gebhart/patrepeval huggingface dataset:
Specific labeling: An effective tool to explore the RNA world (2015)

Our knowledge about the functional diversity and importance of RNA in biology has grown enormously over the past three decades and has driven efforts to develop better tools to characterize RNAs. Amongst these tools are methods for preparing specifically labeled or chemically modified RNAs, which are essential for basic research, biomedical, and clinical applications. Understanding the potential and limits of these different RNA synthesis and labeling strategies is important in deciding how to approach the preparation of a particular RNA molecule. Here, we review these various labeling methods and future directions of the field.
Crystallization of the Secondary Alcohol Dehydrogenase fromThermoanaerobacter ethanolicus 39E. (1996)

Abstract: The secondary alcohol dehydrogenase from the thermophile Thermoanaerobacter ethanolicus 39E has been crystallized at 40°C by vapour difussion using polyethelene glycol as a precipitant. The orthorhombic crystals belong to the space group P 21212 with cell constants of a=170.0A, b=125.7A and c=80.5A.A native X-ray diffraction data set has been collected to 2.7A resolution .
Material Characterization System. (1994)

Abstract : A plurality of elongated test specimens undergo vibrations induced by random noise within an acoustical frequency range establishing standing waves therein having resonant frequencies at which the collection of measurement data through accelerometers mounted at the ends of the specimens provides for calculation of physical material properties. The processing of the data during collection, analysis and calculation is automated by programmed computer control. (MM)
Estimation of particle size variations for laser speckle rheology of materials (2015)

Laser speckle rheology (LSR) is an optical technique for assessing the viscoelastic properties of materials with several industrial, biological, and medical applications. In LSR, the viscoelastic modulus, G*(ω), of a material is quantified by analyzing the temporal fluctuations of speckle patterns. However, the size of scattering particles within the material also influences the rate of speckle fluctuations, independent of sample mechanical properties, and complicates the accurate estimation of G*(ω). Here, we demonstrate that the average particle size may be retrieved from the azimuth-angle dependence of time-averaged speckle intensities, permitting the accurate quantification of the viscoelastic moduli of materials with unknown particle size distribution using LSR.
A Method for Synthesizing Partially Substituted Cucurbit[n]uril (2003)

A novel approach to cucurbituril synthesis is described where partial substitution is introduced into cucurbit[n]uril. The identification of homologues (and their substitution) in reaction mixtures is achieved by a combination of ESMS and the use of the molecular probes (guests) 1,4-dioxane and 1,9-octanediamine. A unique symmetrical hexamethylcucurbit[3,3]uril, the major product, was isolated and characterized.
New catalytic systems for the manufacture of poly(aspartic acid) (1997)

Abstract Aspartic acid (I), when heated to a temperature in excess of 180 °C, undergoes a solid‐state condensation polymerization to afford the useful polymeric intermediate known as poly(succinimide) (II). Treatment of poly(succinimide) with aqueous base, such as sodium hydroxide, affords sodium poly(α,β‐DL‐aspartate) (III) also known as thermal poly(aspartate) (TPA). Acid catalysts, such as phosphoric acid have been added to the aspartic acid to afford higher‐molecular‐weight poly(succinimide) than is obtained in the non‐catalyzed polymerization. Recently, new sulfur‐based catalysts have been disclosed for the polymerization of aspartic acid. The sulfur‐containing catalysts provide a route to highly biodegradable, low‐color poly(aspartate)s in the molecular weight range of 2 000 to 20 000. A comparison of biodegradability, molecular weight, and spectral characteristics of the poly(succinimide)s and poly(aspartate)s derived from the catalyzed and non‐catalyzed polymerizations is presented.
Spherical harmonic decomposition of a sound field based on observations along the equator of a rigid spherical scatterer (2021)

We present a method for computing a spherical harmonic representation of a sound field based on observations of the sound pressure along the equator of a rigid spherical scatterer. Our proposed solution assumes that the captured sound field is height invariant so that it can be represented by a two-dimensional (2D) plane wave decomposition (PWD). The 2D PWD is embedded in a three-dimensional representation of the sound field, which allows for perfectly undoing the effect of the spherical scattering object. If the assumption of height invariance is fulfilled, then the proposed solution is at least as accurate as a conventional spherical microphone array of the same spherical harmonic order, which requires a multiple of the number of sensors. Our targeted application is binaural rendering of the captured sound field. We demonstrate by analyzing the binaural output signals that violations of the assumptions that the solution is based on-particularly height invariance and consequently also horizontal propagation-lead to errors of moderate magnitude.
Experimental Verification of Maximized SNR against RCS from Overrepresented MIMO Virtual Array (2021)

This paper presents experimental verification and results for a novel process of creating an optimized virtual array for a Multi-Input, Multi-Output (MIMO) antenna array. MIMO radars utilize the concept of a virtual array to increased range and angular resolution as compared to non-MIMO phased array radars. There exist certain linear phased array antenna geometries where the MIMO virtual array can become overrepresented. Generation of an optimized MIMO antenna virtual array can be accomplished using full virtualization, the process of creating separate virtual arrays. Experimental results are shown to match with the theoretical prediction of SNR improvement.
Energy-Efficient Computation Offloading and Transmit Power Allocation Scheme for Mobile Edge Computing (2019)

Mobile edge computing (MEC) is considered a promising technique that prolongs battery life and enhances the computation capacity of mobile devices (MDs) by offloading computation-intensive tasks to the resource-rich cloud located at the edges of mobile networks. In this study, the problem of energy-efficient computation offloading with guaranteed performance in multiuser MEC systems was investigated. Given that MDs typically seek lower energy consumption and improve the performance of computing tasks, we provide an energy-efficient computation offloading and transmit power allocation scheme that reduces energy consumption and completion time. We formulate the energy efficiency cost minimization problem, which satisfies the completion time deadline constraint of MDs in an MEC system. In addition, the corresponding Karush–Kuhn–Tucker conditions are applied to solve the optimization problem, and a new algorithm comprising the computation offloading policy and transmission power allocation is presented. Numerical results demonstrate that our proposed scheme, with the optimal computation offloading policy and adapted transmission power for MDs, outperforms local computing and full offloading methods in terms of energy consumption and completion delay. Consequently, our proposed system could help overcome the restrictions on computation resources and battery life of mobile devices to meet the requirements of new applications.
Supporting table partitioning by reference in oracle (2008)

Partitioning is typically employed on large-scale data to improve manageability, availability, and performance. However, for tables connected by a referential constraint (capturing a parent-child relationship), the current approaches require individually partitioning each table thereby burdening the user with the task of maintaining the tables equi-partitioned, which not only is cumbersome but also error prone. This paper proposes a new partitioning method (partition by reference) that allows tables with a parent-child relationship to be logically equi-partitioned by inheriting the partition key from the parent table without duplicating the key columns. The partitioning key is resolved through an existing parent-child relationship, enforced by an active referential constraint. This logical dependency is used to automatically i) cascade partition maintenance operations performed on parent table to child tables, and ii) handle migration of child rows when partition key or parent key in parent table is updated, as a single atomic operation. This method has been introduced in Oracle Database 11gR1 with support for tables with both single level and composite partitioning methods. The paper describes the key concepts of table partitioning by reference method, discusses the design and implementation challenges, and presents an experimental study covering a usage scenario common in Information Life Cycle Management (ILM) applications.
A novel panel to detect microsatellite instability and concordance with clinical reference methods in colorectal cancer patients. (2015)

e22135 Background: Detection of microsatellite instability (MSI) is recommended to identify colorectal cancer (CRC) patients with Lynch syndrome. Current clinical reference methods to detect MSI are immunohistochemistry (IHC) for mismatch repair (MMR) proteins or molecular analysis of markers in the “Bethesda panel”, consisting of DNA repeat regions that are frequently mutated in MSI-high (MSI-H) but not in microsatellite stable (MSS) tumors. Methods: We investigated whether a novel panel of homopolymer repeats (Zhao et al. 2014; eLife 3:e02725) could serve as an alternative method to detect MSI. For this novel panel, repeat length was determined on FFPE DNA by PCR followed by melting curve analysis on CFX96 PCR instruments (Bio-Rad, USA). 70 CRC FFPE samples were analyzed for MSI status using the Bethesda panel markers in the MSI analysis system (Promega, USA; MSI-H cutoff: 3 out of 5 positive markers) or using the novel prototype MSI panel (Biocartis, Belgium; MSI-H cutoff: 2 out of 4 positive markers). A subset of 8 samples was also analyzed by IHC for MLH1, PMS2, MSH2 and MSH6 MMR proteins. Results: For 57 samples with results available on both methods, the overall percent agreement was 98.3% (56/57; 13 samples could not be analysed due to low DNA quality: 4 samples failed for both methods, 7 additional samples for Bethesda and 2 additional samples for the novel MSI panel). The novel MSI panel classified 1 additional sample as MSI-H, which was scored MSS by the Bethesda panel, leading to a positive percent agreement of 96% (24/25) and negative percent agreement of 100% (32/32). For samples of which MSI status was also available by IHC, IHC was 88% (7/8) concordant with both the novel panel and the Bethesda panel. Discordances were due to 1 sample that was MSI-H by both molecular methods but MSS by IHC and 1 other sample that was MSI-H by the novel MSI panel and IHC but MSS by the Bethesda panel. Conclusions: The novel MSI panel showed high concordance with clinical reference methods and detected 1 additional MSI-H sample compared to either the Bethesda panel or IHC in a population of 70 CRC samples. As such, it holds promise for future development of a novel PCR-based diagnostic tool for accurate MSI detection.
Optofluidic Trapping in Exposed Mode Slot Waveguides (2008)

We have demonstrated trapping of 80nm particles in an Integrated Optofluidic Trapping Architecture using an exposed mode waveguides. The exposed mode waveguide allows access to the region of highest optical intensity, providing increased trapping stability.
Acute Administration of n‐3 Triglyceride Emulsion Provides Marked Cardioprotection After Ischemia/Reperfusion (2013)

n‐3 fatty acids may decrease cardiovascular disease risk. We questioned if acute intervention of n‐3 triglyceride (TG) emulsion (48% of fatty acids = EPA+DHA) is protective and improves cardiac function after ischemia/reperfusion (I/R). n‐3 TG were administered after I/R in two models: a) hearts (C57BL/6 mice) were perfused ex‐vivo using the Langendorff technique (LT); b) hearts with acute occlusion of the left anterior descending coronary artery (LAD) in vivo . After LAD occlusion n‐3 TG emulsion (1.5g/kg body weight) was injected intraperitoneally at the end of ischemia and 1h later. In the LT model of I/R, perfusion with KREBS‐Hensleit buffer (KH) led to markedly decreased left ventricular developed pressure (LVDP) (by 60%) and arrhythmias, but reperfusion with KH+ n‐3 TG (300mg/100ml) improved LVDP recovery. In the LAD model, near normal echo‐and electrocardiograms were maintained 48hrs after I/R and left ventricular infarct size was reduced by 80% in TG treated animals vs control. For both I/R models, markers of injury, lactate dehydrogenase and creatine kinase, were significantly reduced in n‐3 TG treated mice. After I/R, in LT model, n‐3 TG increased a marker of apoptosis Bcl‐2 (by 50%), reduced markers of autophagy beclin 1 (by 60%) and HIF1 (by 80%). We conclude that an acute n‐3 TG injection after ischemia provides cardioprotection. This may provide a novel therapy after acute myocardial infarction in humans. Grant Funding Source : Nutrition (ASN)
Rebuilding of a Large Single Hull Tank Barge into Double Hull (2005)

This paper presents Maritrans’ groundbreaking experience in rebuilding very large single hull barges into OPA- 90 compliant double hull barges. Details of the process are described along with interesting case studies involving aspects of analysis and construction. The process by which the American Bureau of Shipping certified this barge to be a “Grade 1” under the ABS SafeHull Condition Assessment Program is described in detail. There is a brief discussion of extending this rebuild process to the double hulling of tankers.
An MRI‐compatible semiautomated vacuum‐assisted breast biopsy system: Initial feasibility study (2005)

Preliminary results demonstrate the feasibility of a vacuum-assisted breast biopsy system in the MRI environment. Small 0.1-mL lesions can be biopsied without needle artifacts obscuring the target.
Provably correct, secrecy preserving computation and its applications in auctions and securities exchanges (2008)

Recent advances in cryptography provide powerful new tools for enhancing trust in electronic commerce at low cost. We construct a general model of provably correct, secrecy preserving computation without relying on any particular cryptographic framework or assumptions. This model employs an Evaluator-Prover that accepts encrypted inputs from many (possibly unaffiliated) parties, computes one or more functions on those inputs, outputs the functions' results and verifies the correctness of the results to one or more verifiers. We distinguish our work from other secure computation approaches as a balance between absolute security and a completely trusted third party, achieving a model enjoying computational tractability and suitability for business applications. 
Our evaluator-prover is not trusted in the traditional sense; it is bound to output only the correct results at all times and prevented from disclosing private data by tools from other areas of computer science research such as trusted computing and network security, rather than the provably secure cryptographic tools employed in many past solutions. We show how to construct an implementation of our model using Paillier's homomorphic encryption scheme. We propose a time-lapse cryptography that produces public encryption keys and guarantees decryption at a particular time by constructing and releasing the corresponding decryption key after a specific interval. This service functions as a new cryptographic commitment primitive with binding, hiding, and nonrepudiation. 
Provided with these tools, we construct four new mechanisms for electronic commerce: a cryptographic sealed-bid auction protocol for one or more identical items, a cryptographic combinatorial auction protocol based on the auction, a cryptographic securities exchange that conducts a continuous double auction for a particular security, and a cryptographic combinatorial securities exchange that provides for efficient atomic exchange of baskets of many securities. 
Along the way, we develop useful building blocks of independent interest, most notably a novel cryptographic mechanism to efficiently prove a solution to a linear or integer program is optimal based on its encrypted inputs and encrypted constraints; this provides unprecedented efficiency in proving the correctness of winner and price determination in our combinatorial clock-proxy auction.
Development of a chitosan‐based adhesive. Application to wood bonding (2012)

Abstract The potential of chitosan (CS) as wood adhesive was investigated in this study. The measurement of the bond strength of different CS‐based formulations was carried out using double‐lap shear tests. The best formulation tested was an adhesive composed of 6% of CS, 1% of glycerol, and 5 mmol/L of trisodium citrate dehydrate. Best bond strength from this formulation was found to be equal to 6.0 MPa in dried conditions and 1.6 MPa in wet conditions (specimens immersed for 3 h at 30°C in water). The failure in the double‐lap joint tests mainly occurred in wood. Finally, the penetration of the rhodamine‐labeled CS at 4% in the pinewood matrix was also studied using microtome and microscopy techniques to show interactions between CS‐based adhesive and wood. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2013
Piezoelectric Wafer Active Sensors for Structural Health Monitoring: State of the Art and Future Directions (2010)

Piezoelectric wafer active sensors (PWAS) are lightweight and inexpensive enablers for a large class of structural health monitoring (SHM) applications. The presentation will start with a brief review of PWAS physical principles and basic modeling. Then, the presentation will consider the several ways in which PWAS can be used for damage detection: (a) embedded guided-wave ultrasonics, i.e., pitch-catch, pulse-echo, phased arrays, thickness mode; (b) high-frequency modal sensing, i.e., the electro-mechanical (E/M) impedance method; (c) passive detection, i.e., acoustic emission and impact detection. Emphasis will be placed on recent developments. Special attention will be given to the mechatronics predictive modeling of the complete cycle from electrical excitation through piezoelectric transduction, ultrasonic acoustic waves, and finally reverse piezoelectric transduction to generate the received electric signal. Power and energy aspects of this process will be considered and discussed. The presentation will end with conclusions and suggestions for further work.
Image Reconstruction in a Wide Aspect Ratio HDTV System (1986)

One of the important characteristics of a high-definition television (HDTV) image is a wide aspect ratio. In some HDTV systems the image is segmented and different formats are used to transmit portions of the image. We address the problem of image reconstruction at the receiver and present an analysis of a wide aspect ratio HDTV system. Several image reconstruction techniques are described, including a channel-dependent design, and their effectiveness discussed. We also present a channel-independent system for image reconstruction that utilizes a vertical interval test line. Performance has been evaluated, via computer simulation, using still images. The results indicate an imperceptible amount of artifacts at the edge-center joints with an overlap as small as one picture element for the channel-independent reconstruction technique.
Role of positively charged residues on the polar and non‐polar faces of amphipathic α‐helical antimicrobial peptides on specificity and selectivity for Gram‐negative pathogens (2017)

We have designed de novo and synthesized eight 26-residue all D-conformation amphipathic α-helical cationic antimicrobial peptides (AMPs), four with "specificity determinants" which provide specificity for prokaryotic cells over eukaryotic cells and four AMPs without specificity determinants. The eight AMPs contain six positively charged Lys residues on the polar face in four different arrangements to understand the role of these residues have on antimicrobial activity against 14 Acinetobacter baumannii strains, seven of which were resistant to polymyxin B and colistin; six diverse Pseudomonas aeruginosa strains and 17 Staphylococcus aureus strains, nine of which were methicillin-sensitive, and eight of which were methicillin-resistant. The four AMPs without specificity determinants are extremely hemolytic. In contrast, the four AMPs with specificity determinants had dramatic improvements in therapeutic indices showing the importance of specificity determinants in removing eukaryotic cell toxicity. The specificity determinants combined with the location of positively charged residues on the polar face provide Gram-negative pathogen selectivity between A. baumannii and S. aureus. Specificity determinants maintain excellent antimicrobial activity in the presence of human sera, whereas the AMPs without specificity determinants were inactive. This study clearly shows the potential of amphipathic α-helical AMPs with specificity determinants as therapeutics to replace existing antibiotics.
Kenaf core as a board raw material. (1993)

Kenaf (Hibiscus cannabinus) is an annual cane-like plant whose outer bast fiber is being considered as a newsprint raw material. In this work, the kenaf core material was examined as a possible raw material for low-density composites. The material was reduced to particles and made into 256 kg/m 3 (16 lb./ft. 3 ) panels. The panel test results were encouraging in comparison to current industrial insulation boards. No problems in processing (adhesive application, felting, or pressing) were encountered. The physical properties were: 1) internal bond about 200 kPa (29 psi); 2) modulus of rupture 1069 kPa (155 psi); 3) 2-hour thickness swell 23 percent
Three-dimensional holographic ring traps (2007)

We describe a class of diffractive optical elements that intended for use in holographic optical trapping systems to project ring-like optical traps. The ring traps' hologram is design by shape-phase algorithm, that incodes amplitude information in Fourier space into shape. The flexibility of the shape-phase algorithm leeds to several advantages over commonly used optical vorteces. While, optical vorteces carry orbital angular momentum which determines the vortex diameter, ring trap dimensions do not depend on the angular momentum. In particular, we formed a ring trap without angular momentum, or tangetial-force. Also unlike most optical vortices or ring-like Bessel beams, these ring traps have strong enough axial intensity gradients to trap objects in three dimensions. We investigated the three dimensional vortex-like trapping experimentaly and by volumetric imaging.
In Vivo Cherenkov Video Imaging during External Beam Radiation Therapy (2014)

In vivo Cherenkov video imaging visualizes the process of external beam radiotherapy. Patient positioning, treatment verification, quality control, superficial dose and skin reactio n estimation were explored for this technique, termed Cherenkoscopy.