gebhart/patrepeval huggingface dataset:
Super-resolution imaging with mid-IR photothermal microscopy on the single particle level (2015)

Photothermal microscopy has achieved single molecule sensitivity. However, the analytes are usually restricted to be natural absorbers in the visible light region. Mid-infrared (MIR) imaging, on the other hand, provides a wealth of information, but encounters difficulties of diffraction-limited spatial resolution and scarcity of ideal detectors. Here we present Mid-IR photothermal heterodyne imaging (MIR-PHI) microscopy as a high sensitivity, super-resolution mid-IR imaging technique. In MIR-PHI, a tunable Mid- IR pulsed laser at 150 kHz is used to excite a micron sized particle. Energy relaxation creates a temperature gradient around the particle, changing the refractive index of the surrounding solvent and creating a thermal lens. A collinear, counter propagating probe beam (a 532 nm CW laser) is modified by the thermal lens and generates a super-resolution photothermal image. We studied 1.1 μm polystyrene beads at the single particle level using this technique. Various solvents with different heat capacities and refractive indices are tested for the best image contrast. The wide applicability and potentially high sensitivity of this technique make it promising for biological imaging and identification.
Consistency of partitionable object groups in a CORBA framework (2002)

The Eternal system provides a novel methodology for the consistent replication of objects in an adaptive, fault-tolerant, CORBA-compliant distributed system that is susceptible to partitioning. Passive and active replication schemes are supported in Eternal, and mechanisms are provided for the interaction of objects with different replication schemes. Nested operations for both passive and active objects are accommodated. Suppression of duplicate operations is ensured by unique message and operation identifiers. Continued operation is allowed in all components of a partitioned system. State transfer mechanisms and fulfillment operations restore the consistency of the states of replicas within the components of a partitioned system when communication is reestablished and the components remerge.
Involving CPUs into Multi-GPU Deep Learning (2018)

The most important part of deep learning, training the neural network, often requires the processing of a large amount of data and can takes days to complete. Data parallelism is widely used for training deep neural networks on multiple GPUs in a single machine thanks to its simplicity. However, its scalability is bound by the number of data transfers, mainly for exchanging and accumulating gradients among the GPUs. In this paper, we present a novel approach to data parallel training called CPU-GPU data parallel (CGDP) training that utilizes free CPU time on the host to speed up the training in the GPUs. We also present a cost model for analyzing and comparing the performances of both the typical data parallel training and the CPU-GPU data parallel training. Using the cost model, we formally show why our approach is better than the typical one and clarify the remaining issues. Finally, we explain how we optimized CPU-GPU data parallel training by introducing chunks of layers and present a runtime algorithm that automatically finds a good configuration for the training. The algorithm is effective for very deep neural networks, which are the current trend in deep learning. Experimental results showed that we achieved speedups of $1.21$, $1.04$, $1.21$ and $1.07$ for four state-of-the-art neural networks: AlexNet, GoogLeNet-v1, VGGNet-16, and ResNet-152, respectively. Weak scaling efficiency greater than $90$ was achieved for all networks across four GPUs.
MemX (2007)

Modern grid computing and enterprise applications increasingly execute on clusters that rely upon virtual machines (VMs) to partition hardware resources and improve utilization efficiency. These applications tend to have memory and I/O intensive workloads, such as large databases, data mining, scientific workloads, and web services, which can strain the limited I/O and memory resources within a single VM. In this paper, we present our experiences in developing a fully transparent distributed system, called MemX, within the Xen VM environment that coordinates the use of cluster-wide memory resources to support large memory and I/O intensive workloads. Applications using MemX do not require specialized APIs, libraries, recompilation, relinking, or dataset pre-partitioning. We compare and contrast the different design choices in MemX and present preliminary performance evaluation using several resource-intensive benchmarks in both virtualized and non-virtualized Linux. Our evaluations show that large dataset applications and multiple concurrent VMs achieve significant speedups using MemX compared against virtualized local and iSCSI disks. As an added benefit, we also show that live Xen VMs using MemX can migrate seamlessly without disrupting any running applications.
Helical antimicrobial polypeptides with radial amphiphilicity (2015)

α-Helical antimicrobial peptides (AMPs) generally have facially amphiphilic structures that may lead to undesired peptide interactions with blood proteins and self-aggregation due to exposed hydrophobic surfaces. Here we report the design of a class of cationic, helical homo-polypeptide antimicrobials with a hydrophobic internal helical core and a charged exterior shell, possessing unprecedented radial amphiphilicity. The radially amphiphilic structure enables the polypeptide to bind effectively to the negatively charged bacterial surface and exhibit high antimicrobial activity against both gram-positive and gram-negative bacteria. Moreover, the shielding of the hydrophobic core by the charged exterior shell decreases nonspecific interactions with eukaryotic cells, as evidenced by low hemolytic activity, and protects the polypeptide backbone from proteolytic degradation. The radially amphiphilic polypeptides can also be used as effective adjuvants, allowing improved permeation of commercial antibiotics in bacteria and enhanced antimicrobial activity by one to two orders of magnitude. Designing AMPs bearing this unprecedented, unique radially amphiphilic structure represents an alternative direction of AMP development; radially amphiphilic polypeptides may become a general platform for developing AMPs to treat drug-resistant bacteria.
Wavelet transform based watermark for digital images (1998)

In this paper, we introduce a new multiresolution watermarking method for digital images. The method is based on the discrete wavelet transform (DWT). Pseudo-random codes are added to the large coefficients at the high and middle frequency bands of the DWT of an image. It is shown that this method is more robust to proposed methods to some common image distortions, such as the wavelet transform based image compression, image rescaling/stretching and image halftoning. Moreover, the method is hierarchical.
Application of the Hilbert-Huang Transform to Financial Data (2005)

A paper discusses the application of the Hilbert-Huang transform (HHT) method to time-series financial-market data. The method was described, variously without and with the HHT name, in several prior NASA Tech Briefs articles and supporting documents. To recapitulate: The method is especially suitable for analyzing time-series data that represent nonstationary and nonlinear phenomena including physical phenomena and, in the present case, financial-market processes. The method involves the empirical mode decomposition (EMD), in which a complicated signal is decomposed into a finite number of functions, called "intrinsic mode functions" (IMFs), that admit well-behaved Hilbert transforms. The HHT consists of the combination of EMD and Hilbert spectral analysis. The local energies and the instantaneous frequencies derived from the IMFs through Hilbert transforms can be used to construct an energy-frequency-time distribution, denoted a Hilbert spectrum. The instant paper begins with a discussion of prior approaches to quantification of market volatility, summarizes the HHT method, then describes the application of the method in performing time-frequency analysis of mortgage-market data from the years 1972 through 2000. Filtering by use of the EMD is shown to be useful for quantifying market volatility.
Repurposing the Clinically Efficacious Antifungal Agent Itraconazole as an Anticancer Chemotherapeutic (2016)

Itraconazole (ITZ) is an FDA-approved member of the triazole class of antifungal agents. Two recent drug repurposing screens identified ITZ as a promising anticancer chemotherapeutic that inhibits both the angiogenesis and hedgehog (Hh) signaling pathways. We have synthesized and evaluated first- and second-generation ITZ analogues for their anti-Hh and antiangiogenic activities to probe more fully the structural requirements for these anticancer properties. Our overall results suggest that the triazole functionality is required for ITZ-mediated inhibition of angiogenesis but that it is not essential for inhibition of Hh signaling. The synthesis and evaluation of stereochemically defined des-triazole ITZ analogues also provides key information as to the optimal configuration around the dioxolane ring of the ITZ scaffold. Finally, the results from our studies suggest that two distinct cellular mechanisms of action govern the anticancer properties of the ITZ scaffold.
Nuclease resistant oligonucleotides with cell penetrating properties (2015)

2'-O-AECM modified oligonucleotides provide an unusual combination of remarkable properties. This includes the combination of high resistance towards enzymatic degradation and the spontaneous cellular uptake of AECM oligonucleotides.
SHALE (2012)

Motivated by the problem of optimizing allocation in guaranteed display advertising, we develop an efficient, lightweight method of generating a compact allocation plan that can be used to guide ad server decisions. The plan itself uses just O(1) state per guaranteed contract, is robust to noise, and allows us to serve (provably) nearly optimally.
Direct printing of aligned carbon nanotube patterns for high-performance thin film devices (2009)

The aligned assembly of carbon nanotubes (CNTs) on substrate presents a significant bottleneck in the fabrication of high-performance thin film devices. Here, we report a direct printing method to prepare laterally aligned thick CNT patterns over large surface regions. In this method, CNT forests were grown selectively on specific regions of one substrate, and the forest patterns were transferred on another SiO2 substrate in a laterally aligned formation while keeping their original shapes. The degree of alignment was characterized via electrical measurement and polarized Raman spectroscopy. Furthermore, we demonstrated high-performance field-effect transistors and gas sensors using our method.
A machine‐independent debugger — revisited (1999)

Most debuggers are notoriously machine-dependent, but some recent research prototypes achieve varying degrees of machine-independence with novel designs. Cdb, a simple source-level debugger for C, is completely independent of its target architecture. This independence is achieved by embedding symbol tables and debugging code in the target program, which costs both time and space. This paper describes a revised design and implementation of cdb that reduces the space cost by nearly one-half and the time cost by 13 per cent by storing symbol tables in external files. A symbol table is defined by a 31-line grammar in the Abstract Syntax Description Language (ASDL). ASDL is a domain-specific language for specifying tree data structures. The ASDL tools accept an ASDL grammar and generate code to construct, read, and write these data structures. Using ASDL automates implementing parts of the debugger, and the grammar documents the symbol table concisely. Using ASDL also suggested simplifications to the interface between the debugger and the target program. Perhaps most important, ASDL emphasizes that symbol tables are data structures, not file formats. Many of the pitfalls of working with low-level file formats can be avoided by focusing instead on high-level data structures and automating the implementation details. Copyright © 1999 John Wiley & Sons, Ltd.
Extreme ultraviolet lithography mask patterning and printability studies with a Ta-based absorber (1999)

Extreme ultraviolet (EUV) lithography masks were fabricated using a stack of TaSi or TaSiN (absorber), SiON (repair buffer), and Cr (conductive etch stop) on a Mo/Si multilayer mirror deposited on a Si wafer. High-resolution structures were exposed using a commercial i-line resist, and the pattern was transferred using both electron cyclotron resonance and reactive ion etching with halogen-based gases. Process temperatures to fabricate these reticles were always maintained below 150 °C. EUV properties after patterning were measured using a synchrotron source reflectometer. Completed masks exhibited a negligible shift in the peak wavelength and less than 2% loss in reflectivity due to processing. Qualified masks were exposed with a 10× EUV exposure system. The exposures were made in 80-nm-thick DUV resist and with numerical apertures (NA) of 0.08, 0.088, and 0.1. Resolution down to 70 nm equal lines and spaces was achieved at a NA of 0.1. Line edge roughness in the resist features was 5.5 nm (3σ, one side), and the depth of focus for ±10% CD control was ±1 μm for 100 nm equal lines and spaces.
A Pilot Randomized Controlled Trial of a New Supplementary Food Designed to Enhance Cognitive Performance during Prevention and Treatment of Malnutrition in Childhood (2017)

These preliminary data suggest that cognitive impairment can be monitored with measurement of CBF. In addition, the findings provide preliminary data that suggest that it may be possible to improve poor cognitive performance in young children through changes in the nutritional formulation of supplementary foods used to prevent and treat MAM. Powered studies of the new supplement formulation are needed. This trial was registered at clinicaltrials.gov as NCT03017209.
Analysis of cone beam reconstruction in computer tomography (2003)

In this work we develop a framework for tomographic reconstruction in both R2 and R3 . Starting with R2 we develop a shift-invariant FBP-type reconstruction formula for the fan-beam data, which allows a very efficient implementation. Then we proceed with a formula for R3 , which is more complicated. This exact formula, known as Katsevich's formula, represents a continuous family of reconstruction algorithms with some parameter ψ. The main topic of this work is to analyze this non-uniqueness of the reconstruction and to show that the result is independent of the choice of ψ, i.e. that all these algorithms are mathematically equivalent. 
In Chapter 1 we introduce the Radon transform, discuss its properties and inversion formulas. In Chapter 2 we introduce the cone beam transform and establish its relation with the Radon transform. Then, in Chapter 3 we discuss the reconstruction problem in R2 and propose a new efficient approximate reconstruction formula. Chapter 4 is devoted to cone beam reconstruction: we introduce the main ideas and describe Katsevich's result. Finally, in Chapter 5 we analyze the nature of non-uniqueness arising in the Katsevich formula. Chapter 6 summarizes the paper.
Stochastic Depth Buffer Compression using Generalized Plane Encoding (2013)

Abstract In this paper, we derive compact representations of the depth function for a triangle undergoing motion or defocus blur. Unlike a static primitive, where the depth function is planar, the depth function is a rational function in time and the lens parameters. Furthermore, we show how these compact depth functions can be used to design an efficient depth buffer compressor/decompressor, which significantly lowers total depth buffer bandwidth usage for a range of test scenes. In addition, our compressor/decompressor is simpler in the number of operations needed to execute, which makes our algorithm more amenable for hardware implementation than previous methods.
Tunable Multiband Microwave Photonic Filters (2017)

The increasing demand for multifunctional devices, the use of cognitive wireless technology to solve the frequency resource shortage problem, as well as the capabilities and operational flexibility necessary to meet ever-changing environment result in an urgent need of multiband wireless communications. Spectral filter is an essential part of any communication systems, and in the case of multiband wireless communications, tunable multiband RF filters are required for channel selection, noise/interference removal, and RF signal processing. Unfortunately, it is difficult for RF electronics to achieve both tunable and multiband spectral filtering. Recent advancements of microwave photonics have proven itself to be a promising candidate to solve various challenges in RF electronics including spectral filtering, however, the development of multiband microwave photonic filtering still faces lots of difficulties, due to the limited scalability and tunability of existing microwave photonic schemes. In this review paper, we first discuss the challenges that were facing by multiband microwave photonic filter, then we review recent techniques that have been developed to tackle the challenge and lead to promising developments of tunable microwave photonic multiband filters. The successful design and implementation of tunable microwave photonic multiband filter facilitate the vision of dynamic multiband wireless communications and radio frequency signal processing for commercial, defense, and civilian applications.
Application of Polymerase Chain Reaction to Determine the Flocculation Properties of Brewer's Lager Yeast (2001)

We developed a polymerase chain reaction method to determine the flocculation ability of yeast based on one of the flocculation genes. More than 30 brewer's lager yeast strains were examined, and the amplification of the targeted flocculation gene was confirmed in all of the flocculating yeast strains. The method was also successfully applied to the early detection of nonflocculating mutants by examining yeast cells individually. In some applications, we were able to determine the cause genetically when yeast suddenly did not flocculate and failed to sediment toward the end of fermentation. This method not only yields rapid results but also offers reliability and reproducibility.
Black Ge Based on Crystalline/Amorphous Core/Shell Nanoneedle Arrays (2009)

Direct growth of black Ge on low-temperature substrates, including plastics and rubber is reported. The material is based on highly dense, crystalline/amorphous core/shell Ge nanoneedle arrays with ultrasharp tips ( approximately 4 nm) enabled by the Ni catalyzed vapor-solid-solid growth process. Ge nanoneedle arrays exhibit remarkable optical properties. Specifically, minimal optical reflectance (<1%) is observed, even for high angles of incidence ( approximately 75 degrees ) and for relatively short nanoneedle lengths ( approximately 1 mum). Furthermore, the material exhibits high optical absorption efficiency with an effective band gap of approximately 1 eV. The reported black Ge could potentially have important practical implications for efficient photovoltaic and photodetector applications on nonconventional substrates.
Edge-guided resolution enhancement in projectors via optical pixel sharing (2012)

Digital projection technology has improved significantly in recent years. But, the relationship of cost with respect to available resolution in projectors is still super-linear. In this paper, we present a method that uses projector light modulator panels (e.g. LCD or DMD panels) of resolution n X n to create a perceptually close match to a target higher resolution cn X cn image, where c is a small integer greater than 1. This is achieved by enhancing the resolution using smaller pixels at specific regions of interest like edges. A target high resolution image ( cn X cn ) is first decomposed into (a) a high resolution ( cn X cn ) but sparse edge image , and (b) a complementary lower resolution ( n X n ) non-edge image . These images are then projected in a time sequential manner at a high frame rate to create an edge-enhanced image -- an image where the pixel density is not uniform but changes spatially. In 3D ready projectors with readily available refresh rate of 120Hz, such a temporal multiplexing is imperceptible to the user and the edge-enhanced image is perceptually almost identical to the target high resolution image. To create the higher resolution edge image, we introduce the concept of optical pixel sharing . This reduces the projected pixel size by a factor of 1/ c 2 while increasing the pixel density by c 2 at the edges enabling true higher resolution edges. Due to the sparsity of the edge pixels in an image we are able to choose a sufficiently large subset of these to be displayed at the higher resolution using perceptual parameters. We present a statistical analysis quantifying the expected number of pixels that will be reproduced at the higher resolution and verify it for different types of images.
Flossing DNA in a Dual Nanopore Device (2019)

Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single-molecule data. Here, an active control technique termed "flossing" that uses a dual nanopore device is presented to trap a proteintagged DNA molecule and up to 100's of back-and-forth electrical scans of the molecule are performed in a few seconds. The protein motifs bound to 48.5 kb λ-DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multiscan data to produce averaged intertag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.