstrated, with depths of the fluorescent targets from the illumination plane between 1cm to 2cm. We show both qualitative and quantitative improvements of our algorithm over reconstructions from only a single measurement.
Electrical impedance myography for the assessment of children with muscular dystrophy: a preliminary study (2013)

Electrical impedance myography (EIM) provides a non-invasive approach for quantifying the severity of neuromuscular disease. Here we determine how well EIM data correlates to functional and ultrasound (US) measures of disease in children with Duchenne muscular dystrophy (DMD) and healthy subjects. Thirteen healthy boys, aged 2-12 years and 14 boys with DMD aged 4-12 years underwent both EIM and US measurements of deltoid, biceps, wrist flexors, quadriceps, tibialis anterior, and medial gastrocnemius. EIM measurements were performed with a custom-designed probe using a commercial multifrequency bioimpedance device. US luminosity data were quantified using a gray-scale analysis approach. Children also underwent the 6-minute walk test, timed tests and strength measurements. EIM and US data were combined across muscles. EIM 50 kHz phase was able to discriminate DMD children from healthy subjects with 98% accuracy. In the DMD patients, average EIM phase measurements also correlated well with standard functional measures. For example the 50 kHz phase correlated with the Northstar Ambulatory Assessment test (R = 0.83, p = 0.02). EIM 50 kHz phase and US correlated as well, with R = -0.79 (p < 0.001). These results show that EIM provides valuable objective measures Duchenne muscular dystrophy severity.
Significant Survival Benefit to Patients with Advanced Non-Small-Cell Lung Cancer from Treatment with Clarithromycin (1997)

We carried out a randomized study of 49 consecutive patients with unresectable primary lung cancer to determine whether clarithromycin (CAM), a 14-membered ring macrolide, can improve outcome. A total of 49 patients (42 patients with non-small-cell lung cancer and 7 patients with small-cell lung cancer) had received prior chemotherapy, radiotherapy or both during their hospital stay. They were randomly allocated into two study groups on the first visit after discharge: 25 patients (22 patients with non-small-cell lung cancer, 3 patients with small-cell lung cancer) were assigned to receive CAM (400 mg/day, orally), and 24 patients (20 patients with non-small-cell lung cancer, 4 patients with small-cell lung cancer) did not receive CAM. CAM treatment after randomization was open and the treatment was to be continued as long as the patients could tolerate CAM. There was no significant difference in the median survival time for small-cell lung cancer between the CAM group and the non-CAM group. However, CAM treatment significantly increased the median survival time for non-small-cell lung cancer patients, the median survival for the CAM group was 535 days and that for the non-CAM group was 277 days. Analyses of prognostic factors showed that only treatment with CAM was predictive of longer survival for non-small-cell lung cancer, and other tested covariates had no effects on the prognosis. There were no remarkable side effects observed in the CAM group throughout treatment. We conclude that long-term treatment using CAM is beneficial for unresectable non-small-cell lung cancer patients and that it can increase the median survival of patients with advanced disease.
A Unique Mucin Immunoenhancing Peptide with Antitumor Properties (2004)

Implantation of DA-3 mammary tumor cells into BALB/c mice results in tumor growth, metastatic lesions, and death. These cells were transfected with genes encoding for either the transmembrane (DA-3/TM) or secreted (DA-3/sec) form of human mucin 1 (MUC1). Although the gene for the secreted form lacks the transmembrane and cytoplasmic domains, the 5' sequences of these mucins are identical; however, the gene for the secreted mucin isoform ends with a sequence encoding for a unique 11 amino acid peptide. The DA-3/TM or DA-3 cells transfected with the neomycin vector only (DA-3/neo) have the same in vivo growth characteristics as the parent cell line. In contrast, DA-3/sec cells fail to grow when implanted in immunocompetent BALB/c animals. DA-3/sec cells implanted in nude mice resulted in tumor development verifying the tumorigenic potential of these cells. Pre-exposure of BALB/c mice to DA-3/sec cells afforded protection against challenge with DA-3/TM or DA-3/neo mammary tumors and the unrelated tumors K7, an osteosarcoma, and RENCA, a renal cell carcinoma. Partial protection against subsequent tumor challenges was also achieved by substituting the 11 amino acid peptide found only in the secreted MUC1 isoform, for the live DA-3/sec cells. Notably, the efficacy of this peptide is not strain restricted because it also retarded the growth of Lewis lung carcinoma cells in C57 BL/6 mice. These findings reveal that a unique peptide present in the secreted MUC1 has immunoenhancing properties and may be a potential agent for use in immunotherapy.
Optical polarization characteristics of InGaN∕GaN light-emitting diodes fabricated on GaN substrates oriented between (101¯) and (101¯1¯) planes (2008)

Optical polarization characteristics of InGaN∕GaN light-emitting diodes (LEDs) were studied. Light-emitting diode samples were fabricated on four types of GaN substrates near (101¯0) orientation with intentional off-axis cuts of 0°, 5°, 10°, and 27° towards [0001¯]. A confocal microscope was used to characterize the optical polarization of electroluminescence at various currents. The highest polarization ratio of 0.91 was measured on samples fabricated on a 5° off-cut substrate. First moments were calculated on emission spectra to assess emission peak shifts of two polarization components. We drew a conclusion that substrate off-axis cut is a technique to improve optical polarization characteristics of nonpolar-oriented InGaN∕GaN LEDs.
Exploiting LTE white space using dynamic spectrum access algorithms based on survival analysis (2017)

In this study, we design and implement two algorithms for dynamic spectrum access (DSA) that are based on survival analysis. They use a non-parametric estimate of the cumulative hazard function to predict the remaining idle time available for secondary transmission subject to the constraint of a preset probability of successful completion. To show that the algorithms are effective in real-world scenarios even at fine time scales, we evaluate their performance using data collected from an LTE band to model primary user activity. The algorithms are run in different configurations, i.e., they are trained and run on a few combinations of data sets. Our results show that as long as the cumulative hazard functions are fairly similar across datasets, the algorithms can be trained on one day's dataset and run on that of another day's without any significant degradation of performance. The algorithms achieve fairly high white space utilization and have a measured probability of interference which always stays below the preset threshold.
Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly (2015)

Metagenomics approach involves extraction, sequencing and characterization of the genomic content of entire community of microbes present in a given environment. In contrast to genomic data, accurate assembly of metagenomic sequences is a challenging task. Given the huge volume and the diverse taxonomic origin of metagenomic sequences, direct application of single genome assembly methods on metagenomes are likely to not only lead to an immense increase in requirements of computational infrastructure, but also result in the formation of chimeric contigs. A strategy to address the above challenge would be to partition metagenomic sequence datasets into clusters and assemble separately the sequences in individual clusters using any single-genome assembly method. The current study presents such an approach that uses tetranucleotide usage patterns to first represent sequences as points in a three dimensional (3D) space. The 3D space is subsequently partitioned into "Grids". Sequences within overlapping grids are then progressively assembled using any available assembler. We demonstrate the applicability of the current Grid-Assembly method using various categories of assemblers as well as different simulated metagenomic datasets. Validation results indicate that the Grid-Assembly approach helps in improving the overall quality of assembly, in terms of the purity and volume of the assembled contigs.
Profiling of 95 MicroRNAs in Pancreatic Cancer Cell Lines and Surgical Specimens by Real‐Time PCR Analysis (2008)

Pancreatic cancer tissues or cell lines have a unique miRNA profiling pattern at the individual basis compared with relatively normal pancreatic tissues or cells as well as pancreatitis tissue. Upregulation of eight miRNAs occurs in most pancreatic cancer tissues and cell types. These miRNAs may share common pathways in pancreatic cancer pathogenesis. This study may provide useful information for further investigations of functional roles of miRNAs in pancreatic cancer development, progression, diagnosis, and prognosis.
The role of mixed cubic/hexagonal nucleation layers on threading dislocation reduction in epitaxial GaN films (1996)

The defect density and their configuration in epitaxial GaN films on sapphire are strongly related to the optical and electrical properties of the films. The crystalline quality of GaN on sapphire can be greatly improved by introducing a low temperature GaN buffer layer. However, recent studies in our group demonstrate that the pre-growth substrate treatment can significantly change the defects structure and electron properties of the films. In this paper, we present our results on studies of the film microstructures and their corresponding nucleation layers. We propose a novel mechanism for dislocation reduction for GaN on sapphire. The growths for this study were achieved in a horizontal flow reactor operating at atmospheric pressure. Basal plane AI 2 O 3 (Union Carbide) substrates were first cleaned in solvents and then heated in flowing H 2 at 1050°C. Sample A was exposed to an ammonia flow of 3 1/min for 60s, sample B for 400s before the temperature was then reduced to 600°C and a nominal 190 Å thick GaN layer was grown.
Enterococcus faecium QU 50: a novel thermophilic lactic acid bacterium for high-yield l-lactic acid production from xylose (2014)

Production of optically pure lactic acid from lignocellulosic material for commercial purposes is hampered by several difficulties, including heterofermentation of pentose sugars and high energy consumption by mesophilic lactic acid bacteria. Here, we report a novel lactic acid bacterium, strain QU 50, that has the potential to produce optically pure l-lactic acid (≥99.2%) in a homofermentative manner from xylose under thermophilic conditions. Strain QU 50 was isolated from Egyptian fertile soil and identified as Enterococcus faecium QU 50 by analyzing its sugar fermentation pattern and 16S rRNA gene sequence. Enterococcus faecium QU 50 fermented xylose efficiently to produce lactic acid over wide pH (6.0-10.0) and temperature ranges (30-52°C), with a pH of 6.5 and temperature of 50°C being optimal. To our knowledge, this is the first report of homofermentative lactic acid production from xylose by a thermophilic lactic acid bacterium.
G-Matrix Fourier Transform NOESY-Based Protocol for High-Quality Protein Structure Determination (2005)

A protocol for high-quality structure determination based on G-matrix Fourier transform (GFT) NMR is presented. Five through-bond chemical shift correlation experiments providing 4D and 5D spectral information at high digital resolution are performed for resonance assignment. These are combined with a newly implemented (4,3)D GFT NOESY experiment which encodes information of 4D 15N/15N-, 13C(alipahtic)/15N-, and 13C(aliphatic)/13C(aliphatic)-resolved [1H,1H]-NOESY in two subspectra, each containing one component of chemical shift doublets arising from 4D --> 3D projection at omega1:Omega(1H) +/- Omega(X) [X = 15N,13C(aliphatic)]. The peaks located at the centers of the doublets are obtained from simultaneous 3D 15N/13C(aliphatic)/13C(aromatic)-resolved [1H,1H]-NOESY, wherein NOEs detected on aromatic protons are also obtained. The protocol was applied for determining a high-quality structure of the 14 kDa Northeast Structural Genomics consortium target protein, YqfB (PDB ID ). Through-bond correlation and NOESY spectra were acquired, respectively, in 16.9 and 39 h (30 h for shift doublets, 9 h for central peaks) on a 600 MHz spectrometer equipped with a cryogenic probe. The rapidly collected highly resolved 4D NOESY information allows one to assign the majority of NOEs directly from chemical shifts, which yields accurate initial structures "within" approximately 2 angstroms of the final structure. Information theoretical "QUEEN" analysis of initial distance limit constraint networks revealed that, in contrast to structure-based protocols, such NOE assignment is not biased toward identifying additional constraints that tend to be redundant with respect to the available constraint network. The protocol enables rapid NMR data collection for robust high-quality structure determination of proteins up to approximately 20-25 kDa in high-throughput.
Generation of ultra-broadband pulses in the near-IR by non-collinear optical parametric amplification in potassium titanyl phosphate (2008)

Non-collinear optical parametric amplification in potassium-titanyl phosphate (KTP) pumped with 800 nm pulses is reported. Broadband phase matching is achieved with non-collinear geometry and a slightly divergent signal seed. This enables a gain bandwidth up to approximately 2500 cm(-1) in near-IR region. Introducing a chirp into the pump pulse makes it possible to amplify the white light seed in a broad spectral region from approximately 1050 to approximately 1400 nm simultaneously. Pulse compression to sub-40 fs is readily achieved, while the spectrum should support approximately 8.5 fs pulses. Angular dispersion of the broadband output is discussed.
Complex Modulation Computer-Generated Hologram with Occlusion Effect by a Fast Hybrid Point-source/Wave-field Approach (2015)

We propose a fast Computer-Generated Hologram (CGH) computation method with occlusion effect based on a hybrid point-source/wave-field approach. Whereas previously proposed methods tried to reduce the computational complexity of the point-source or the wave-field approaches independently, the proposed method uses the two approaches together and therefore takes advantages from both of them. Our algorithm consists of three steps. First, the 3D scene is sliced into several depth layers parallel to the hologram plane. Then, light scattered by the scene is propagated and shielded from one layer to another, starting from the farthest layer. For each layer, light propagation and light shielding are performed using either a point-source or a wave-field approach according to a threshold criterion on the number of points within the layer. Finally, we compute light propagation from the nearest layer to the hologram plane in order to obtain the final CGH. Experimental results reveal that this combination of approaches does not produce any visible artifact and outperforms both the point-source and wavefield approaches.
Efficient fuzzy type-ahead search in TASTIER (2010)

TASTIER is a research project on the new information-access paradigm called type-ahead search, in which systems find answers to a keyword query on-the-fly as users type in the query. In this paper we study how to support fuzzy type-ahead search in TASTIER. Supporting fuzzy search is important when users have limited knowledge about the exact representation of the entities they are looking for, such as people records in an online directory. We have developed and deployed several such systems, some of which have been used by many people on a daily basis. The systems received overwhelmingly positive feedbacks from users due to their friendly interfaces with the fuzzy-search feature. We describe the design and implementation of the systems, and demonstrate several such systems. We show that our efficient techniques can indeed allow this search paradigm to scale on large amounts of data.
LMI Based Control of Stick-Slip Oscillations in Drilling (2014)

This paper investigates control of stick-slip oscillations in drilling from a linear matrix inequality perspective. Stick-slip oscillations include a period of no angular motion at the bit caused by a large static friction torque followed by a period of rapid angular motion at the bit caused by a build up of torque in the drilling pipe. Many of the model parameters are uncertain but belong to convex sets, and the friction torques are not easily modeled. The linear matrix inequality approach facilitates design of state feedback controllers in the presence of polytopic uncertainties and can be optimized to reject disturbance effects relative to outputs. Results indicate that the linear matrix inequality approach leads to a simple controller, successfully alleviates the stick-slip problem, and is robust to uncertainties.
Dissolution Douce of Single Walled Carbon Nanotubes (2005)

This report deals with the “dissolution douce” or mild dissolution of single wall carbon nanotubes (SWNT), i.e a gentle way to obtain concentrated true solutions of SWNTs without functionalization, strongly acidic treatment and /or sonication thus keeping full integrity of the SWNT samples. Chemical reduction of SWNTs yields polyelectrolyte alkali metal salts of nanotubes, spontaneously soluble in polar organic solvent. The resulting solutions are indefinitely stable if kept under inert atmosphere.
Pattern-integrated interference lithography: single-exposure fabrication of photonic-crystal structures (2012)

Multibeam interference represents an approach for producing one-, two-, and three-dimensional periodic optical-intensity distributions with submicrometer features and periodicities. Accordingly, interference lithography (IL) has been used in a wide variety of applications, typically requiring additional lithographic steps to modify the periodic interference pattern and create integrated functional elements. In the present work, pattern-integrated interference lithography (PIIL) is introduced. PIIL is the integration of superposed pattern imaging with IL. Then a pattern-integrated interference exposure system (PIIES) is presented that implements PIIL by incorporating a projection imaging capability in a novel three-beam interference configuration. The purpose of this system is to fabricate, in a single-exposure step, a two-dimensional periodic photonic-crystal lattice with nonperiodic functional elements integrated into the periodic pattern. The design of the basic system is presented along with a model that simulates the resulting optical-intensity distribution at the system sample plane where the three beams simultaneously interfere and integrate a superposed image of the projected mask pattern. Appropriate performance metrics are defined in order to quantify the characteristics of the resulting photonic-crystal structure. These intensity and lattice-vector metrics differ markedly from the metrics used to evaluate traditional photolithographic imaging systems. Simulation and experimental results are presented that demonstrate the fabrication of example photonic-crystal structures in a single-exposure step. Example well-defined photonic-crystal structures exhibiting favorable intensity and lattice-vector metrics demonstrate the potential of PIIL for fabricating dense integrated optical circuits.