Miracle-dz/UniFAR-FTUs huggingface dataset:
An approach to prevent aggregation during the purification and crystallization of wild type acyl coenzyme A: Isopenicillin acyltransferase from

Acyl coenzyme A: isopenicillin N acyltransferase (AT) from Penicillium chrysogenum is an enzyme of interest for the biosynthesis of -lactam antibiotics. Severe aggregation problems with wild type AT have, however, prevented signiWcant progress in the structure–function analysis of this enzyme for a decade. In this study, we show an approach to solve this aggregation problem by using dynamic light scattering (DLS) analysis to probe the aggregation state of the protein in the presence of various additives. After a onestep puriWcation of recombinant wild type AT with a C-terminal His-tag using Ni2+ aYnity chelate chromatography, addition of a combination of 5 mM DTT, 250 mM NaCl, and 5 mM EDTA to the puriWed AT eVectively prevented aggregation. In the presence of these additives, the DLS proWle of AT shows a narrow size distribution indicative of a homogeneous protein solution and the absence of aggregation. The purity and mono-dispersity of wild type AT was suYcient for the growth of high quality crystals diVracting to 1.64 Å resolution.  2005 Elsevier Inc. All rights reserved.
Fauna insectil asociada a cultivos de dos especies de Physalis (Solanaceae) en Argentina

Con el fin de conocer la fauna insectil asociada a cultivos de Physalis peruviana L. y P. ixocarpa Brot se realizaron monitoreos semanales durante dos campanas anuales determinandose las principales especies perjudiciales y beneficas. Se realizaron graficos de fluctuacion poblacional de las especies consideradas mas importantes por el dano que produjeron y su densidad alcanzada. La especie mas perjudicial fue Heliothis subflexa Guenee 1852 (Lepidoptera: Noctuidae) debido al dano producido en frutos. Se relaciona la presencia de esta especie en P. peruviana con el desarrollo de las plantas y fecha de siembra.
Pathogenic fungi in humans and animals.

An Introduction to the Taxonomy of Zoopathic Fungi, D.H. Howard The Peronosporomycetes and Other Flagellate Fungi, M.W. Dick Zygomycetes: The Order Mucorales, M.A.A. Schipper and J.A Stalpers Zygomycetes: The Order Entomophthorales, S. -C. Jong and F.M. Dugan Onygenales: Arthrodermataceae, D.H. Howard, I. Weitzman, and A.A. Padhye Ascomycetes: The Onygenaceae and Other Fungi from the Order Onygenales, L. Sigler Aspergillus, Fusarium, Sporothrix, Piedraia, and Their Relatives, R. Summerbell Yeasts: Blastomycetes and Endomycetes, K.C. Hazen and S.A. Howell Basidiomycetous Yeasts, T. Boekhout and E. Gueho Dematiaceous Hyphomycetes, W.A. Schell Miscellaneous Opportunistic Fungi: Microascaceae and Other Ascomycetes, Hyphomycetes, Coelomycetes, and Basidiomycetes, L. Sigler Molecular Methods to Identify Pathogenic Fungi, T.G. Mitchell and J. Xu Population Genetic Analyses of Medically Important Fungi, J. Xu and T.G. Mitchell Genetic Instability of Candida albicans, E. Rustchenko and F. Sherman Index
Application of molecular methods to microbial community analysis of activated sludge

In the last decade, molecular biology has made significant progress, and innovative molecular methods have become available to analyze microbial community structures. Among them, we applied the FISH (Fluorescent in situ Hybridization) method to analyze activated sludge in wastewater treatment plants (WWTPs). As a result, domain- or division-level community structures in activated sludge were determined successfully without cultivation. We also applied the PCR (polymerase chain reaction) -DGGE (Denaturing Gradient Gel Electrophoresis) method for laboratory nitrifying sludge in order to investigate more detailed microbial community structure. By this method, genus- or species-level community structures were characterized well. This method was also found to be powerful for monitoring the change of microbial community structures. For example, the behavior of Nitrosomonas group was successfully detected in the reactor with nitrification by the PCR-DGGE method.
Application of a rapid and sensitive combined phage-PCR method for the detection of Mycobacterium avium subspecies paratuberculosis in raw milk

The objective of this study was to evaluate a new combined phage-PCR method by investigating levels of MAP in milking herds in the UK and throughout the Republic of Cyprus. Bulk milk samples were collected from 54 UK farms and 225 dairy farms in Cyprus and were tested using both the phage assay and a conventional culture method for the presence of MAP. The identity of MAP cells detected was confirmed in both cases by IS900 PCR. None of the UK samples were culture positive whereas 1 was phage-PCR positive. In Cyprus MAP 50 of the 225 samples were MAP positive using the combined phage-PCR and MAP was cultured from 2 samples, despite the fact that the animals tested were not displaying clinical symptoms of Johne’s disease. Total viable count was also determined as an indicator of the general hygiene status of the samples. Comparison of MAP status with TVC suggests that these were not introduced by faecal contamination. Typing of the two MAP strains isolated from cow’s milk in Cyprus by culture was performed using REA IS1311 PCR and identified one of these to be an S strain and the other C strain. The results confirm that the phage-based detection test is more sensitive than conventional culture and demonstrate the efficacy and practicality of the phage-based test as a routine rapid method for the detection of viable MAP in milk.
Morphological convergence and molecular divergence: the taxonomic status of Sceloporus serrifer (squamata, phrynosomatidae) subspecies

Martínez‐Méndez, N. , Mejía, O. , Rocha‐Gómez, A. & Méndez‐De La Cruz, F. R. (2012) Morphological convergence and molecular divergence: the taxonomic status of Sceloporus serrifer (squamata, phrynosomatidae) subspecies. —Zoologica Scripta, 41, 97–108.
Quantitative quality control and background correction for two-colour microarray data

Two-colour microarrays are a popular tool for measuring relative gene expression between RNA populations for thousands of genes simultaneously. This thesis develops methods for assessing the quality and variability of data from such experiments and for incorporating these assessments into algorithms for discovering differential expression. The variability of microarray data depends not only on the quality of the arrays, but also on how they are processed and normalised. The intimate relationship between variability of expression logratios and the method used for background correcting the expression values is specifically explored. The performance of different estimators of the background level and various model-based processing methods, including a novel normal-exponential convolution model are compared in search of a ‘best’ alternative. The results indicate that the choice of method should be guided by the specific question of interest; the model-based methods give gene expression measures with low bias, and do very well at choosing differentially expressed genes, while subtracting low background estimates, or not background correcting the data produces low variance estimates which are the most biased, however perform best at choosing DE genes. All of these alternatives give better results than those obtained by the standard approach of subtracting high local background estimates from the foreground signal, which is not recommended. Another important low level analysis issue is that of data quality. Filtering microarray data according to different criteria to remove suspect arrays and/or spots from further analysis is widely used. This thesis investigates a more graduated approach to quality involving the use of array and spot quality weights in the linear model analysis of expression log-ratios. For array weights, a heteroscedastic linear model is fitted using a novel gene-by-gene update algorithm to calculate the array variance parameters. These variances are used as inverse weights in re-fits of the mean
Isolasi dan Kultivasi Mikrob Endofit Penghasil Senyawa Alkaloid Kinkona dari Cinchona spp.

Some endophytic microbes had been isolated from some Cinchona spp. collected from Gunung Mas Tea Plantation, Cibodas Botanical Garden, and Tea & Cinchona Research Centre, Gambung, Bandung. The isolates were grown onto liquid culture medium for 7 days. Thin layer chromatography and high pressure liquid chromatography analysis showed that some microbes (bacteria, yeast, and mold) were capable in producing cinchona alkaloid compound. Quinine was used as a standard compound. Key words: Endophyte, alkaloid, quinine, Cinchona spp. , bacteria, fungi, yeast
Aumento da resistência ao estresse oxidativo induzido pelo Extrato Hidroalcoólico de Carqueja (Baccharis trimera) no Caenorhabditis elegans: seria através de um mecanismo SKN-1/p38 MAPK e DAF-16 dependente?

iv LISTA DE TABELAS viii LISTA DE FIGURAS ix ABREVIATURAS x 1. INTRODUCAO 1 1.1 ESTRESSE OXIDATIVO . 2 1.2 MECANISMOS ENZIMATICOS E NAO-ENZIMATICOS DE COMBATE AO ERO 3 1.3 CONTROLE DA EXPRESSAO GENICA DAS ENZIMAS ANTIOXIDANTES EM MAMIFEROS 4 1.3.1 Proteinas Nrf2 (Nuclear factor-erythroid-2-related factor 2) 5 1.3.2 Proteinas FoxO (Forkhead Box) 6 1.4 PLANTAS MEDICINAIS E FITOQUIMICOS COMO MECANISMO DE COMBATE AO ERO . 6 1.5 PROPRIEDADES ANTIOXIDANTES DA CARQUEJA (BACCHARIS TRIMERA) 9 1.6 O NEMATODO CAENORHABDITIS ELEGANS 11 1.7 CONTROLE DA EXPRESSAO GENICA DAS ENZIMAS ANTIOXIDANTES NO C. ELEGANS 12 1.7. 1 A via de sinalizacao SKN-1/Nrf2 13 1.7. 2 A via de sinalizacao de DAF-2/Ins/IGF-1 16 1.7. 3 C. elegans como um modelo para estudos de fitoquimicos 17 2. OBJETIVOS 19 2.1 OBJETIVO GERAL . 20 2.2 OBJETIVOS ESPECIFICOS 20 3. METODOLOGIA 21 3.1 CEPAS E LINHAGENS 22 3.2 CRESCIMENTO E MANUTENCAO DO C. ELEGANS 22 3.3 SINCRONIZACAO CRONOLOGICA DO C. ELEGANS 23 3.4 EXTRATO DE CARQUEJA 23 3.4. 1 Coleta do material botânico 23
A Revision Of The Genus Sarcophyton Lesson (Octocorallia, Alcyonacea)

The author refers 35 valid species to the genus Sarcophyton. The holotypes of nearly all species could be examined; of only three species (S. elegans, S. glaucum, and S. latum) their depository is unknown. The holotypes of eight species were described earlier by the present author, in four cases in co-operation with other authors; the reader is referred to the literature given in the list of valid species. Among the species described in the present paper there is a new one: S. buitendijki. A list of invalid taxa is added. Four keys may help with the identification of the corals.
Optimally managing under imperfect detection: A method for plant invasions

Summary 1. Failing to account for uncertainty in the detection of invasive plants may lead to inefficient management strategies and wasted resources. Smart strategies to manage plant invasions requires consideration of the economic costs and benefits, and plant life-history characteristics as well as imperfect detection. 2. We develop a partially observable Markov decision process (POMDP) to provide optimal management actions when we are uncertain about the presence of invasive plants. The optimal strategy depends on the probability of being in a particular state. We ask the question, ‘When is it preferable to use a less efficient, less costly action to a more efficient, more costly action? ’ We apply the POMDP to branched broomrape Orobanche ramosa, a parasitic plant species at the centre of a national eradication campaign in South Australia. 3. The optimal strategy depends on the ability to detect the invasive species and the location of the infested site. For high detection rates, if the site is a satellite infestation, management should employ the more efficient, more costly action (i.e. soil fumigation) the year the weed is detected followed by monitoring. When the detection probability is low, then it is optimal to employ the less efficient, low cost action (i.e. host denial) in the years the species is not detected. For sites in the centre of the infestation, management should employ the less costly, less efficient action. While the optimal strategy is insensitive to colonization, the likelihood of local eradication diminishes as colonization probability increases, highlighting the importance of limiting colonization if eradication is to be achieved. 4. Synthesis and applications. Providing decision support for managing ecological systems is a key role of applied research. Formulating this support within a decision theory context provides a framework for good decision-making. The POMDP model is a novel decision support tool for optimal sequential decision making when invasive plants are difficult to detect. The model can determine the best management action to employ based on the location of the infestation and can inform when to switch to alternative management actions that buffer against imperfect detection.
Replication data for: From \"Made in China\" to \"Innovated in China\": Necessity, Prospect, and Challenges

After more than three decades of high growth based on its low-wage advantage and relatively favorable demographics--in combination with market-oriented reforms and openness to the world economy--China is at a crossroads with a much higher wage and a shrinking workforce. Future growth will depend, by necessity, more on the generation of increased productivity, and domestic innovation will play an important part in this. In this paper, we assess the likelihood that China can make the necessary transition. Using data on expenditure on research and development, and patent applications, receipts, and citations, we show that the Chinese economy has become increasingly innovative. We will argue that rising wages and expanding markets are among the important drivers of China's growth in innovation. On the other hand, we find evidence of resource misallocation in the innovation area: while state-owned firms receive more subsidies, private firms exhibit more innovation results. Innovation can presumably progress even faster if resource misallocation can be tackled.
Effects of ant behaviour and presence of extrafloral nectaries on seed dispersal of the Neotropical myrmecochore Turnera ulmifolia L. (Turneraceae)

This paper describes the myrmecochory system of Turnera ulmifolia in a coastal sand dune matorral in Mexico. Turnera ulmifolia has elaiosome-bearing seeds and extrafloral nectaries (EFNs). In ten quadrants (4 × 15 m) ant–seed interaction was monitored, and an interaction intensity index calculated and correlated with the number of seedlings. Seed removal rates by ants were surveyed every 2 h for 24 h, the ants being observed both on and beneath the plants. The role of the elaiosome in seed removal was evaluated by offering seeds with and without elaiosomes, and elaiosomes only. Finally, the effect of ant manipulation in seed germination was evaluated. There were 25 ant species associated with seeds and/or EFNs, the most frequently recorded being Monomorium cyaneum and Forelius analis. There was a positive correlation between the intensity index and seedling number per quadrant. There was significantly higher mean seed removal during the day than during the night (19.3% and 12.3%, respectively), and from beneath than on the plant (21.9% and 9.5%, respectively). The preference for elaiosomes only was also greater during the diurnal period, and when gathered on, rather than beneath, the plant. Seed manipulation by F. analis enhanced germination by T. ulmifolia. Seed removal, dispersal distances, seed predation and germination were largely determined by ant behaviour. The presence of EFNs may be influencing seed removal on the plant by attracting a specific assemblage of omnivorous ants. Among such assemblages associated with T. ulmifolia we encountered a variety of behaviours, with ant species either good at defending plants but bad at dispersing seeds, or vice versa. We discuss the way in which these two rewards, and the processes involved (defence and dispersion), could have interacted with each other and evolved. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86, 67–77.
A preliminary molecular phylogenetic assessment of the lichen moths (Lepidoptera: Erebidae: Arctiinae: Lithosiini) with comments on palatability and chemical sequestration

The lichen moth tribe Lithosiini is best known for its hypothesized larval feeding behaviour, lichenivory. The larvae of some species have been found to be capable of sequestering polyphenolics, and the adults of some species are unpalatable to vertebrate predators. However, the chemical basis for the defence is unknown. Here we reconstruct a phylogenetic hypothesis using likelihood methods (maximum likelihood, Bayesian inference) for 65 species of Lithosiini representing 37 genera and seven outgroup species using 2806 bp of sequence data obtained from two mitochondrial gene fragments (COI barcoding region, CytB), and two nuclear gene fragments (RpS5 and ribosomal gene region 28S). Lithosiine species representing four of the seven subtribes and unplaced taxa are included in the analysis. The deeper relationships within the tribe are not strongly supported, and the monophyly of three of the four subtribes is not supported. The placement of the fourth subtribe, Acsalina, is weakly supported. We also conduct a survey of the secondary metabolites present within adults of five species. The species are examined for the presence of lichen polyphenolics and plant secondary metabolites sequestered by arctiines. Seven lichen polyphenolics are identified in the taxa examined, but no plant secondary metabolites are found using either analytical method. The results of this study and prior reports in the literature of chemical sequestration and unpalatability are plotted onto the resulting Bayesian inference phylogeny to examine the evolution of chemical defence within Lithosiini. Species that sequester lichen polyphenolics and unpalatable species occur in each of the major clades recovered in the analysis.
Field identification guide to the living marine resources of the eastern and southern Mediterranean.

The field identification guide surveys marine organisms of commercial and potential commercial importance. The region covered extends from the Mediterranean coast of Turkey proceeding in a general southwestern direction to that of Morocco. Species were selected carefully according to economic interest, commonness and sometimes according to their endangered or invasive status. A total of 372 marine species were considered, including the most common exotic ones. Also presented are their relevant diagnostic features, biological information, and geographical distribution while highlighting their importance on local fisheries. The entire field guide was translated into Arabic for a better accessibility among non scientists in Arabic speaking countries.
Penalized regression techniques for prediction: a case study for predicting tree mortality using remotely sensed vegetation indices

Constructing models can be complicated when the available fitting data are highly correlated and of high dimension. However, the complications depend on whether the goal is prediction instead of estimation. We focus on predicting tree mortality (measured as the number of dead trees) from change metrics derived from moderate-resolution imaging spectroradiometer satellite images. The high dimensionality and multicollinearity inherent in such data are of particular concern. Standard regression techniques perform poorly for such data, so we examine shrinkage regression techniques such as ridge regression, the LASSO, and partial least squares, which yield more robust predictions. We also suggest efficient strategies that can be used to select optimal models such as 0.632+ bootstrap and generalized cross validation. The techniques are compared using simulations. The techniques are then used to predict insect-induced tree mortality severity for a Pinus radiata D. Don plantation in southern New South Wales, Austr.
An adaptive space-time discontinuous Galerkin method for reservoir flows

Numerical simulation has become a vital tool for predicting engineering quantities of interest in reservoir flows. However, the general lack of autonomy and reliability prevents most numerical methods from being used to their full potential in engineering analysis. This thesis presents work towards the development of an efficient and robust numerical framework for solving reservoir flow problems in a fully-automated manner. In particular, a space-time discontinuous Galerkin (DG) finite element method is used to achieve a high-order discretization on a fully unstructured space-time mesh, instead of a conventional time-marching approach. Anisotropic mesh adaptation is performed to reduce the error of a specified output of interest, by using a posteriori error estimates from the dual weighted residual method to drive a metric-based mesh optimization algorithm. An analysis of the adjoint equations, boundary conditions and solutions of the Buckley-Leverett and two-phase flow equations is presented, with the objective of developing a theoretical understanding of the adjoint behaviors of porous media models. The intuition developed from this analysis is useful for understanding mesh adaptation behaviors in more complex flow problems. This work also presents a new bottomhole pressure well model for reservoir simulation, which relates the volumetric flow rate of the well to the reservoir pressure through a distributed source term that is independent of the discretization. Unlike Peaceman-type models which require the definition of an equivalent well-bore radius dependent on local grid length scales, this distributed well model is directly applicable to general discretizations on unstructured meshes. We show that a standard DG diffusive flux discretization of the two-phase flow equations in mass conservation form results in an unstable semi-discrete system in the advection-dominant limit, and hence propose modifications to linearly stabilize the discretization. Further, an artificial viscosity method is presented for the BuckleyLeverett and two-phase flow equations, as a means of mitigating Gibbs oscillations in high-order discretizations and ensuring convergence to physical solutions. Finally, the proposed adaptive solution framework is demonstrated on compress3 ible two-phase flow problems in homogeneous and heterogeneous reservoirs. Comparisons with conventional time-marching methods show that the adaptive space-time DG method is significantly more efficient at predicting output quantities of interest, in terms of degrees-of-freedom required, execution time and parallel scalability. Thesis Supervisor: David L. Darmofal Title: Professor of Aeronautics and Astronautics Thesis Committee Member: Steven R. Allmaras Title: Research Engineer of Aeronautics and Astronautics Thesis Committee Member: Ali H. Dogru Title: Saudi Aramco Fellow Thesis Committee Member: Youssef M. Marzouk Title: Professor of Aeronautics and Astronautics
NOTES ON THE GENUS CYLINDROCLADIUM (Fungi: Mucedinaceae)

The genus Cylindrocladivm was erected by Morgan in 1892 for a Mucedinaceous fungus with Penicillium-like branching and long,cylindrical,two-celled conidia.The original diagnosis runs: — Cylindrocladium Morgan. "Hyphae steriles repentes,fertiles erectae,dichoto mice ramosae,septatae, basidia in apice ramorum subterna fusoidea,conidia cylin- dracea, 1-septata. " The type and only species,Cylindrocladium scoparium Morgan,was found on dead pods of Gleditschia triacanthos L.In 1900 the same fungus was reported by Ellis and Everhart on dead leaves of Asimina triloba Dun.They considered it a new species of the genus Diplocladhim Bonord.and described it accordingly as Diplocladium cylindrosporum Ell. & Everh.In 1912 Hawley (see Rea and Hawley) erected the genus Candelospora with the following diagnosis