gebhart/patrepeval huggingface dataset:
The major hormone-specific discontinuous epitopes on human chorionic gonadotrophin (2004)

The hormone human chorionic gonadotrophin (hCG) shows extensive sequence homology with LH. Thus, many of the antigenic epitopes on hCG are shared with LH, leading to immunological cross-reaction between these two hormones. Anti-fertility and anti-cancer vaccines based upon hCG should ideally target only the hCG-specific epitopes. The hCG-unique linear epitopes located in the C-terminal peptide of the hCG beta-chain are well characterised. In contrast, the hCG-specific discontinuous epitopes, termed beta1, beta6 and beta7, have remained poorly defined. By generating hCG beta-chain molecules containing single amino acid substitutions we have identified R10, N13, R60 and Q89 as being important in the formation of the beta1 epitope, with R60 providing a particularly dominant residue. We also show that the amino acid residue Q89 contributes to the beta7 epitope, whilst D61 plays a role in both the beta6 and beta7 epitopes.
Story Detection Using Generalized Concepts and Relations (2015)

A major challenge in automated text analysis is that different words are used for related concepts. Analyzing text at the surface level would treat related concepts (i.e. actors, actions, targets, and victims) as different objects, potentially missing common narrative patterns. Shallow parsers reveal semantic roles of words leading to subject-verb-object triplets. We developed a novel algorithm to extract information from triplets by clustering them into generalized concepts by utilizing syntactic criteria based on common contexts and semantic corpus-based statistical criteria based on "contextual synonyms". We show that generalized concepts representation of text (1) overcomes surface level differences (which arise when different keywords are used for related concepts) without drift, (2) leads to a higher-level semantic network representation of related stories, and (3) when used as features, they yield a significant 36% boost in performance for the story detection task.
Advanced Modeling of Micromirror Devices (1995)

The flexure-beam micromirror device (FBMD) is a phase only piston style spatial light modulator demonstrating properties which can be used for phase adaptive corrective optics. This paper presents a complete study of a square FBMD, from advanced model development through final device testing and model verification. The model relates the electrical and mechanical properties of the device by equating the electrostatic force of a parallel-plate capacitor with the counter-acting spring force of the device's support flexures. The capacitor solution is derived via the Schwartz-Christoffel transformation such that the final solution accounts for non-ideal electric fields. The complete model describes the behavior of any piston-style device, given its design geometry and material properties. It includes operational parameters such as drive frequency and temperature, as well as fringing effects, mirror surface deformations, and cross-talk from neighboring devices. The steps taken to develop this model can be applied to other micromirrors, such as the cantilever and torsion-beam designs, to produce an advanced model for any given device. The micromirror devices studied in this paper were commercially fabricated in a surface micromachining process. A microscope-based laser interferometer is used to test the device in which a beam reflected from the device modulates a fixed reference beam. The mirror displacement is determined from the relative phase which generates a continuous set of data for each selected position on the mirror surface. Plots of this data describe the localized deflection as a function of drive voltage.
Characterization of a Variable Angle Reflection Fourier Transform Infrared Accessory Modified for Surface Plasmon Resonance Spectroscopy (2010)

The Harrick AutoSeagull variable angle reflection accessory for Fourier transform infrared (FT-IR) spectrometers provides access to various spectroscopic techniques in a highly flexible platform. In particular, its ability to perform total internal reflection measurements is of interest because it also forms the basis for surface plasmon resonance (SPR) spectroscopy in prism-based configurations. The work presented here discusses the modification of the AutoSeagull to perform SPR spectroscopy, allowing for easy incorporation of the technique into most common FT-IR spectrometers. The wavelength dependency of the dielectric constant of the plasmon-supporting metal (in our case, gold) is largely responsible for the sensitivity attributed to changes in the sample's refractive index (RI) monitored by SPR spectroscopy. Furthermore, the optical properties of gold are such that when near-infrared (NIR) and/or mid-infrared (mid-IR) wavelengths are used to excite surface plasmons, higher sensitivities to RI changes are experienced compared to surface plasmons excited with visible wavelengths. The result is that in addition to instrumental simplicity, SPR analysis on FT-IR spectrometers, as permitted by the modified AutoSeagull, also benefits from the wavelength ranges accessible. Adaptation of the AutoSeagull to SPR spectroscopy involved the incorporation of slit apertures to minimize the angular spread reaching the detector, resulting in sharper SPR "dips" but at the cost of noisier spectra. In addition, discussion of the system's analytical performance includes comparison of dip quality as a function of slit size, tailoring of the dip minima location with respect to incident angle, and sensitivity to bulk RI changes.
Folksonomy-based term extraction for word cloud generation (2011)

In this work we study the task of term extraction for word cloud generation. We present a folksonomy-based term extraction method, called tag-boost, which boosts terms that are frequently used by the public to tag content. Our experiments with tag-boost-based term extraction over different domains demonstrate tremendous improvement in word cloud quality, as reflected by the agreement between extracted terms and manually assigned tags of the testing items. Additionally, we show that tag-boost can be effectively applied even in non-tagged domains, by using an external rich folksonomy borrowed from a well-tagged domain.
Full color waveguide liquid crystal display (2017)

We developed a waveguide liquid crystal display from a liquid crystal (LC)/polymer composite. It does not need polarizers or color filters. It is illuminated by color LEDs installed on its edge. The light produced by the edge LEDs is coupled into the display and then waveguided through the display. When the LC is in the transparent state, the incident light is waveguided through and no light comes out of the viewing side of the display. When the LC is in the scattering state, the incident light is scattered and comes out of the display. It can be used either for transparent display or for direct view display. The composite has a submillisecond response time, and a field sequential scheme can be used to display full color images. Because the display does not need polarizers or color filters, its energy efficiency is much higher than current liquid crystal displays.
The Commons: A Toolkit for the Quantitative Analysis of Factors in the Success or Failure of Electronic Societies (1998)

In this paper, we introduce The Commons, which is a novel methodology and toolkit to aid in the design and study of online societies. We first discuss the foundations which led to its inception, and explain the design decisions made along the way to its completion. Next, we describe the system itself. We then describe and analyze the results of a user study, which shows that this methodology is valid, and that the toolkit produces results comparable to the existing social science literature. In this study we examine a particular form of online communication-- synchronous text chat- and report on its effects in increasing trust and cooperation in online interactions. It is a common intuition that communication leads to more cooperative online relationships but intuition is not proof, nor does intuition provide a precise mapping of the effects and dynamics of various forms of communication on cooperation. Next, we will examine the usefulness of The Commons in the design of successful electronic societies by exploring its advantages over those methods most commonly used today. Finally, we discuss the importance of this platform for continued experimental research in both the social science and computer-human interaction research communities.
Reawakening Retrocyclins: Ancestral Human Defensins Active Against HIV-1 (133.49) (2009)

Abstract Human alpha and beta defensins contribute substantially to innate immune defenses against microbial and viral infections. Certain nonhuman primates also produce theta-defensins - 18 residue cyclic peptides that act as HIV-1 entry inhibitors. Multiple human theta-defensin genes exist, but they harbor a premature stop codon that blocks translation. Consequently, the theta-defensins (retrocyclins) encoded within the human genome are not expressed as peptides. In vivo production of theta-defensins in rhesus macaques involves the post-translational ligation of two nonapeptides. Neither the mechanism of this unique process nor its existence in human cells is known. To ascertain if human cells retained the ability to process demidefensins, we transfected human promyelocytic cells with plasmids containing repaired retrocyclin-like genes. The expected peptides were isolated, their sequences were verified by mass spectrometric analyses, and their anti-HIV-1 activity was confirmed in vitro. Our study reveals for the first time that human cells have the ability to make cyclic theta-defensins. Given this evidence that human cells could make theta-defensins, we attempted to restore endogenous expression of retrocyclin peptides. Since human theta-defensin genes are transcribed, we used aminoglycosides to read-through the premature stop codon found in the mRNA transcripts. This treatment induced the production of intact, bioactive retrocyclin-1 peptide by human epithelial cells and cervicovaginal tissues. Since retrocyclins are broadly antiviral, the ability to reawaken retrocyclin genes from their 7 million years of slumber could provide a novel way to secure enhanced resistance to several major viral pathogens. AI052017; AI065430
Trustworthy data from untrusted databases (2013)

Ensuring the trustworthiness of data retrieved from a database is of utmost importance to users. The correctness of data stored in a database is defined by the faithful execution of only valid (authorized) transactions. In this paper we address the question of whether it is necessary to trust a database server in order to trust the data retrieved from it. The lack of trust arises naturally if the database server is owned by a third party, as in the case of cloud computing. It also arises if the server may have been compromised, or there is a malicious insider. In particular, we reduce the level of trust necessary in order to establish the authenticity and integrity of data at an untrusted server. Earlier work on this problem is limited to situations where there are no updates to the database, or all updates are authorized and vetted by a central trusted entity. This is an unreasonable assumption for a truly dynamic database, as would be expected in many business applications, where multiple clients can update data without having to check with a central server that approves of their changes. We identify the problem of ensuring trustworthiness of data at an untrusted server in the presence of transactional updates that run directly on the database, and develop the first solutions to this problem. Our solutions also provide indemnity for an honest server and assured provenance for all updates to the data. We implement our solution in a prototype system built on top of Oracle with no modifications to the database internals. We also provide an empirical evaluation of the proposed solutions and establish their feasibility.
A New Platform for Attitude Determination and Declination Correction (1999)

Abstract Conventional directional measurement methods for MWD and Survey systems rely on measurement of the borehole orientation relative to the geomagnetic field. The borehole orientation can then be referred to the geographical coordinate system from the knowledge of the magnetic field orientation relative to True North and the horizontal plane. Calibration of the directional sensors relies on knowledge of the Geomagnetic Field intensity. The geomagnetic field intensity is obtained annually from look up tables referred to as the British Geological Survey Model (BGSM) taken as a function of time and location. However, the Earth's Magnetic Field is not stable and may have noticeable, short term fluctuations due to diurnal variations, proximity to masses of magnetic material, local anomalies originating in the upper mantle, crust, or surface, and other phenomenon like solar activities. As a result, declination calculation and magnetic survey measurement will not be as accurate as they seem to be in most cases for the above mentioned reasons. This new method is introduced to measure the local earth magnetic field, local magnetic dip angle, apparatus platform orientation with respect to the axis of the earth local magnetic field, the roll and tilt of that platform, and its longitudinal axis with respect to true north. This is done using the following combination of sensors: Inertial Motion Reference Unit (IMRU)tri-axial magnetometertri-axial accelerometerGlobal Positioning System (GPS) receiver antenna matrix. Based on these measurements, an accurate declination calculation can be performed in real time. Thus, performing magnetic corrections and detection of magnetic anomalies can then be compensated. This is particularly critical in high latitude locations. Very promising results were obtained through lab testing in Houston and Field Testing in Canada (the system shows excellent added value in high latitude locations). This paper presents the results of the lab and field testing of the system that will be of great value to the drilling industry due to the enhanced accuracy provided by the system.
New antiarrhythmic agents. N-Aryl-8-pyrrolizidinealkanamides (1985)

The synthesis and antiarrhythmic activity of N-aryl-8-pyrrolizidinealkanamides are described. The target compounds were evaluated for their ability to protect against chloroform-induced fibrillation in mice. Many of them were found to have antifibrillatory activity comparable to that of lidocaine; several are more potent than lidocaine. N-(2,6-Dimethylphenyl)-8-pyrrolizidineacetamide which was found to be more potent and less toxic (LD50) than lidocaine, also showed a long duration of action in dogs with ventricular arrhythmias after oral administration.
Somatic PKD2 Mutations in Individual Kidney and Liver Cysts Support a “Two-Hit” Model of Cystogenesis in Type 2 Autosomal Dominant Polycystic Kidney Disease (1999)

An intriguing feature of autosomal dominant polycystic kidney disease (ADPKD) is the focal and sporadic formation of renal and extrarenal cysts. Recent documentation of somatic PKD1 mutations in cystic epithelia of patients with germ-line PKD1 mutations suggests a "two-hit" model for cystogenesis in type 1 ADPKD. This study tests whether the same mechanism for cystogenesis might also occur in type 2 ADPKD. Genomic DNA was obtained from 54 kidney and liver cysts from three patients with known germ-line PKD2 mutations, using procedures that minimize contamination of cells from noncystic tissue. Using intragenic and microsatellite markers, these cyst samples were screened for loss of heterozygosity. The same samples were also screened for somatic mutations in five of the 15 exons in PKD2 by single-stranded conformational polymorphism analysis. Loss of heterozygosity was found in five cysts, and unique intragenic mutations were found in seven other cysts. In 11 of these 12 cysts, it was also determined that the somatic mutation occurred nonrandomly in the copy of PKD2 inherited from the unaffected parent. These findings support the "two-hit" model as a unified mechanism for cystogenesis in ADPKD. In this model, the requirement of a somatic mutation as the rate-limiting step for individual cyst formation has potential therapeutic implications.
Nuclear magnetic resonance: Beyond physical imaging: A powerful new diagnostic tool that uses magnetic fields and radio waves creates pictures of the body's internal chemistry (1983)

Reviews the physics, history, advantages and applications of NMR imaging. The technique yields high-resolution anatomical information using computerised image reconstruction methods and the weak interaction of static and time dependent magnetic fields with the atomic nuclei of the body.
Exploiting similarity in adjacent slices for compressed sensing MRI (2014)

Due to fundamental characteristics of MRI that limit scan speedup, sub-sampling techniques such as compressed sensing (CS) have been developed for rapid MRI. Current CS MRI approaches utilize sparsity of the image in the wavelet or other transform domains to speed-up acquisition. Another drawback of MRI is its poor signal-to-noise ratio (SNR), which is proportional to the image slice thickness. In this paper, we use the difference between adjacent slices as the sparse domain for CS MRI. We propose to acquire thick MRI slices and to reconstruct the thin slices from the thick slices' data, utilizing the similarity between adjacent thin slices. The acquisition of thick slices, instead of thin ones, improves the total SNR of the reconstructed image. Experimental results show that the image reconstruction quality of the proposed method outperforms existing CS MRI methods using the same number of measurements.
Exome sequencing, histoincompatibility and long-term kidney allograft function (2015)

BACKGROUND: Kidney transplantation is the treatment of choice for most patients with end-stage renal disease and existing data suggest that post transplant graft function is a predictor of kidney graft failure. METHODS: Exome sequencing of DNA from kidney graft recipients and their donors was used to determine recipient and donor mismatches at the amino acid level. The number of mismatches that are more likely to induce an immune response in the recipient was computationally estimated and designated the allogenomics mismatch score. The relationship between the allogenomics score and post transplant kidney allograft function was examined using linear regression. RESULTS: A significant inverse correlation between the allogenomics mismatch score and kidney graft function at 36 months post transplantation was observed in a discovery cohort of kidney recipient-donor pairs (r 2 >=0.57, P<0.05, the score vs. level of serum creatinine or estimated glomerular filtration rate). This relationship was confirmed in an independent validation cohort of kidney recipient-donor pairs. We observed that the strength of the correlation increased with time post-transplantation. This inverse correlation remained after excluding HLA loci from the calculation of the score. Exome sequencing yielded allogenomics scores with stronger correlations with graft function than simulations of genotyping assays which measure common polymorphisms only. CONCLUSIONS: The allogenomics mismatch score, derived by exome sequencing of recipient-donor pairs, facilitates quantification of histoincompatibility between the organ donor and recipient impacting long-term post transplant graft function. The allogenomics mismatch score, by serving as a prognostic biomarker, may help identify patients at risk for graft failure.
Exploring Genomic Variants Related to Residual Feed Intake in Local and Commercial Chickens by Whole Genomic Resequencing (2018)

Improving feed efficiency is a major goal in poultry production to reduce production costs and increase profitability. The genomic variants and possible molecular mechanisms responsible for residual feed intake (RFI) in chickens, however, remain poorly understood. In this study, using both local and commercial breeds, genome re-sequencing of low RFI and high RFI chickens was performed to elucidate the genomic variants underlying RFI. Results showed that 8,505,214 and 8,479,041 single nucleotide polymorphisms (SNPs) were detected in low and high RFI Beijing-You chickens, respectively; 8,352,008 and 8,372,769 SNPs were detected in low- and high-RFI Cobb chickens, respectively. Through a series of filtering processes, 3746 candidate SNPs assigned to 1137 genes in Beijing-You chickens and 575 candidate SNPs (448 genes) in Cobb chickens were found. The validation of the selected 191 SNPs showed that 46 SNPs were significantly associated with the RFI in an independent population of 779 Cobb chickens, suggesting that the method of screening associated SNPs with whole genome sequencing (WGS) strategy was reasonable. Functions annotation of RFI-related genes indicated that genes in Beijing-You were enriched in lipid and carbohydrate metabolism, as well as the phosphatase and tensin homolog (PTEN) signaling pathway. In Cobb, however, RFI-related genes were enriched in the feed behavior process and cAMP responsive element binding protein (CREB) signaling pathway. For both breeds, organismal development physiological processes were enriched. Correspondingly, <i>NOS1</i>, <i>PHKG1</i>, <i>NEU3</i> and <i>PIP5K1B</i> were differentially expressed in Beijing-You, while <i>CDC42</i>, <i>CSK</i>, <i>PIK3R3</i>, <i>CAMK4</i> and <i>PLCB4</i> were differentially expressed in Cobb, suggesting that these might be key genes that contribute to RFI. The results of the present study identified numerous novel SNPs for RFI, which provide candidate biomarkers for use in the genetic selection for RFI. The study has improved knowledge of the genomic variants and potential biological pathways underlying RFI in chickens.
An 8-18-GHz all-optical microwave downconverter with channelization (2001)

A wide-band fiber-optic image-rejection downconverter capable of channelizing received signals into a 500-MHz intermediate frequency band is demonstrated. The downconverter utilizes phase modulators to convert received signals into optical side-bands prior to heterodyne detection with the system local oscillator. Experimental measurements performed on a two-channel system which maps 8-18-GHz signals into intermediate frequencies between 2 and 2.5 GHz reveal an image rejection of 20 dB and a spur-free dynamic range of 107 dB/Hz/sup 2/3/.
Fourier Transform Interferometer Alignment Method (2002)

A rapid and convenient method has been developed to facilitate the alignment of the image-plane components of point-diffraction interferometers, including the phase-shifting point-diffraction interferometer. In real time, the Fourier transform of the detected image is used to calculate a pseudoimage of the electric field in the image plane of the test optic where the critical alignment of various optical components is performed. Reconstruction of the pseudoimage is similar to off-axis, Fourier transform holography. Intermediate steps in the alignment procedure are described. Fine alignment is aided by the introduction and optimization of a global-contrast parameter that is easily calculated from the Fourier transform. Additional applications include the alignment of image-plane apertures in general optical systems, the rapid identification of patterned image-plane alignment marks, and the probing of important image-plane field properties.