gebhart/patrepeval huggingface dataset:
Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs (1994)

A 30 base pair parallel-stranded (ps) duplex ps-L1.L2 composed of two adjoined purine-purine and purine-pyrimidine sequence blocks has been characterized thermodynamically and spectroscopically. The 5'-terminal 15 residues in both strands ('left-half') consisted of the alternating d(GA)7G sequence that forms a ps homoduplex secondary structure stabilized by d(G.G) and d(A.A) base pairs. The 3'-terminal 15 positions of the sequence ('right-half') were combinations of A and T with complementary reverse Watson-Crick d(A.T) base pairing between the two strands. The characteristics of the full length duplex were compared to those of the constituent left and right halves in order to determine the compatibility of the two ps helical forms. The thermal denaturation curves and hyperchromicity profiles of all three duplexes determined by UV absorption spectroscopy were characteristic of ps-DNA, in accordance with previous studies. The thermodynamic properties of the 30 bp duplex corresponded within experimental error to the linear combination of the two 15-mers. Thus, the Tm and delta HvH of ps-L1.L2 in 10 mM MgCl2, derived from analyses according to a statistical mechanical formulation for the helix-coil transition, were 43 degrees C and 569 kJ mol-1, compared to 21 degrees C, 315 kJ mol-1 (ps-F5.F6) and 22 degrees C, 236 kJ mol-1 (ps-GA15). The UV absorption and CD spectra of ps-L1.L2 and the individual 15-mer ps motifs were also compared quantitatively. The sums of the two constituent native spectra (left+right halves) accurately matched that of the 30 bp duplex, with only small deviations in the 195-215 nm (CD) and 220-240 nm (absorption) regions. Based on analysis by native gel electrophoresis, the sequences studied formed duplex structures exclusively; there were no indications of higher order species. Chemical modification with diethyl pyrocarbonate showed no hyperreactivity of the junctional bases, indicating a smooth transition between the two parallel-stranded conformations. We conclude that under given salt conditions, oligonucleotides with normal primary chemical structures can readily form a parallel-stranded double helix based on blocks of very disparate non-canonical purine-purine and purine-pyrimidine base pairs and without perceptible destabilization at the junction. There are biological implications of these findings in relation to genetic structure and expression.
A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens (2016)

Abstract Anthrax is a zoonotic disease that occurs naturally in wild and domestic animals but has been used by both state-sponsored programs and terrorists as a biological weapon. The 2001 anthrax letter attacks involved less than gram quantities of Bacillus anthracis spores while the earlier Soviet weapons program produced tons. A Soviet industrial production facility in Sverdlovsk proved deficient in 1979 when a plume of spores was accidentally released and resulted in one of the largest known human anthrax outbreak. In order to understand this outbreak and others, we have generated a B. anthracis population genetic database based upon whole genome analysis to identify all SNPs across a reference genome. Only ~12,000 SNPs were identified in this low diversity species and represents the breadth of its known global diversity. Phylogenetic analysis has defined three major clades (A, B and C) with B and C being relatively rare compared to A. The A clade has numerous subclades including a major polytomy named the Trans-Eurasian (TEA) group. The TEA radiation is a dominant evolutionary feature of B. anthracis , many contemporary populations, and must have resulted from large-scale dispersal of spores from a single source. Two autopsy specimens from the Sverdlovsk outbreak were deeply sequenced to produce draft B. anthracis genomes. This allowed the phylogenetic placement of the Sverdlovsk strain into a clade with two Asian live vaccine strains, including the Russian Tsiankovskii strain. The genome was examined for evidence of drug resistance manipulation or other genetic engineering, but none was found. Only 13 SNPs differentiated the virulent Sverdlovsk strain from its common ancestor with two vaccine strains. The Soviet Sverdlovsk strain genome is consistent with a wild type strain from Russia that had no evidence of genetic manipulation during its industrial production. This work provides insights into the world's largest biological weapons program and provides an extensive B. anthracis phylogenetic reference valuable for future anthrax investigations. Importance The 1979 Russian anthrax outbreak resulted from an industrial accident at the Soviet anthrax spore production facility in the city of Sverdlovsk. Deep genomic sequencing of two autopsy specimens generated a draft genome and phylogenetic placement of the Soviet Sverdlovsk anthrax strain. While it is known that Soviet scientists had genetically manipulated Bacillus anthracis , with the potential to evade vaccine prophylaxis and antibiotic therapeutics, there was no genomic evidence of this from the Sverdlovsk production strain genome. The whole genome SNP genotype of the Sverdlovsk strain was used to precisely identify it and its close relatives in the context of an extensive global B. anthracis strain collection. This genomic identity can now be used for forensic tracking of this weapons material on a global scale and for future anthrax investigations.
Discrete Lagrangian methods for optimizing the design of multiplierless QMF banks (1999)

In this paper, we present a new discrete Lagrangian method for designing multiplierless quadrature mirror filter banks. The filter coefficients in these filter banks are in powers-of-two, where numbers are represented as sums or differences of powers of two (also called canonical signed digit representation), and multiplications are carried out as additions, subtractions, and shifts. We formulate the design problem as a nonlinear discrete constrained optimization problem, using reconstruction error as the objective, and stopband and passband energies, stopband and passband ripples, and transition bandwidth as constraints. Using the performance of the best existing designs as constraints, we search for designs that improve over the best existing designs with respect to all the performance metrics. We propose a new discrete Lagrangian method for finding good designs and study methods to improve the convergence speed of Lagrangian methods without affecting their solution quality. This is done by adjusting dynamically the relative weights between the objective and the Lagrangian part. We show that our method can find designs that improve over Johnston's benchmark designs using a maximum of three to six ONE bits in each filter coefficient instead of using floating-point representations. Our approach is general and is applicable to the design of other types of multiplierless filter banks.
Study on the anodizing of AZ31 magnesium alloys in ethanol solution (2016)

Magnesium is one of the most prevalent elements in the earth’s crust. It is also present in large quantities in seawater. Magnesium has some promising properties, such as its combination of high strength and low density, and also its high dimensional stability, high thermal conductivity, good electromagnetic shielding characteristics, high damping, and good machinability (Salman & Okido 2013). These properties make it an attractive proposition and an excellent choice when weight reduction is needed. There are several applications of magnesium alloys, such as in vehicles, electronic parts, and aerospace equipment. Unfortunately, the high chemical and electrochemical activity of magnesium leads to a poor corrosion resistance and consequently prevents the widespread use of magnesium alloys in many applications. The internal galvanic corrosion from second phases or impurities and the weakness of the surface hydroxide film on magnesium are other reasons for the poor corrosion resistance of magnesium alloys. Furthermore, the oxide film produced is less stable than the anodic films formed on Al alloys and steel.
Fiberoptic surgery by ultrabright lamp light (2006)

We report the first realization of interstitial surgery by ultrabright lamp light, on the kidneys and livers of live animals. A high-flux optic concentrates lamp emissions into an optical fiber for power delivery inside the body. The trials reveal surgical efficacy comparable to corresponding laser fiber optic treatments, as well as pronounced delayed tissue death.
Predicting Surface Reflectance Properties of Outdoor Scenes Under Unknown Natural Illumination (2021)

Estimating and modelling the appearance of an object under outdoor illumination conditions is a complex process. Although there have been several studies on illumination estimation and relighting, very few of them focus on estimating the reflectance properties of outdoor objects and scenes. This paper addresses this problem and proposes a complete framework to predict surface reflectance properties of outdoor scenes under unknown natural illumination. Uniquely, we recast the problem into its two constituent components involving the BRDF incoming light and outgoing view directions: (i) surface points' radiance captured in the images, and outgoing view directions are aggregated and encoded into reflectance maps, and (ii) a neural network trained on reflectance maps of renders of a unit sphere under arbitrary light directions infers a low-parameter reflection model representing the reflectance properties at each surface in the scene. Our model is based on a combination of phenomenological and physics-based scattering models and can relight the scenes from novel viewpoints. We present experiments that show that rendering with the predicted reflectance properties results in a visually similar appearance to using textures that cannot otherwise be disentangled from the reflectance properties.
A self-embedded watermarking scheme based on relationship function of corresponding inter-blocks DCT coefficient (2009)

In the realm of computer supported cooperative work in design (CSCWD), how to ensure the authenticity and integrity of an image plays important roles. This paper presents a novel semi-fragile image watermarking scheme for authenticating and recovering image content. The scheme also shows strong robustness on those images' content reserved operations. It can precisely detect and locate malicious operations and tampers, and recover main content of tampered image region. Firstly, it assigns the exclusive precursor block and successor block for every block to be a block circle link, and regards the function mapping result of DCT coefficients of neighboring blocks as watermark, and embeds it into middle-frequency domain of DCT coefficients of successor block to form a watermarked image. Secondly, it verifies the blocks, which have been maliciously operated and tampered, by detecting whether the DCT coefficients of neighboring blocks satisfy the relationship function after operations. Thirdly, it uses corresponding relationship function of neighboring blocks in the link to estimate DCT direct current coefficients (DC) and low-frequency coefficients of the tampered blocks and recovers their main content. The experimental results show that the scheme is effective and feasible.
Factors that exaggerate the deleterious effects of pulmonary insufficiency on the right ventricle after tetralogy repair. Surgical implications. (1987)

Postoperative cardiac catheterization data of 74 patients with pulmonary insufficiency after tetralogy repair were analyzed. Two groups were identified: Group A, 26 patients with normal right ventricular function (ejection fraction 95% +/- 5.5%, end-systolic volume 110% +/- 17% of predicted normal) and Group B, 48 patients with right ventricular dysfunction (ejection fraction 80% +/- 18% [p less than 0.001], and end-systolic volume 218% +/- 75% of predicted normal [p less than 0.001]). There was no significant difference between the two groups with respect to frequency of previous palliative procedures, age at operative repair, operative techniques, methods of myocardial protection, and follow-up period. Right ventricular dysfunction in Group B was associated with significant distal pulmonary stenosis (right ventricle-pulmonary artery pressure gradient 28 +/- 13 torr in Group A versus 55 +/- 20 torr in Group B, p less than 0.001), moderate pulmonary regurgitation (regurgitant fraction 18% +/- 11% in Group A versus 32% +/- 10% in Group B, p less than 0.001), and large transannular outflow patch (ratio of patch diameter to descending aorta diameter 1.31 +/- 0.16 in Group A versus 2.50 +/- 0.28 in Group B, p less than 0.001). Pulmonary valve insertion was performed in 42 patients in Group B. Eighteen had subsequent cardiac catheterization. Right ventricular function recovered completely (end-systolic volume 122% +/- 24%, and ejection fraction 92% +/- 7% of predicted) in five of six patients (83%) who had valve insertion within the first 2 years after tetralogy repair. In contrast, right ventricular function remained abnormal in all 12 patients who had valve insertion later than 2 years after tetralogy repair (p less than 0.05). Patients with residual pulmonary stenosis and/or a large transannular outflow patch are at risk for the development of right ventricular dysfunction from pulmonary insufficiency after tetralogy repair. Early correction of these residual lesions and control of pulmonary insufficiency may prevent long-term deterioration in right ventricular function.
Selective oxidative dehydrogenation of propane to propene using boron nitride catalysts (2016)

The exothermic oxidative dehydrogenation of propane reaction to generate propene has the potential to be a game-changing technology in the chemical industry. However, even after decades of research, selectivity to propene remains too low to be commercially attractive because of overoxidation of propene to thermodynamically favored CO<sub>2</sub> Here, we report that hexagonal boron nitride and boron nitride nanotubes exhibit unique and hitherto unanticipated catalytic properties, resulting in great selectivity to olefins. As an example, at 14% propane conversion, we obtain selectivity of 79% propene and 12% ethene, another desired alkene. Based on catalytic experiments, spectroscopic insights, and ab initio modeling, we put forward a mechanistic hypothesis in which oxygen-terminated armchair boron nitride edges are proposed to be the catalytic active sites.
Piece-Wise Multiplicative Scatter Correction Applied to Near-Infrared Diffuse Transmittance Data from Meat Products (1993)

This paper presents a nonlinear scatter correction method, called piece-wise multiplicative scatter correction (PMSC), that is a further development of the multiplicative scatter correction (MSC) method. Near-infrared diffuse transmittance (NIT) data from meat and meat product samples were used to test the predictive performances of the PMSC and the MSC methods. With the use of PMSC, the prediction errors, expressed as the root mean square error of prediction (RMSEP), were improved by up to 36% for protein, up to 55% for fat, and up to 37% for water, in comparison to uncorrected data. The corresponding improvements by using PMSC compared to MSC were up to 22%, 24%, and 31% for protein, fat, and water, respectively.
High-speed, low-power InSb transistors (2002)

High-speed, low-power consumption field-effect transistors fabricated from InSb/In/sub 1-x/Al/sub x/Sb are demonstrated. A 0.7 /spl mu/m gate-length enhancement-mode device shows an f/sub T/, of 74 GHz, and an f/sub max/ of 89 GHz, at a drain voltage below 0.5 V. This is the fastest reported transistor for its gate length, as far as is known.
Linking product design in CAD with assembly operations in CAM for virtual product assembly (2007)

Purpose Virtual product design has become a key technology in reducing costly design errors that are often difficult to detect manually. In order to evaluate product assembly in a virtual environment, it is important to link a product's design in CAD with the constrained complexity of assembly operations in CAM so that the design can be evaluated and modified in a virtual environment before production begins. The paper aims to focus on this. Design/methodology/approach The proposed virtual system includes the following components: a product assembly coding model, named Open Structured Assembly Coding System (OSACS), that codes part‐mating operations for assembling any two parts in CAM; a rule‐based code extractor that identifies OSACS codes for assembling product from the part‐mating information encoded in Standard for the Exchange of Product Model Data AP‐203 CAD data; and an assembly‐sequence generator that generates a binary assembly‐tree for the designed product coded with OSACS assembly codes, representing assembly operations in CAM for product assembly. Findings The proposed system links the design phase in CAD with the manufacturing phase in CAM. Simulation studies were made using CAD Ap‐203 data files from an actual mobile phone housing assembly. A binary assembly‐tree assigned with OSACS assembly codes was generated for assembling the product. The assembling complexity between any two parts was coded with the unique OSACS assembly codes. The final binary assembly tree represents how the product is going to be assembled in CAM with the mating complexity encoded in the assigned OSACS codes. Research limitations/implications The advantage of this virtual product assembly system is that a design can be validated first in a virtual environment without building the expensive physical production system. Moreover, additional design iterations can be performed in the same amount of time to improve product quality. Practical implications Linking product design in CAD with assembly operations in CAM can help realize significant cost savings by preventing future manufacturing problems. With the proposed virtual system, a company can prevent a potential problematic design from reaching production. Originality/value This paper introduces the conceptual design of a virtual system that links product design in CAD with assembly operations in CAM. This system provides a designer with a virtual product assembly process to evaluate a designed product.
Software-Defined LTE Evolution Testbed Enabling Rapid Prototyping and Controlled Experimentation (2017)

The long-term evolution (LTE) has spread around the globe for deploying 4G cellular networks for commercial use. These days, it is gaining interest for new applications where mobile broadband services can be of benefit to society. Whereas the basic concepts of LTE are well understood, its long-term evolution has just started. New areas of Ramp;amp;D look into operation in unlicensed and shared bands, where new versions of LTE need to coexist with other communication systems and radars. Virginia Tech has developed an LTE testbed with unique features to spur LTE research and education. This pa-per introduces Virginia Tech's LTE testbed, its main features and components, access and configuration mechanisms, and some of the research thrusts that it enables. It is unique in several aspects, including the extensive use of software-defined radio technology, the combination of industry-grade hardware and software-based systems, and the remote access feature for user- defined configurations of experiments and radio frequency paths.
Physical Characterization of Solid-Liquid Slurries at High Weight Fractions Using Optical and Ultrasonic Methods (2002)

The goal of this proposed work is to directly address the need for rapid on-line characterization of the physical properties of HLW slurries during all phases of the remediation process, from in-tank characterization of sediments to monitoring of the concentration, particle size, and degree of agglomeration and gelation of slurries during transport. This will be done with both optical and ultrasonic methods. There are three tasks: (1) develop optical and acoustic measurements to provide the fundamental science needed for successful device development and implementation, (2) develop theories that describe the interrelationship between wave propagation and the physical properties of the slurry, and (3) solve, in the framework of these theories, the inversion problem and compare them with the experimental measurements to non-intrusively characterize slurries.
BhGLM: Bayesian hierarchical GLMs and survival models, with applications to genomics and epidemiology (2018)

The package is freely available from the public GitHub repository, https://github.com/nyiuab/BhGLM.
Efficiency and Technological Change at U.S. Research Universities (2005)

This paper investigates the determinants of efficiency and technological progress at US research universities. It relies on a unique panel data set of multiple outputs and inputs from 92 universities covering the period 1981-1998. Over that time span, US universities experienced large increases in industry funding and in academic patenting activity. In this context, the directional distance function and a nonparametric representation of the underlying production technology are combined to obtain estimates of productivity growth and technical efficiency. A pooled-Tobit estimator is used to examine the determinants of technical efficiency and the rate of technological progress. The results show how changes in funding sources for U.S. research universities affects research performance.
Normal Values of Myocardial Deformation Assessed by Cardiovascular Magnetic Resonance Feature Tracking in a Healthy Chinese Population: A Multicenter Study (2018)

Reference values on atrial and ventricular strain from cardiovascular magnetic resonance (CMR) are essential in identifying patients with impaired atrial and ventricular function. However, reference values have not been established for Chinese subjects. One hundred and fifty healthy volunteers (75 Males/75 Females; 18-82 years) were recruited. All underwent CMR scans with images acceptable for further strain analysis. Subjects were stratified by age: Group 1, 18-44 years; Group 2, 45-59 years; Group 3, ≥60 years. Feature tracking of CMR cine imaging was used to obtain left atrial global longitudinal (LA <i>E</i><sub>ll</sub>) and circumferential strains (LA <i>E</i><sub>cc</sub>) and respective systolic strain rates, left ventricular longitudinal (LV <i>E</i><sub>ll</sub>), circumferential (LV <i>E</i><sub>cc</sub>) and radial strains (LV <i>E</i><sub>rr</sub>) and their respective strain rates, and right ventricular longitudinal strain (RV <i>E</i><sub>ll</sub>) and strain rate. LA <i>E</i><sub>ll</sub> and LA <i>E</i><sub>cc</sub> were 32.8 ± 9.2% and 40.3 ± 13.4%, respectively, and RV <i>E</i><sub>ll</sub> was -29.3 ± 6.0%. LV <i>E</i><sub>ll</sub>, LV <i>E</i><sub>cc</sub> and LV <i>E</i><sub>rr</sub> were -22.4 ± 2.9%, -24.3 ± 3.1%, and 79.0 ± 19.4%, respectively. LV <i>E</i><sub>ll</sub> and LV <i>E</i><sub>cc</sub> were higher in females than males (<i>P</i> < 0.05). LA <i>E</i><sub>ll</sub>, LA <i>E</i><sub>cc</sub>, and LV <i>E</i><sub>cc</sub> decreased, while LV <i>E</i><sub>rr</sub> increased with age (<i>P</i> < 0.05). LV <i>E</i><sub>ll</sub> and RV <i>E</i><sub>ll</sub> were not shown to be associated with age. Normal ranges for atrial and ventricular strain and strain rates are provided using CMR feature tracking in Chinese subjects.