gebhart/patrepeval huggingface dataset:
Investigating Computational Models of Development for the Construction of Shape and Form (2004)

A central problem in Artificial Life is that of construction. Researchers have been investigating methods of constructing solutions to problems that overcome fundamental issues of adaptation, scalability and repetition. For example, what is the correct configuration of thousands of basic elements needed to give rise to a complex adaptive solution? Such questions and the sophisticated developmental processes and mechanisms of construction evolved by natural selection provide the general source of inspiration and motivation for the field of Computational Development (CD), and consequently, the subject matter of this thesis. This thesis investigates computational models of development for the construction of shape and form. To this end, seven sets of experiments using different computational models of development are reported. A comparison of the performance and behaviour of three classes of developmental encodings for the construction of shape and form is made, and their properties, advantages and disadvantages are identified. Traditional genetic encodings are shown to suffer from severe problems of scalability, while computational models of development are shown to offer plausible solutions. A computer software testbed, the Evolutionary Developmental System, is used to investigate the self-organising construction of 3D shape and form, such as a planes, spheres, cubes and cylinders. The EDS uses a novel genetic representation inspired by developmental genetics to evolve genetic regulatory networks (GRNs). The EDS additional mechanism of receptor-mediated signal transduction is shown to construct designs that exhibit phenomena resembling biological cellular differentiation. This thesis also shows that computational models of development are useful for biologists. It presents the first ever study of the evolution of robust mechanisms of morphogen gradient maintenance for positional information in biology using genetic algorithms. Evolved mechanisms of morphogen gradient maintenance over 3- to 10-cells are shown to provide positional information leading to the emergence of spatial patterns of cellular differentiation.
Enzymes for Purine Synthesis and Scavenging in Pathogenic Mycobacteria and Their Distribution in Mycobacterium leprae (1987)

Three enzymes catalysing the synthesis of four intermediates (phosphoribosylglycinamide, phosphoribosylaminoimidazole-succinocarboxamide, phosphoribosylaminoimidazole-carboxamide and AMP) in the purine biosynthetic pathway were detected in extracts of Mycobacterium microti and M. avium, even when the organisms had been grown in mice. However only one of the three enzymes, adenylosuccinate AMP-lyase (catalysing the synthesis of the last two of the four intermediates listed above) was detected in M. leprae. Phosphoribosyltransferases, which convert adenine, guanine and hypoxanthine to the corresponding nucleoside monophosphates, and adenosine kinase were the major enzymes for purine scavenging in all mycobacteria studied. In contrast to enzymes in the synthetic pathway, evidence for metabolic regulation of the purine-scavenging enzymes was obtained. In particular, 20-80-fold differences in the activities of guanine phosphoribosyltransferase and adenosine kinase were observed when M. microti was grown in media with or without purines, or in mice. In M. leprae, activities of all phosphoribosyltransferases were low in comparison with activities in M. microti and M. avium (specific activity less than 2% when comparisons were made between extracts of host-grown mycobacteria). However, activity of adenosine kinase was higher in host-grown M. leprae than in host-grown M. microti or M. avium.
The Relative Effectiveness of Different Approaches to the Surveillance of Infections among Hospitalized Patients (1969)

A method for estimating the effectiveness of systems designed to monitor the occurrence of events within a population is described. Specific application of this model to the analysis of a control program for the surveillance of infectious disease in a university hospital is presented. A reporting system with three sources—physicians, nurses, and bacteriology laboratory—was instituted. The effectiveness of the system ranged from 61 to S3 per cent over a period of 12 months. There was considerable variation among the three sources in terms of their relative effectiveness in identification of patients with infections. Under the circumstances described, the most effective two–source reporting system would have been the physicians' discharge reports and bacteriology laboratory records.
Hydrophilicity-controllable Microporous Hybrid Materials by Anion Exchange (2008)

Abstract Poly(acrylic acid) (PAA)/silica hybrids having imidazolium chloride [IL(Cl−)] moieties could be prepared by utilizing ionic interactions between anionic carboxylic acid groups of PAA and cationic imidazolium groups of silica phase. By removing PAA from the obtained hybrids, we could obtain hydrophilicity-controllable microporous hybrids by means of anion-exchange reaction of imidazolium moieties.
Virtual DOM: An Efficient Virtual Memory Representation for Large XML Documents (2008)

Standardized main memory representation methods (DOM) are quite inadequate to represent large XML documents, both in terms of space (necessary amount of memory) and, consequently, in time: it easily happens that it is not possible to load large XML documents in main memory. In this paper, we present virtual DOM, a Java package that provides an efficient representation technique for large XML documents. It adopts a specifically designed virtual memory technique: memory blocks allocated to represent the document are swapped, when necessary, by skipping the operating system swapping mechanism; this way, the actual main memory needs are kept under control, the thrashing phenomenon is avoided even for large documents.
Production of polysaccharide and surfactin by Bacillus subtilis ATCC 6633 using rehydrated whey powder as the fermentation medium (2012)

The aim of this research was to assess the amounts of polysaccharide and surfactin produced by Bacillus subtilis ATCC 6633 in rehydrated whey powder (RWP) as the growth medium. One-day-old cultures of B. subtilis (∼4.6 log cfu/mL) were inoculated into 100mL of 10, 15, or 20% (wt/vol) RWP and incubated at 30°C for 72 h. To analyze the effects of lactose and protein on polysaccharide and surfactin production, 6 RWP solutions containing different levels of lactose and protein were also used as media. The number of vegetative cells and spores, pH, viscosity, and the concentration of lactose were determined at 0, 24, 48, or 72 h of fermentation. The levels of polysaccharide and surfactin produced after 72 h of fermentation were measured using HPLC and the phenol-sulfuric acid method, respectively. During 72 h of fermentation, B. subtilis populations increased from 4.6 to 10.54, 9.82, and 9.67 log(10) cfu/mL in 10, 15, and 20% RWP, respectively. The number of B. subtilis spores in 10% RWP increased from 3.91 to 4.72 log(10) cfu/mL after 48 and 72 h of fermentation, respectively. The increased level of lactose or protein in RWP did not significantly change the vegetative growth. After 72h of fermentation, the pH of RWP decreased from 5.70 to 4.99 with a slight increase in viscosity. Polysaccharide levels in 10, 15, and 20% RWP after fermentation were 513.6, 613.5, and 768.3mg/L, respectively, with B. subtilis producing 0.18 to 0.29 g/L of surfactin after 72 h of fermentation. The polysaccharide or surfactin production was not changed significantly by addition of protein or lactose to RWP. These results indicate that RWP is a good fermentation substrate for surfactin and polysaccharide production.
STUDIES IN THE HETEROCYCLIC COMPOUNDS V<sup>1</sup>. SOME REACTIONS OF 5-CHLORO-2-THIOPHENESULFONYL DERIVATIVES (1982)

Abstract The reactions of 5-chloro-2-thiophenesulfonyl chloride are described. Treatment of the sulfonyl chloride with ammonia, hydrazine hydrate, sodium azide, indole and imidazole gave the sulfonamides (5), sulfonohydrazide (4), sulfonyl azide (3), 1-(5-chloro-2-thiophenesulfonyl)indole (27) and 1-(5-chloro-2-thiophenesulfonyl)-imidazole (26), respectively. The sulfonyl chloride was reacted further with 20 aryl-and cycloalkyl-amines to give the corresponding sulfonamides (6)-(25). Attempted chlorination of the sulfonyl chloride (2) with sulfuryl chloride or bromination of the sulfonyl azide (3) with pyridinium bromide perbromide failed. However, nitration of the sulfonyl chloride (2) with fuming nitric acid gave the 4-nitro-sulfonyl chloride (28), which with sodium azide afforded the 5-chloro-4-nitro-sulfonyl azide (29). The sulfonyl azides, (3) and (29), have been reacted with triphenylphosphine, triethylphosphite, norbornene and cyclohexene. The azides reacted further with indole and 1-methylindole to give the 2-sulfonyl-iminoindolines (34)-(36). The infra-red spectra and mass spectra of some of the substituted thiophenesulfonyl derivatives are discussed.
Effect of an induced conformational change on the physical properties of two chemotactic receptor molecules (1979)

The physical properties and conformational dynamics of the Salmonella typhimurium ribose and galactose receptors have been examined. Studies involving circular dichroism, fluorescence, absorption spectroscopy, and sedimentation analysis show that the two receptor proteins have different morphologies and exhibit diverse responses to sugar binding. The ribose receptor lacks both tryptophan and disulfide residues, and the galactose receptor lacks disulfides and has only a single tryptophan residue. By virtue of these fortuitous properties, the conformational changes induced in these proteins by sugar binding can be dissected by utilizing a variety of physical probes. A ligand-induced conformational change in the ribose receptor is shown by circular dichroism and fluorescence spectroscopy, which reveal spectral changes assignable to tyrosine, phenylalanine, and methionine residues. A conformational change in the galactose receptor has been demonstrated by fluorescence spectroscopy involving the distant reporter group method, which shows changes assignable to tryptophan and methionine sites and which is corroborated by sedimentation analysis. It is clear that there are extensive conformational changes in the two receptor proteins and that the different physical methods provide complementary information on the nature of these changes.
Anomalous optical bistability and robust entanglement of mechanical oscillators using two-photon coherence (2015)

We analyze the optical bistability and the entanglement of two movable mirrors coupled to a two-mode laser in a doubly resonant cavity. We show that in stark contrast to the usual red-detuned condition for observing bistability in single-mode optomechanics, the optical intensities exhibit bistability for all values of cavity laser detuning due to intermode coupling induced by two-photon atomic coherence. Interestingly, an unconventional bistability with “ribbon”-shaped hysteresis can be observed for a certain range of cavity laser detuning. We also demonstrate that the atomic coherence leads to a strong entanglement between the movable mirrors in the adiabatic regime. Surprisingly, the mirror–mirror entanglement is shown to persist for environment temperatures of the phonon bath up to 12 K using experimental parameters.
Dimer acid structures. the thermal dimer of methyl 10‐<i>trans</i>, 12‐<i>trans</i>, linoleate (1964)

Abstract Thermal dimerization of the conjugated 10‐ trans , 12‐ trans linoleate (250C, 5 hr) produced a dimer whose structure is shown to be that of the Diels‐Alder reaction between two molecules of monomer, with one molecule acting as diene, and either one of the two double bonds of the second molecule acting as dieneophile. This produces four skeletal isomers of a tetrasubstituted (1,2,3,4) cyclohexene structure with ॅ‐ ॆ unsaturation on one chain. The isomers formed depend on whether the 10 or the 12 double bond acts as dieneophile, and whether the monomers add 舠head to head舡 or 舠head to tail.舡 Evidences for the structures include chemical analyses, ozonolysis, nuclear magnetic resonance, IR and UV spectrometry and particularly mass spectrometry of the distilled dimer, of the completely hydrogenated dimer, and of the aromatized dimer formed by catalytic dehydrogenation. The hydrogenated dimer can be separated into two components by TLC. These are probably related to 舠head to head舡 vs. 舠head to tail舡 addition.
Statistical Size Distributions in Economics and Actuarial Sciences (2003)

A comprehensive account of economic size distributions around the world and throughout the years In the course of the past 100 years, economists and applied statisticians have developed a remarkably diverse variety of income distribution models, yet no single resource convincingly accounts for all of these models, analyzing their strengths and weaknesses, similarities and differences. Statistical Size Distributions in Economics and Actuarial Sciences is the first collection to systematically investigate a wide variety of parametric models that deal with income, wealth, and related notions. Christian Kleiber and Samuel Kotz survey, compliment, compare, and unify all of the disparate models of income distribution, highlighting at times a lack of coordination between them that can result in unnecessary duplication. Considering models from eight languages and all continents, the authors discuss the social and economic implications of each as well as distributions of size of loss in actuarial applications. Specific models covered include: Pareto distributions Lognormal distributions Gamma-type size distributions Beta-type size distributions Miscellaneous size distributions Three appendices provide brief biographies of some of the leading players along with the basic properties of each of the distributions. Actuaries, economists, market researchers, social scientists, and physicists interested in econophysics will find Statistical Size Distributions in Economics and Actuarial Sciences to be a truly one-of-a-kind addition to the professional literature.
Performance of sub-carrier synchronized OFDM (2002)

This work analyses the performance of an OFDM system with frequency equalization. The equalizers, using a learning sequence, estimate the frequency response of the channel at each sub-carrier. The global performance of the system is then analyzed using the importance sampling technique. With this fast Monte Carlo method, a BER of the order of 10/sup -5/ only requires 1000 simulations. The gain in simulation time is exceptional.
Real-time hidden surface removal in a flight simulator (2002)

The authors investigate four different concepts which are candidates to resolve the hidden surface removal problem without the use of priorities. All four are based on determining a linear depth order consistent with the partial order of primitives in a span. A span is a small subimage of the image being generated. The first approach examines parallel sorting of all the depth values of all primitives in a span. The second approach, for each pixel in a span, builds a list of all the primitives in that span, totally ordered by depth. These lists represent the partial order of the primitives, and are later enumerated to give a total order. The third approach performs up to k pairwise comparisons in parallel between primitives to determine if a depth relationship exists. If one exists, the pair is stored in a partial order graph which is later enumerated to create a total order. The fourth approach involves the use of a pipeline of length k, which, at any given time, contains up to k primitives which are closest. If there are more than k primitives in a span, more than one iteration is needed. The fourth approach appears to be the most promising, even though there are situations in which it generates an incorrect ordering.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A2A Adenosine Receptors on Bone Marrow-Derived Cells Protect Liver from Ischemia-Reperfusion Injury (2005)

Activation of the A2A adenosine receptor (A(2A)R) during reperfusion of various tissues has been found to markedly reduce ischemia-reperfusion injury. In this study, we used bone marrow transplantation (BMT) to create chimeric mice that either selectively lack or selectively express the A(2A)R on bone marrow-derived cells. Bolus i.p. injection of the selective A2A agonist, 4-[3-[6-amino-9-(5-cyclopropylcarbamoyl-3,4-dihydroxy-tetrahydro-furan-2-yl)-9H-purin-2-yl]-prop-2-ynyl]-piperidine-1-carboxylic acid methyl ester (ATL313; 3 microg/kg), at the time of reperfusion protects wild-type (wt) mice from liver ischemia-reperfusion injury. ATL313 also protects wt/wt (donor/recipient BMT mouse chimera) and wt/knockout chimera but produces modest protection of knockout/wt chimera as assessed by alanine aminotransferase activity, induction of cytokine transcripts (RANTES, IFN-gamma-inducible protein-10, IL-1alpha, IL-1-beta, IL-1Ralpha, IL-18, IL-6, and IFN-gamma), or histological criteria. ATL313, which is highly selective for the A(2A)R, produces more liver protection of chimeric BMT mice than 4-[3-[6-amino-9-(5-ethylcarbamoyl-3,4-dihydroxy-tetrahydro-furan-2-yl)-9H-purin-2-yl]-prop-2-ynyl]-cyclohexanecarboxylic acid methyl ester, which is rapidly metabolized in mice to produce 4-[3-[6-amino-9-(5-ethylcarbamoyl-3,4-dihydroxy-tetrahydro-furan-2-yl)-9H-purin-2-yl]-prop-2-ynyl]-cyclohexanecarboxylic acid, which has similar affinity for the A(2A)R and the proinflammatory A3 adenosine receptor. GFP chimera mice were created to show that vascular endothelial cells in the injured liver do not account for liver protection because they are not derived by transdifferentiation of bone marrow precursors. The data suggest that activation of the A(2A)R on bone marrow-derived cells is primarily responsible for protecting the liver from reperfusion injury.
Simultaneous Emergence of Multidrug-Resistant <i>Candida auris</i> on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses (2016)

C. auris is an emerging healthcare-associated pathogen associated with high mortality. Treatment options are limited, due to antifungal resistance. WGS analysis suggests nearly simultaneous, and recent, independent emergence of different clonal populations on 3 continents. Risk factors and transmission mechanisms need to be elucidated to guide control measures.
Carbon Source-Mediated Catabolite Repression (2014)

Catabolite repression is a regulatory mechanism by which the cell (i) coordinates metabolism of carbon a n d energy sources to maximize efficiency and (ii) regulates other metabolic processes as well. The objective of this review is to examine what is known about the molecular mechanisms by which catabolite repression operates in gram-positive bacteria, especially Bacillus subtilis. In this chapter, the author uses the term catabolite repression to refer specifically to carbon source-mediated regulation and not to regulation by nitrogen or other nutrient sources. The phenomenon of catabolite repression has been best characterized in Escherichia coli. The chapter briefly reviews the basic mechanism by which E. coli accomplishes the type of global regulation. Catabolite repression in E. coli is interference with a positive regulatory mechanism in which the catabolite repressor protein (CRP or CAP) in complex with the cyclic nucleotide cyclic AMP (cAMP) binds to a specific site in the promoter region of catabolite repression-sensitive genes or operons. In the three genera of gram-positive bacteria (S. aureus, Streptomyces spp, and B. subtilis), the molecular mechanism by which catabolite repression functions appears to be fundamentally different from that in E. coli. To date, few studies have been directed at elucidating the molecular mechanism by which carbon source-mediated catabolite repression operates. The mechanism by which B. subtilis monitors its environment for the presence of readily metabolized carbohydrates and translates that information into regulatory signals is unknown.
Transform domain adaptive linear phase filter (1996)

Describes a new adaptive linear-phase filter whose weights are updated by the normalized least-mean-square (LMS) algorithm in the transform domain. This algorithm provides a faster convergence rate compared with the time domain linear phase LMS algorithm. Various real-valued orthogonal transforms are investigated such as the discrete cosine transform (DCT), discrete Hartley transform (DHT), and power of two (PO2) transform, etc. By using the symmetry property of the transform matrix, an efficient implementation structure is proposed. A system identification example is presented to demonstrate its performance.
ShowMeHow (2011)

Many people learn how to use complex authoring applications through tutorials. However, user interfaces for authoring tools differ between versions, platforms, and competing products, limiting the utility of tutorials. Our goal is to make tutorials more useful by enabling users to repurpose tutorials between similar applications. We introduce UI translation interfaces which enable users to locate commands in one application using the interface language of another application. Our end-user tool, ShowMeHow, demonstrates two interaction techniques to accomplish translations: 1) direct manipulation of interface facades and 2) text search for commands using the vocabulary of another application. We discuss tools needed to construct the translation maps that enable these techniques. An initial study (n=12) shows that users can locate unfamiliar commands twice as fast with interface facades. A second study showed that users can work through tutorials written for one application in another application.
Similarity index for seismic data sets using adaptive curvelets (2014)

Summary In this paper, we propose a distance measure to evaluate visual similarity between two images. The algorithm searches for adaptive curvelet parameters that better represent a reference image. Next, the distance between the reference image and other images is computed as a weighted sum of distances between histograms of adaptive curvelet coefficients. The algorithm is tested on a data set of exemplary seismic activities. The developed measure is shown to be effective in extracting correct matches from the data set.
Flow-Fiber Coupled Viscosity in Injection Molding Simulations of Short Fiber Reinforced Thermoplastics (2019)

Abstract The main objective of this paper is to numerically investigate the use of fiber-dependent viscosity models in injection molding simulations of short fiber reinforced thermoplastics with latest commercial software. We propose to use the homogenization-based anisotropic rheological model to take into account flow-fiber coupling effects. The 4th-order viscosity tensor is approximated by an optimal scalar model and then implemented in the Moldflow Insight API framework. Numerical simulations are performed for a test-case rectangular plate with three fiber orientation models. The resulting coupled flow kinematics and fiber evolutions are then compared to the standard uncoupled simulations. Interpretations are given based on detailed post-processing of the field results. Certain deformation conditions are expected to be better taken into account, which may also in return lead to an improved fiber orientation prediction. Preliminary confrontation between flow-fiber coupled simulations and existing experimental data is then presented at the end of the paper.