gebhart/patrepeval huggingface dataset:
An Effective Method for Evolving Reaction Networks in Synthetic Biochemical Systems (2015)

In this paper, we introduce our approach for evolving reaction networks. It is an efficient derivative of the neuroevolution of augmenting topologies algorithm directed at the evolution of biochemical systems or molecular programs. Our method addresses the problem of meaningful crossovers between two chemical reaction networks of different topologies. It also builds on features such as speciation to speed up the search, to the point where it can deal with complete, realistic mathematical models of the biochemical processes. We demonstrate this framework by evolving credible biochemical answers to challenging autonomous molecular problems: in vitro batch oscillatory networks that match specific oscillation shapes. Our experimental results suggest that the search space is efficiently covered and that, by using crossover and preserving topological innovations, significant improvements in performance can be obtained for the automatic design of molecular programs.
Quantitative methods for linking transcriptional profiles to physiology (2004)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2004.
Process Development and Scale-up of Fully Synthetic Tetracycline TP-2758: A Potent Antibacterial Agent with Excellent Oral Bioavailability (2015)

Process research and development of the fully synthetic broad spectrum tetracycline TP-2758, with a chiral pyrrolidine side chain at the C-8 position, is described. The process utilizes two key intermediates, 7 and 10, in a convergent approach that allows for manufacturing of sufficient quantities of API to supply preclinical and early clinical development. The pyrrolidine moiety was introduced into the left-hand piece (LHP) 10 with high enantioselectivity using Ellman’s sulfinamide chemistry, and the absolute configuration was confirmed by X-ray crystal structure analysis.
The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x‐ray structure “maintained”? (1996)

We present molecular dynamics simulations on ubiquitin with explicit solvent molecules and investigate the influence of different force fields [Weiner et al. (J. Am. Chem. Soc. 106:765-784, 1984; J. Comput. Chem. 7:230-252, 1986) vs. Cornell et al. (J. Am. Chem. Soc. 117:5179-5197, 1995)], different treatments of the long-range electrostatic interaction (8 A cutoff vs. particle mesh Ewald), and different solvation models (periodic box vs. small shell of water molecules) on the structure and the dynamics of the protein. Structural data are monitored by atomic root mean square deviations (RMSDs) from the crystal structure, the radius of gyration, the solvent-accessible surface area, and the pattern of the backbone hydrogen bonds. The dynamic behavior is assessed by the atomic fluctuations and the order parameters of the N-H backbone vectors. With the Cornell et al. force field and a periodic box model, the simulated structures stay much closer to the experimental X-ray structure than with the older Weiner et al. force field. A further improvement of the simulation is found when the electrostatic interaction is evaluated with the particle mesh Ewald method; after 1.2 ns of simulation the backbone RMSD amounts to only 1.13 A. The analysis of the dynamic parameters shows that this good structural agreement is not due to a damping of internal motion in the protein. For a given length of simulation time, the shell models achieve an agreement between simulated and experimental structures that is comparable to the best models that employ a periodic box of solvent models. However, compared with the box models, the fluctuations of the protein atoms in the shell models are smaller, and only with simulation times as long as 2 ns do they become of comparable size to the experimental ones.
ChemInform Abstract: Continuous‐Flow Technology — A Tool for the Safe Manufacturing of Active Pharmaceutical Ingredients (2015)

Abstract Review: [202 refs.
Review. Tannins and ruminant nutrition (2004)

Tannins are a complex group of polyphenolic compounds found in a wide range of plant species commonly consumed by ruminants. They are conventionally classified into two major groups: the hydrolysable and the condensed tannins. Although for a long time tannins were thought to be detrimental to ruminants, their effect may be either beneficial or harmful depending on the type of tannin consumed, its chemical structure and molecular weight, the amount ingested, and the animal species involved. High concentrations of tannins reduce voluntary feed intake and nutrient digestibility, whereas low to moderate concentrations may improve the digestive utilisation of feed mainly due to a reduction in protein degradation in the rumen and a subsequent increase in amino acid flow to the small intestine. These effects on nutrition are reflected in animal performance.
Rendering fur with three dimensional textures (1989)

We present a method for rendering scenes with fine detail via an object called a texel, a rendering primitive inspired by volume densities mixed with anisotropic lighting models. This technique solves a long outstanding problem in image synthesis: the rendering of furry surfaces.
Fractal relations for the diameter and trace length of disc‐shaped fractures (1997)

Analytic relations are developed between the fractal parameters of a random, isotropic population of disc‐shaped fractures and the parameters of the corresponding population of fracture traces expressed in outcrop. These relations indicate that a fractal distribution of fracture diameters translates to a fractal distribution of trace lengths and that the parameters for diameter may be uniquely determined from the parameters for trace length. Probabilistic results demonstrate the accuracy of the analytic relations and identify nonideal behaviors at the limits of the computed trace length data. It is expected that these relations will be useful in the three‐dimensional characterization of fracture systems in rock from in situ trace length data.
FLF4DoS. Dynamic DDoS Mitigation based on TTL field using fuzzy logic. (2007)

DoS is an attack which overwhelm victims servers and services. Distributed DoS attacks do not let legitimate users to access services provided by servers. Several techniques have been proposed to mitigate such attacks. Preventive techniques have proven their effectiveness. However, most of those techniques require historic data and training. We propose a dynamic algorithm based on the concept of fuzzy logic applied to hop-count filtering technique to mitigate distributed DoS. Very promising results of this technique is shown through this paper
[Characterization of Alcaligenes species using analysis of esterase electrophoretic polymorphism and analysis of antibiotic resistance profiles]. (1992)

The species of an Alcaligenes bacterial strain may be difficult to determine on the basis of conventional phenotype features. Esterase pattern analysis using acrylamide-agar gel electrophoresis and determination of the antimicrobial resistance profile (agar diffusion method) were performed for A. faecalis (34 strains). A. denitrificans subsp xylosoxydans (16 strains) and A. piechaudi (5 strains). The Cistat program (D2 Software) was used for statistical representation of results. The homogeneous, species-specific esterase patterns ensured correct assignment of each strain to one of the three species. Antimicrobial susceptibility was greatest for A. faecalis which was susceptible to both cephalosporins of all generations and aminoglycosides. A. xylosoxydans was the species with the greatest resistance to antimicrobials. A. piechaudii exhibited intermediate susceptibility.
Censoring sensors: a low-communication-rate scheme for distributed detection (1996)

We consider a new scheme for distributed detection based on a "censoring" or "send/no-send" idea. The sensors are assumed to "censor" their observations so that each sensor sends to the fusion center only "informative" observations, and leaves those deemed "uninformative" untransmitted. The main result of this work is that with conditionally independent sensor data and under a communication rate constraint, in order to minimize the probability of error, transmission should occur if and only if the local likelihood ratio value observed by the sensor does not fall in a certain single interval. Similar results are derived from Neymarr-Pearson and distance-measure viewpoints. We also discuss simplifications for the most interesting case that the fusion center threshold is high and the communication constraint is severe. We compare censoring with the more common binary-transmission framework and observe its considerable decrease in communication needs. Finally, we explore the use of feedback to achieve optimal performance with very little communication.
Nanoscale in-plane displacement evaluation by AFM scanning and digital image correlation processing (2005)

A quantitative evaluation of the structure deformation of microfabricated electromechanical systems is important for the design and functional control of microsystems. When the displacement measurement of the microstructure's surface is to be made in a domain smaller than a few microns, both spatial sampling resolution and measuring sensitivity should reach nanoscale levels. In this paper, an atom force microscope (AFM) is used to scan surface topographies of silicon beam structures under electrostatic actuation, and then the AFM images are utilized to evaluate the in-plane deformation field based on digital image correlation (DIC) processing. It is shown that the AFM topographic maps provide a kind of carrier pattern to include the displacement information of the deformed surface, whose high scanning resolution and good image correlation makes it possible to search the in-plane displacement components on the nanometre scale from the images with statistics resembling grey level distributions. By using the proposed DIC algorithms, the deformation fields in the beam-end regions are obtained for the folded silicon flexures actuated by electrostatic comb drives.
Complete Spin Polarization for a Carbon Nanotube with an Adsorbed Atomic Transition-Metal Chain (2004)

Our calculations indicate that a chromium or vanadium atomic chain adsorbed on an armchair carbon nanotube opens up a band gap for the minority spin, making the whole system a 100% spin-polarized conductor. The gaps are 0.49 and 0.44 eV for V and Cr, respectively. The adsorption of manganese, iron, cobalt, or nickel chains leads to large but not complete spin polarization. These hybrid structures can function as basic building blocks for the nanoscale construction of hitherto elusive perfect spin polarizers, which promise wide-ranging applications in spintronics research.
Transverse electric field scattering by a Kerr media deposited on a conducting planar surface (1990)

The scattering of a transverse electric plane wave incident from a linear media by a nonlinear Kerr film deposited on a good conductor is studied. Self-focusing and self-defocusing are included both above and below the critical angle. The solution to the complex second-order nonlinear differential wave equation is constrained at the nonlinear/conductor planar interface by mixed boundary conditions and at the linear/nonlinear interface by the continuity of the tangential electric and magnetic fields. A potential-well approach is employed to classify and isolate the various solutions. Several examples illustrate the two nonlinear analogies of the evanescent and harmonic field solutions. Additionally, we obtain the surface-wave solutions and the transitional, hybrid, fields. Finally, we show that the reflectivity is multistable with respect to the incident intensity and that the reflected intensity is multistable as the incident angle changes for a constant input intensity.
Pharmacological doses of dietary curcumin increase colon epithelial cell proliferation <i>in vivo</i> in rats (2007)

Although curcumin has preventive actions in animal models of colon cancer, whether the mechanism of action is through anti-proliferation in normal environment is not clearly understood. Here, we studied the effects of chemopreventive doses of curcumin on the proliferation rate of colon epithelial cells (CEC), using a recently developed stable isotope-mass spectrometric method for measuring DNA synthesis rate. Adult male F344 rats were given diets containing 0, 2 and 4% curcumin for 5 weeks. 4% (2)H(2)O was given in drinking water to label DNA, after a priming bolus, for 4 days prior to sacrifice. The isotopic enrichment of the deoxyribose moiety of deoxyadenosine from DNA was measured by gas chromatography - mass spectrometry. Cell cycle analysis was performed after propidium iodide staining of CECs. Curcumin administration did not reduce but instead resulted in dose-dependent increases in CEC proliferation rate (p < 0.05) for 2% and 4% curcumin vs 0%). The length of the colon crypts and the fraction of cells in S-phase were also increased in the 2% and 4% curcumin groups (p < 0.05). Thus, pharmacological doses of curcumin increase CEC proliferation rate and pool size in normal rats. Reduction of CEC proliferation therefore cannot explain the proposed chemopreventive actions of curcumin in colon cancer.
Internetworking with Bluetooth Low Energy (2015)

Recent developments in the Bluetooth SIG have made Bluetooth Low Energy (LE), marketed as Bluetooth Smart, a strong contender for the underlying wireless technology in many IoT applications. The key strengths of Bluetooth LE are its very low power and widespread adoption. Recently, many indoor location applications have turned to Bluetooth LE. However, IEEE 802.11 and 802.15.4 based Zigbee have the lead in networking with IP. The new Bluetooth 4.2 Core Specification and Internet Protocol Support Profile improves the IP capabilities of Bluetooth. For networked IoT applications that demand the lowest power, Bluetooth LE may become the technology of choice.
Vitamin A status and metabolism of cutaneous polyamines in the hairless mouse after UV irradiation: action of beta-carotene and astaxanthin. (1995)

Solar radiations (UV A and B) can cause epidermis photoaging and skin cancers. These frequently irreversible effects result from the in situ generation of free radicals. However, it has been noted that nutritional factors can modulate photochemical damage, in particular the common carotenoids present in food, which can be considered as potential prophylactic agents against carcinogenesis. We investigated the effect of UV A and B radiations on the skin of the SKH1 hairless mouse fed a diet either lacking in vitamin A or supplemented with retinol, beta-carotene or astaxanthin. The latter is an oxygenated carotenoid (like canthaxanthin) without provitamin A activity and with strong singlet oxygen quenching ability. After analysing of vitamin status of each group (plasma retinol concentrations and hepatic reserves), we searched for UV-induced modifications of polyamine metabolism by measuring epidermal ornithine decarboxylase (ODC) activity and free polyamines concentration (putrescine, spermidine and spermine). In the basal state without irradiation, differences in ODC activity between groups were nonsignificant; but after UV stimulation, ODC increased markedly in the skin of vitamin A-deficient animals, much more than in other groups. Curiously, the addition of astaxanthin or beta-carotene to the regimen containing retinol reduced the protective effect of retinol alone. Regarding polyamines after irradiation, putrescine was significantly increased in the skin of deficient animals, in parallel with ODC activity. However, astaxanthin had a stronger inhibitory effect on putrescine accumulation than retinol, and decreased spermidine and spermine concentrations: this suggests a specific action on transglutaminases.
Eigenvalues of Laplacians on a closed Riemannian manifold and its nets (1995)

We show that the eigenvalues of the Laplacian of a closed manifold <italic>M</italic> is approximated in a certain sense by the eigenvalues of the Laplacian of the graph of a <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartFraction 1 Over n EndFraction"> <mml:semantics> <mml:mfrac> <mml:mn>1</mml:mn> <mml:mi>n</mml:mi> </mml:mfrac> <mml:annotation encoding="application/x-tex">\frac {1}{n}</mml:annotation> </mml:semantics> </mml:math> </inline-formula>-net in <italic>M</italic> as <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="n right-arrow normal infinity"> <mml:semantics> <mml:mrow> <mml:mi>n</mml:mi> <mml:mo stretchy="false">→</mml:mo> <mml:mi mathvariant="normal">∞</mml:mi> </mml:mrow> <mml:annotation encoding="application/x-tex">n \to \infty</mml:annotation> </mml:semantics> </mml:math> </inline-formula>. Our approximation needs no assumption on <italic>M</italic> except for dimension.
Broad-Band Fourier Transform Quadrupole Ion Trap Mass Spectrometry (1996)

Broad-band nondestructive ion detection is achieved in a quadrupole ion trap mass spectrometer by impulsive excitation of a collection of trapped ions of different masses and recording of ion image currents induced on a small detector electrode embedded in but isolated from the adjacent end cap electrode. The image currents are directly measured using a simple differential preamplifier, filter, and amplifier combination and then Fourier analyzed to obtain broad-band frequency domain spectra characteristic of the sample ions. The use of the detector electrode provides a significant reduction in capacitive coupling with the ring electrode. This minimizes coupling of the rf drive signal, which can saturate the front-end stage of the detection circuit and prevent measurement of the relatively weaker ion image currents. Although impulsive excitation is preferred due to its broad-band characteristics and simplicity of use, results are also given for narrow-band ac and broad-band SWIFT (stored wave-form inverse Fourier transform) excitation. Data using argon, acetophenone, and n-butylbenzene show that a resolution of better than 1000 is obtained with a detection bandwidth of 400 kHz. An advantage of nondestructive ion detection is the ability to measure a single-ion population multiple times. This is demonstrated using argon as the sample gas with an average remeasurement efficiency of >90%. Tandem mass spectrometry experiments using a population of acetophenone ions are also shown.
Fluorescence Monitoring of Viscosity and Chemical Changes During Polymerization (1987)

Three approaches using fluorescent dyes dissolved in epoxy resins were used to determine the viscosity changes during the curing process. First, the intensity of excimer fluorescence from a dye which forms an intramolecular excimer was measured to determine the viscosity changes. In another approach, we used a dye whose fluorescence intensity increases with the increase in the local viscosity, and a second dye whose fluorescence intensity is insensitive to the local viscosity. The ratio of the fluorescence intensities of the two dyes was measured to monitor the cure of epoxy resins. In a third approach, we measured the diffusion coefficient of a fluorescent dye by a photobleaching technique to monitor the curing process. Finally, we used a fluorescence technique to monitor the formation of a polyimide polymer from poly(amide acid).
Why Has 'Historic' Public Disclosure of Hospital Performance Data Attracted So Little Attention? (1995)

CONSUMERS, COMPETITORS, and payers aren't exactly rushing to snap up the first national reports on hospital performance. "After a huge amount of hullabaloo nationally, this has become a great nonevent," says Dennis S. O'Leary, MD, president of the Joint Commission on Accreditation of Healthcare Organizations. Two years ago, when the Joint Commission announced plans to permit public access to some of the information it compiles during the accreditation process, the move was called historic. But during the first 6 weeks that the reports became available, 97 callers placed orders for 167 of the performance profiles. "This is bearing out my expectations," O'Leary adds. <h3>Measuring Hospital Performance</h3> The Joint Commission accredits more than 5200 hospitals and 6000 other health care organizations nationwide. Performance reports currently are available for only about 850 hospitals because they're produced according to the Commission's 3-year accreditation cycle. Reports for all Joint Commission—accredited facilities will be completed
Learn$^{++}$.NC: Combining Ensemble of Classifiers With Dynamically Weighted Consult-and-Vote for Efficient Incremental Learning of New Classes (2008)

We have previously introduced an incremental learning algorithm Learn(++), which learns novel information from consecutive data sets by generating an ensemble of classifiers with each data set, and combining them by weighted majority voting. However, Learn(++) suffers from an inherent "outvoting" problem when asked to learn a new class omega(new) introduced by a subsequent data set, as earlier classifiers not trained on this class are guaranteed to misclassify omega(new) instances. The collective votes of earlier classifiers, for an inevitably incorrect decision, then outweigh the votes of the new classifiers' correct decision on omega(new) instances--until there are enough new classifiers to counteract the unfair outvoting. This forces Learn(++) to generate an unnecessarily large number of classifiers. This paper describes Learn(++).NC, specifically designed for efficient incremental learning of multiple new classes using significantly fewer classifiers. To do so, Learn (++).NC introduces dynamically weighted consult and vote (DW-CAV), a novel voting mechanism for combining classifiers: individual classifiers consult with each other to determine which ones are most qualified to classify a given instance, and decide how much weight, if any, each classifier's decision should carry. Experiments on real-world problems indicate that the new algorithm performs remarkably well with substantially fewer classifiers, not only as compared to its predecessor Learn(++), but also as compared to several other algorithms recently proposed for similar problems.