gebhart/patrepeval huggingface dataset:
Hepatitis B virus polymerase-specific T cell epitopes shift in a mouse model of chronic infection (2021)

Our data show that in different stains of mice including those that carry a human major histocompatibility complex (MHC) class I antigen HBV vaccines adjuvanted with a checkpoint inhibitor induce potent and broad HBV-specific CD8<sup>+</sup> T cell responses and lower but still detectable CD4<sup>+</sup> T cell responses. CD8<sup>+</sup> T cell responses are reduced and their epitope specificity changes in mice that are chronically exposed to HBV antigens. Implications for the design of therapeutic HBV vaccines are discussed.
Early dental caries detection using a fibre-optic coupled polarization-resolved Raman spectroscopic system (2008)

A new fibre-optic coupled polarization-resolved Raman spectroscopic system was developed for simultaneous collection of orthogonally polarized Raman spectra in a single measurement. An application of detecting incipient dental caries based on changes observed in Raman polarization anisotropy was also demonstrated using the developed fibre-optic Raman spectroscopic system. The predicted reduction of polarization anisotropy in the Raman spectra of caries lesions was observed and the results were consistent with those reported previously with Raman microspectroscopy. The capability of simultaneous collection of parallel- and cross-polarized Raman spectra of tooth enamel in a single measurement and the improved laser excitation delivery through fibre-optics demonstrated in this new design illustrates its future clinical potential.
Dipolar Alignment for Second Harmonic Generation: Host-Guest Inclusion Compounds (1987)

Solid, polycrystalline inclusion complexes between β-cyclodextrin, tris-ortho-thymotide, or thiourea hosts and a variety of polarizable organic and organometallic guests have been prepared. The inclusion complexes generate second harmonic light at 530 nm when irradiated with high power 1.06 µ light from a Nd-YAG laser. The relative SHG ability of the complexes has been measured relative to urea by powder techniques. The solid state structure of several of the complexes has been determined. The structure and activity of the materials is correlated using a simple two state model for the SHG process.
Audio Summarization for Podcasts (2021)

We propose a novel system to automatically generate audio summaries for podcasts, allowing listeners to quickly preview podcast episodes. The proposed system first transcribes the audio from a podcast using automatic speech recognition (ASR), then summarizes the transcript using extractive text summarization, and finally returns the audio associated with the text summary. Motivated by a lack of relevant datasets for this task, we created our own by transcribing the audio from various podcasts and generating summaries for these transcripts using a manual annotation tool. Using these text summaries, we fine-tuned a recent Transformer-based summarization model to specifically handle podcast summaries. Our system achieves ROUGE-(1/2/L) F-scores of 0.63/0.53/0.63, respectively, showing good performance for podcast summarization. We present some examples of podcast audio summaries here: https://github.com/aneeshvartakavi/podsumm.
Different patterns of serum chromogranin A in patients with prostate cancer with and without undergoing hormonal therapy (1999)

Elevated serum chromogranin A (CgA) levels have been detected in patients with prostate cancer who have developed resistance to hormonal therapy. We would like to re-examine these cases by using serial specimens to determine whether such elevated levels are also detectable in prostate cancer patients not undergoing hormonal therapy. Serum CgA was measured in both random and serial specimens from prostate cancer patients with and without undergoing hormonal therapy. We found that serum CgA levels became elevated much earlier than did the levels of serum PSA in approximately one-third of prostate cancer patients developing resistance to hormonal therapy. On the other hand, serum CgA levels became elevated at later, more advanced stages of the disease in patients not undergoing hormonal therapy. Elevated serum CgA levels were usually detected in specimens containing highly elevated PSA. The early rise of serum CgA levels provides an early signal allowing a change of therapy to be made before the disease progresses to a fatal stage. Drugs targeting neuroendocrine cells should be considered for prostate cancer patients with elevated serum CgA levels. J. Clin. Lab. Anal. 13:308–311, 1999. © 1999 Wiley-Liss, Inc.
Enabling Signal Processing over Data Streams (2017)

Internet of Things applications analyze the data coming from large networks of sensor devices using relational and signal processing operations and running the same query logic over groups of sensor signals. To support such increasingly important scenarios, many data management systems integrate with numerical frameworks like R. Such solutions, however, incur significant performance penalties as relational data processing engines and numerical tools operate on fundamentally different data models with expensive inter-communication mechanisms. In addition, none of these solutions supports efficient real-time and incremental analysis.
A novel Trench Fast Recovery Diode with injection control (2014)

A novel Trench Fast Recovery Diode (FRD) structure with injection control is proposed in this paper. The proposed structure achieves improved carrier profile without the need for excess lifetime control. This substantially improves the device performance, especially at extreme temperatures (-40 °C to 175 °C). The device maintains low leakage at high temperatures, and its Qrr and Irm do not degrade as is the usual case in heavily electron radiated devices. A 1600 diode using this structure is proposed in this paper, with a low Vf and good reverse recovery properties. The experimental results show that the structure maintains its performance at high temperatures.
Induction of allergic inflammation by interleukin‐18 in experimental animal models (2004)

Interleukin-18 (IL-18) has been regarded as a proinflammatory cytokine because of its potent interferon-gamma-inducing activity. However, mutant mice that release excess amounts of IL-18 spontaneously develop pruritic chronic dermatitis-like atopic dermatitis (AD), suggesting the importance of IL-18 for the development of AD. Intriguingly, depletion of il-18 but not stat6, an essential transcriptional factor for IL-4 signaling, rescues the mice from AD, indicating IL-18-dependent, T-helper 2 (Th2) cell-independent AD. This type of AD is classified as innate-type allergy in contrast to Th2 cell-dependent ordinary allergy. Consistent with the previous studies, mice transferred with antigen-specific Th1 cells exhibit no airway hyperresponsiveness and respiratory eosinophilic inflammation after challenge with antigen alone. However, they suffer from asthma upon challenge with antigen plus IL-18, with comparable levels of both the alterations as in those transferred with Th2 cells following challenge with antigen. The former type of asthma is categorized as Th1-associated allergy. Therefore, it is definitely necessary to evaluate whether individual allergic disorders involve either of these IL-18-mediated pathways or a Th2-mediated one.
Pressure effect on diamond nucleation in a hot-filament CVD system (1997)

Using extraordinarily low pressure (0.1--1 Torr) we obtained high-density nucleation of diamond on mirror-polished silicon in a hot-filament chemical vapor deposition (HF-CVD) system. A diamond nuclei density as high as ${10}^{10}$--${10}^{11}$ ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}2}$ was achieved, which was comparable to the largest nuclei density obtained in a microwave-plasma chemical vapor deposition system. The low-pressure nucleation technique and the pressure effect on diamond nucleation were discussed in detail based on molecular dynamics. The enhanced nucleation at low pressure was attributed to an increased mean free path, which gave rise to an increased concentration of nucleating species at the substrate and other beneficial nucleating factors. The present work suggests that very low pressure may be an effective approach to nucleate and grow diamond films on untreated substrates via HF-CVD.
Cancellation of capacitor parasitic parameters for noise reduction application (2006)

In this paper, a method is proposed to reduce the equivalent series inductance and equivalent series resistance of capacitors. The method is, first, theoretically analyzed and then verified through experiments. This method will show that it can be used for both film capacitors and electrolytic capacitors, greatly improving the performance of both. Applications in practical power converters prove that the proposed technique can significantly reduce high frequency (HF) electromagnetic interference noise. The technique can also be very useful to reduce HF voltage ripple.
Conventional free radical polymerization in room temperature ionic liquids: a green approach to commodity polymers with practical advantages (2002)

Free-radical polymerization of methyl methacrylate and styrene using conventional organic initiators in the room temperature ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([C4mim][PF6]) is rapid and produces polymers with molecular weights up to 10x higher than from benzene; both polymerization and isolation of products were achieved without using VOCs, offering economic as well as environmental advantages.
Fast image registration via joint gradient maximization: application to multimodal data (2006)

We present a computationally inexpensive method for multi-modal image registration. Our approach employs a joint gradient similarity function that is applied only to a set high spatial gradient pixels. We obtain motion parameters by maximizing the similarity function by gradient ascent method, which secures a fast convergence. We apply our technique to the task of affine model based registration of 2D images which undergo large rigid motion, and show promising results.
Integrating Histology and Imaging Mass Spectrometry (2004)

MALDI (matrix-assisted laser desorption/ionization) imaging mass spectrometry (IMS) is a new technology that generates molecular profiles and two-dimensional ion density maps of peptide and protein signals directly from the surface of thin tissue sections. This allows specific information to be obtained on the relative abundance and spatial distribution of proteins. One important aspect of this is the opportunity to correlate these specific ion images with histological features observed by optical microscopy. To facilitate this, we have developed protocols that allow MALDI mass spectrometry imaging and optical microscopy to be performed on the same section. Key components of these protocols involve the use of conductive glass slides as sample support for the tissue sections and MS-friendly tissue staining protocols. We show the effectiveness of these with protein standards and with several types of tissue sections. Although stain-specific intensity variations occur, the overall protein pattern and spectrum quality remain consistent between stained and control tissue samples. Furthermore, imaging mass spectrometry experiments performed on stained sections showed good image quality with minimal delocalization of proteins resulting from the staining protocols.
Closed loop control of excitation parameters for high speed switched-reluctance generators (2003)

This paper presents a new approach to the automatic control of excitation parameters for the switched-reluctance generator (SRG) where the SRG system operates at sufficiently high speed that it operates in the single pulse mode. The turn-on and turn-off angles are the two parameters through which we can control the electric power generation. The objective of the work is to develop an easily implementable control algorithm that automatically maintains the most efficient excitation angles in producing the required amount of electric power. The work is focused on finding the most efficient excitation angles and characterizing them for easy implementation under closed loop control. Through modeling of an experimental SRG and extensive simulation, it can be seen that the optimal-efficiency turn-off angles can be characterized as a function of power and speed level. Within the closed-loop power controller, the optimal-efficiency turn-off angle is determined from an analytic curve fit. The turn-on angle is then used as the degree of freedom necessary to regulate the power produced by the SRG. Given that the turn-off angle is associated with optimal-efficiency at each speed and power point, overall operation is achieved at optimal-efficiency. The SRG, inverter and control system are modeled in Simulink to demonstrate the operation of the system when implemented within a voltage regulation system. The control technique is then applied to an experimental SRG system. Experimental operation documents that the technique provides for efficient operation of the SRG system through tuning the controller at only four operating points.
Genetic variation in the <i>pro‐melanin‐concentrating hormone</i> gene affects carcass traits in <i>Bos taurus</i> cattle (2008)

Mammalian pro-melanin-concentrating hormone (PMCH) has previously been shown to affect feed intake in rodent species. The objectives of this study were to sequence the Bos taurus PMCH gene in order to identify any existing genetic variants and to evaluate whether these affected carcass traits. An A-to-T SNP was identified at position -134 relative to the ATG start codon (g.-134A>T). The alleles at this SNP were significantly associated with average fat and grade fat in two crossbred populations of Bos taurus cattle. The g.-134T allele may introduce a binding site for the transcriptional repressor, adenovirus E4 promoter binding protein, which may contribute to this effect. The g.-134A allele occurred in 67% of cattle examined and was associated with higher fat levels.
3D-Sensing MIMO Radar for UAV Formation Flight and Obstacle Avoidance (2019)

This paper presents a millimeter-wave (mmW), multiple-input, multiple-output (MIMO) radar capable of three-dimensional (3D) sensing for applications in UAV formation flight (FF) and obstacle avoidance (OA). The radar consists of a custom, 3D-sensing, MIMO antenna array integrated with a commercial automotive radar. The antenna array is optimized for FF and OA. Specifically, the antenna is designed for wide scan range in azimuth while sacrificing scan range in elevation. This tradeoff reduces the complexity, size, weight, and power of the radar while maintaining sufficient coverage of 3D space for nearby obstacles and UAV peers, which are often arranged in a common azimuthal plane for FF. Experimental results are provided which verify the 3D-sensing capability of the radar against a small peer/obstacle drone hovering at various prescribed aerial locations. The standard deviation of the position estimation is 0.61° in azimuth, 2.6° in elevation, and 0.13 meters in range.
Short communication: Validation of in vitro fertility genes in a Holstein bull population (2010)

Previously, we constructed an in vitro fertilization system for the identification of genes affecting fertility traits in dairy cattle. The efficiency of this system has been demonstrated by the identification of several genes affecting fertilization rate and early embryonic survival. However, to employ these genetic markers in marker- and gene-assisted selection programs, there is a need to validate in vitro results in phenotypic data sets collected in vivo. Thus, the objective of this study was to validate, in a population of Holstein bulls, the fertility trait genes we previously identified in an in vitro system. Estimated relative conception rate (ERCR) data from 222 Holstein bulls were obtained from 5 different artificial insemination companies in the United States. Bulls were genotyped for the genes FGF2, POU1F1, PRL, PRLR, GH, GHR, STAT5A, OPN, and UTMP, and the data were analyzed for association with ERCR using a mixed effects sire model. A stepwise model selection procedure revealed evidence of association with ERCR for FGF2 and STAT5A polymorphisms. The in vivo validation suggests that these genes can be used in gene-assisted selection programs for reproductive performance in dairy cattle. The genotypes found to be associated with low bull fertility in this study have been reported to be associated with high milk composition in previous studies. These findings provide molecular evidence for the antagonistic relationship between milk production and fertility observed for many years in different breeds of dairy cattle.
miRNA profiling in renal carcinoma suggest the existence of a group of pro-angionenic tumors in localized clear cell renal carcinoma (2019)

Abstract Renal cell carcinoma comprises a variety of entities, the most common being the clear-cell, papillary and chromophobe subtypes. These subtypes are related to different clinical evolution; however, most therapies have been developed for clear-cell carcinoma and there is not a specific treatment based on different subtypes. In this study, one hundred and sixty-four paraffin samples from primary nephrectomies for localized tumors were analyzed. MiRNAs were isolated and measured by microRNA arrays. Significance Analysis of Microarrays and Consensus Cluster algorithm were used to characterize different renal subtypes. The analyses showed that chromophobe renal tumors are a homogeneous group characterized by an overexpression of miR 1229, miR 10a, miR 182, miR 1208, miR 222, miR 221, miR 891b, miR 629-5p and miR 221-5p. On the other hand, clear cell renal carcinomas presented two different groups inside this histological subtype, with differences in miRNAs that regulate focal adhesion, transcription, apoptosis and angiogenesis processes. Specifically, one of the defined groups had an overexpression of proangiogenic microRNAs miR185, miR126 and miR130a. In conclusion, differences in miRNA expression profiles between histological renal subtypes were established. In addition, clear cell renal carcinomas had different expression of proangiogenic miRNAs. With the emergence of antiangiogenic drugs, these differences could be used as therapeutic targets in the future or as a selection method for tailoring personalized treatments.
Target detection and recognition improvements by use of spatiotemporal fusion (2004)

We developed spatiotemporal fusion techniques for improving target detection and automatic target recognition. We also investigated real IR (infrared) sensor clutter noise. The sensor noise was collected by an IR (256 x 256) sensor looking at various scenes (trees, grass, roads, buildings, etc.). More than 95% of the sensor pixels showed near-stationary sensor clutter noise that was uncorrelated between pixels as well as across time frames. However, in a few pixels (covering the grass near the road) the sensor noise showed nonstationary properties (with increasing or decreasing mean across time frames). The natural noise extracted from the IR sensor, as well as the computer-generated noise with Gaussian and Rayleigh distributions, was used to test and compare different spatiotemporal fusion strategies. Finally, we proposed two advanced detection schemes: the double-thresholding the reverse-thresholding techniques. These techniques may be applied to complicated clutter situations (e.g., very-high clutter or nonstationary clutter situations) where the traditional constant-false-alarm-ratio technique may fail.
Assay for Recombinant and Native Human Intraacrosomal Antigen SP‐10 (1993)

The assay system described is useful to monitor the yield of recombinant SP-10 during scale-up production of the SP-10 vaccine.
Activity Modeling in Email (2016)

Ashequl Qadir, Michael Gamon, Patrick Pantel, Ahmed Hassan Awadallah. Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2016.
Construction of Nano-vesicles Containing Sweet Taste Receptor Derived from Artificial Sweet Taste Cell for Development of Bioelectronic Tongue (2010)

Development of artificial tongue is important for quality control in the food and beverage industry. However, artificial tongue using inorganic synthetic materials as sensing elements, so called ‘Electronic tongues’, still have problems in terms of sensitivity and selectivity. Bioelectorinctongue using biological taste receptor proteins as sensing elements is expected to overcome limitations of electronic tongue. In this study, nano-vesicles containing sweet taste receptor, heterodimer composed of hTAS1R2 and hTAS1R3, derived from artificial sweet taste cells wereconstructed. We created each artificial sweet taste cells stably expressing hTAS1R2 and hTAS1R3 and then the cells were transfected to express both receptor proteins. The artificial cells expressing sweet taste receptors were treated with cytochalasin B to obtain nano-vesicles budded out form the cells. The diameter of the nano-vesicles was nanometer scale which issuitable for applying to nano-material-based sensor platform to detect specific tastant binding to receptors. This nano-vesicle production method is useful for development of receptor protein-based bioelectronic tongue. Furthermore, this work also offers useful tool for basic research on taste receptors and opens up opportunities for many industrial applications.
Development of Mucoadhesive Drug Delivery System Using Phenylboronic Acid Functionalized Poly(<scp>D</scp>,<scp>L</scp>‐lactide)‐<i>b</i>‐Dextran Nanoparticles (2012)

Mucoadhesive NP drug carriers have attracted substantial interest as a potential treatment for anterior eye diseases. NPs composed of PLA-Dex surface functionalized with a mucoadhesive ligand, PBA, were developed as drug carriers with particle sizes ranging from 25 to 28 nm. Using CycA as a model drug, we showed that NPs encapsulated up to 13.7 wt% CycA and exhibited sustained release for up to 5 d in vitro at a clinically relevant dose. We fine-tuned the PBA density on the NP surface to maximize the mucin-NP interaction without compromising the particle stability in vitro. This block copolymer conjugate may be useful to improve the bioavailability of topical formulations.
Attribute-Based Encryption with Fast Decryption. (2013)

Attribute-based encryption (ABE) is a vision of public key encryption that allows users to encrypt and decrypt messages based on user attributes. This functionality comes at a cost. In a typical implementation, the size of the ciphertext is proportional to the number of attributes associated with it and the decryption time is proportional to the number of attributes used during decryption. Specifically, many practical ABE implementations require one pairing operation per attribute used during decryption. This work focuses on designing ABE schemes with fast decryption algorithms. We restrict our attention to expressive systems without system-wide bounds or limitations, such as placing a limit on the number of attributes used in a ciphertext or a private key. In this setting, we present the first key-policy ABE system where ciphertexts can be decrypted with a constant number of pairings. We show that GPSW ciphertexts can be decrypted with only 2 pairings by increasing the private key size by a factor of |Γ|, where Γ is the set of distinct attributes that appear in the private key. We then present a generalized construction that allows each system user to independently tune various efficiency tradeoffs to their liking on a spectrum where the extremes are GPSW on one end and our very fast scheme on the other. This tuning requires no changes to the public parameters or the encryption algorithm. Strategies for choosing an individualized user optimization plan are discussed. Finally, we discuss how these ideas can be translated into the ciphertext-policy ABE setting at a higher cost. 1