gebhart/patrepeval huggingface dataset:
Implications of Biofilm Formation on Urological Devices (2008)

Despite millions of dollars and several decades of research targeted at their prevention and eradication, biofilm‐associated infections remain the major cause of urological device failure. Numerous strategies have been aimed at improving device design, biomaterial composition, surface properties and drug delivery, but have been largely circumvented by microbes and their plethora of attachment, host evasion, antimicrobial resistance, and dissemination strategies. This is not entirely surprising since natural biofilm formation has been going on for millions of years and remains a major part of microorganism survival and evolution. Thus, the fact that biofilms develop on and in the biomaterials and tissues of humans is really an extension of this natural tendency and greatly explains why they are so difficult for us to combat. Firstly, biofilm structure and composition inherently provide a protective environment for microorganisms, shielding them from the shear stress of urine flow, immune cell attack and some antimicrobials. Secondly, many biofilm organisms enter a metabolically dormant state that renders them tolerant to those antibiotics and host factors able to penetrate the biofilm matrix. Lastly, the majority of organisms that cause biofilm‐associated urinary tract infections originate from our own oral cavity, skin, gastrointestinal and urogenital tracts and therefore have already adapted to many of our host defenses. Ultimately, while biofilms continue to hold an advantage with respect to recurrent infections and biomaterial usage within the urinary tract, significant progress has been made in understanding these dynamic microbial communities and novel approaches offer promise for their prevention and eradication. These include novel device designs, antimicrobials, anti‐adhesive coatings, biodegradable polymers and biofilm‐disrupting compounds and therapies.
Modeling local and global deformations in Deep Learning: Epitomic convolution, Multiple Instance Learning, and sliding window detection (2015)

Deep Convolutional Neural Networks (DCNNs) achieve invariance to domain transformations (deformations) by using multiple `max-pooling' (MP) layers. In this work we show that alternative methods of modeling deformations can improve the accuracy and efficiency of DCNNs. First, we introduce epitomic convolution as an alternative to the common convolution-MP cascade of DCNNs, that comes with the same computational cost but favorable learning properties. Second, we introduce a Multiple Instance Learning algorithm to accommodate global translation and scaling in image classification, yielding an efficient algorithm that trains and tests a DCNN in a consistent manner. Third we develop a DCNN sliding window detector that explicitly, but efficiently, searches over the object's position, scale, and aspect ratio. We provide competitive image classification and localization results on the ImageNet dataset and object detection results on Pascal VOC2007.
A Second‐Generation Total Synthesis of Spirastrellolide A Methyl Ester (2012)

Marine macrolides: an improved second-generation total synthesis of the anticancer macrolide spirastrellolide A methyl ester has been achieved. The synthesis features a uniformly high level of stereocontrol combined with more expedient fragment assembly, and demonstrates a critical dependence of the crucial macrolactonization step on the substitution pattern of the C22-C24 linker region.
X-ray properties of active galaxies with high intrinsic absorption (1993)

We present the results of Ginga observations of three narrow emission line X-ray galaxies, NGC 7172, NGC 7582, and ESO 103-G35. In each of these galaxies the column density along the line of sight to the active nucleus is extremely high |$(\text {i.e}. {n}_\text {H} \gtrsim {10}^{23}\enspace \text {cm}^{-2})$|⁠. A comparison of the optical depth in the iron K-edge with the low-energy absorption in the X-ray spectrum indicates an apparent iron abundance in excess of the solar value in these sources. Measurements of the iron K-edge energy show that the bulk of the X-ray-absorbing gas is not strongly photoionized, with only ESO 103-G35 exhibiting an edge energy significantly above that for neutral iron. In the case of NGC 7582, the line-of-sight column density may have increased by a factor of ~ 3 over an interval of about 4 yr. The implications of these results for current models of the state and distribution of gaseous material in low-luminosity active galactic nuclei are briefly discussed.
Optimal structure screening for large-scale multi-state series-parallel systems based on structure ordinal optimization (2020)

Multi-state series-parallel systems are widely-used for representing engineering systems. In real-life cases, engineers need to select an optimal system structure among many different multi-state series-parallel system structures. Screening of system structures is meaningful and critical. Moreover, to design a reliable structure, reliability evaluation is an indispensable part of the process. Due to the large number of available system structures, the computational burden can be huge when selecting the optimal one. Also, the number of components and possible states of each system can be enormous when the system scale is large, which causes significant complexity in exact reliability evaluation. To effectively select the optimal structure among numerous multi-state series-parallel systems under a reliability constraint, this article proposes an optimal structure screening method called the structure ordinal optimization. The proposed method combines the fuzzy universal generating function technique with an ordinal optimization algorithm. The fuzzy universal generating function technique is applied to reduce the computational time by approximately evaluating the reliability. Based on the approximate reliabilities, ordinal optimization helps to reduce the number of structure options and thus accelerate the screening process. Numerical examples show that the structure ordinal optimization method has advantages in computational efficiency with satisfactory accuracy.
An in vivo study of dynamic effects of wrist traction on the radiolunate and capitolunate joints (2015)

Introduction We described the dynamic effects of traction on the radiolunate and capitolunate joints in a living body to explore the possibility of range of motion exercise of the wrist joint under traction as a new method of exercise. Methods Dynamic radiography was conducted while creating wrist passive movements by using manual traction and machinery traction with a measurement device. Subjects were 20 healthy men. The change in the percentage of contribution of the radiolunate and capitolunate joints with or without traction was calculated. Results Manual traction: During palmar flexion, the percentage of contribution of the radiolunate angle was increased from 39.4% to 49.9%, and the capitolunate angle was decreased from 60.6% to 50.1% with traction. During dorsiflexion, the radiolunate angle was increased from 60.2% to 70.0%, and the capitolunate angle was decreased from 39.8% to 30.0% with traction. Machinery traction: During palmar flexion, the radiolunate angle was increased from 46.1% to 56.4%, and the capitolunate angle was decreased from 53.9% to 43.6% with traction. During dorsiflexion, the radiolunate angle was increased from 68.7% to 72.0%, and the capitolunate angle was decreased from 31.3% to 28.0% with traction. Conclusions The movement of the radiolunate joint was increased and that of the capitolunate joint decreased with the addition of traction. Range of motion exercise with traction has the potential to be applied to an advanced rehabilitation program targeting the radiolunate joint under specific pathological conditions.
<title>SEM performance evaluation using the sharpness criterion</title> (1996)

Fully automated or semi-automated scanning electron microscopes (SEM) are now commonly used in semiconductor production and other forms of manufacturing. The industry requires that an automated instrument must be routinely capable of 5 nm resolution (or better) at 1.0 kV accelerating voltage for the measurement of nominal 0.25 - 0.35 micrometer semiconductor critical dimensions. Testing and proving that the instrument is performing at this level on a day-by-day basis is an industry need and concern and is addressed in this paper. Furthermore, with the introduction of fully automated inspection and metrology instrumentation, not only does an appropriate, easy to obtain or manufacture measurement sample have to exist, but also an objective and automated algorithm developed for its analysis. Both of these have been the objects of a study at NIST and the fundamentals are discussed in this paper. In scanning electron microscopy, two of the most important instrument parameters are the size and shape of the primary electron beam and any image taken in a scanning electron microscope is the result of the sample and electron probe interaction. The low frequency changes in the video signal, collected from the sample, contains information about the larger features and the high frequency ones carry information of finer details. In principle, if the sample geometry is known, the geometric parameters of the primary electron beam are mathematically determinable from an acquired image. The method described in this paper is based on the frequency domain representation of a scanning electron microscope image and can also be used to check and optimize two basic parameters of the primary electron beam, the focus and the astigmatism. The application of this technique to regularly check the resolution of the SEM in quantitative form also is discussed.
Botulinum neurotoxin type A (BoNTA) decreases the mechanical sensitivity of nociceptors and inhibits neurogenic vasodilation in a craniofacial muscle targeted for migraine prophylaxis (2010)

The mechanism by which intramuscular injection of BoNTA into the craniofacial muscles decreases migraine headaches is not known. In a blinded study, the effect of BoNTA on the mechanical and chemical responsiveness of individual temporalis muscle nociceptors and muscle neurogenic vasodilation was investigated in female rats. Mechanical threshold was measured for 3h following intramuscular injection of BoNTA or vehicle, and for 10 min after a subsequent injection of the algogen glutamate. Injection of BoNTA significantly increased the mechanical threshold of muscle nociceptors without altering the muscle surface temperature and blocked glutamate-induced mechanical sensitization and neurogenic vasodilation. None of these effects were reproduced by pancuronium-induced muscle paralysis. Western blot analysis of temporalis muscles indicated that BoNTA significantly decreased SNAP-25. Measurement of interstitial glutamate concentration with a glutamate biosensor indicated that BoNTA significantly reduced glutamate concentrations. The mechanical sensitivity of muscle nociceptors is modulated by glutamate concentration through activation of peripheral NMDA receptors. Immunohistochemical experiments were conducted and they indicated that half of the NMDA-expressing temporalis nerve fibers co-expressed substance P or CGRP. Additional electrophysiology experiments examined the effect of antagonists for NMDA, CGRP and NK1 receptors on glutamate-induced effects. Glutamate-induced mechanical sensitization was only blocked by the NMDA receptor antagonist, but muscle neurogenic vasodilation was attenuated by NMDA or CGRP receptor antagonists. These data suggest that injection of BoNTA into craniofacial muscles acts to decrease migraine headaches by rapidly decreasing the mechanical sensitivity of temporalis muscle nociceptors through inhibition of glutamate release and by attenuating the provoked release of CGRP from muscle nociceptors.
Metabolic Profiles of Patients with Subarachnoid Hemorrhage Treated by Early Surgery (1998)

SAH treated by surgery induces a profound stress response. A significant difference of increased catabolism but not decreased anabolism between the mild and severe groups was noted.
Interpreting pre-Quaternary climate from the geologic record (1998)

Foreword Introduction Marine Biotic Indicators of Paleoclimate Continental Biotic Indicators of Paleoclimate Marine Lithologic Indicators of Paleoclimate Continental Lithologic Indicators of Paleoclimate Integrating Marine and Continental Paleoclimatic Records Models Case Histories of Paleoclimatic Studies
Microbially Enhanced Oil Recovery by Sequential Injection of Light Hydrocarbon and Nitrate in Low- And High-Pressure Bioreactors (2015)

Microbially enhanced oil recovery (MEOR) often involves injection of aqueous molasses and nitrate to stimulate resident or introduced bacteria. Use of light oil components like toluene, as electron donor for nitrate-reducing bacteria (NRB), offers advantages but at 1-2 mM toluene is limiting in many heavy oils. Because addition of toluene to the oil increased reduction of nitrate by NRB, we propose an MEOR technology, in which water amended with light hydrocarbon below the solubility limit (5.6 mM for toluene) is injected to improve the nitrate reduction capacity of the oil along the water flow path, followed by injection of nitrate, other nutrients (e.g., phosphate) and a consortium of NRB, if necessary. Hydrocarbon- and nitrate-mediated MEOR was tested in low- and high-pressure, water-wet sandpack bioreactors with 0.5 pore volumes of residual oil in place (ROIP). Compared to control bioreactors, those with 11-12 mM of toluene in the oil (gained by direct addition or by aqueous injection) and 80 mM of nitrate in the aqueous phase produced 16.5 ± 4.4% of additional ROIP (N = 10). Because toluene is a cheap commodity chemical, HN-MEOR has the potential to be a cost-effective method for additional oil production even in the current low oil price environment.
Visual landmark extraction and recognition for autonomous robot navigation (2002)

The robot navigation using visual landmark approach is described. The landmarks are not preselected or otherwise defined a priori, but rather, they are extracted automatically during a learning phase. To facilitate this, a saliency map is constructed which highlights potential landmarks. This is used in conjunction with a qualitative segregation of the workspace, to further delineate the search areas for environment landmarks. For the sake of robustness, no semantic information is attached to the landmarks; they are stored as raw patterns along with information readily available from the workspace segregation, that facilitates their accurate rate recognition at a later, navigation session. During such a session, similar steps with the learning phase are employed to locate landmarks. The stored information is used to transform a previously leaned landmark pattern, according to the current position of the observer, achieving thus accurate landmark recognition. Results obtained from our approach demonstrate its validity and applicability in indoor workspaces.
Inhibition of monocyte adhesion and fibrinogen adsorption on glow discharge plasma deposited tetraethylene glycol dimethyl ether (2001)

Monocytes and macrophages play important roles in host responses to implanted biomedical devices. Monocyte and macrophage interactions with biomaterial surfaces are thought to be mediated by adsorbed adhesive proteins such as fibrinogen and fibronectin. Non-fouling surfaces that minimize protein adsorption may therefore minimize monocyte adhesion, activation, and the foreign body response. Radio-frequency glow discharge plasma deposition (RF-GDPD) of tetraethylene glycol dimethyl ether (tetraglyme) was used to produce polyethylene oxide (PEO)-like coatings on a fluorinated ethylene-propylene (FEP) surface. Electron spectroscopy for chemical analysis (ESCA) and static time of flight secondary ion mass spectrometry (ToF-SIMS) were used to characterize the surface chemistry of tetraglyme coating. Fibrinogen adsorption to the tetraglyme surface was measured with 125I-labeled fibrinogen and ToF-SIMS. Adsorption of fibrinogen to plasma deposited tetraglyme was less than 10 ng cm(-2), a 20-fold decrease compared to untreated FEP or tissue culture polystyrene (TCPS). Monocyte adhesion to plasma deposited tetraglyme was significantly lower than adhesion to FEP or TCPS. In addition, when the surfaces were preadsorbed with fibrinogen, fibronectin, or blood plasma, monocyte adhesion to plasma deposited tetraglyme after 2 h or 1 day was much lower than adhesion to FEP. RF-GDPD tetraglyme coating provides a promising approach to make non-fouling biomaterials that can inhibit non-specific material-host interactions and reduce the foreign body response.
Hypertonic Saline Is Effective in the Prevention and Treatment of Mucus Obstruction, but Not Airway Inflammation, in Mice with Chronic Obstructive Lung Disease (2013)

Recent evidence suggests that inadequate hydration of airway surfaces is a common mechanism in the pathogenesis of airway mucus obstruction. Inhaled hypertonic saline (HS) induces osmotic water flux, improving hydration of airway surfaces. However, trials in patients with obstructive lung diseases are limited. The aim of this study was to investigate effects of HS on mucus obstruction and airway inflammation in the prevention and treatment of obstructive lung disease in vivo. We, therefore, used the β-epithelial Na(+) channel (βENaC)-overexpressing mouse as a model of chronic obstructive lung disease and determined effects of preventive and late therapy with 3% HS and 7% HS on pulmonary mortality, airway mucus obstruction, and inflammation. We found that preventive treatment with 3% HS and 7% HS improved growth, reduced mortality, and reduced mucus obstruction in neonatal βENaC-overexpressing mice. In adult βENaC-overexpressing mice with chronic lung disease, mucus obstruction was significantly reduced by 7% HS, but not by 3% HS. Treatment with HS triggered airway inflammation with elevated keratinocyte chemoattractant levels and neutrophils in airways from wild-type mice, but reduced keratinocyte chemoattractant in chronic neutrophilic inflammation in adult βENaC-overexpressing mice. Our data demonstrate that airway surface rehydration with HS provides an effective preventive and late therapy of mucus obstruction with no consistent effects on inflammation in chronic lung disease. These results suggest that, through mucokinetic effects, HS may be beneficial for patients with a spectrum of obstructive lung diseases, and that additional strategies are required for effective treatment of associated airway inflammation.
The differentiation of cytotoxic T cells in vitro. IV. Interleukin-2 production in primary mixed lymphocyte cultures involves cooperation between Qa-1+ and Qa-1- "helper" T cells. (1981)

Studies with C57BL/6-TIaa mice have established that both Qa-1+ and Qa-1- helper T cells are required for the optimal production of Interleukin 2(IL-2) activity in primary MLC. This was established both by depletion of Qa-1 bearing cells by treatment of responder cells with anti-Qa-1 serum in the presence of complement and by positive selection (using FACS II analysis) of those cells displaying Qa-1. Furthermore, microfluoremetry revealed that the great majority of C57BL/6-TIaa and of A/J splenic T cells bore Qa-1 alloantigen but that only those with the highest antigen density were susceptible to complement-mediated lysis.
Clinical Application of Compton and Photo-Electric Reconstruction in Computed Tomography: Preliminary Results (1978)

Although computed tomography has demonstrated some promise in the direction of quantative radiology, valuable information related to the varying response of tissues to x-rays of different energy is still not utilized on a routine basis. Advancements in a method proposed by Alvarez and Macovski for decomposing dual-spectra CT projection data into its material-dependent Compton and photo-electric components are described. Results are presented to demonstrate that such a separation can be performed. Reconstructed images of separated Compton and photo-electric data obtained from clinical scans are shown. With the improvements described, the Compton images begin to approach the quality of conventional reconstructions with evidence of improved polychromatic correction. The photo-electric data, while separable, suffers from unacceptable noise level. Analysis of this difficulty is presented, with recommendations for future improvement by careful selection of the effective energy of the low energy spectrum. The encouraging results suggest that this technique warrants continued development and evaluation.
Synthesis of Key Intermediate of Phosphonosulfonates (BPH-652), 1-(3-Iodopropyl)-3-Phenoxy Benzene (2014)

A convenient and efficient four-step synthesis of 1-(3-iodopropyl)-3-phenoxy benzene can be achieved by 3-phenoxybenzaldehyde and malonic acid in the presence of piperidine and pyridine to yield (E)-3-(3-phenoxyphenyl)-2-propenoic acid, esterification with methanol in the present of p-toluene sulfonic acid, reduction with sodium borohydride to give 3-(3-phenoxyphenyl)propan-1-ol and iodination of 3-(3-phenoxy phenyl) propan-1-ol using iodine and triphenylphosphine in the present of potassium iodide and imidazole and to afford the title compound in an overall yield of 55.6 %.
A uniform analysis method for DSP architectures and instruction sets with a comprehensive example (2002)

As digital signal processing finds broader areas of application, more processors are adapting to the need for DSP operations. MMX instructions have been added to the Pentium, high-performance RISC have done similar things for workstations, and microcontrollers are doing it for embedded applications. Digital signal processors too are changing as there are increased demands for higher performance. With new processors having such vastly different architectures and employing different processing strategies, it is increasingly difficult to make meaningful DSP performance comparisons between them. This paper reviews the normal representations or views of a processor: hardware architecture, programming model, instruction set architecture and benchmarks, and their role in DSP performance estimation in four critical areas. A uniform model is proposed for the first three views, which includes a new annotated form of programming model using signal-flow-graph-like techniques. Finally, one of the new types of processors, the Siemens TriCore Microcontroller-DSP, is analyzed to test and illustrate the new models and methodology.
Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering (2020)

The use of optogenetics in metabolic engineering for light-controlled microbial chemical production raises the prospect of utilizing control and optimization techniques routinely deployed in traditional chemical manufacturing. However, such mechanisms require well-characterized, customizable tools that respond fast enough to be used as real-time inputs during fermentations. Here, we present OptoINVRT7, a new rapid optogenetic inverter circuit to control gene expression in <i>Saccharomyces cerevisiae</i>. The circuit induces gene expression in only 0.6 h after switching cells from light to darkness, which is at least 6 times faster than previous OptoINVRT optogenetic circuits used for chemical production. In addition, we introduce an engineered inducible <i>GAL1</i> promoter (P<sub>GAL1-S</sub>), which is stronger than any constitutive or inducible promoter commonly used in yeast. Combining OptoINVRT7 with P<sub>GAL1-S</sub> achieves strong and light-tunable levels of gene expression with as much as 132.9 ± 22.6-fold induction in darkness. The high performance of this new optogenetic circuit in controlling metabolic enzymes boosts production of lactic acid and isobutanol by more than 50% and 15%, respectively. The strength and controllability of OptoINVRT7 and P<sub>GAL1-S</sub> open the door to applying process control tools to engineered metabolisms to improve robustness and yields in microbial fermentations for chemical production.