gebhart/patrepeval huggingface dataset:
Abstract 649: A three-gene DNA methylation signature for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer. (2013)

Abstract Purpose: Diagnostic and prognostic tools for prostate cancer (PC) are suboptimal causing overtreatment of indolent PC and risk of delayed treatment of aggressive PC. Here, we identify six novel candidate DNA methylation markers for PC with promising diagnostic and prognostic potential. Methods: Microarray-based screening and bisulfite sequencing of 20 non-malignant and 29 PC tissue specimens were used to identify new candidate DNA hypermethylation markers for PC. Diagnostic and prognostic potential was evaluated in 35 formalin-fixed paraffin-embedded (FFPE) nonmalignant prostate tissue samples, 293 FFPE malignant radical prostatectomy (RP) samples (cohort 1), and 148 fresh-frozen malignant RP samples (cohort 2) collected in Denmark, Switzerland, Germany, and Finland. Sensitivity and specificity for PC was evaluated by receiver operating characteristic analyses. Correlations between DNA methylation levels and biochemical recurrence were assessed by log rank tests as well as uni- and multivariate cox regression analyses. A methylation-based prognostic model was developed in cohort 1 and validated in cohort 2. Results: Hypermethylation of AOX1, C1orf114, GAS6, HAPLN3, KLF8, and MOB3B was highly cancer-specific (AUCs 0.89-0.98). Furthermore, a three-gene methylation signature (AOX1/C1orf114/HAPLN3) was developed in cohort 1 and validated in cohort 2. High AOX1/C1orf114/HAPLN3 methylation was significantly associated with biochemical recurrence in multivariate analysis (P&lt;0.05) with hazard ratios of 1.79 (1.20-2.68) and 1.98 (1.02-3.83), respectively, independently of routine clinicopathological variables in both cohorts. Conclusion: We identified six novel candidate DNA methylation markers for PC and developed a three-gene methylation signature, which was an independent predictor of time to biochemical recurrence after RP in two PC patient cohorts. Citation Format: Christa Haldrup, Kamilla Mundbjerg, Else Marie Vestergaard, Philippe Lamy, Peter Wild, Wolfgang A. Schulz, Christian Arsov, Michael Borre Borre, Søren Høyer, Torben F. Ørntoft, Karina D. Sørensen. A three-gene DNA methylation signature for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 649. doi:10.1158/1538-7445.AM2013-649
Poly(aniline boronic acid):  A New Precursor to Substituted Poly(aniline)s (2001)

A novel strategy for preparing a wide range of substituted poly(aniline)s from a single precursor is described. This approach relies on a boron activation/electrophilic displacement reaction resulting in ipso-substitution. Specifically, we demonstrate this strategy to prepare a few of the many possible structures that can be generated from poly(aniline boronic acid), including poly(hydroxyaniline) and halogenated poly(aniline)s. The ability to tune the properties of poly(aniline) through the generation of these new structures will be useful in diverse fields where poly(aniline) is used ranging from polymer-based electronics to sensors.
Compensating For Movement Of Eye In Laser Surgery (1991)

Conceptual system for laser surgery of retina includes subsystem that tracks position of retina. Tracking signal used to control galvanometer-driven mirrors keeping laser aimed at desired spot on retina as eye moves. Alternatively or additionally, indication of position used to prevent firing of laser when eye moved too far from proper aiming position.
Therapeutic compositions and uses of alpha1-antitrypsin: a patent review (2012 – 2015) (2016)

A molecule no longer patentable per se, presents with novel clinical applications; its mechanism still unfolding. While modified protein sequences are patentable and potentially superior, they are burdened by regulatory setbacks. Thus, recent approaches in the context of AAT appear in patents that describe combinations with other drugs, redefined clinical subclasses, and unique recombinant entities, carefully skirting saturated areas of AAT patentology. It will be fascinating to follow technologies and creative patenting as AAT navigates the trying trades of pharmaceutical industry towards an increasing lineup of unmet clinical needs.
The Clock-Proxy Auction: A Practical Combinatorial Auction Design (2005)

Abstract This chapter reports on the clock-proxy auction, a hybrid combinatorial auction design in which the process of auction begins with a clock phase and ends with a proxy round to promote efficiency. This format combines the advantages of both the designs as the efficiency of the proxy auction is complemented with the logical price discovery of the clock auction. A comparison between the clock-proxy auction and the simultaneous ascending auction that establishes the superiority of the former on the efficiency and revenues front is also made. The chapter concludes that this auction format has been used in more than two dozen high-stake auctions across a range of industries in several countries as it has no exposure problem, eliminates incentives for demand reduction, and does not allow the use of collusive bidding strategies.
Memory T Cells Specific for Novel Human Papillomavirus Type 16 (HPV16) E6 Epitopes in Women Whose HPV16 Infection Has Become Undetectable (2008)

Human papillomavirus (HPV)-specific T-cell response to the HPV type 16 (HPV16) E6 protein has been shown to be associated with successful viral clearance. The patterns of CD8 T-cell epitopes within HPV16 E6 protein were previously studied in two women with HPV16 clearance. The goal of this study was to characterize these epitopes in terms of their minimal and optimal amino acid sequences and the human leukocyte antigen (HLA) restriction molecules. The presence of the epitope-specific memory T cells after viral clearance was also examined. In subject A, the dominant epitope was characterized to be E6 75-83 (KFYSKISEY), restricted by the HLA-B62 molecule, while that of subject B was E6 133-142 (HNIRGRWTGR), restricted by the HLA-A6801 molecule. Homologous epitopes were identified in five other high-risk HPV types for both of these epitopes, but they were not recognized by respective T-cell clone cells. An enzyme-linked immunospot assay or tetramer analysis was performed on peripheral blood mononuclear cells from blood samples collected after viral clearance but prior to isolation of the T-cell clones. The presence of epitope-specific memory T cells was demonstrated. These data suggest that HPV-specific memory T cells were generated in vivo and that they may remain in circulation many months, if not years, after viral clearance. Our findings broaden the spectrum of the CD8 T-cell epitopes of the HPV16 E6 protein. The characterization of novel T-cell epitopes and long-lasting epitope-specific memory T cells may be useful for the development of a potential epitope-based vaccine.
Noise reduction in three‐dimensional phase‐contrast MR velocity measurementsl (1993)

The authors have developed a method to reduce noise in three-dimensional (3D) phase-contrast magnetic resonance (MR) velocity measurements by exploiting the property that blood is incompressible and, therefore, the velocity field describing its flow must be divergence-free. The divergence-free condition is incorporated by a projection operation in Hilbert space. The velocity field obtained with 3D phase-contrast MR imaging is projected onto the space of divergence-free velocity fields. The reduction of noise is achieved because the projection operation eliminates the noise component that is not divergence-free. Signal-to-noise ratio (S/N) gains on the order of 15%-25% were observed. The immediate effect of this noise reduction manifests itself in higher-quality phase-contrast MR angiograms. Alternatively, the S/N gain can be traded for a reduction in imaging time and/or improved spatial resolution.
Low-cost fabrication of functional plasmonic fiber-optic-based sensors using microsphere photolithography (2019)

This paper studies the use of Microsphere Photolithography (MPL) as an alternative to Focused Ion Beam milling or e-beam lithography to pattern plasmonic fiber-optic based sensors. In the MPL approach, silica microspheres are self-assembled to form a Hexagonal Close-Packed (HCP) array on top of a layer of photoresist. The microspheres serve as an optical element and focus collimated UV radiation to an array of photonic jets inside the photoresist layer. The exposed region is dependent on the angle of incidence of the UV radiation which facilitates hierarchical patterning. Pattern transfer can be accomplished using either etching or lift-off with the size of the features dependent on the exposure dose. While low-cost and very scalable, the use of MPL influences the design and performance of the fiber probe in several ways. Specifically, the entire cleaved face is patterned without alignment to the fiber core and any defects in the self-assembled microsphere lattice are transferred to the surface. This paper presents the low-cost fabrication of Extraordinary Optical Transmission (EOT) type plasmonic fiber-optic based sensors. The sensors consist of a thin aluminum film on the cleaved face of single mode optical fiber, perforated with a HCP hole-array. At resonance, Extraordinary Optical Transmission (EOT), decreases the reflection from the fiber tip. The conditions for resonance are dependent on the local environment surrounding the fiber tip and the resonant wavelength can be used to measure the index of refraction of a liquid. Experiments show that viable sensors can be created with MPL. The reflection spectra of the sensors was measured in various concentrations of sugar water with a measured sensitivity of 8.33 mg/mL/nm. These results are compared to simulation results which provides a sensitivity analysis of the sensors.
Ansamycin Biogenesis: Studies on a Novel Rifamycin Isolated from a Mutant Strain of <i>Nocardia mediterranei</i> (1974)

A novel ansamycin, rifamycin W, was isolated from a mutant strain of Nocardia mediterranei. The metabolic origin of rifamycin W was studied by (13)C nuclear magnetic resonance spectroscopy. Examination of the proton-decoupled pulse and Fourier transform (13)C spectra of rifamycin W biogenetically enriched with [1-(13)C]-, [2-(13)C]-, and [3-(13)C]propionate and with [1-(13)C]acetate has revealed that the alignment of acetate and propionate units corresponds to that previously proposed for rifamycin S. Washed mycelium from a rifamycin B-producing strain of N. mediterranei transformed rifamycin W into rifamycin B. We suggest that rifamycin W is a normal intermediate in the biosynthesis of the other rifamycins. These results, together with the structural similarity of rifamycin W to the streptovaricins, reinforce our hypothesis that a common progenitor is involved in the biogenesis of all naphthalenic ansamycins.
Distributed query evaluation with performance guarantees (2007)

Partial evaluation has recently proven an effective technique for evaluating Boolean XPath queries over a fragmented tree that is distributed over a number of sites. What left open is whether or not the technique is applicable to generic data-selecting XPath queries. In contrast to Boolean queries that return a single truth value, a generic XPath query returns a set of elements, and its evaluation introduces difficulties to avoiding excessive data shipping. This paper settles this question in positive by providing evaluation algorithms and optimizations for generic XPath queries in the same distributed and fragmented setting. These algorithms explore parallelism and retain the performance guarantees of their counterpart for Boolean queries, regardless of how the tree is fragmented and distributed. First, each site is visited at most three times, and down to at most twice when optimizations are in place. Second, the network traffic is determined by the final answer of the query, rather than the size of the tree, without incurring unnecessary data shipping. Third, the total computation is comparable to that of centralized algorithms on the tree stored in a single site. We show both analytically and experimentally that our algorithms and optimizations are scalable and efficient on large trees and complex XPath queries.
Purification and Characterization of Shiga Toxin 2f, an Immunologically Unrelated Subtype of Shiga Toxin 2 (2013)

Here, we detail the purification, biochemical properties, and toxicity of Stx2f, from an E. coli strain isolated from a feral pigeon. Information obtained in this study will be valuable for characterizing Stx2f and explaining the differences of Stx2a and Stx2f in host specificity and cytotoxicity.
Applying MSTDM to packet voice and data in cellular radio systems (2002)

Movable slot TDM (MSTDM) is a variant of the Ethernet protocol that provides quality of service guarantees for voice. The protocol has been applied to LANs and CATV networks. However cellular networks are different. (1) Each cell has a base station: when mobile units communicate through the base station, frequency reuse increases and collisions are detected. (2) The objective is to connect mobile units to the communication infrastructure: communications between units is only used to share the channel. (3) The base station broadcasts packets from the communications infrastructure to the mobile units: this channel can also provide timing and control. Rapid contention resolution techniques make it unnecessary to transmit voice during silent intervals. Taking advantage of the cellular characteristics and TASI increases the number of voice connections by a factor of 8.
Abstract 4326: Mitochondrial genetics and cellular metabolism regulate tumorigenicity and metastatic potential (2014)

Abstract Current paradigms of carcinogenic risk suggest that genetic, hormonal, and environmental factors combine to influence an individual's predilection for breast cancer and related metastatic tumor formation. The genetic component, in particular, has become the focus of many emergent studies. A renewed focus on cancer metabolism and the Warburg Effect has similarly cast a spotlight on the role, if any, of the mitochondrion in directing disease progression. Analysis of the direct contribution of mitochondrial DNA on tumorigenicity is made possible through the use of mitochondrial-nuclear exchange (MNX) mice in which nuclei from normal FVB mice (the background strain of the tg: MMTV-PyMT) were transferred onto cytoplasms containing C57BL/6 or BALB/c mitochondria. Crossing male FVB:tg:MMTV:PyMT mice with FVB(nDNA)C57BL/6(mtDNA) or FVB(nDNA)BALB/c(mtDNA) females maintained nuclear FVB nDNA and takes advantage of maternal inheritance of mtDNA. These PyMT transgene positive female progeny are then scored for primary tumor onset and pulmonary metastatic density. Present data indicate primary tumor latency segregating by mitochondrial DNA as PyMT-FVB wild-type animals develop primary tumors in 57 days compared to PyMT-FVB(n)C57BL/6(mt) which develop primary tumors in 65 days and PyMT-FVB(n)BALB/c(mt) animals having detectable tumors in 52 days. One group of animals were aged 40 days following primary tumor detection and a second group were sacrificed when aged to 70 days, allowing for evaluation of metastatic severity and confirmation of differential primary tumor growth, respectively. This work hypothesizes that the pre-existent “normal” mitochondrial haplotype harbored by an individual conveys risk in determining tumor latency and metastatic susceptibility. Furthermore, these changes in susceptibility will be accompanied by altered mitochondrial functional characteristics that can be attributed to differences in mitochondrial haplotype. To address those mitochondrial differences, primary mammary epithelial cells were isolated from resected tumors which were then assessed for Complex I and Complex IV activity. In addition, isolated mammary epithelial cells from tumor and healthy animals had bioenergetic profiles generated using the Seahorse XF24 analyzer. Markers of ROS production will also be assessed as they too have been implicated increasingly frequently in cancer aggressiveness. Citation Format: Kyle P. Feeley, Alexander W. Bray, Jessica L. Fetterman, David G. Westbrook, Larry W. Johnson, Robert A. Kesterson, Danny R. Welch, Scott W. Ballinger. Mitochondrial genetics and cellular metabolism regulate tumorigenicity and metastatic potential. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4326. doi:10.1158/1538-7445.AM2014-4326
Genome-wide specificity profiles of CRISPR-Cas Cpf1 nucleases in human cells (2016)

CRISPR-Cas Cpf1 nucleases have recently been described as an alternative genomeediting platform 1 , yet their activities and genome-wide specificities remain largely undefined.
MouseLight (2010)

MouseLight is a spatially-aware standalone mobile projector with the form factor of a mouse that can be used in combination with digital pens on paper. By interacting with the projector and the pen bimanually, users can visualize and modify the virtually augmented contents on top of the paper, and seamlessly transition between virtual and physical information. We present a high fidelity hardware prototype of the system and demonstrate a set of novel interactions specifically tailored to the unique properties of MouseLight. MouseLight differentiates itself from related systems such as PenLight in two aspects. First, MouseLight presents a rich set of bimanual interactions inspired by the ToolGlass interaction metaphor, but applied to physical paper. Secondly, our system explores novel displaced interactions, that take advantage of the independent input and output that is spatially aware of the underneath paper. These properties enable users to issue remote commands such as copy and paste or search. We also report on a preliminary evaluation of the system which produced encouraging observations and feedback.
Synthesis and pharmacological activity of angiotensin-converting enzyme inhibitors: N-(mercaptoacyl)-4-substituted-(S)-prolines (1988)

The synthesis of a series of N-(mercaptoacyl)-4-substituted-(S)-prolines (2 and 3) is described. These compounds were evaluated in vitro for inhibition of angiotensin-converting enzyme (ACE), and selected compounds were evaluated in vivo for ACE inhibition. The most potent compounds in vitro are 108, 109, 111, 114, and 116, having relative potencies of 1.0, 1.0, 1.3, 1.1, and 2.6 as compared to the potency of captopril. The most potent compounds in vivo intravenously are 108, 111, 114, 116, 117, and 97.
On the computation and reduction of the peak-to-average power ratio in multicarrier communications (2000)

For any code C defined over an equal energy constellation, it is first shown that at any time instance, the problem of determining codewords of C with high peak-to-average power ratios (PAPR) in a multicarrier communication system is intimately related to the problem of minimum-distance decoding of C. Subsequently, a method is proposed for computing the PAPR by minimum-distance decoding of C at many points of time. Moreover an upper bound on the error between this computed value and the true one is derived. Analogous results are established for codes defined over arbitrary signal constellations. As an application of this computational method, an approach for reducing the PAPR of C proposed by Jones and Wilkinson (1996) is revisited. This approach is based on introducing a specific phase shift to each coordinate of all the codewords where phase shifts are independent of the codewords and known both to the transmitter and the receiver. We optimize the phase shifts offline by applying our method for computing the PAPR for the coding scenario proposed by the ETSI BRAN Standardization Committee. Reductions of order 4.5 dB can be freely obtained using the computed phase shifts. Examples are provided showing that most of the gain is preserved when the computed optimal phase shifts are rounded to quantenary phase-shift keying (PSK), 8-PSK, and 16-PSK type phase shifts.
Nanocomposites for radiation sensing (2012)

The use of light emitting nanoparticles in polymer and glass matrices was studied for the detection of radiation. These nanocomposite scintillators were produced by various approaches including quantum dot/polymer, fluoride nanophosphor/epoxy and halide nanophosphor containing glass-ceramic composites. The synthesis and characterization of these nanoparticles as well as their incorporation into composites is discussed. Further, the application of these composites for radiation detection and spectroscopy is described.
DEVELOPMENT OF NEW GUARDRAIL END TREATMENTS. FINAL REPORT (1988)

This report describes the development of two new end treatments for W-beam guardrail. The first design, called the rail end treatment, consists of weakened W-beam segments, with slots cut along the length of the rail to reduce the buckling strength of the rail. The end of the rail is flared and anchored with standard breakaway-cable-terminal hardware. The split rail design was crash tested and shown to be in compliance with nationally recognized impact performance standards. The second design, called the extruder terminal, consists of a device that, when struck, causes the W-beam to be flattened and projected in front of the impacting vehicle and behind the guardrail. Vehicular energy is dissipated in the process, resulting in a uniform, controlled deceleration of the vehicle. The guardrail extruder terminal was crash tested and shown to be in compliance with nationally recognized impact performance standards. Of the two designs, the guardrail extruder terminal offers the greatest improvement in comparison to present guardrail end treatments. It is advantageous in terms of cost, impact performance, and design.
An intelligent fitting room using multi-camera perception (2008)

In this paper, we describe the architecture of the vision system for the Responsive Mirror, a novel system for retail fitting rooms that enables online fashion comparisons in physical stores based on multi-camera perception. This vision system provides implicitly controlled real-time interaction for self and social clothing comparisons by automatically tracking user's motion as she tries on clothes. We describe the key components of the motion-tracking and clothes-recognition systems and evaluate their effectiveness against images collected during a previous user study and a dataset of images representing content from a fashion network.
Phenotype, genotype, and worldwide genetic penetrance of LRRK2-associated Parkinson's disease: a case-control study (2008)

UK Medical Research Council; UK Parkinson's Disease Society; UK Brain Research Trust; Internationaal Parkinson Fonds; Volkswagen Foundation; National Institutes of Health: National Institute of Neurological Disorders and Stroke and National Institute of Aging; Udall Parkinson's Disease Centre of Excellence; Pacific Alzheimer Research Foundation Centre; Italian Telethon Foundation; Fondazione Grigioni per il Morbo di Parkinson; Michael J Fox Foundation for Parkinson's Research; Safra Global Genetics Consortium; US Department of Veterans Affairs; French Agence Nationale de la Recherche.