Double Hybrid Functionals and the Π-System Bond Length Alternation Challenge: Rivaling Accuracy of Post-HF Methods

Predicting accurate bond length alternations (BLAs) in long conjugated oligomers has been a significant challenge for electronic-structure methods for many decades, made particularly important by the close relationships between BLA and the rich optoelectronic properties of π-delocalized systems. Here, we test the accuracy of recently developed, and increasingly popular, double hybrid (DH) functionals, positioned at the top of Jacobs Ladder of DFT methods of increasing sophistication, computational cost, and accuracy, due to incorporation of MP2 correlation energy. Our test systems comprise oligomeric series of polyacetylene, polymethineimine, and polysilaacetylene up to six units long. MP2 calculations reveal a pronounced shift in BLAs between the 6-31G(d) basis set used in many studies of BLA to date and the larger cc-pVTZ basis set, but only modest shifts between cc-pVTZ and aug-cc-pVQZ results. We hence perform new reference CCSD(T)/cc-pVTZ calculations for all three series of oligomers against which we assess the performance of several families of DH functionals based on BLYP, PBE, and TPSS, along with lower-rung relatives including global- and range-separated hybrids. Our results show that DH functionals systematically improve the accuracy of BLAs relative to single hybrid functionals. xDH-PBE0 (N4 scaling using SOS-MP2) emerges as a DH functional rivaling the BLA accuracy of SCS-MP2 (N5 scaling), which was found to offer the best compromise between computational cost and accuracy the last time the BLA accuracy of DFT- and wave function-based methods was systematically investigated. Interestingly, xDH-PBE0 (XYG3), which differs to other DHs in that its MP2 term uses PBE0 (B3LYP) orbitals that are not self-consistent with the DH functional, is an outlier of trends of decreasing average BLA errors with increasing fractions of MP2 correlation and HF exchange.

The teaching of reading English in a foreign language in Libyan universities: methods and models

This study focuses on the learning and teaching of Reading in English as a Foreign Language (REFL), in Libya. The study draws on an action research process in which I sought to look critically at students and teachers of English as a Foreign Language (EFL) in Libya as they learned and taught REFL in four Libyan research sites. The Libyan EFL educational system is influenced by two main factors: the method of teaching the Holy-Quran and the long-time ban on teaching EFL by the former Libyan regime under Muammar Gaddafi. Both of these factors have affected the learning and teaching of REFL and I outline these contextual factors in the first chapter of the thesis. This investigation, and the exploration of the challenges that Libyan university students encounter in their REFL, is supported by attention to reading models. These models helped to provide an analytical framework and starting point for understanding the many processes involved in reading for meaning and in reading to satisfy teacher instructions. The theoretical framework I adopted was based, mainly and initially, on top-down, bottom-up, interactive and compensatory interactive models. I drew on these models with a view to understanding whether and how the processes of reading described in the models could be applied to the reading of EFL students and whether these models could help me to better understand what was going on in REFL. The diagnosis stage of the study provided initial data collected from four Libyan research sites with research tools including video-recorded classroom observations, semi-structured interviews with teachers before and after lesson observation, and think-aloud protocols (TAPs) with 24 students (six from each university) in which I examined their REFL reading behaviours and strategies. This stage indicated that the majority of students shared behaviours such as reading aloud, reading each word in the text, articulating the phonemes and syllables of words, or skipping words if they could not pronounce them. Overall this first stage indicated that alternative methods of teaching REFL were needed in order to encourage ‘reading for meaning’ that might be based on strategies related to eventual interactive reading models adapted for REFL. The second phase of this research project was an Intervention Phase involving two team-teaching sessions in one of the four stage one universities. In each session, I worked with the teacher of one group to introduce an alternative method of REFL. This method was based on teaching different reading strategies to encourage the students to work towards an eventual interactive way of reading for meaning. A focus group discussion and TAPs followed the lessons with six students in order to discuss the 'new' method. Next were two video-recorded classroom observations which were followed by an audio-recorded discussion with the teacher about these methods. Finally, I conducted a Skype interview with the class teacher at the end of the semester to discuss any changes he had made in his teaching or had observed in his students' reading with respect to reading behaviour strategies, and reactions and performance of the students as he continued to use the 'new' method. The results of the intervention stage indicate that the teacher, perhaps not surprisingly, can play an important role in adding to students’ knowledge and confidence and in improving their REFL strategies. For example, after the intervention stage, students began to think about the title, and to use their own background knowledge to comprehend the text. The students employed, also, linguistic strategies such as decoding and, above all, the students abandoned the behaviour of reading for pronunciation in favour of reading for meaning. Despite the apparent efficacy of the alternative method, there are, inevitably, limitations related to the small-scale nature of the study and the time I had available to conduct the research. There are challenges, too, related to the students’ first language, the idiosyncrasies of the English language, the teacher training and continuing professional development of teachers, and the continuing political instability of Libya. The students’ lack of vocabulary and their difficulties with grammatical functions such as phrasal and prepositional verbs, forms which do not exist in Arabic, mean that REFL will always be challenging. Given such constraints, the ‘new’ methods I trialled and propose for adoption can only go so far in addressing students’ difficulties in REFL. Overall, the study indicates that the Libyan educational system is underdeveloped and under resourced with respect to REFL. My data indicates that the teacher participants have received little to no professional developmental that could help them improve their teaching in REFL and skills in teaching EFL. These circumstances, along with the perennial problem of large but varying class sizes; student, teacher and assessment expectations; and limited and often poor quality resources, affect the way EFL students learn to read in English. Against this background, the thesis concludes by offering tentative conclusions; reflections on the study, including a discussion of its limitations, and possible recommendations designed to improve REFL learning and teaching in Libyan universities.

In Vitro Evaluation Of Sun Protection Factor And Stability Of Commercial Sunscreens Using Mass Spectrometry.

Sunlight exposure causes several types of injury to humans, especially on the skin; among the most common harmful effects due to ultraviolet (UV) exposure are erythema, pigmentation and lesions in DNA, which may lead to cancer. These long-term effects are minimized with the use of sunscreens, a class of cosmetic products that contains UV filters as the main component in the formulation; such molecules can absorb, reflect or diffuse UV rays, and can be used alone or as a combination to broaden the protection on different wavelengths. Currently, worldwide regulatory agencies define which ingredients and what quantities must be used in each country, and enforce companies to conduct tests that confirm the Sun Protection Factor (SPF) and the UVA (Ultraviolet A) factor. Standard SPF determination tests are currently conducted in vivo, using human subjects. In an industrial mindset, apart from economic and ethical reasons, the introduction of an in vitro method emerges as an interesting alternative by reducing risks associated to UV exposure on tests, as well as providing assertive analytical results. The present work aims to describe a novel methodology for SPF determination directly from sunscreen formulations using the previously described cosmetomics platform and mass spectrometry as the analytical methods of choice.

Phenotypic Polymorphism Of Chrysomya Albiceps (wiedemann) (diptera: Calliphoridae) May Lead To Species Misidentification.

Species identification is an essential step in the progress and completion of work in several areas of biological knowledge, but it is not a simple process. Due to the close phylogenetic relationship of certain species, morphological characters are not always sufficiently distinguishable. As a result, it is necessary to combine several methods of analysis that contribute to a distinct categorization of taxa. This study aimed to raise diagnostic characters, both morphological and molecular, for the correct identification of species of the genus Chrysomya (Diptera: Calliphoridae) recorded in the New World, which has continuously generated discussion about its taxonomic position over the last century. A clear example of this situation was the first record of Chrysomya rufifacies in Brazilian territory in 2012. However, the morphological polymorphism and genetic variability of Chrysomya albiceps studied here show that both species (C. rufifacies and C. albiceps) share very similar character states, leading to misidentification and subsequent registration error of species present in our territory. This conclusion is demonstrated by the authors, based on a review of the material deposited in major scientific collections in Brazil and subsequent molecular and phylogenetic analysis of these samples. Additionally, we have proposed a new taxonomic key to separate the species of Chrysomya found on the American continent, taking into account a larger number of characters beyond those available in current literature.

New methods to quantify NH3 volatilization from fertilized surface soil with urea

Gaseous N losses from soil are considerable, resulting mostly from ammonia volatilization linked to agricultural activities such as pasture fertilization. The use of simple and accessible measurement methods of such losses is fundamental in the evaluation of the N cycle in agricultural systems. The purpose of this study was to evaluate quantification methods of NH3 volatilization from fertilized surface soil with urea, with minimal influence on the volatilization processes. The greenhouse experiment was arranged in a completely randomized design with 13 treatments and five replications, with the following treatments: (1) Polyurethane foam (density 20 kg m-3) with phosphoric acid solution absorber (foam absorber), installed 1, 5, 10 and 20 cm above the soil surface; (2) Paper filter with sulfuric acid solution absorber (paper absorber, 1, 5, 10 and 20 cm above the soil surface); (3) Sulfuric acid solution absorber (1, 5 and 10 cm above the soil surface); (4) Semi-open static collector; (5) 15N balance (control). The foam absorber placed 1 cm above the soil surface estimated the real daily rate of loss and accumulated loss of NH3N and proved efficient in capturing NH3 volatized from urea-treated soil. The estimates based on acid absorbers 1, 5 and 10 cm above the soil surface and paper absorbers 1 and 5 cm above the soil surface were only realistic for accumulated N-NH3 losses. Foam absorbers can be indicated to quantify accumulated and daily rates of NH3 volatilization losses similarly to an open static chamber, making calibration equations or correction factors unnecessary.

An analytical solution for the critical number of particles for stable bose-einstein condensation under the influence of an anisotropic potential

We have considered a Bose gas in an anisotropic potential. Applying the the Gross-Pitaevskii Equation (GPE) for a confined dilute atomic gas, we have used the methods of optimized perturbation theory and self-similar root approximants, to obtain an analytical formula for the critical number of particles as a function of the anisotropy parameter for the potential. The spectrum of the GPE is also discussed.

Study of mural paintings by Fulvio Pennacchi in São Paulo City by mineralogical techniques

The present research deals with two mural paintings made in 1947 with the fresco technique by Fulvio Pennacchi in the Catholic Chapel of the Hospital das Clínicas (São Paulo City, Brazil), namely the Virgin Annunciation and the Supper at Emmaus. This study regards the materials and painting techniques used by the artist, based on historical research,on in situ observations and laboratory analytical techniques (stereomicroscopy,scanning electron microscopy with an energy dispersive spectrometer, X-ray diffractometry, electron microprobe, images obtained with UV-light), aiming to improve the methods of characterization of objects of our cultural heritage, and to enhance its preservation accordingly. The results lead to the identification of the plaster components and of distinct layers in the frescoes, besides further information on grain size, impurities and textures, composition of pigments, and features of deterioration, such as efflorescences. The degree of degradation of the murals painting was assessed by this way. Our data suggest that a single layer of plaster was used by Pennacchi, as a common mortar with fine- and medium-grained aggregates. Differences in texture were obtained by adding gypsum to the plaster.

Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in Sao Paulo, Brazil

Background: The genetic diversity of the human immunodeficiency virus type 1 (HIV-1) is critical to lay the groundwork for the design of successful drugs or vaccine. In this study we aimed to characterize and define the molecular prevalence of HIV-1 subclade F1 currently circulating in Sao Paulo, Brazil. Methods: A total of 36 samples were selected from 888 adult patients residing in Sao Paulo who had previously been diagnosed in two independent studies in our laboratory as being infected with subclade F1 based on pol subgenomic fragment sequencing. Proviral DNA was amplified from the purified genomic DNA of all 36 blood samples by 5 fragments overlapping PCR followed by direct sequencing. Sequence data were obtained from the 5 fragments of pure subclade F1 and phylogenetic trees were constructed and compared with previously published sequences. Subclades F1 that exhibited mosaic structure with other subtypes were omitted from any further analysis Results: Our methods of fragment amplification and sequencing confirmed that only 5 sequences inferred from pol region as subclade F1 also holds true for the genome as a whole and, thus, estimated the true prevalence at 0.56%. The results also showed a single phylogenetic cluster of the Brazilian subclade F1 along with non-Brazilian South American isolates in both subgenomic and the full-length genomes analysis with an overall intrasubtype nucleotide divergence of 6.9%. The nucleotide differences within the South American and Central African F1 strains, in the C2-C3 env, were 8.5% and 12.3%, respectively. Conclusion: All together, our findings showed a surprisingly low prevalence rate of subclade F1 in Brazil and suggest that these isolates originated in Central Africa and subsequently introduced to South America.

Determination of Threshold Dose of Photodynamic Therapy to Measure Superficial Necrosis

Background Data: Photodynamic therapy (PDT) involves the photoinduction of cytotoxicity using a photosensitizer agent, a light source of the proper wavelength, and the presence of molecular oxygen. A model for tissue response to PDT based on the photodynamic threshold dose (Dth) has been widely used. In this model cells exposed to doses below Dth survive while at doses above the Dth necrosis takes place. Objective: This study evaluated the light Dth values by using two different methods of determination. One model concerns the depth of necrosis and the other the width of superficial necrosis. Materials and Methods: Using normal rat liver we investigated the depth and width of necrosis induced by PDT when a laser with a gaussian intensity profile is used. Different light doses, photosensitizers (Photogem, Photofrin, Photosan, Foscan, Photodithazine, and Radachlorin), and concentrations were employed. Each experiment was performed on five animals and the average and standard deviations were calculated. Results: A simple depth and width of necrosis model analysis allows us to determine the threshold dose by measuring both depth and surface data. Comparison shows that both measurements provide the same value within the degree of experimental error. Conclusion: This work demonstrates that by knowing the extent of the superficial necrotic area of a target tissue irradiated by a gaussian light beam, it is possible to estimate the threshold dose. This technique may find application where the determination of Dth must be done without cutting the tissue.

Chemical similarities between Galactic bulge and local thick disk red giant stars

Context. The evolution of the Milky Way bulge and its relationship with the other Galactic populations is still poorly understood. The bulge has been suggested to be either a merger-driven classical bulge or the product of a dynamical instability of the inner disk. Aims. To probe the star formation history, the initial mass function and stellar nucleosynthesis of the bulge, we performed an elemental abundance analysis of bulge red giant stars. We also completed an identical study of local thin disk, thick disk and halo giants to establish the chemical differences and similarities between the various populations. Methods. High-resolution infrared spectra of 19 bulge giants and 49 comparison giants in the solar neighborhood were acquired with Gemini/Phoenix. All stars have similar stellar parameters but cover a broad range in metallicity. A standard 1D local thermodynamic equilibrium analysis yielded the abundances of C, N, O and Fe. A homogeneous and differential analysis of the bulge, halo, thin disk and thick disk stars ensured that systematic errors were minimized. Results. We confirm the well-established differences for [O/Fe] (at a given metallicity) between the local thin and thick disks. For the elements investigated, we find no chemical distinction between the bulge and the local thick disk, which is in contrast to previous studies relying on literature values for disk dwarf stars in the solar neighborhood. Conclusions. Our findings suggest that the bulge and local thick disk experienced similar, but not necessarily shared, chemical evolution histories. We argue that their formation timescales, star formation rates and initial mass functions were similar.

Age distribution of the central stars of galactic disk planetary nebulae

Context. Determination of the ages of central stars of planetary nebulae (CSPN) is a complex problem, and there is presently no single method that can be generally applied. We have developed several methods of estimating the ages of CSPN, based on both the observed nebular properties and some properties of the stars themselves. Aims. Our aim is to estimate the ages and the age distribution of CSPN and to compare the derived results with mass and age determinations of CSPN and white dwarfs based on empirical determinations of these quantities. Methods. We considered a sample of planetary nebulae in the galactic disk, most of which (similar to 69%) are located in the solar neighbourhood, within 3 kpc from the Sun. We discuss several methods of deriving the age distribution of CSPN, namely; (i) the use of an age-metallicity relation that also depends on the galactocentric distance; (ii) the use of an age-metallicity relation obtained for the galactic disk; and (iii) the determination of ages from the central star masses obtained from the observed nitrogen abundances. Results. We estimated the age distribution of CSPN with average uncertainties of 1-2 Gyr, and compared our results with the expected distribution based both on the observed mass distribution of white dwarfs and on the age distribution derived from available mass distributions of CSPN. Based on our derived age distributions, we conclude that most CSPN in the galactic disk have ages under 6 Gyr, and that the age distribution is peaked around 2-4 Gyr.

Cyclic variability of the circumstellar disk of the Be star zeta Tauri I. Long-term monitoring observations

Context. Emission lines formed in decretion disks of Be stars often undergo long-term cyclic variations, especially in the violet-to-red (V/R) ratio of their primary components. The underlying structural and dynamical variations of the disks are only partly understood. From observations of the bright Be-shell star. Tau, the possibly broadest and longest data set illustrating the prototype of this behaviour was compiled from our own and archival observations. It comprises optical and infrared spectra, broad-band polarimetry, and interferometric observations. Aims. The dense, long-time monitoring permits a better separation of repetitive and ephemeral variations. The broad wavelength coverage includes lines formed under different physical conditions, i.e. different locations in the disk, so that the dynamics can be probed throughout much of the disk. Polarimetry and interferometry constrain the spatial structure. All together, the objective is a better understand the dynamics and life cycle of decretion disks. Methods. Standard methods of data acquisition, reduction, and analysis were applied. Results. From 3 V/R cycles between 1997 and 2008, a mean cycle length in Ha of 1400-1430 days was derived. After each minimum in V/R, the shell absorption weakens and splits into two components, leading to 3 emission peaks. This phase may make the strongest contribution to the variability in cycle length. There is no obvious connection between the V/R cycle and the 133-day orbital period of the not otherwise detected companion. V/R curves of different lines are shifted in phase. Lines formed on average closer to the central star are ahead of the others. The shell absorption lines fall into 2 categories differing in line width, ionization/excitation potential, and variability of the equivalent width. They seem to form in separate regions of the disk, probably crossing the line of sight at different times. The interferometry has resolved the continuum and the line emission in Br gamma and HeI 2.06. The phasing of the Br gamma emission shows that the photocenter of the line-emitting region lies within the plane of the disk but is offset from the continuum source. The plane of the disk is constant throughout the observed V/R cycles. The observations lay the foundation for the fully self-consistent, one-armed, disk-oscillation model developed in Paper II.

Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence

Background: Mites (Acari) have traditionally been treated as monophyletic, albeit composed of two major lineages: Acariformes and Parasitiformes. Yet recent studies based on morphology, molecular data, or combinations thereof, have increasingly drawn their monophyly into question. Furthermore, the usually basal (molecular) position of one or both mite lineages among the chelicerates is in conflict to their morphology, and to the widely accepted view that mites are close relatives of Ricinulei. Results: The phylogenetic position of the acariform mites is examined through employing SSU, partial LSU sequences, and morphology from 91 chelicerate extant terminals (forty Acariformes). In a static homology framework, molecular sequences were aligned using their secondary structure as guide, whereby regions of ambiguous alignment were discarded, and pre-aligned sequences analyzed under parsimony and different mixed models in a Bayesian inference. Parsimony and Bayesian analyses led to trees largely congruent concerning infraordinal, well-supported branches, but with low support for inter-ordinal relationships. An exception is Solifugae + Acariformes (P. P = 100%, J. = 0.91). In a dynamic homology framework, two analyses were run: a standard POY analysis and an analysis constrained by secondary structure. Both analyses led to largely congruent trees; supporting a (Palpigradi (Solifugae Acariformes)) clade and Ricinulei as sister group of Tetrapulmonata with the topology (Ricinulei (Amblypygi (Uropygi Araneae))). Combined analysis with two different morphological data matrices were run in order to evaluate the impact of constraining the analysis on the recovered topology when employing secondary structure as a guide for homology establishment. The constrained combined analysis yielded two topologies similar to the exclusively molecular analysis for both morphological matrices, except for the recovery of Pedipalpi instead of the (Uropygi Araneae) clade. The standard (direct optimization) POY analysis, however, led to the recovery of trees differing in the absence of the otherwise well-supported group Solifugae + Acariformes. Conclusions: Previous studies combining ribosomal sequences and morphology often recovered topologies similar to purely morphological analyses of Chelicerata. The apparent stability of certain clades not recovered here, like Haplocnemata and Acari, is regarded as a byproduct of the way the molecular homology was previously established using the instrumentalist approach implemented in POY. Constraining the analysis by a priori homology assessment is defended here as a way of maintaining the severity of the test when adding new data to the analysis. Although the strength of the method advocated here is keeping phylogenetic information from regions usually discarded in an exclusively static homology framework; it still has the inconvenience of being uninformative on the effect of alignment ambiguity on resampling methods of clade support estimation. Finally, putative morphological apomorphies of Solifugae + Acariformes are the reduction of the proximal cheliceral podomere, medial abutting of the leg coxae, loss of sperm nuclear membrane, and presence of differentiated germinative and secretory regions in the testis delivering their products into a common lumen.

COUNTABLE GROUPS OF ISOMETRIES ON BANACH SPACES

A group G is representable in a Banach space X if G is isomorphic to the group of isometrics on X in some equivalent norm. We prove that a countable group G is representable in a separable real Banach space X in several general cases, including when G similar or equal to {-1,1} x H, H finite and dim X >= vertical bar H vertical bar or when G contains a normal subgroup with two elements and X is of the form c(0)(Y) or l(p)(Y), 1 <= p < +infinity. This is a consequence of a result inspired by methods of S. Bellenot (1986) and stating that under rather general conditions on a separable real Banach space X and a countable bounded group G of isomorphisms on X containing -Id, there exists an equivalent norm on X for which G is equal to the group of isometrics on X. We also extend methods of K. Jarosz (1988) to prove that any complex Banach space of dimension at least 2 may be renormed with an equivalent complex norm to admit only trivial real isometries, and that any complexification of a Banach space may be renormed with an equivalent complex norm to admit only trivial and conjugation real isometrics. It follows that every real Banach space of dimension at least 4 and with a complex structure may be renormed to admit exactly two complex structures up to isometry, and that every real Cartesian square may be renormed to admit a unique complex structure up to isometry.

Molluscicidal and ovicidal activities of plant extracts of the Piperaceae on Biomphalaria glabrata (Say, 1818)

Schistosomiasis is a tropical disease caused by Schistosoma and occurs in 54 countries, mainly in South America, the Caribbean region, Africa and the eastern Mediterranean. Currently, 5 to 6 million Brazilian people are infected and 30,000 are under infection risk. Typical of poor regions, this disease is associated with the lack of basic sanitation and very frequently to the use of contaminated water in agriculture, housework and leisure. One of the most efficient methods of controlling the disease is application of molluscicides to eliminate or to reduce the population of the intermediate host snail Biomphalaria glabrata. Studies on molluscicidal activity of plant extracts have been stimulated by issues such as environmental preservation, high cost and recurrent resistance of snails to synthetic molluscicides. The aim of this study was to determine the molluscicide action of extracts from Piperaceae species on adult and embryonic stages of B. glabrata. Fifteen extracts from 13 Piperaceae species were obtained from stems, leaves and roots. Toxicity of extracts was evaluated against snails at two different concentrations (500 and 100 ppm) and those causing 100% mortality at 100 ppm concentration were selected to obtain the LC(90) (lethal concentration of 90% mortality). Piper aduncum, P. crassinervium, P. cuyabanum, P. diospyrifolium and P. hostmannianum gave 100% mortality of adult snails at concentrations ranging from 10 to 60 ppm. These extracts were also assayed on embryonic stages of B. glabrata and those from P. cuyabanum and P. hostmannianum showed 100% ovicidal action at 20 ppm.