gebhart/patrepeval huggingface dataset:
Assessing genetic diversity and similarity of 435 KPC-carrying plasmids (2019)

The global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (bla<sub>KPC</sub>) has been spreading over the last decade in the health care setting. bla<sub>KPC</sub> seems to have rapidly diversified and has been found in various species and on different plasmid types. To review the progress and dynamics of this diversification, all currently available KPC plasmids in the NCBI database were analysed in this work. Plasmids were grouped into 257 different representative KPC plasmids, of which 79.4% could be clearly assigned to incompatibility (Inc) group or groups. In almost half of all representative plasmids, the KPC gene is located on Tn4401 variants, emphasizing the importance of this transposon type for the transmission of KPC genes to other plasmids. The transposons also seem to be responsible for the occurrence of altered or uncommon fused plasmid types probably due to incomplete transposition. Moreover, many KPC plasmids contain genes that encode proteins promoting recombinant processes and mutagenesis; in consequence accelerating the diversification of KPC genes and other colocalized resistance genes.
Homocereulide, an Extremely Potent Cytotoxic Depsipeptide from the Marine Bacterium Bacillus cereus (1995)

Abstract Homocereulide (1) and cereulide (2), isolated from the marine bacterium Bacillus cereus SCRC, showed extremely potent cytotoxicity. Their structures were elucidated by spectroscopic analysis and chemical degradation.
Genetic Engineering of Enterobacter asburiae Strain JDR-1 for Efficient Production of Ethanol from Hemicellulose Hydrolysates (2009)

Dilute acid pretreatment is an established method for hydrolyzing the methylglucuronoxylans of hemicellulose to release fermentable xylose. In addition to xylose, this process releases the aldouronate methylglucuronoxylose, which cannot be metabolized by current ethanologenic biocatalysts. Enterobacter asburiae JDR-1, isolated from colonized wood, was found to efficiently ferment both methylglucuronoxylose and xylose in acid hydrolysates of sweet gum xylan, producing predominantly ethanol and acetate. Transformation of E. asburiae JDR-1 with pLOI555 or pLOI297, each containing the PET operon containing pyruvate decarboxylase (pdc) and alcohol dehydrogenase B (adhB) genes derived from Zymomonas mobilis, replaced mixed-acid fermentation with homoethanol fermentation. Deletion of the pyruvate formate lyase (pflB) gene further increased the ethanol yield, resulting in a stable E. asburiae E1(pLOI555) strain that efficiently utilized both xylose and methylglucuronoxylose in dilute acid hydrolysates of sweet gum xylan. Ethanol was produced from xylan hydrolysate by E. asburiae E1(pLOI555) with a yield that was 99% of the theoretical maximum yield and at a rate of 0.11 g ethanol/g (dry weight) cells/h, which was 1.57 times the yield and 1.48 times the rate obtained with the ethanologenic strain Escherichia coli KO11. This engineered derivative of E. asburiae JDR-1 that is able to ferment the predominant hexoses and pentoses derived from both hemicellulose and cellulose fractions is a promising subject for development as an ethanologenic biocatalyst for production of fuels and chemicals from agricultural residues and energy crops.
Perceptually based techniques for image segmentation and semantic classification (2007)

We present a new approach for semantic image analysis that combines knowledge of human perception with an understanding of signal characteristics to segment natural scenes into perceptually uniform regions, and then uses the region statistics to extract semantic information. Applications include content-based image retrieval and region of interest extraction for efficient compression/transmission over heterogeneous networks
Reactions of Carbonyl Compounds in Basic Solutions. Part 351: The Alkaline Hydrolysis and Reactivity – Structure – Spectra Correlations of (Z)-4-(Substituted Benzylidene)-2-Phenyl-4H-Oxazol-5-Ones (2002)

The kinetics of the alkaline hydrolysis and the configuration, conformation and electronic structure were studied using IR, NMR spectroscopy, X-ray analysis and AM1 theoretical calculations for a series of (Z)-4-(substituted benzylidene)-2-phenyl-4H-oxazol-5-ones (1) and compared with analogous results reported for (E)-4-benzylidene-2-phenyl-4H-furan-5-ones (5) and related compounds.
Subject-oriented composition rules (1995)

Subject-oriented programming supports composition of object-oriented programs or program fragments called subjects. This paper presents an approach to the composition rules used to specify composition details. Rules can be generic, allowing different subrules to be "plugged into" higher-level rules, and they include a means of specifying exceptions to general rules. We give definitions of a number of useful, generic rules, including merge and override, as a first step towards a generally-useful composition rule library. We also outline an object-oriented framework for implementing rules, which we are currently building as part of our support for subject-oriented programming in C++.
Risk-Informed Design Changes in a Passive Decay Heat Removal System (2008)

The failure probability of a passive decay heat removal (DHR) system after a loss-of-coolant accident (LOCA) is evaluated as part of a risk-informed design process for a helium-cooled fast reactor. The system was modeled using RELAP5-3D. The epistemic uncertainties in input parameters as well as the epistemic model uncertainties in the code were assessed and propagated through the model using Latin hypercube sampling. The changes in the design that we investigated reduced the overall failure probability of the system by reducing the impact of the major contributor to the failure probability. Sensitivity analyses led to two unexpected results. First, the key factors affecting the system failure probability are the location of the thermal insulation (inside or outside the hot leg) and the uncertainty in the insulation thermal conductivity. Second, the heat transfer coefficient in the core is not as important as one might expect. Our results show that the heat transfer coefficient in the containment structures is more important. Different methods for sensitivity analysis were applied and gave consistent results. The calculated conditional (given a LOCA) failure probability of the passive DHR system was deemed to be unacceptable and led the Massachusetts Institute of Technology design team to adopt an active DHR system as the main mode of DHR for the gas-cooled fast reactor
Safety, speed, and effectiveness of air transportation for neonates (2020)

Neonatal transportation by air is as safe as land transportation, and time to first aid and intensive care are significantly reduced by transportation by air than by land. Air transport could also contribute to the prevention of IVH in neonatal transportation.
Development of a Transabdominal Anchoring System for Trocar-Less Laparoscopic Surgery (2003)

Compared with open surgery, laparoscopy results in significantly less pain, faster convalescence, and less morbidity. However, eye-hand dissociation, a two-dimensional field-of-view and fixed instrumentation with limited degrees of freedom contribute to a steep learning curve and demanding dexterity requirements for many laparoscopic procedures. One of the main limitations of laparoscopy is the fixed working envelope surrounding each trocar, often necessitating placement of multiple ports to accomodate changes in position of the instruments or laparoscope to improve visibility and efficiency. The placement of additional working ports contributes to post-operative pain and carries a small risk of bleeding or adjacent organ damage. In order to provide for greater flexibility of endoscopic viewing and instrument usage and to further reduce morbidity, a novel adjunct laparoscopic system has been developed consisting of a platform capable of supporting various laparoscopic tools which is secured magnetically to the abdominal wall and subsequently positioned within the abdominal cavity through surgeon-controlled, external magnetic couples on the patient’s abdomen. Using this technique, instruments such as miniature endoscopic cameras used to augment the surgical field of view and surgical retractors have been successfully evaluated in a dry laboratory as well as in porcine models, with several others currently under investigation. This document elaborates on the theoretical and empirical process which has led to anchoring designs optimized for size, strength and surgical compatibility, as well as the benefits, limitations and prospects for the use of incisionless, magnetically-coupled tooling in laparoscopic surgery.
Two-Dimensional Modeling of the Metallization-Induced Recombination Losses of Screen-Printed Solar Cells (2014)

We present an approach of implementing the experimental microscopic observations at metal-Si emitter interface into a 2-D simulation model to investigate the metallization-induced recombination losses of crystalline Si solar cells with firing through metallization. This metal-Si interface is typically characterized by few Ag crystallites grown into Si, whereas the main part of the interface area is covered by a glass layer. By using this simulation model, we were able to disentangle the effect that each of these microscopic features has on solar cell performance. The model assumes the metal-Si interface to be either Ohmic or Schottky, with current extraction occurring only through the direct Ag crystallites-Si interface. The simulation results show negligible degradation in open-circuit voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OC</sub> ) and pseudo-fill factor (pF F) if the metal-Si interface comprises the sole presence of Ag crystallites, as long as these crystallites grow only superficially and are not penetrating the p-n junction. A more detrimental effect is observed if the emitter area beneath the glass layer is affected by etching. For more aggressive metallization pastes or for overfiring scenarios where larger in-grown crystallites are observed that are protruding through the p-n junction, the model assuming a Schottky contact qualitatively explains the shunting behavior observed experimentally.
A new technique of D/A conversions (2002)

In this paper, we present a new technique to convert a digital signal to an analog signal by interpolation method. For three sample points d/sub i/, d/sub i+/spl Upsi// and d/sub i+2T/ of a given digital signal, we use a part of a sine wave A sin /spl beta/t to connect the sample points d/sub i/ and d/sub i+T/ so that we get an analog signal between sampling interval i and i+T. When the same process is carried out with every sample point, a perfect analog signal without switching noises can be obtained. Also, we propose a circuit to realize this technique.
A Highly Dense, Low Power, Programmable Analog Vector-Matrix Multiplier: The FPAA Implementation (2011)

This paper presents a solid foundation for implementing analog vector-matrix multipliers (VMMs) in field-programmable analog arrays (FPAAs). Custom analog VMMs have been demonstrated to be 1000 times more power efficient than commercial digital implementations. However, no previous analog VMM discussion has carefully provided all of the implementation and performance considerations needed to utilize such a system. We utilize the FPAA because it provides an ideal platform for embedding low-power analog processing into larger systems. FPAAs allow the analog processing system to be rapidly prototyped, implemented at low cost, and easily reconfigured in the field. This paper can double as a complete analog VMM design specification, as well as a systematic tutorial on developing general systems with FPAA hardware. We detail the aspects of VMM topology choice, completely analyze the performance metrics, and describe the methods and tools involved in FPAA synthesis.
Extent of Cardiac Sympathetic Neuronal Damage Is Determined by the Area of Ischemia in Patients With Acute Coronary Syndromes (2000)

Sympathetic neuronal damage measured by (123)I-MIBG SPECT is larger than infarct size and is closely related to risk area, suggesting high sensitivity of neuronal structures to ischemia compared with myocardial cells.
Design Considerations for a Combined MicroCT and Fluorescence Diffuse Optical Tomography System (2008)

An imaging system combining x-ray microCT and fluorescence diffuse optical tomography is being developed for small animal functional imaging. The methodology for selecting the optimal source-detector geometry and subsequent system design are presented.
Wall Representations of Rectangular Dissections and Their Use in Automated Space Allocation (1978)

A procedure is described which generates dissections of rectangles into rectangular components in order to obtain solutions to space-allocation problems which arc restricted through topological and dimensional constraints, Solutions are generated in two steps: step 1 determines basic geometric properties of the arrangements to be produced, and step 2 computes the dimensions of the spaces in such an arrangement. Both steps are based on ‘wall representations’ of the solutions. These representations allow geometric relations and operations to be transformed into relations and operations defined on character strings. They furthermore allow the (possibly infinite) set of solutions to be systematically searched for a finite set of ‘principal options’. The importance of linear-programming techniques for step 2 is described.
On Heterogeneous Database Retrieval: A Cognitively Guided Approach (2001)

Retrieving information from heterogeneous database systems involves a complex process and remains a challenging research area. We propose a cognitively guided approach for developing an information-retrieval agent that takes the user's information request, identifies relevant information sources, and generates a multidatabase access plan. Our work is distinctive in that the agent design is based on an empirical study of how human experts retrieve information from multiple, heterogeneous database systems. To improve on empirically observed information-retrieval capabilities, the design incorporates mathematical models and algorithmic components. These components optimize the set of information sources that need to be considered to respond to a user query and are used to develop efficient multidatabase-access plans. This agent design, which integrates cognitive and mathematical models, has been implemented using Soar, a knowledge-based architecture.
Simulating commercial Java throughput workloads: a case study (2006)

We present our study on the simulation methodology for SPECjbb2000. The result shows that CPI can be practically used as a performance metric in place of throughput in the simulation. It is shown that SimPoint can successfully identify phases. With only a small number of clusters the user can reap most of the benefits of clustering analysis. A stationary main phase dominates the execution of the benchmark. We propose a method to accurately measure the CPI for the main phase with only one checkpoint. The error in the result can be quantified with a confidence interval.
Pregnanes, Part 1: Progestins (2010)

This chapter contains sections titled: Biological Activity Sources of Progesterone Modified Pregnanes Some Drugs Based on Progestins
Metamaterial Based High Impedance Surface with Band-Pass Frequency Response (2012)

We introduce a metamaterial based parallel-plate waveguide, devised in microstrip technology that features two electromagnetic band-gaps. Since one of the band-gaps extends from zero frequency, the structure can be used as a band-pass filter. We perform a parametric study in view of facilitating design and optimisation.
DEOXYGENATION OF EPOXIDES TO OLEFINS WITH FeCl3–n-BuLi SYSTEM (1974)

Abstract Deoxygenation reaction of epoxides with iron(III) chloride–n-butyllithium system gave olefins in high yields under mild reaction conditions.
Cover Feature: Few‐layer Black Phosphorous Catalyzes Radical Additions to Alkenes Faster than Low‐valence Metals (ChemCatChem 8/2020) (2020)

The Cover Feature shows how phosphorene can catalyse different radical additions to alkenes. These catalysts have an initial turnover frequency up to two orders of magnitude higher than representative state–of–the–art metal complex catalysts at room temperature. In their Full Paper, M. Tejeda-Serrano et al. describe how the electron–richness of the 2D material, either phosphorene or graphene, parallels the catalytic activity of different low-valence iron compounds as metal catalysts. These results showcase the advantages of substituting metals by p–block main-group elements not only because of their positive economic and ecological fingerprint, but also because of their higher catalytic efficiency in some organic reactions, which opens the door for cross–fertilization between 2D materials and metal catalysts in organic synthesis. More information can be found in the Full Paper by M. Tejeda-Serrano et al..
Enhanced binding of peptide antigen to purified class II major histocompatibility glycoproteins at acidic pH. (1991)

Helper T lymphocytes recognize peptide antigens stably associated with class II major histocompatibility complex (MHC) glycoproteins on the surface of antigen-presenting cells and serve to regulate a wide variety of immune responses. A previous study from our laboratory had demonstrated that the functional association of various peptide antigens with the antigen-presenting cell membrane was increased at pH 5 as compared to pH 7, consistent with the potential role of acidic endosomal compartments in antigen processing. The mechanism for this effect was not determined. In the present study, assays using purified class II glycoprotein were used to further define this mechanism. The potential requirement for pH-dependent interactions involving non-MHC membrane components was excluded in functional assays with purified class II reconstituted in artificial membranes containing only neutral phospholipids and cholesterol. The association of HEL(104-120) with I-Ed, and OVA(323-339) with I-Ad, was increased at pH 5, as measured by activation of specific T cell hybridomas. An enzyme immunoassay was developed to measure the binding of biotin-labeled peptides to purified class II in detergent micelles. The pH dependence of binding paralleled our previous functional results. Optimum binding of biotin-HEL(104-120) to I-Ed was observed at pH approximately 4.5, whereas maximum binding of biotin-Myo(106-118) to I-Ad occurred at pH approximately 5.5. The latter peptide also bound weakly to I-Ed, but with a pH dependence similar to that observed using HEL(104-120). Further experiments with biotin-HEL(104-120)/I-Ed indicated that both the apparent affinity and the apparent concentration of peptide-binding sites are increased as hydrogen ion concentration is increased from pH 7 to pH 5. The effect of pH in this range was largely reversible and was not associated with a change in peptide dissociation that could be measured with our assay system. Binding was not inhibited in the presence of 1.5 M NaCl, suggesting that electrostatic interactions between HEL(104-120) and I-Ed are not essential for binding. It is proposed that protonation of a critical group(s) in the class II molecule regulates its capacity to form stable complexes with peptide. However, this effect alone does not fully account for the rapid kinetics of peptide binding observed in experiments with intact antigen-presenting cells.
On the origins of observations of heterostyly in Primula (2015)

In 1862, Charles Darwin published his landmark study on the different forms of flower in Primula; he coined the term distyly and subsequently expanded his studies to other species, including those with tristyly. Darwin is widely recognized as the first to study pin and thrum flowers in Primula, and to provide an explanation for the functional significance of the two floral morphs. Our laboratory is pursuing the genes that underpin floral heteromorphy in Primula, work influenced by Darwin's observations. One day, while appreciating a print of Primula vulgaris from William Curtis' Flora Londinensis, I was struck by the fact that I was looking at images of dimorphic Primula flowers captured in a late-1700s copper-plate engraving that predated Darwin's observations by over 70 yr. This realization triggered a journey into archives of botanical texts, herbals and florilegia from the 16(th) to 19(th) Centuries, and correspondence archives, in search of earlier documents that could have influenced Darwin and the origins of an idea. Darwin was not the first to observe floral heteromorphy in Primula, but he was the first to realize the significance of the two floral morphs. Darwin's insight and exposition of purpose have underpinned all consequent work on the subject.
Mesoporous Titania Microspheres with Highly Tunable Pores as an Anode Material for Lithium Ion Batteries (2017)

Mesoporous titania microspheres (MTMs) have been employed in many applications, including (photo)catalysis as well as energy conversion and storage. Their morphology offers a hierarchical structural design motif that lends itself to being incorporated into established large-scale fabrication processes. Despite the fact that device performance hinges on the precise morphological characteristics of these materials, control over the detailed mesopore structure and the tunability of the pore size remains a challenge. Especially the accessibility of a wide range of mesopore sizes by the same synthesis method is desirable, as this would allow for a comparative study of the relationship between structural features and performance. Here, we report a method that combines sol-gel chemistry with polymer micro- and macrophase separation to synthesize porous titania spheres with diameters in the micrometer range. The as-prepared MTMs exhibit well-defined, accessible porosities with mesopore sizes adjustable by the choice of the polymers. When applied as an anode material in lithium ion batteries (LIBs), the MTMs demonstrate excellent performance. The influence of the pore size and an in situ carbon coating on charge transport and storage is examined, providing important insights for the optimization of structured titania anodes in LIBs. Our synthesis strategy presents a facile one-pot approach that can be applied to different structure-directing agents and inorganic materials, thus further extending its scope of application.
Determining Quality of Microcrystal Silicon Thin films Based on Infrared Absorption Coefficients (2010)

We proposed the absorption coefficient ratio of (1.4 eV)/ (0.8 eV) as the quality factor of microcrystalline silicon thin films. It is convinced that a proportional relationship is between quality factor and solar cell efficiency.