gebhart/patrepeval huggingface dataset:
Phase Boundaries of Microemulsion Systems Help to Increase Productivity (2011)

Abstract Formation damage may be caused by in-situ emulsions, changes in wettability and by deposition of asphaltenes, wax and scales. It is widely recognized that these damage mechanisms may be removed by using microemulsion technology, resulting in enhanced productivity of oil and gas wells. It is also known that microemulsion systems are composed of surfactants, oil, brine and optional co-surfactants and acids. These systems can be very complex, due to the number of variables that influence formulation behavior, including temperature, type of oil, type and concentration of salt, surfactant, co-surfactant, and acid. The development of microemulsions for specific oilfield applications requires a systematic study of phase behavior as a tool to select a treatment composition that satisfies specific parameters defined by the application. Phase behavior studies are necessary in order to identify microemulsion phase boundaries. Phase behavior diagrams of microemulsion systems developed for wellbore damage remediation considered the following variables: temperature, type and concentration of co-surfactants, type and concentration of brine, oils, surfactants and acids. Laboratory studies of surfactant-oil-brine systems used successfully in the field confirm that they undergo phase transitions from Winsor I (oil-in-water with excess oil), to Winsor III (microemulsion), to Winsor II (water-in-oil with excess water). This paper presents formulations positioned in an area of the phase diagram that correspond to maximum detergency and optimum interfacial properties required for field applications. The relationship between phase diagrams, interfacial properties (interfacial tension and contact angle) and well productivity are discussed.
Purification, Characterization, and Sequence Analysis of a Potential Virulence Factor from <i>Porphyromonas gingivalis</i> , Peptidylarginine Deiminase (1999)

The initiation and progression of adult-onset periodontitis has been associated with infection of the gingival sulcus by Porphyromonas gingivalis. This organism utilizes a multitude of virulence factors to evade host defenses as it establishes itself as one of the predominant pathogens in periodontal pockets. A feature common to many other oral pathogens is the production of ammonia due to its protective effect during acidic cleansing cycles in the mouth. Additionally, ammonia production by P. gingivalis has been proposed as a virulence factor due to its negative effects on neutrophil function. In this study, we describe the first purification of a peptidylarginine deiminase (PAD) from a prokaryote. PAD exhibits biochemical characteristics and properties that suggest that it may be a virulence agent. PAD deiminates the guanidino group of carboxyl-terminal arginine residues on a variety of peptides, including the vasoregulatory peptide-hormone bradykinin, to yield ammonia and a citrulline residue. The soluble protein has an apparent mass of 46 kDa, while the DNA sequence predicts a full-length protein of 61.7 kDa. PAD is optimally active at 55 degrees C, stable at low pH, and shows the greatest activity above pH 9.0. Interestingly, in the presence of stabilizing factors, PAD is resistant to limited proteolysis and retains significant activity after short-term boiling. We propose that PAD, acting in concert with arginine-specific proteinases from P. gingivalis, promotes the growth of the pathogen in the periodontal pocket, initially by enhancing its survivability and then by assisting the organism in its circumvention of host humoral defenses.
Femtosecond laser polishing of optical materials (2015)

Technologies including magnetorheological finishing and CNC polishing are commonly used to finish optical elements, but these methods are often expensive, generate waste through the use of fluids or abrasives, and may not be suited for specific freeform substrates due to the size and shape of finishing tools. Pulsed laser polishing has been demonstrated as a technique capable of achieving nanoscale roughness while offering waste-free fabrication, material-specific processing through direct tuning of laser radiation, and access to freeform shapes using refined beam delivery and focusing techniques. Nanosecond and microsecond pulse duration radiation has been used to perform successful melting-based polishing of a variety of different materials, but this approach leads to extensive heat accumulation resulting in subsurface damage. We have experimentally investigated the ability of femtosecond laser radiation to ablate silicon carbide and silicon. By substituting ultrafast laser radiation, polishing can be performed by direct evaporation of unwanted surface asperities with minimal heating and melting, potentially offering damage-free finishing of materials. Under unoptimized laser processing conditions, thermal effects can occur leading to material oxidation. To investigate these thermal effects, simulation of the heat accumulation mechanism in ultrafast laser ablation was performed. Simulations have been extended to investigate the optimum scanning speed and pulse energy required for processing various substrates. Modeling methodologies and simulation results will be presented.
Avalanche Diodes and Circuits for Infrared Photon Counting and Timing: Retrospect and Prospect. (2006)

The evolution of single-photon avalanche diodes (SPAD) and associated avalanche-quenching circuits for extending beyond 1 micron wavelength the spectral range of photon counting and timing is reviewed and the prospect of further progress is discussed
Production of high-brightness continuous wave proton beams with very high proton fractions (abstract)a) (1996)

This article demonstrates a new technique to significantly enhance the proton fraction of an ion beam extracted from a plasma ion source. We employ a magnetically confined microwave driven source, though the technique is not source specific and can probably be applied equally effectively to other plasma sources such as Penning and multicusp types. Specifically, we dope the plasma with about 1% H2O, which increases the proton fraction of a 45 keV 45 mA beam from 75% to 90% with 375 W 2.45 GHz power to the source and from 84% to 92% for 500 W when the source is operated under nonresonant conditions. Much of the remaining fraction of the beam comprises a heavy mass ion we believe to be N+ impurity ions resulting from the conditions under which the experiments were performed. If so, this impurity can easily be removed and much higher proton fractions could be expected. Preliminary measurements show the additive has no adverse effect on the emittance of the extracted beam, and source stability is greatly improved.
Finite Impulse Response Cyclic Shift Transmit Diversity for Broadband Mobile OFDM (2007)

This paper introduces an open-loop transmit diversity method called finite impulse response cyclic shift diversity (FIR-CSD) for broadband mobile OFDM systems. Ordinary CSD operates in OFDM by cyclically shifting the same time- domain signal by different cyclic shift values on each transmit antenna branch. Unfortunately, in some channels (such as a line of sight channel or a heavily spatially correlated channel), ordinary CSD introduces deep spectral nulls in the composite frequency response seen by the receiver, which results in a performance loss relative to the single transmit antenna case. FIR-CSD is an extension of the CSD concept wherein multiple weighted and circular shifted copies of the time-domain signal are combined and transmitted on each antenna. Each transmit antenna essentially uses a different FIR filter that combines multiple weighted and circularly-shifted copies of the time-domain signal to be transmitted. Careful selection of the circular shift values and weighting factors on each transmit antenna can significantly reduce or eliminate the deep spectral nulls that ordinary CSD would produce in the above mentioned channels. This paper shows that FIR-CSD provides a significant performance improvement over the original cyclic shift diversity method, especially in correlated channels and with high-rate coding.
Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing (2009)

We report on a new algorithm for combining the information from several mass spectra of the same peptide. The algorithm automatically learns peptide fragmentation patterns, so that it can handle spectra from any instrument and fragmentation technique. We demonstrate the utility of the algorithm, and the power of multiple spectra, by showing that combining pairs of spectra (one CID and one ETD) greatly improves de novo sequencing success rates.
Fabrication of dual damascene BEOL structures using a multilevel multiple exposure (MLME) scheme, part 1: lithographic patterning (2010)

In this work, the conventional via-first dual damascene (DD) patterning scheme is replaced by a cost-efficient Multi-Level Multiple Exposure (MLME) patterning and etching approach. A two-layer positive-tone photoresist stack is sequentially imaged using 193 nm dry lithography, to produce a DD resist structure that is subsequently transferred into an auxiliary dual organic underlayer stack, and then further into a dielectric layer. This novel integration approach eliminates inter-tool wafer exchange sequences as performed in a conventional litho-etch-litho-etch process flow, while simultaneously being applicable to all back-end-of-the-line (BEOL) levels, ensuring throughput increase. The top and bottom resist layers are chemically designed in such a way that they feature differential solubility in organic solvents making it possible to coat the top photoresist onto the bottom resist layer without intermixing to enable a strict litholitho- etch processing sequence. Independent registration of the via and trench structures in the bottom and top resist layers is achieved by selective photospeed decoupling of the respective layers, so that the bottom resist is largely insensitive at nominal resist exposure dose for the top resist. Imaging performance evaluation of the newly introduced MLME technology includes the resist materials selection process and their required properties (solvent compatibility, adhesion, photospeed, defectivity and correction of via dose bias due to trench exposure) as well as metrology work. Image transfer of the patterned DD resist structure into an underlying transfer layer stack and then further into a dielectric layer using Reactive Ion Etching (RIE) followed by electroplating, polishing and electrical testing was also thoroughly investigated and is described in detail in an accompanying paper.
Determining configuration parameter dependencies via analysis of configuration data from multi-tiered enterprise applications (2009)

Multi-tiered enterprise applications, which comprise of many (heterogeneous and possibly loosely coupled) components at various layers of the IT stack, typically have configuration dependencies between these different components. A change in the value of a configuration parameter of a component may require changing one or more parameters of other components to the same value. Keeping track of these dependencies is not a mean task as they are typically cross product and requires in-depth product/system knowledge.Our aim in this paper is to introduce techniques that do not require a system administrator to have in-depth knowledge about a multi-tiered system in order to be aware of the possible configuration dependencies in a system. Our focus in this paper does not include, for example, the performance-related dependencies such as the one that exists between the maximum number of threads and session timeout in an Apache server. In this paper we provide a method for analyzing existing deployments (that are functioning properly) to infer the configuration dependencies in a probabilistic sense. Firstly, we analyze the values of the configuration parameters of the various components to determine a candidate list of dependencies which includes both true and false ones. We then provide a heuristic that makes use of the statistics on the parameter name and value strings, computed from the configuration data and also the information on the web, to compute a rank for a dependency to be true. We provide a rank-ordered list of dependencies so that administrators can consult it to quickly and systematically identify the true dependencies. To complement our proposed approach we have performed an extensive study and experimentation to show the efficacy of our technique on data from two real-world solutions.
Implantable phototherapy device to treat diabetic retinopathy (2017)

This paper reports on the first implantable phototherapy device to treat diabetic retinopathy by modulating rod cell metabolism through reduction of dark current. Utilizing a tritium-based radioluminescent light source capable of emitting around 505nm, the device achieves phototherapeutic activity for up to a 12-year service lifetime and <;30mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> size. The unique scleral anchoring system facilitates simple, rapid, and robust implantation into the eye. Implantation into a rabbit model demonstrated safety over a 4-week period with no adverse effects observed.
IC‐P‐134: Differential Diagnosis of Dementia with FDG‐PET and Voxel‐Based Statistical Analysis: Impact of Alternative Normal Databases (2010)

For differential diagnosis of dementia using FDG-PET, several studies have highlighted increased accuracy of image interpretation when significant local intensity deviations are detected and visualized. This requires the statistical comparison of the patient's image data to a normal database (NL-DB). The database is ideally created using the same scanner and acquisition / reconstruction protocol as the test image. This poses a significant barrier to the widespread use of statistical analysis for clinical FDG-PET dementia evaluation, as a custom NL-DB is not available at many institutions. This study investigated the accuracy of visual diagnostic interpretation of statistical maps using various NL-DBs. FDG-PET brain scans were obtained for 97 subjects with suspected dementia, including healthy subjects (NL, n = 30) and patients with probable Alzheimer's disease (AD, n = 30), fronto-temporal dementia (FTD, n = 25) and dementia with Lewy bodies (LBD, n = 12). Images were acquired at two institutions using three different PET scanner and local protocol (Allegro, n = 28; Gemini-GXL, n = 33; ECAT-EXACT, n = 36), and NL-DBs were obtained for each scanner (n = 24/19/26, age = 72.2 ± 6.8/68.1 ± 8.1/49.6 ± 13.2 respectively). Voxel-wise statistical comparison to each NL-DB yielded 3 different statistical maps per subject, one from the same scanner (“own DB”) and two from different scanners (“other DB”). These maps were overlaid on the template image, and presented (48 axial slices covering the brain) in random order to two expert readers who assigned diagnostic classes (NL/AD/FTD/LBD) to each map. Inter-rater agreement (Cohen's kappa) was 0.73 (substantial) for “own DB”, and 0.50 (moderate) for “other DB”. Overall accuracy of visual interpretation over both readers was 80% with “own DB”, and 68% with “other DB”. Sensitivity for the diagnostic classes NL/AD/FTD/LBD was 97/82/84/25% for “own DB”, and 61/73/84/38% for “other DB”. Average specificity was 93% and 89% respectively. Inter-rater agreement and diagnostic accuracy of visual statistical map interpretation is significantly reduced when the NL-DB is not from the same scanner. The most evident effect of using another NL-DB is false-positive assignment of healthy subjects to one of the disease classes. This suggests that loss of accuracy might be reduced using simple methods to adapt an external NL-DB to local conditions.
A cell wall‐associated polysaccharide is required for bacteriophage adsorption to the <i>Streptococcus thermophilus</i> cell surface (2020)

Streptococcus thermophilus strain ST64987 was exposed to a member of a recently discovered group of S. thermophilus phages (the 987 phage group), generating phage-insensitive mutants, which were then characterized phenotypically and genomically. Decreased phage adsorption was observed in selected bacteriophage-insensitive mutants, and was partnered with a sedimenting phenotype and increased cell chain length or aggregation. Whole genome sequencing of several bacteriophage-insensitive mutants identified mutations located in a gene cluster presumed to be responsible for cell wall polysaccharide production in this strain. Analysis of cell surface-associated glycans by methylation and NMR spectroscopy revealed a complex branched rhamno-polysaccharide in both ST64987 and phage-insensitive mutant BIM3. In addition, a second cell wall-associated polysaccharide of ST64987, composed of hexasaccharide branched repeating units containing galactose and glucose, was absent in the cell wall of mutant BIM3. Genetic complementation of three phage-resistant mutants was shown to restore the carbohydrate and phage resistance profiles of the wild-type strain, establishing the role of this gene cluster in cell wall polysaccharide production and phage adsorption and, thus, infection.
IMMEDIATE LOCAL TRANSPLANTATION OF MESENCHYMAL STEM CELLS AFTER SEVERE SKELETAL MUSCLE INJURY IMPROVES THE FUNCTIONAL OUTCOME COMPARABLE TO DELAYED TRANSPLANTATION (2010)

Skeletal muscle injuries often lead to severe functional deficits. Mesenchymal stem cell (MSC) therapy is a promising but still experimental tool in the regeneration of muscle function after severe trauma. One of the most important questions, which has to be answered prior to a possible future clinical application is the ideal time of transplantation. Due to the initial inflammatory environment we hypothesized that a local injection of the cells immediately after injury would result in an inferior functional outcome compared to a delayed transplantation. Twenty-seven female Sprague Dawley rats were used for this study. Bone marrow was aspirated from both tibiae of each animal and autologous MSC cultures obtained from the material. The animals were separated into three groups (each n=9) and the left soleus muscles were bluntly crushed in a standardized manner. In group 1 2×106 MSCs were transplanted into the injured muscle immediately after trauma, whereas group 2 and 3 received an injection of saline. Another week later the left soleus muscles of the animals of group 2 were transplanted with the same number of MSCs. Group 1 and 3 received a sham treatment with the application of saline solution in an identical manner. In vivo functional muscle testing was performed four weeks after trauma to quantify muscle regeneration. Maximum contraction forces after twitch stimulation decreased to 39 ± 18 % of the non injured right control side after crush trauma of the soleus muscles as measured in group 3. Tetanic stimulation showed a reduction of the maximum contraction capacity of 72 ± 12 % of the value obtained from intact internal control muscles. The transplantation of 2 x 106 MSCs one week after trauma improved the functional regeneration of the injured muscles as displayed by significantly higher contraction forces in group 2 (twitch: p = 0.014, tetany: p = 0.018). Local transplantation of the same number of MSCs immediately after crush injury was able to enhance the regeneration process to a similar extent with an increase of maximum twitch contraction forces by 73.3 % (p = 0.006) and of maximum tetanic contraction forces by 49.6 % (p = 0.037) compared to the control group. The presented results underline the effectivity of MSC transplantation in the treatment of severe skeletal muscle injuries. The most surprising finding was that despite of the fundamental differences of the local environment into which MSCs had been transplanted, similar results could be obtained in respect to functional skeletal muscle regeneration. We assume that the effect of the MSC after immediate injection can partly be explained by their known immunomodulatory competences. The data of our study provide evidence for a large time window of MSC transplantation after muscle trauma.
On-resin dimerization incorporates a diverse array of π-conjugated functionality within aqueous self-assembling peptide backbones (2010)

We report a convenient method to incorporate pi-electron units into peptides that assemble into amyloid-like supramolecular polymers, discussing the scope of the process and preliminary characterization of the resulting nanomaterials. Self-assembly manipulates these "electronic peptides" into delocalized sub-10 nm 1-D nanostructures under completely aqueous conditions.
Compensation of the differential floating capacitance between dual microelectrodes (2000)

A circuit for compensating the floating differential capacitance appearing between two recording microelectrodes is presented. It is shown how this floating capacitance can be neutralized so that current in any microelectrode can be injected without any significant crosstalk picked up by the other.
Herpes simplex virus type-1(HSV-1) oncolytic and highly fusogenic mutants carrying the NV1020 genomic deletion effectively inhibit primary and metastatic tumors in mice (2008)

These results show that the attenuated, but highly fusogenic OncSyn and OncdSyn viruses can effectively reduce primary and metastatic breast tumors in immuncompetent mice. The available bac-cloned OncSyn and OncdSyn viral genomes can be rapidly modified to express a number of different anti-tumor and immunomodulatory genes that can further enhance their anti-tumor potency.
Antigenic Profiling of a<i>Chlamydia trachomatis</i>Gene‐Expression Library (2008)

The obligate intracellular bacterium Chlamydia trachomatis is the causative agent of sexually transmitted chlamydia infections. A panel of 116 recombinant C. trachomatis proteins was evaluated comparatively to characterize both cell-mediated and humoral immune responses in patients with confirmed C. trachomatis genital infection. The antigens identified were categorized as being recognized exclusively by T cells (CT004, CT043, CT184, CT509, and CT611), B cells (CT082, CT089, CT322, CT396, and CT681), or both T cells and B cells (CT110 and CT443). This grouping of C. trachomatis antigens was correlated to their predicted cellular localization. The comparative evaluation presented here indicates that T cell antigens are located in all bacterial compartments, whereas antibody targets are mainly localized to the outer membrane (P = .0013). Overall, we have identified 5 T cell antigens, 5 B cell antigens, and 2 T/B cell antigens that are potential components for a future chlamydia vaccine.
Laser Pulse Heating Simulation of Firing Damage on Coated Gun Bore Surfaces (2001)

Abstract : Laser pulse heating was used to simulate thermal effects on plated gun bore surfaces during firing. The aim is to provide new insights into the erosion process and develop the method as an evaluation tool for developmental coatings. This report discusses results of cyclic thermal pulsing experiments on high contractile and low contractile chromium plated gun steel, sputtered tantalum coated gun steel, and uncoated steel.
Coherent Optical Noise Suppression Device (1974)

In optical data processing the quality of the output image is usually degraded by diffraction noise generated by the optical components of the system. The suitability of previously suggested techniques to a dc spatial filtering processor is discussed. A new system is proposed that overcomes the problems of the previous noise suppression techniques. Experimental results of the new system are presented along with a determination of the resolution of the system. The errors and limits of the new coherent noise suppression system are discussed.