gebhart/patrepeval huggingface dataset:
Generation of photoacoustic sound for gases in an open environment (2000)

Photoacoustics is the generation of acoustic waves due to unsteady heating from a light source. It was discovered over 119 years ago and is commonly used for trace gas detection and molecular spectroscopy when the photoactive gas or gas mixture is contained in a chamber. However, photoacoustic phenomena are less well characterized in an open environment. In this presentation, scaling laws for radiated photoacoustic sound pressure are developed from dimensional analysis and verified with experiments using a carbon dioxide laser tuned to 10.6 μm and small plumes of sulfur hexafluoride, a photoactive tracer gas. In addition, a forced wave equation that includes laser-gas heating is developed to predict the generation and propagation of photoacoustic sound. Using this forced wave equation, the shape and amplitude of photoacoustic sound pulses are determined based on the shape of the tracer-gas plume and the extent of laser-beam absorption through the Lambert–Beer law. The model results are compared to measured photoacoustic signal pulses and show favorable agreement. [Work supported by Ford Motor Company.]
Design of inhibitors against HIV, HTLV-I, and Plasmodium falciparum aspartic proteases (2004)

Aspartic proteases have emerged as targets for substrate-based inhibitor design due to their vital roles in the life cycles of the organisms that cause AIDS, malaria, leukemia, and other infectious diseases. Based on the concept of mimicking the substrate transition-state, we designed and synthesized a novel class of aspartic protease inhibitors containing the hydroxymethylcarbonyl (HMC) isostere. An unnatural amino acid, allophenylnorstatine [Apns; (2 S ,3 S )-3-amino-2-hydroxy-4-phenylbutyric acid], was incorporated at the P1 site in a series of peptidomimetic compounds that mimic the natural substrates of the HIV, HTLV-I, and malarial aspartic proteases. From extensive structure-activity relationship studies, we were able to identify a series of highly potent peptidomimetic inhibitors of HIV protease. One highly potent inhibitor of the malarial aspartic protease (plasmepsin II) was identified. Finally, a promising lead compound against the HTLV-I protease was identified.
Metal wire waveguides for broadband terahertz pulses (2004)

Guided propagation of terahertz pulses on metal wires, characterized with the direct measurement of the electric field in the time domain, shows record low loss and negligible group velocity dispersion.
Ferrohydrodynamic relaxometry for magnetic particle imaging (2011)

The ferrohydrodynamic properties of magnetic nanoparticles govern resolution and signal strength in magnetic particle imaging (MPI), a medical imaging modality with applications in small animals and humans. Here, we discuss the development and key results of a magnetic particle relaxometer that measures the core diameter and relaxation constant of magnetic nanoparticles. This instrument enables us to directly measure the one-dimensional MPI point spread function. To elucidate our results, we develop a simplified ferrohydrodynamic model that assumes nanoparticles respond to time varying magnetic fields according to a Debeye model of Brownian relaxation, which we verify with experimental data.
Direct Fluorescent Visualization of HSC Competitive Repopulation in Transparent Adult Zebrafish (2008)

Abstract Transplanted hematopoietic stem cells (HSCs) home to the marrow space, engraft and self-renew. The process of engraftment is difficult to study in most vertebrates because it is impossible to visualize the engraftment directly. Here we have developed competitive transplantation of fluorescent donor marrow samples into a completely transparent adult zebrafish called casper. This allows the direct visualization of engraftment and the process of HSC competition. Transplantation of zebrafish whole kidney marrow (WKM) cells, containing HSCs, progenitors and mature blood cells, can rescue lethally irradiated recipient fish and repopulate all the blood lineages. We used different GFP-/DsRed-labeled transgenic fish as donors in WKM transplantation, such as the myeloid specific Tg(mpo:GFP), or the ubiquitous expression of Tg(β-actin:GFP), and Red GloFish® to study the kinetics of engraftment. Engraftment can be visualized with a simple fluorescent microscope, and was evident in the recipient kidney as early as 2 weeks post transplant (wpt). By 4 wpt, mature hematopoietic cells differentiated from donor HSCs or progenitors can be observed in the recipient circulation as well as in epidermis as tissue residential macrophages. At 8 wpt, donor-derived lymphoid cells also repopulate the recipient immune system. The fluorescence intensity of engrafted cells was quantified by image analysis software and positively correlated with the engraftment efficiency quantified by FACS. Using Red GloFish® as competitor donor and Tg(β-actin:GFP) as test donor, we were able to see the competition between the two donors both by fluorescence intensity analysis and FACS analysis. To test the sensitivity of this competitive transplant system to the alteration of the ratios between the two colors, we increased the ratio of the test vs. competitor donor from 1:3 to 1:2 to 1:1. At 4wpt, in the 1:3 ratio group, only 14% of the recipients had stronger GFP intensity than the red (n=7), while the rest had weaker or equivalent GFP intensity than the red; however, this percentage increased to 43% and 50% in the 1:2 (n=7) and 1:1(n=8) groups respectively. Therefore, the relative engraftment ratio can be fast detected in vivo by direct fluorescent visualization with the transparent zebrafish recipients. Next, we treated the test donor cells with 16,16-methyl prostaglandin E2 (dmPGE2) or DMSO for 2 hours in vitro at room temperature before transplant. The engraftment efficiency of the dmPGE2 group dramatically increased by at least 2 folds compared with the DMSO group. The colors of competitor and test donors were switched, and the increase of engraftment efficiency by dmPGE2 treatment of the test donor was still evident. In conclusion, direct visualization of competitive marrow repopulation greatly facilitates the developmental, physiological or pathological study of HSCs and progenitors and should provide a new platform for the assay of specific genes or chemicals that could alter homing, engraftment or self-renewal.
Towards a manufacturable back-contact emitter-wrap-through silicon solar cell (2005)

The emitter-wrap-through (EWT) silicon solar cell is an all back-contact cell design that features a high efficiency while using solar-grade silicon materials. This paper reports on progress towards a low-cost manufacturable back-contact cell using the EWT design. We first show that the EWT cell is particularly well suited for thin (<200 /spl mu/m) silicon solar cells. In particular, the EWT cell structure is inherently able to obtain high efficiencies (17% range) from low-quality materials by using thinner substrates and due to the double-sided carrier collection afforded by the n/sup +/pn/sup +/ structure. Secondly, we show that the manufacturing process is largely similar to conventional solar cells. Detailed estimates of manufacturing costs find that the EWT module could potentially reduce costs by one-half compared to current technology using front-contacted cells with screen-printed metallizations. Finally, we report on progress on several key processing steps required for a low-cost EWT cell design and process.
Extending G.1070 for video quality monitoring (2011)

In 2007, the International Telecommunication Union (ITU) standardized a multimedia quality assessment model as ITU-T Recommendation G.1070. The video quality estimation model proposed in this document uses the encoded bit rate and frame rate of the compressed video, along with the expected packet loss rate of the channel, to predict the subjective video quality. The model was designed as a video quality planning tool and requires prior knowledge of or assumptions about the video and channel parameters. This paper considers the use of the G.1070 video quality estimation model for monitoring applications, where the input parameters themselves must be estimated from the observed bitstream. We address the issues that arise when estimating these video and channel parameters from a real-time video stream.
Experimental study of a microstrip patch antenna with an L-shaped probe (2000)

The L-shaped probe is shown to be an attractive feed for the thick microstrip antenna (thickness around 10% of the operating wavelength). A parametric study on the rectangular patch antenna is presented. It is found that the antenna attains 36% impedance bandwidth (SWR/spl les/2) as well as gain bandwidth and about 7-dBi average gain. A two-element array fed by L-probes is also proposed. Experiments show that the array design can substantially suppress the cross polarization of the proposed antenna. Both the antennas have stable radiation patterns across the passband. Moreover, the measured resonant frequencies of the proposed antenna agree well with an existing formula and the L-probe does not have much effect on the resonant frequency.
Dimeric quinacrines as chemical tools to identify PPT1, a new regulator of autophagy in cancer cells (2017)

DQ661 is a novel dimeric quinacrine that affects multiple lysosomal functions (autophagy and macropinocytosis) and mTORC1 (mechanistic target of rapamycin) activity by specifically targeting protein-palmitoyl thioesterase 1 (PPT1). DQ661 has <i>in vivo</i> activity in immunocompetent mouse models of cancer, and constitutes a new tool compound for the study of lysosomal function in cancer and therapeutic resistance.
Robust semantic sketch based specific image retrieval (2010)

Specific images refer to images one has a certain episodic memory about, e.g. a picture one has ever seen before. Specific image retrieval is a frequent daily information need and the episodic memory is the key to find a specific image. In this paper, we propose a novel semantic sketch-based interface to incorporate the episodic memory for specific image retrieval. The interface allows a user to specify the semantic category and rough area/color of the objects in his memory. To bridge the semantic gap between the query sketch and database images, in the back end, a sampling method selects exemplars from a reference dataset which contains many object instances with user-provided tags and bounding boxes. After that, an exemplar matching algorithm ranks images to retrieve the target image to match the user's memory. In practice, we have observed that query sketches are usually error prone. That is, the position or the color of an object may not be accurate. Meanwhile, the annotations in the reference dataset are also noisy. Thus, the search algorithm has to handle two kinds of errors: 1) reference dataset label noise; 2) user sketch error such as position or scale. For the former, we propose a robust sampling method. For the latter, we derive an efficient spatial reranking algorithm to tolerate inaccurate user sketches. Detailed experimental results on the LabelMe dataset show that the proposed approach is robust to both kinds of errors.
Molecular cloning of an aldehyde dehydrogenase implicated in artemisinin biosynthesis in <i>Artemisia annua</i>This paper is one of a selection of papers published in a Special Issue from the National Research Council of Canada – Plant Biotechnology Institute. (2009)

Limitations in the supply of the antimalarial compound artemisinin from Artemisia annua L. have led to an interest in understanding its biosynthesis and enhancing its production. Recent biochemical and molecular genetic data have implicated dihydroartemisinic aldehyde as a precursor to the corresponding acid, which is then converted to artemisinin. Thus, it is important to understand the enzyme or enzymes involved in dihydroartemisinic aldehyde oxidation. Given its activity on artemisinic aldehyde, the cytochrome P450 CYP71AV1 was investigated for its ability to oxidize dihydroartemisinic aldehyde. However, no net activity was detected. In a search for alternative enzymes that could catalyze the oxidation, an expressed sequence tag (EST) collection from A. annua was investigated for relevant cDNAs. This led to the isolation of a full-length cDNA encoding an aldehyde dehydrogenase homologue, named Aldh1, which is highly expressed in trichomes. Expression of the cDNA in E. coli and characterization of the purified recombinant enzyme revealed that the gene product catalyses the NAD(P)-dependent oxidation of the putative artemisinin precursors, artemisinic and dihydroartemsinic aldehydes, and a limited range of other aldehydes. The observed enzyme activity of Aldh1 and the expression pattern of the corresponding gene suggest a role in artemisinin biosynthesis in the glandular secretory trichomes of A. annua.
Generalized and stationary scrolling (1999)

We present a generalized definition of scrolling that unifies a wide range of existing interaction techniques, from conventional scrolling through pan and zoom systems and fish-eye views. Furthermore it suggests a useful class of new scrolling techniques in which objects do not move across the display. These “stationary scrolling” techniques do not exhibit either of two problems that plague spatial scrolling system: discontinuity in salience and the undermining of the user's spatial memory.
Memristor-based multilevel memory (2010)

A method to utilize the memristor as a multilevel memory has been proposed. There are several roadblocks in the practical use of memristors for multilevel memory. A difficulty comes from the nonlinearity in the ¿ vs. q curve which makes it difficult to determine the proper pulse width for desired resistance values. Another one comes from the property of the memristor which integrates any kind of signals including noise that appeared at the memristor and causes memristors to be perturbed from their original values. The proposed method enables the memristor to be used as multilevel memory using a reference resistance array by forcing the memristor to stick at a set of predetermined fixed reference resistance values. We propose the write-in (programming) circuit and the readout/restoration circuit which share the information storing technique using the reference resistance array.
Association between <i>BRCA1</i> and <i>BRCA2</i> mutations and cancer phenotype in Spanish breast/ovarian cancer families: Implications for genetic testing (2001)

Index cases from a clinically relevant cohort of 102 Spanish families with at least 3 cases of breast and/or ovarian cancer (at least 1 case diagnosed before age 50) in the same lineage were screened for germline mutations in the entire coding sequence and intron boundaries of the breast cancer susceptibility genes BRCA1 and BRCA2. Overall, the prevalence of mutations was 43% in female breast/ovarian cancer families, 15% in female breast cancer families and 100% in male breast cancer families. Three recurrent mutations (185delAG, 589delCT and A1708E) explained 63% of BRCA1-related families. Early age at diagnosis of breast cancer, ovarian cancer, bilateral breast cancer, concomitant breast/ovarian cancer in a single patient and prostate cancer but not unilateral breast cancer were associated with BRCA1 and BRCA2 mutations. Male breast cancer was associated with BRCA2 mutations. The presence of male breast cancer was the only cancer phenotype that distinguished BRCA2- from BRCA1-related families. We have developed a logistic regression model for predicting the probability of harbouring a mutation in either BRCA1 or BRCA2 as a function of the cancer phenotype present in the family. The predictive positive and negative values of this model were 77.4% and 79%, respectively (probability cutoff of 30%). The findings of our work may be a useful tool for increasing the cost-effectiveness of genetic testing in familial cancer clinics.
RapidCDC (2019)

I/O deduplication is a key technique for improving storage systems' space and I/O efficiency. Among various deduplication techniques content-defined chunking (CDC) based deduplication is the most desired one for its high deduplication ratio. However, CDC is compute-intensive and time-consuming, and has been recognized as a major performance bottleneck of the CDC-based deduplication system.
Compressive sampling in active and passive millimeter-wave imaging (2011)

We have developed a compressive sampling method based on Hadamard transform for active and passive millimeter wave (mmW) imaging. Hadamard masks of subwavelength sized pixels were used for collecting spatial mmW modulated data with a single-pixel detector system. The image reconstruction from subsampled data was based on a real time, iterative interpolation relaxation technique in the Hadamard space. Compressive sampled active and passive imaging results show that high-fidelity images of objects may be obtained with as small as 1/9 of the data needed for a full set of acquisitions.
Robust Superhydrophobic Conical Pillars from Syringe Needle Shape to Straight Conical Pillar Shape for Droplet Pancake Bouncing (2019)

Superhydrophobic conical pillars have great industrial application potential in, for example, anti-icing of aircraft wings and protecting high voltage transmission lines from freezing rain because of their droplet pancake bouncing phenomenon, which is recognized to further reduce the liquid-solid contact time. However, there are still no methods that can fabricate robust superhydrophobic conical pillars in large scale. Here, a mold replication technology was proposed to realize the large-scale fabrication of superhydrophobic conical pillars with high mechanical strength. An Al mold with intensive conical holes decorated with micro/nanometer-scale structures was fabricated by nanosecond laser drilling and HCl etching. The conical shape originated from a near Gaussian spatial distribution of the energy and temperature in the radial direction in the laser drilling processes. Robust superhydrophobic conical pillars from syringe needle shape to straight conical pillar shape were easily fabricated through replication from the Al mold without any extra spray of superhydrophobic nanoparticles. It was also found that although all superhydrophobic conical pillars with different shapes could generate the droplet pancake bouncing, the shape had a great influence on the critical bottom space and the critical Weber number (<i>We</i>) to generate pancake bouncing. The pancake bouncing with the shortest contact time of a 68.5% reduction appeared on superhydrophobic straight conical pillars with the shape angle of 180°. Overcoming the difficulties in the large-scale fabrication and robustness of superhydrophobic conical pillars will promote practical applications of the droplet pancake bouncing phenomenon.
Aerodynamic design using neural networks (2000)

The design of aerodynamic components of aircraft, such as wings or engines, involves a process of obtaining the most optimal component shape that can deliver the desired level of component performance, subject to various constraints, e.g., total weight or cost, that the component must satisfy. Aerodynamic design can thus be formulated as an optimization problem that involves the minimization of an objective function subject to constraints. A new aerodynamic design optimization procedure based on neural networks and response surface methodology (RSM) incorporates the advantages of both traditional RSM and neural networks. The procedure uses a strategy, denoted parameter-based partitioning of the design space, to construct a sequence of response surfaces based on both neural networks and polynomial fits to traverse the design space in search of the optimal solution. Some desirable characteristics of the new design optimization procedure include the ability to handle a variety of design objectives, easily impose constraints, and incorporate design guidelines and rules of thumb. It provides an infrastructure for variable fidelity analysis and reduces the cost of computation by using less-expensive, lower fidelity simulations in the early stages of the design evolution. The initial or starting design can be far from optimal. The procedure is easy and economical to use in large-dimensional design space and can be used to perform design tradeoff studies rapidly. Designs involving multiple disciplines can also be optimized. Some practical applications of the design procedure that have demonstrated some of its capabilities include the inverse design of an optimal turbine airfoil starting from a generic shape and the redesign of transonic turbines to improve their unsteady aerodynamic characteristics.
Design of non‐peptidic helix/sheet topomimetics: applications to bacterial endotoxin neutralization and inhibition of angiogenesis and tumor growth in mice (2006)

We report here the design of non‐peptidic calixarene‐based compounds that display chemical substituents to approximate the molecular dimensions and surface topology of amphipathic α‐helix and β‐sheet peptides. From a small library of these calixarene‐based topomimetics, we demonstrate that some of them mimic the biological activities of model peptides SC4 and anginex by neutralizing bacterial endotoxin lipopolysaccharide (LPS), and by inhibiting angiogenesis and tumor growth in mice. Several calixarene‐based topomimetics neutralize LPS in the 10‐8 to 10‐9 M range in vitro , and a few of these are protective in vivo against LPS challenge to mice. Other compounds within the library are potent angiogenesis inhibitors, as determined by endothelial cell proliferation and migration assays in vitro , and by the chick embryo chorioallantoic membrane (CAM) assay in vivo . In human ovarian carcinoma and murine melanoma tumor models in mice, these compounds are highly effective at inhibiting tumor angiogenesis and tumor growth. Our results demonstrate the feasibility of designing non‐peptidic helix/sheet topomimetics as novel therapeutic agents. This work was supported by a research grant to KHM from the National Institute of Allergy and Infectious Diseases through the Greater Lakes Research Center of Excellence (GLRCE) for Biodefense and Emerging Infectious Diseases (U54 AI057153).
Zero-Shot Object Detection (2021)

We introduce and tackle the problem of zero-shot object detection (ZSD), which aims to detect object classes which are not observed during training. We work with a challenging set of object classes, not restricting ourselves to similar and/or fine-grained categories as in prior works on zero-shot classification. We present a principled approach by first adapting visual-semantic embeddings for ZSD. We then discuss the problems associated with selecting a background class and motivate two background-aware approaches for learning robust detectors. One of these models uses a fixed background class and the other is based on iterative latent assignments. We also outline the challenge associated with using a limited number of training classes and propose a solution based on dense sampling of the semantic label space using auxiliary data with a large number of categories. We propose novel splits of two standard detection datasets - MSCOCO and VisualGenome, and present extensive empirical results in both the traditional and generalized zero-shot settings to highlight the benefits of the proposed methods. We provide useful insights into the algorithm and conclude by posing some open questions to encourage further research.