gebhart/patrepeval huggingface dataset:
Limit cycle oscillations in compartmental chemical systems (1974)

The dynamics of a chemical system which is localized in two compartments between which mass transport occurs at a rate proportional to the difference in chemical concentrations between the two compartments have been studied. Pursuing a problem posed by Smale, we have tried to find a set of reactions such that when the cells are uncoupled there is a single unique stable steady state in each compartment, but when the cells are coupled there is a single unique global limit cycle oscillator in the combined system. We have analyzed open systems far from equilibrium in which there are two reacting chemicals. A linear stability analysis in the region of the homogeneous steady state has been performed for the case in which identical reactions are occurring in both compartments. We have also studied, using both local and global techniques, a class of systems in which different reactions are occuring in each compartment. For this latter class of systems we have been able to find evidence that there can be limit cycle oscillations which require transport in order to be sustained.
Développement d'une librairie de code et d'outils bio-informatiques faciliant l'analyse de grandes quantités de données génomiques (2016)

Thèse décrivant l'écriture d'outils spécialisés facilitant l'analyse de grandes quantités de données provenant de technologie de séquencage haut débit.
Optical and Electrical Characterization of Poly(3-hexylthiophene-2,5-diyl) Interface with Al and LiF (2008)

The qualitative nature of the interface of poly(3-hexylthiophene-2,5-diyl) (P3HT) with aluminum (Al) and lithium fluoride (LiF) have been studied by photoluminescence (PL) spectra and photo induced memory techniques. The PL quenching and photo induced memory effect are clearly distinguishable in P3HT films coated with Al and LiF coated separately. It has been observed that LiF only forms an insulating barrier while aluminum creates a depletion layer with P3HT. The observed effects have been explained, based on carrier diffusion and band bending models.
MEMS-based gray-scale lithography (2002)

Micro-electro-mechanical systems (MEMS) fabrication technologies originated directly from integrated circuit (IC) fabrication. IC devices require only two-dimensional or planar structures to be fabricated, because there are no mechanical operations taking place. Therefore structures fabricated for MEMS devices have been traditionally designed with nominally vertical sidewalls (dry anisotropic etching), undercut sidewalls (wet isotropic etching), or sidewalls that have limited angles due to the crystallographic orientation of the substrate (wet anisotropic etching). Assorted novel techniques have been developed in the MEMS field that can achieve 3-D structures. Such techniques include SU-8 molding using microstereolithography, directing ions in DRIE using buried dielectric layers, and by inclined rotating UV lithography and electroplating. These techniques however are very time consuming and/or are limited in the structures that can be created, especially for large MEMS structures. A technique called gray-scale lithography, typically in diffractive optics, is applied using a one level development process to create 3-D structures in photoresist. This technique utilizes planar processing and provides additional flexibility that is not supported in conventional IC, fabrication technologies. The key components for the development of gray-scale lithography in MEMS applications are presented and include the design of the optical mask and the use of a photolithography stepper system.
Using undiagnosed data to enhance computerized breast cancer analysis with a three stage data labeling method (2014)

A novel three stage Semi-Supervised Learning (SSL) approach is proposed for improving performance of computerized breast cancer analysis with undiagnosed data. These three stages include: (1) Instance selection, which is barely used in SSL or computerized cancer analysis systems, (2) Feature selection and (3) Newly designed ‘Divide Co-training’ data labeling method. 379 suspicious early breast cancer area samples from 121 mammograms were used in our research. Our proposed ‘Divide Co-training’ method is able to generate two classifiers through split original diagnosed dataset (labeled data), and label the undiagnosed data (unlabeled data) when they reached an agreement. The highest AUC (Area Under Curve, also called Az value) using labeled data only was 0.832 and it increased to 0.889 when undiagnosed data were included. The results indicate instance selection module could eliminate untypical data or noise data and enhance the following semi-supervised data labeling performance. Based on analyzing different data sizes, it can be observed that the AUC and accuracy go higher with the increase of either diagnosed data or undiagnosed data, and reach the best improvement (&Delta;AUC = 0.078, &Delta;Accuracy = 7.6%) with 40 of labeled data and 300 of unlabeled data.
Enhanced Adsorption of Hydroxyl- and Amino-Substituted Aromatic Chemicals to Nitrogen-Doped Multiwall Carbon Nanotubes: A Combined Batch and Theoretical Calculation Study (2015)

A large effort is being made to develop nanosorbents with tunable surface chemistry for enhanced adsorption affinity and selectivity toward target organic contaminants. Heteroatom N-doped multiwall carbon nanotubes (N-MCNT) were synthesized by chemical vapor deposition of pyridine and were further investigated for the adsorptive removal of several aromatic chemicals varying in electronic donor and acceptor ability from aqueous solutions using a batch technique. Compared with commercial nondoped multiwall carbon nanotubes (MCNT), N-MCNT had similar specific surface area, morphology, and pore-size distribution but more hydrophilic surfaces and more surface defects due to the doping of graphitic and pyridinic N atoms. N-MCNT exhibited enhanced adsorption (2-10 folds) for the π-donor chemicals (2-naphthol and 1-naphthalmine) at pH ∼6 but similar adsorption for the weak π-donor chemical (naphthalene) and even lower adsorption (up to a 2-fold change) for the π-acceptor chemical (1,3-dinitrobenzene). The enhanced adsorption of 2-naphthol and 1-naphthalmine to N-MCNT was mainly attributed to the favored π-π electron-donor-acceptor (EDA) interaction between the π-donor adsorbate molecule and the polarized N-heterocyclic aromatic ring (π-acceptor) on N-MCNT. The proposed adsorption enhancement mechanisms were further tested through the pH effects on adsorption and the density function theory (DFT) calculation. The results show for the first time that the adsorptive interaction of π-donor aromatic compounds with carbon nanomaterials can be facilitated by N-doping.
Interplay of cysteine exposure and global protein dynamics in small‐molecule recognition by a regulator of G‐protein signaling protein (2018)

Regulator of G protein signaling (RGS) proteins play a pivotal role in regulation of G protein-coupled receptor (GPCR) signaling and are therefore becoming an increasingly important therapeutic target. Recently discovered thiadiazolidinone (TDZD) compounds that target cysteine residues have shown different levels of specificities and potencies for the RGS4 protein, thereby suggesting intrinsic differences in dynamics of this protein upon binding of these compounds. In this work, we investigated using atomistic molecular dynamics (MD) simulations the effect of binding of several small-molecule inhibitors on perturbations and dynamical motions in RGS4. Specifically, we studied two conformational models of RGS4 in which a buried cysteine residue is solvent-exposed due to side-chain motions or due to flexibility in neighboring helices. We found that TDZD compounds with aromatic functional groups perturb the RGS4 structure more than compounds with aliphatic functional groups. Moreover, small-molecules with aromatic functional groups but lacking sulfur atoms only transiently reside within the protein and spontaneously dissociate to the solvent. We further measured inhibitory effects of TDZD compounds using a protein-protein interaction assay on a single-cysteine RGS4 protein showing trends in potencies of compounds consistent with our simulation studies. Thermodynamic analyses of RGS4 conformations in the apo-state and on binding to TDZD compounds revealed links between both conformational models of RGS4. The exposure of cysteine side-chains appears to facilitate initial binding of TDZD compounds followed by migration of the compound into a bundle of four helices, thereby causing allosteric perturbations in the RGS/Gα protein-protein interface.
Synthesis and mesomorphic properties of laterally fluorinated alkyl 4′′-alkylterphenyl-4-yl carbonate liquid crystals (2013)

Fifteen series of homologues of a variety of mono-, di- and trifluorosubstituted alkyl 4′′-alkylterphenyl-4-yl carbonates have been synthesized and their mesomorphic properties have been determined. From among 95 prepared compounds, 40 pure nematogens have been found, as well as 55 mesogens with orthogonal and tilted smectic phases in broad temperature ranges. The type and combination of the LC phase strongly depend on the position and number of the fluorine atoms. Physical properties and correlations between the molecular core fluorosubstitution, the length of the terminal chains and the type and sequence of the liquid crystalline phases, have been determined. The compounds are useful for the formulation of nematic mixtures as well as ferroelectric ones.
Semi-automatic calibration of a projector-camera system using arbitrary objects with known geometry (2015)

We propose a new semi-automatic calibration approach for projector-camera systems that - unlike existing auto-calibration approaches - additionally recovers the necessary global scale by projecting on an arbitrary object of known geometry from one view. Our method therefore combines surface registration with bundle adjustment optimization on points reconstructed from structured light projections. In simulations on virtual data and experiments with real data we demonstrate that our approach estimates the global scale robustly and is furthermore able to improve incorrectly guessed intrinsic and extrinsic calibration parameters.
The Theory of Rotating Fluids (1968)

The monograph gives the first unified and comprehensive account of the theory of rotating fluids. The mathematical development focuses on fundamental principles as revealed through the systematic study of simply constructed experiments, many of which are described for the first time. Special features of the book include a separate chapter devoted to non-linear processes and methods of solution, several sections reporting the results of previously unpublished research, and the identification of important unsolved problems. The discussion of basic concepts also allows for a wide range of engineering applications and a chapter is devoted to the laboratory simulation of large-scale oceanic circulations. The book will be of direct use to many applied mathematicians, engineers and physical oceanographers. (Author)
ing Leading to Format Transpare ncorporating Noninve (1996)

We demonstrate a unique semiconductor optical amplifier based system that performs the converting functions of: 1) RZ-to-NRZ; and 2) NRZ-to-RZ-to-NRZ by using noninverting cross-gain compression wavelength shifting. Our robust NRZ-to- RZ-to-NRZ reconverter was tested using 80 km of fiber and 4 EDFA's. We show that at l-Gb/s, both functions can be realized with low power penalties (<2.0 dB). UTURE all-optical wavelength-division-multiplexed (WDM) networks may be required to support a variety of modulation and data formats. Two standard data formats that have found extensive use are the return-to-zero (RZ) and nonreturn-to-zero (NRZ) formats. Although the RZ data format requires twice the NRZ transmission bandwidth, it is quite useful in applications including passive time-division- multiplexing and -demultiplexing, soliton generation, and the suppression of stimulated Brillouin scattering (l), (2). Also, since some optical processing operations unintentionally change the data format (3), fully functional WDM networks should have the capability of all-optically converting between the RZ and NRZ formats. Previous work (4) has demonstrated all-optical RZ-to- conversion using a nonlinear optical loop mirror at 10-Gb/s, but the performance of this system was shown to be highly sensitive to the polarization state of the loop mirror. We demonstrate a unique polarization insensitive semincon- ductor optical amplifier (SOA) based system that performs the desirable function of converting an RZ WDM channel into the NRZ format (RZ + NE). Our system allows the input RZ wavelength to be either preserved or wavelength shifted to a different wavelength during the conversion process. In an earlier paper (5), we demonstrated a complementary NRZ-to- RZ (NRZ -+ RZ) converter that uses SOA gain modulation to convert an input NRZ signal into an output RZ signal at the same wavelength. We use this NRZ -+ RZ converter and the RZ ---f NRZ converter presented in this work, to realize
Computational and Experimental Studies of Methyl Group Exchange between Palladium(II) Centers (2010)

The disproportionation of 2 equiv of (L)2Pd(CH3)(X) to form 1 equiv of (L)2Pd(CH3)2 and 1 equiv of (L)2Pd(X)2 could serve as a key step in the catalytic oxidative oligomerization of methane. The thermodynamics associated with this transformation have been evaluated as a function of the supporting ligands L and X using DFT calculations. With these calculations as a guide, we demonstrate the first experimental example of disproportionation of a PdII monomethyl complex to generate a PdII dimethyl species using (tBu-bpy)Pd(CH3)(CH2COCH3) (tBu-bpy = 4,4′-di-tert-butyl-2,2′-bipyridine) as the starting material.
Improved Synthesis of 1-Chloroadamantane by Hydride Transfer Induced by Tertiarybutylchloride (1989)

Abstract Adamantane was chlorinated, without chlorine, by tertiarybutylchloride and Lewis acids. The result with AlCl3 gives the best yield (90.5%) and selectivity (95.4%) in 1-chloroadamantane so far reported. The results are consistent with an hydride transfer mechanism.
NaNet: a flexible and configurable low-latency NIC for real-time trigger systems based on GPUs. (2016)

ABSTRACT: NaNet is an FPGA-based PCIe X8 Gen2 NIC supporting 1/10 GbE links and the custom 34 Gbps APElink channel. The design has GPUDirect RDMA capabilities and features a network stack protocol offloading module, making it suitable for building low-latency, real-time GPU-based computing systems. We provide a detailed description of the NaNet hardware modular architecture. Benchmarks for latency and bandwidth for GbE and APElink channels are presented, followed by a performance analysis on the case study of the GPU-based low level trigger for the RICH detector in the NA62 CERN experiment, using either the NaNet GbE and APElink channels. Finally, we give an outline of project future activities.
Mesh Representation Driven by Variance Normalized Neighborhood in Scale Space (2008)

In this paper, we extend our previous work on regular mesh simplification using scale-space filtering (SSF), to arbitrary meshes. Additional challenges in using arbitrary meshes involve accurately defining a geodesic distance and a structure attribute. Since our SSF method is based on Laplacian smoothing, which filters finer local details before larger global structures, it preserves perceptual quality that is consistent with how the human visual system looks at 3D objects moving from close to farther away. By keeping the simplified mesh vertices as a subset of the denser meshes, versus using the vertex split operation, bandwidth is utilized more efficiently during refinement. Our contribution lies in applying the shortest path normalized by variance, instead of using an un-normalized geodesic distance to weight the influence of a neighborhood. Variance normalization ensures that the global smoothing property is preserved. We build a priority list to facilitate vertex removal and insertion. Experimental results are presented to support our approach.
Effectiveness of a killed whole-cell oral cholera vaccine in Bangladesh: further follow-up of a cluster-randomised trial (2021)

For the Bengali translation of the abstract see Supplementary Materials section.
Economic selection index in small rural dairy farms (2019)

This study aimed to calculate economic values (EVs) and economic selection indices for milk production systems in small rural properties. The traits 305-d milk yield in kg (MY), fat (FP) and protein (PP) percentage, daily fat (FY) and protein (PY) yield, cow live weight in kg (LW), calving interval (CI), and logarithm of daily somatic cell count (SCC) in milk were considered the goals and selection criteria. The production systems were identified from 29 commercial properties based on the inventory of revenues and costs and of zootechnical field data. Later, bioeconomic models were developed to calculate the productive performance, revenues, and costs concerning milk production to estimate EVs, which were calculated as the difference in annual profit with dairy production resulting from a change in one unit of the trait while keeping the others constant and dividing the value by the number of cows. After the EVs were known, ten economic selection indices were estimated for each system so they could be compared by modifying the selection criteria and calculating the relative importance of each selection criteria, the accuracy of the economic selection index, and response expected to the selection in USD, among other parameters. One of the systems detected was called less intensive (LS) and was characterized by having ten cows in lactation that produced 13·5 l/d and consumed 1·8 kg of concentrate/d. The second system detected was called more intensive (IS) and had 22 cows in lactation that produced 17·5 l/d and consumed 3·4 kg of concentrate/d. Monthly profits per cows in lactation of USD 2·60 and USD 68·77 were recorded for LS and IS, respectively. The EVs of the traits MY, FP, and PP were all positive, while for the other traits they were all negative in all situations. The best economic selection indices were those featuring selection criteria MY, LW, and CI, while the trait LW had the greatest importance in both systems. These results indicate that animal frame must be controlled in order to maximize the system's profit.
Shape-based image indexing and retrieval for diagnostic pathology (2002)

A prototype system performing analysis, indexing and retrieval of pathology images to assist physicians in differential diagnosis of lymphoproliferative disorders is presented. Robust color segmentation is used to automatically analyse regions of interest in images of leukocytes. The shape of leukocyte nuclei, described through similarity invariant shape descriptors, represents the main attribute in the search query. Monte Carlo tests for stability and goal-directed evaluations of the system performance are also shown.
Particle-bed gas-cooled fast reactor (PB-GCFR) design. Project final technical report (Sept 2001 - Aug 2003). (2003)

The objective of this project is to develop a conceptual design of a particle-bed, gas-cooled fast reactor (PB-GCFR) core that meets the advanced reactor concept and enhanced proliferation-resistant goals of the US Department of Energy's NERI program. The key innovation of this project is the application of a fast neutron spectrum environment to enhance both the passive safety and transmutation characteristics of the advanced particle-bed and pebble-bed reactor designs. The PB-GCFR design is expected to produce a high-efficiency system with a low unit cost. It is anticipated that the fast neutron spectrum would permit small-sized units ({approx} 150 MWe) that can be built quickly and packaged into modular units, and whose production can be readily expanded as the demand grows. Such a system could be deployed globally. The goals of this two-year project are as follows: (1) design a reactor core that meets the future needs of the nuclear industry, by being passively safe with reduced need for engineered safety systems. This will entail an innovative core design incorporating new fuel form and type; (2) employ a proliferation-resistant fuel design and fuel cycle. This will be supported by a long-life core design that is refueled infrequently, and hence, reduces the potential for fuel diversion; (3) incorporate design features that permit use of the system as an efficient transmuter that could be employed for burning separated plutonium fuel or recycled LWR transuranic fuel, should the need arise; and (4) evaluate the fuel cycle for waste minimization and for the possibility of direct fuel disposal. The application of particle-bed fuel provides the promise of extremely high burnup and fission-product protection barriers that may permit direct disposal.
BIOFÁBRICAS PARA PRODUÇÃO DE MUDAS POR MICROPROPAGAÇÃO: ESTRATÉGIA PARA O AUMENTO DA PRODUTIVIDADE DE CANA-DE-AÇÚCAR NO RIO DE JANEIRO (2015)

Historicamente importante, a Regiao Norte Fluminense responde por mais de 90% da producao de cana-de-acucar (Saccharum spp L.) do Estado do Rio de Janeiro, sendo o municipio de Campos dos Goytacazes responsavel por mais de 50% dessa producao. Todavia, a baixa produtividade (55,6 t/ha) e um fator limitante para o crescimento do setor, tal condicao poderia ser revertida com a insercao de biotecnologias pertinentes que possam aumentar a oferta e qualidade genetica de mudas clonais para as agroindustrias. Um levantamento feito junto aos produtores mostrou que a producao de mudas e uma forte preocupacao entre eles. Estudos mostram que mudas micropropagadas podem aumentar a produtividade e a longevidade dos canaviais em ate 30%, uma vez que possibilita melhor padrao fitossanitario, controle das condicoes ambientais do processo, producao o ano todo e otimizacao da area utilizada quando comparada com o metodo convencional. Entretanto, a pouca oferta deste material na regiao limita sua aplicacao, mostrando a necessidade de ampliacao deste sistema de producao de mudas. A producao em larga escala e feita em instalacoes denominadas biofabricas, as mudas micropropagadas de cana-de-acucar produzidas neste sistema podem aumentar a competitividade do produtor, iniciando uma recuperacao do setor canavieiro na Regiao. Isto implicaria em aumento na renda do produtor rural, principalmente nas pequenas e medias propriedades. Alem disso, a aplicacao dessa biotecnologia permitiria obter o aumento na producao, pelo oferecimento em larga escala de uma gama de variedades adaptadas e pela alta qualidade genetica e fisiologicas das mudas oferecidas, sem a necessidade de avancar sobre areas de preservacao ambiental.
THE CYTOCHEMICAL APPLICATION OF NEW POTENT INHIBITORS OF ALKALINE PHOSPHATASES (1973)

The inhibitory properties of levamisole and its analogue R 8231 on alkaline phosphatases of various rat tissues were investigated cytochemically. Very low concentrations, respectively, 0.5 and 0.1 mM, sufficed to achieve complete inhibition in most tissues except intestine. The inhibition was reversible as for other known uncompetetive inhibitors but was found to be substrate-independent. The influence of fixation and incubation procedures was negligable. Other phosphatases as acid phosphatase, adenosine triphosphatase, thiamine pyrophosphatase, glucose 6-phosphatase and 5'-nucleotidase remained unchanged in the presence of the inhibitors.