gebhart/patrepeval huggingface dataset:
Communication Lower-Bounds for Distributed-Memory Computations for Mass\n Spectrometry based Omics Data (2020)

Mass spectrometry (MS) based omics data analysis require significant time and\nresources. To date, few parallel algorithms have been proposed for deducing\npeptides from mass spectrometry-based data. However, these parallel algorithms\nwere designed, and developed when the amount of data that needed to be\nprocessed was smaller in scale. In this paper, we prove that the communication\nbound that is reached by the \\emph{existing} parallel algorithms is\n$\\Omega(mn+2r\\frac{q}{p})$, where $m$ and $n$ are the dimensions of the\ntheoretical database matrix, $q$ and $r$ are dimensions of spectra, and $p$ is\nthe number of processors. We further prove that communication-optimal strategy\nwith fast-memory $\\sqrt{M} = mn + \\frac{2qr}{p}$ can achieve\n$\\Omega({\\frac{2mnq}{p}})$ but is not achieved by any existing parallel\nproteomics algorithms till date. To validate our claim, we performed a\nmeta-analysis of published parallel algorithms, and their performance results.\nWe show that sub-optimal speedups with increasing number of processors is a\ndirect consequence of not achieving the communication lower-bounds. We further\nvalidate our claim by performing experiments which demonstrate the\ncommunication bounds that are proved in this paper. Consequently, we assert\nthat next-generation of \\emph{provable}, and demonstrated superior parallel\nalgorithms are urgently needed for MS based large systems-biology studies\nespecially for meta-proteomics, proteogenomic, microbiome, and proteomics for\nnon-model organisms. Our hope is that this paper will excite the parallel\ncomputing community to further investigate parallel algorithms for highly\ninfluential MS based omics problems.\n
Fluorocarbon−Organosilicon Copolymer Synthesis by Hot Filament Chemical Vapor Deposition (2002)

Hot-filament chemical vapor deposition has been used to deposit copolymer thin films consisting of fluorocarbon and organosilicon groups from hexafluoropropylene oxide (HFPO) and hexamethylcyclotrisiloxane (D3). This method offers an easy route to the production of such copolymers as the process does not require a solvent and can be performed in a single step. The presence of covalent bonds between the fluorocarbon and organosilicon moieties in the thin films has been confirmed by infrared spectroscopy; X-ray photoelectron spectroscopy (XPS); and solid-state 19F, 13C, and 29Si nuclear magnetic resonance (NMR) spectroscopy. The film structure consists of chains with linear and cyclic siloxane groups and CF2 groups as repeat units. Cross-linking and termination occur mainly via the siloxane units.
MicroRNA-Cancer Connection: The Beginning of a New Tale (2008)

Cancer initiation and progression can involve microRNAs (miRNA), which are small noncoding RNAs that can regulate gene expression. Their expression profiles can be used for the classification, diagnosis, and prognosis of human malignancies. Loss or amplification of miRNA genes has been reported in a variety of cancers, and altered patterns of miRNA expression may affect cell cycle and survival programs. Germ-line and somatic mutations in miRNAs or polymorphisms in the mRNAs targeted by miRNAs may also contribute to cancer predisposition and progression. We propose that alterations in miRNA genes play a critical role in the pathophysiology of many, perhaps all, human cancers.
H-Plane Mode Conversion and Application in Printed Microwave Integrated Circuit (2000)

This paper presents a novel MIC (microwave integrated circuit) design methodology, which consistently applies the H-plane discontinuity structures to integrate a multi-function microwave RF module using conventional PCB (printed-circuit-board) fabrication process. Two distinct types of waveguide, namely, microstrip and metallic rectangular waveguide, are simultaneously integrated on the same substrate(s) through the interface mode converters. An X-band MIC filter prototype, consisting of two H-plane mode converters and six H-plane waveguide slits, is built and tested, showing an attractive filter performance and a great potential for implementing the proposed MIC design methodology.
Pancreatic Cancer Stem Cells: Implications for the Treatment of Pancreatic Cancer (2008)

Pancreatic cancer is a highly lethal disease that is usually diagnosed at a late stage for which there are few effective therapies. Emerging evidence has suggested that malignant tumors are quite heterogeneous and that they are composed of a small subset of distinct cancer cells (usually defined by cell surface marker expression) that are responsible for tumor initiation and propagation, termed cancer stem cells. These cells are termed cancer stem cells because, like normal stem cells, they possess the ability to self-renew and make differentiated progeny. Recent studies of human pancreatic cancers have shown a population of pancreatic cancer stem cells that have aberrantly activated developmental signaling pathways, are resistant to standard chemotherapy and radiation, and have up-regulated signaling cascades that are integral for tumor metastasis. An improved understanding of the biological behavior of these cells may lead to more effective therapies to treat pancreatic cancer. In this review, approaches to develop and test therapeutics targeting pancreatic cancer stem cells are discussed.
Millimeter-wave spectrometer for pollution research (1977)

A microwave spectrometer for the detection of gaseous pollutants is described.The spectrometer operates at frequencies in the vicinity of 70 GHz and employs a Fabry-Perot interferometer as a sample cell.The interferometer is voltage tuned by means of a piezoelectric transducer which enables it to track the microwave source frequency.The operation and performance of the instrument is discussed and illustrated by measurements of diluted samples of sulfur dioxide.The noise contributions which limit the sensitivity are described and suggestions for future improvements are noted.
Two elephants in the room (2015)

Recent advances in NMR and mass spectrometry-based metabolomics and their synergistic use promises to significantly improve metabolomics sample characterization both in terms of identification and quantitation, and accelerate metabolite discovery.
Short-Range Radio Communications System for Military Operations in Built-up Areas (1977)

Abstract : Dispersive-surface-acoustic wave devices were employed in an experimental spread-spectrum communications system for the transmission of voice and tone signals via radio and via urban media. A short-range clandestine communications capability was demonstrated with this system competing with standard VHF radio transceivers.
Mid-infrared lasers in hydrogen and deuterium (1982)

New laser lines at 3.71 and 3.84 μm in hydrogen and lines at 4.52, 4.60, and 4.71 μm in deuterium excited by a pulsed electrical discharge have been obtained. The lines in hydrogen are assigned to the a 3Σ+g → c 3Πu triplet band, but the lines in deuterium have not yet been assigned. Direct electronic excitation from the ground state to the a 3Σ+g state is believed to be the excitation mechanism, and indicates that an excimer-type laser from the a 3Σ+g upper state to the dissociative b 3Σ+u state may be possible.
Cardiovascular effect of L-arginine (1998)

Most of the known cardiovascular effects of L-arginine are exerted via its conversion to nitric oxide by nitric oxide synthase. Accumulating evidence indicates that supplemental administration of L-arginine is sufficient to restore endothelium-derived nitric oxide production in many disorders in which endothelium-derived nitric oxide production is altered. L-arginine may enhance nitric oxide production by competing as a substrate with an endogenous antagonist for nitric oxide synthase. In other cases, L-arginine may act by competing with molecular oxygen as a substrate so as to reduce the production of superoxide anion. It is likely that other mechanisms exist by which the nitric oxide synthase pathway can be perturbed. Regardless of the mechanism, a wide array of cardiovascular disorders characterized by endothelial dysfunction are reversible by L-arginine.
Strategies for lung regeneration (2011)

Due to the limited ability of the adult lung to regenerate and the frequency of lung disease, the lung is a tissue that can especially benefit from regenerative medicine. Prospects for lung regeneration have made great strides in the past year. In this review, we summarize recent progress and key challenges for approaches in lung regenerative medicine. With a focus on the matrix components critical for the development of regenerative lung tissues, we discuss possible cell sources for lung regeneration, key matrix effects on cell repopulation, and physical stimuli that will aid in the growth of lung tissues in vitro.
Evaluation of Distillation and Diffusion Techniques for Estimating Hydrolyzable Amino Sugar‐Nitrogen as a Means of Predicting Nitrogen Mineralization (2008)

A rapid method to estimate soil N mineralization to improve N fertilizer recommendations has long been sought. Over the years, numerous methods to predict N mineralization have been proposed, but no one method has been widely accepted. Recently, researchers observed the concentration of hydrolyzable amino sugar‐N in the soil correlated with crop N response. The objective of this study was to determine if developmental methods that quantify hydrolyzable amino sugar‐N accurately predict N mineralization when compared to net‐N mineralization by anaerobic incubation. Methods evaluated to predict hydrolyzable amino sugar‐N were the Illinois soil nitrogen test (ISNT) by diffusion, and 2, 5, and 10 M NaOH direct steam distillation procedures. It was observed that the hydrolyzable amino sugar‐N was a somewhat accurate predictor of N mineralization ( R 2 = 0.38). However, when the hydrolyzable amino sugar‐N concentrations were combined with the hydrolyzable NH 4 –N concentrations, the ability to predict N mineralization improved ( R 2 = 0.61). Suggesting more labile soil organic N forms along with amino sugar‐N are potentially mineralizable. Rapid analytical procedures like the ISNT diffusion method and the 2, 5, and 10 M NaOH direct steam distillation techniques accurately predicted hydrolyzable amino sugar‐N as well as hydrolyzable (NH 4 + amino sugar)‐N. These methods also accurately predicted NH 4 –N mineralized after anaerobic incubation. It could be assumed that this predictability may increase when soils are analyzed based on soil management, geographic area, and crop rotation. Glucosamine recovery was significant ( >85%, P = 0.05) for both methods showing their ability to quantify amino sugar‐N in the soil as well as estimate the amount of potentially mineralizable‐N. Lastly, in soil‐testing facilities where the ISNT is already implemented as a procedure, the much quicker and equally reliable 10 M NaOH distillation technique may be used to achieve near identical test values.
Using Small Molecules to Improve Generation of Induced Pluripotent Stem Cells from Somatic Cells (2010)

Induction of pluripotent stem cells from somatic cells by defined factors was shown to be possible only recently, but already several laboratories have made tremendous strive toward improving and understanding the process. Originally, Oct4, Sox2, Klf4, and cMyc were identified as being the combination of genes necessary to induce reprogramming. It was later shown that cMyc was dispensable; however, in its absence the process was less efficient and took a considerably longer period of time to occur. Furthermore, others have shown that the combination of Oct4, Sox2, Nanog, and Lin28 could also induce reprogramming. One major caveat associated with these techniques remains the need for overexpression of several genes using viral systems. Until very recently, most studies were done using integrating viruses such as retroviruses and lentiviruses. This method ensured that the protein of interested would be expressed at a high concentration and for an adequate period of time necessary to induce reprogramming. Up to date, others have now been able to use different nonintegrative method such as adenovirus and plasmid transfection to induce reprogramming. Furthermore, piggyBac transposition was successfully used to induce reprogramming of murine cells. Most importantly, it was recently published that reprogramming can be induced in the absence of virus, with proteins and small molecules. All of the later methods are appealing since they do not require the integration of the virus or plasmid to exert its effect. However, one avenue that would be all the more therapeutically appealing would be to induce reprogramming in the absence of gene overexpression systems, using small molecules to modulate signaling pathways in the somatic cells. A few molecules have already been identified with the ability to either improve the process or replace one or two of the genes deemed necessary for reprogramming. We have screened successfully for compounds that can replace some of these factors, and share the methods developed following these screens.
Direct patterning of composite biocompatible microstructures using microfluidics (2007)

This study demonstrates a versatile and fast method for patterning three-dimensional (3D) monolithic microstructures made of multiple (up to 24 demonstrated) types of materials, all spatially aligned, inside a microchannel. This technique uses confocal scanning or conventional fluorescence microscopy to polymerize selected regions of a photocurable material, and microfluidics to automate the delivery of a series of washes and photocurable reagents. Upon completion of lithographic cycles, the aligned 3D microstructures are suitable for microfluidic manipulation and analysis. We demonstrated the fabrication of composite 3D microstructures with various geometries, size scales (up to 1 mm2), spatial resolution (down to 3 microm), and materials. For a typical multi-cycle process, the total fabrication time was tens of minutes, compared to tens of hours for conventional methods. In the case of 3D hydrogels, a potential use is the direct patterning of inhomogeneous 3D microenvironments for studying cell behavior.
Nondestructive Identification of Individual Leukemia Cells by Laser Trapping Raman Spectroscopy (2008)

Currently, a combination of technologies is typically required to assess the malignancy of cancer cells. These methods often lack the specificity and sensitivity necessary for early, accurate diagnosis. Here we demonstrate using clinical samples the application of laser trapping Raman spectroscopy as a novel approach that provides intrinsic biochemical markers for the noninvasive detection of individual cancer cells. The Raman spectra of live, hematopoietic cells provide reliable molecular fingerprints that reflect their biochemical composition and biology. Populations of normal T and B lymphocytes from four healthy individuals and cells from three leukemia patients were analyzed, and multiple intrinsic Raman markers associated with DNA and protein vibrational modes have been identified that exhibit excellent discriminating power for cancer cell identification. A combination of two multivariate statistical methods, principal component analysis (PCA) and linear discriminant analysis (LDA), was used to confirm the significance of these markers for identifying cancer cells and classifying the data. The results indicate that, on average, 95% of the normal cells and 90% of the patient cells were accurately classified into their respective cell types. We also provide evidence that these markers are unique to cancer cells and not purely a function of differences in their cellular activation.
Human Adenovirus Type 36 Enhances Glucose Uptake in Diabetic and Nondiabetic Human Skeletal Muscle Cells Independent of Insulin Signaling (2008)

Ad-36 infection increases glucose uptake in HSKM cells via Ras-activated PI 3-kinase pathway in an insulin-independent manner. These findings may provide impetus to exploit the role of Ad-36 proteins as novel therapeutic targets for improving glucose handling.
A New Predictive Modality of Cranial Bone Thickness (1999)

The objective of this study was to evaluate A-mode ultrasound in the assessment of cranial bone thickness utilizing an in vivo animal model. A prospective study was performed that identified four standardized calvarial points in 10 Landrace porcine skulls. The individual points were scanned with an A-mode ultrasonic transducer to obtain bone thickness measurements. The same points were measured subsequently using digital calipers for objective comparison. The accuracy of each of the measurement modalities was evaluated for inter- and intrarater reliability. The association between ultrasonic and caliper measurements was evaluated using Student's t-test, Pearson's correlation coefficient, and linear regression models to assess the effect of confounding variables. The mean difference between the ultrasonic and the caliper values was 0.31 +/- 0.22 mm (standard deviation). The statistical analyses employed strongly supported the predictive value of ultrasound as a function of the true calvarial thickness (p < 0.05, r > 0.88, R2 = 0.89). The results suggest that ultrasound is an accurate reflection of cranial bone thickness in an in vivo animal skull model. The development of a portable, noninvasive ultrasonic device can have substantial clinical implications for craniomaxillofacial surgery.
Acoustic Device Would Measure Density Of Gas (1992)

Proposed acoustic sensor measures density of flowing gas or mixture of gases. Constructed in variety of configurations for use in monitoring industrial processes. Basic configuration, sensor comprises narrow tube closed at one end and open at other, sound transmitter located in closed end, and microphone located part way along tube. Entire sensor, or at least open end of tube, placed inside pipe or vessel containing gas, density of which measured. Transducer produces constant-velocity-amplitude sound waves at frequency lower than fundamental resonant frequency of tube.
Film thickness dependence of magneto-optical and magnetic properties in Co/Pt and Co/Pd multilayers (1990)

Co/Pt and Co/Pd multilayers were prepared by two source dc-magnetron sputtering. It was found that magneto-optical and magnetic properties of the multilayers were affected by total film thickness. Kerr rotation angle of the films was remarkably enhanced at the film thickness below several hundred angstroms. The theoretical calculation clarified that the increase of Kerr rotation was due to optical interference and multiple reflection. The shape of Kerr loop also depends upon the film thickness and a perfect squareness is attained only at the ultrathin region. The improvement in the squareness of Kerr loop can be explained by the change in the domain structure from a stripe domain to a single domain. These behaviors at the ultrathin region in the multilayers are suitable for new magneto-optical recording media.
Miniaturized-element frequency selective surfaces with narrowband, higher-order bandpass responses (2015)

The selectivity and response type of the frequency response of a frequency selective surface (FSS) are important factors that determine the suitability of an FSS for a given application. A common application of FSSs is to use them to shield sensitive electronic devices form unwanted interference or jamming signals with frequencies close to the main transmission band of the device. In such situations, spatial filters with highly-selective and narrowband transmission windows are required. FSSs with higher-order bandpass or bandstop responses acts similar to coupled-resonator filters. Therefore, their operational bandwidths are inversely related to quality factors of their resonators. Thus, to achieve a narrow-band response, higher quality factors are needed. For the case of traditional FSSs, these resonators are created using resonant elements within a unit cell. Miniaturized-element frequency selective surfaces (MEFSSs), on the other hand, use the combination of non-resonant reactive surfaces with capacitive and inductive surface impedances to create distributed-type resonators. For both approaches, the minimum-attainable feature sizes used in the metallic patterns of the structures are the bottleneck of achieving high quality-factor resonators. In practice, the minimum gap spacing and trace widths are determined by the minimum feature size that can be reliably fabricated using standard PCB lithography techniques. Therefore, achieving very high-quality factors and accordingly narrowband frequency responses for both configurations is rather challenging.
An Augmented Reality Guided Capture Platform for Structured and Consistent Product Reference Imagery (2021)

Within e-commerce, vendors require high quality, consistent reference imagery to showcase products. Capturing correct images is difficult when photographic intent has to be conveyed through written instructions, as lack of real-time guidance leads to subjectivity in the interpretation of directions. Hiring professional photographers to conform to specific aesthetics can be expensive. The ubiquity of mobile devices and rapid improvements in augmented reality have facilitated the creation of experiences with in-situ guidance. We present Guided Capture, a mobile application utilizing augmented reality to enable structured capture of consistent user-generated content for reference imagery with real-time feedback. Results from user studies have shown that our system creates a streamlined feedback loop to reduce possible user error, scalable across large groups of people.
Enhancement of contrast echocardiography by image variability analysis (2001)

CVI can substantially enhance endocardial border delineation and improve echocardiographic image quality and image interpretation.
Optical processing of composite pattern structured light projection for high-speed depth measurement (2004)

Structured light pattern projection is a well known method of accurately extracting 3-Dimensional information of a scene. Traditional multi-frame structured light methods require several different patterns to recover the depth, without ambiguity and albedo sensitivity, and are corrupted by object motion during the projection/capture process. The authors have developed a methodology for combining multiple patterns into a single composite pattern by using spatial modulation techniques. A single composite pattern projection does not require synchronization with the camera so the data acquisition rate is only limited by the video rate and therefore suitable for high-speed depth measurement. However, the composite pattern is restrained by the spatial bandwidth directly related to the number of embedded patterns and the lateral resolution of the camera. Another problem is the processing requires image demodulation which is computational intensive. As part of a NASA Phase I STTR, we address the first limitation by analysis of the source of the error and post-processing the reconstruction data with dynamic programming approach. For the second problem we propose the use of a 4-f optical correlator, not as a correlator, but instead as an optical demodulator. Simulation results show reasonable depth reconstruction using our strategy for composite pattern after the post-processing.