A topologia molecular QTAIM e a descrição mecânico-quântica de ligações de hidrogênio e ligações de di-hidrogênio

Hydrogen bonds formed through the interaction between a high electronic density center (lone electron pairs, π or pseudo-π bonds) and proton donors cause important electronic and vibrational phenomena in many systems. However, it was demonstrated that proton donors interact with hydrides, such as alkali and alkaline earth metals (BeH2, MgH2, LiH and NaH), what yields a new type of interaction so-called dihydrogen bonds. The characterization of these interactions has been performed at light of the Quantum Theory of Atoms in Molecules (QTAIM), by which the electronic densities ρ are quantified and the intermolecular regions are characterized as closed-shell interactions through the analysis of the Laplacian field ∇2ρ.

Estudio de usabilidad de visualización molecular educativa en un teléfono inteligente

Chemistry students have difficulty understanding molecular structures and their functions. To aide their comprehension, molecular visualization software has been developed to run on smart phones, but in order to positively influence learning it must have a high degree of usability (usability measures how software is used in terms of efficiency, efficacy and satisfaction). This paper describes a usability study of molecular visualization software running on a smart phone, where chemistry students analyzed molecular models. Results showed very good usability and 95% of students wanted to use it in further classes.

EFEITO DA ESTRUTURA MOLECULAR DE LIGANTES DE SUPERFÍCIE EM PONTOS QUÂNTICOS DE CdTe DISPERSOS EM ÁGUA

Water-soluble CdTe quantum dots are synthesized to investigate how short-chain surface ligands bearing -SH, -COOH, and -NH2 groups interact with CdTe during nucleation/growth processes. Their optical properties and colloidal stability after the ligand exchange are also investigated. We then characterize the resulting CdTe by fluorescence, UV–Vis absorption, and infrared spectroscopies. The stability of the colloidal dispersions was determined by their Zeta potentials. The results show that in the synthesis of water-soluble CdTe, surface ligands with at least two functional groups are required and the hard/soft character of them is an important factor in the stability of CdTe.

Molecular characterization of Brazilian strains of Xanthomonas campestris pv. viticola by rep-PCR fingerprinting

Bacterial canker of grapevine (Vitis vinifera), caused by Xanthomonas campestris pv. viticola was first detected in Brazil in 1998, affecting grapevines in the São Francisco river basin, state of Pernambuco. The disease was also reported in Juazeiro, Bahia and later in Piauí and Ceará. Due to its limited geographical distribution and relatively recent detection in Brazil, very little is known about the pathogen's biology and diversity. Repetitive DNA based-PCR (rep-PCR) profiles were generated from purified bacterial DNA of 40 field strains of X. campestris pv. viticola, collected between 1998 and 2001 in the states of Pernambuco, Bahia and Piauí. Combined analysis of the PCR patterns obtained with primers REP, ERIC and BOX, showed a high degree of similarity among Brazilian strains and the Indian type strain NCPPB 2475. Similar genomic patterns with several diagnostic bands, present in all strains, could be detected. Fingerprints were distinct from those of strains representing other pathovars and from a yellow non-pathogenic isolate from grape leaves. The polymorphism observed among the Brazilian strains allowed their separation into five subgroups, although with no correlation with cultivar of origin, geographic location or year collected.

Pathogenicity, molecular characterization, and cercosporin content of Brazilian isolates of Cercospora kikuchii

Cercospora kikuchii, involved with the defoliation of soybean (Glycine max) plants, is normally associated with Septoria glycines in late season. Seventy-two isolates from different regions in Brazil, obtained mainly from purple stained seeds, showed phenotypic variation. Cercosporin content and rate of colony growth was higly variable among isolates. A strong correlation between cercosporin content and virulence was identified. Genetic variation among and within populations was evaluated based on 86 RAPD loci. The RAPD analysis clustered all isolates into seven groups. No relationship was observed between RAPD groups and geographic origin or cercosporin content. The sequence of the internal spacer regions (ITS1-5.8S-ITS2) from 13 isolates chosen according to the previous RAPD and clustering analysis showed high similarity (97%-100%) to the GenBank sequences of C. kikuchii (AY266160, AY266161, AY152577 and AF291708). It is clear from this work that Brazilian isolates of C. kikuchii from different geographic regions, are variable in relation to virulence, RAPD profiles and cercosporin content. Cercosporin content could be a good parameter for choosing an adequate isolate for screening resistant or tolerant cultivars. Considering that this pathogen is easily seed-borne, findings are expected to show the same haplotypes in different regions. Migration could be favoured by infected seeds as demonstrated by RAPD analysis.

Comparison measures of maps generated by geostatistical methods

This study uses several measures derived from the error matrix for comparing two thematic maps generated with the same sample set. The reference map was generated with all the sample elements and the map set as the model was generated without the two points detected as influential by the analysis of local influence diagnostics. The data analyzed refer to the wheat productivity in an agricultural area of 13.55 ha considering a sampling grid of 50 x 50 m comprising 50 georeferenced sample elements. The comparison measures derived from the error matrix indicated that despite some similarity on the maps, they are different. The difference between the estimated production by the reference map and the actual production was of 350 kilograms. The same difference calculated with the mode map was of 50 kilograms, indicating that the study of influential points is of fundamental importance to obtain a more reliable estimative and use of measures obtained from the error matrix is a good option to make comparisons between thematic maps.

Molecular characterization of group A bovine rotavirus in southeastern and central-western Brazil, 2009-2010

Rotavirus is an important cause of neonatal diarrhea in humans and several animal species, including calves. A study was conducted to examine 792 fecal samples collected from calves among 65 dairy and beef herds distributed in two of Brazil's major livestock producing regions, aiming to detect the occurrence of rotavirus and perform a molecular characterization of the rotavirus according to G and P genotypes in these regions. A total of 40 (5.05%) samples tested positive for rotavirus by the polyacrylamide gel electrophoresis (PAGE) technique. The molecular characterization was performed by multiplex semi-nested RT-PCR reactions, which indicated that the associations of genotypes circulating in herds in Brazil's southeastern region were G6P[11], G10P[11], G[-]P[5] + [11], G[-]P[6] in the state of São Paulo and G6P[11], G8P[5], G11P[11], G10P[11] in the state of Minas Gerais. In the central-western region, the genotypes G6P[5] + [11], G6P[5], G8P[-], G6P[11], G [-] P[1], G[-] P[11], and G[-] P[5] were detected in the state of Goiás, while the genotypes G6P[5], G8[P11], G6[P11], G8[P1], G8[P5], G6[P1] were circulating in herds in the state of Mato Grosso do Sul. The genotypic diversity of bovine rotavirus found in each region under study underlines the importance of characterizing the circulating samples in order to devise the most effective prophylactic measures.

Molecular characterization of DDX26, a human DEAD-box RNA helicase, located on chromosome 7p12

DEAD-box proteins comprise a family of ATP-dependent RNA helicases involved in several aspects of RNA metabolism. Here we report the characterization of the human DEAD-box RNA helicase DDX26. The gene is composed of 14 exons distributed over an extension of 8,123 bp of genomic sequence and encodes a transcript of 1.8 kb that is expressed in all tissues evaluated. The predicted amino acid sequence shows a high similarity to a yeast DEAD-box RNA helicase (Dbp9b) involved in ribosome biogenesis. The new helicase maps to 7p12, a region of frequent chromosome amplifications in glioblastomas involving the epidermal growth factor receptor (EGFR) gene. Nevertheless, co-amplification of DDX26 with EGFR was not detected in nine tumors analyzed.

Use of molecular epidemiology to monitor the nosocomial dissemination of methicillin-resistant Staphylococcus aureus in a University Hospital from 1991 to 2001

Methicillin-resistant Staphylococcus aureus (MRSA) has been the cause of major outbreaks and epidemics among hospitalized patients, with high mortality and morbidity rates. We studied the genomic diversity of MRSA strains isolated from patients with nosocomial infection in a University Hospital from 1991 to 2001. The study consisted of two periods: period I, from 1991 to 1993 and period II from 1995 to 2001. DNA was typed by pulsed-field gel electrophoresis and the similarity among the MRSA strains was determined by cluster analysis. During period I, 73 strains presented five distinctive DNA profiles: A, B, C, D, and E. Profile A was the most frequent DNA pattern and was identified in 55 (75.3%) strains; three closely related and four possibly related profiles were also identified. During period II, 80 (68.8%) of 117 strains showed the same endemic profile A identified during period I, 18 (13.7%) closely related profiles and 18 (13.7%) possibly related profiles and, only one strain presented an unrelated profile. Cluster analysis showed a 96% coefficient of similarity between profile A from period I and profile A from period II, which were considered to be from the same clone. The molecular monitoring of MRSA strains permitted the determination of the clonal dissemination and the maintenance of a dominant endemic strain during a 10-year period and the presence of closely and possibly related patterns for endemic profile A. However, further studies are necessary to improve the understanding of the dissemination of the endemic profile in this hospital.

Epidemiological and functional implications of molecular variants of human papillomavirus

Human papillomavirus genomes are classified into molecular variants when they present more than 98% of similarity to the prototype sequence within the L1 gene. Comparative nucleotide sequence analyses of these viruses have elucidated some features of their phylogenetic relationship. In addition, human papillomavirus intratype variability has also been used as an important tool in epidemiological studies of viral transmission, persistence and progression to clinically relevant cervical lesions. Until the present, little has been published concerning the functional significance of molecular variants. It has been shown that nucleotide variability within the long control region leads to differences in the binding affinity of some cellular transcriptional factors and to the enhancement of the expression of E6 and E7 oncogenes. Furthermore, in vivo and in vitro studies revealed differences in E6 and E7 biochemical and biological properties among molecular variants. Nevertheless, further correlation with additional functional information is needed to evaluate the significance of genome intratypic variability. These results are also important for the development of vaccines and to determine the extent to which immunization with L1 virus-like particles of one variant could induce antibodies that cross-neutralize other variants.

Non-Markovian dynamics in quantum optical dephasing channels

Quantum computation and quantum communication are two of the most promising future applications of quantum mechanics. Since the information carriers used in both of them are essentially open quantum systems it is necessary to understand both quantum information theory and the theory of open quantum systems in order to investigate realistic implementations of such quantum technologies. In this thesis we consider the theory of open quantum systems from a quantum information theory perspective. The thesis is divided into two parts: review of the literature and original research. In the review of literature we present some important definitions and known results of open quantum systems and quantum information theory. We present the definitions of trace distance, two channel capacities and superdense coding capacity and give a reasoning why they can be used to represent the transmission efficiency of a communication channel. We also show derivations of some properties useful to link completely positive and trace preserving maps to trace distance and channel capacities. With the help of these properties we construct three measures of non-Markovianity and explain why they detect non-Markovianity. In the original research part of the thesis we study the non-Markovian dynamics in an experimentally realized quantum optical set-up. For general one-qubit dephasing channels we calculate the explicit forms of the two channel capacities and the superdense coding capacity. For the general two-qubit dephasing channel with uncorrelated local noises we calculate the explicit forms of the quantum capacity and the mutual information of a four-letter encoding. By using the dynamics in the experimental implementation as a set of specific dephasing channels we also calculate and compare the measures in one- and two-qubit dephasing channels and study the options of manipulating the environment to achieve revivals and higher transmission rates in superdense coding protocol with dephasing noise. Kvanttilaskenta ja kvanttikommunikaatio ovat kaksi puhutuimmista tulevaisuuden kvanttimekaniikan käytännön sovelluksista. Koska molemmissa näistä informaatio koodataan systeemeihin, jotka ovat oleellisesti avoimia kvanttisysteemejä, sekä kvantti-informaatioteorian, että avointen kvanttisysteemien tuntemus on välttämätöntä. Tässä tutkielmassa käsittelemme avointen kvanttisysteemien teoriaa kvantti-informaatioteorian näkökulmasta. Tutkielma on jaettu kahteen osioon: kirjallisuuskatsaukseen ja omaan tutkimukseen. Kirjallisuuskatsauksessa esitämme joitakin avointen kvanttisysteemien ja kvantti-informaatioteorian tärkeitä määritelmiä ja tunnettuja tuloksia. Esitämme jälkietäisyyden, kahden kanavakapasiteetin ja superdense coding -kapasiteetin määritelmät ja esitämme perustelun sille, miksi niitä voidaan käyttää kuvaamaan kommunikointikanavan lähetystehokkuutta. Näytämme myös todistukset kahdelle ominaisuudelle, jotka liittävät täyspositiiviset ja jäljensäilyttävät kuvaukset jälkietäisyyteen ja kanavakapasiteetteihin. Näiden ominaisuuksien avulla konstruoimme kolme epä-Markovisuusmittaa ja perustelemme, miksi ne havaitsevat dynamiikan epä-Markovisuutta. Oman tutkimuksen osiossa tutkimme epä-Markovista dynamiikkaa kokeellisesti toteutetussa kvanttioptisessa mittausjärjestelyssä. Yleisen yhden qubitin dephasing-kanavan tapauksessa laskemme molempien kanavakapasiteettien ja superdense coding -kapasiteetin eksplisiittiset muodot. Yleisen kahden qubitin korreloimattomien ympäristöjen dephasing-kanavan tapauksessa laskemme yhteisen informaation lausekkeen nelikirjaimisessa koodauksessa ja kvanttikanavakapasiteetin. Käyttämällä kokeellisen mittajärjestelyn dynamiikkoja esimerkki dephasing-kanavina me myös laskemme konstruoitujen epä-Markovisuusmittojen arvot ja vertailemme niitä yksi- ja kaksi-qubitti-dephasing-kanavissa. Lisäksi käyttäen kokeellisia esimerkkikanavia tutkimme, kuinka ympäristöä manipuloimalla superdense coding –skeemassa voidaan saada yhteinen informaatio ajoittain kasvamaan tai saavuttaa kaikenkaikkiaan korkeampi lähetystehokkuus.

Extreme Observables and Optimal Measurements in Quantum Theory

Optimization of quantum measurement processes has a pivotal role in carrying out better, more accurate or less disrupting, measurements and experiments on a quantum system. Especially, convex optimization, i.e., identifying the extreme points of the convex sets and subsets of quantum measuring devices plays an important part in quantum optimization since the typical figures of merit for measuring processes are affine functionals. In this thesis, we discuss results determining the extreme quantum devices and their relevance, e.g., in quantum-compatibility-related questions. Especially, we see that a compatible device pair where one device is extreme can be joined into a single apparatus essentially in a unique way. Moreover, we show that the question whether a pair of quantum observables can be measured jointly can often be formulated in a weaker form when some of the observables involved are extreme. Another major line of research treated in this thesis deals with convex analysis of special restricted quantum device sets, covariance structures or, in particular, generalized imprimitivity systems. Some results on the structure ofcovariant observables and instruments are listed as well as results identifying the extreme points of covariance structures in quantum theory. As a special case study, not published anywhere before, we study the structure of Euclidean-covariant localization observables for spin-0-particles. We also discuss the general form of Weyl-covariant phase-space instruments. Finally, certain optimality measures originating from convex geometry are introduced for quantum devices, namely, boundariness measuring how ‘close’ to the algebraic boundary of the device set a quantum apparatus is and the robustness of incompatibility quantifying the level of incompatibility for a quantum device pair by measuring the highest amount of noise the pair tolerates without becoming compatible. Boundariness is further associated to minimum-error discrimination of quantum devices, and robustness of incompatibility is shown to behave monotonically under certain compatibility-non-decreasing operations. Moreover, the value of robustness of incompatibility is given for a few special device pairs.

On the effect of molecular structure and composition on the photofragmentation of biomolecules

The research on the interaction between radiation and biomolecules pro-vides valuable information for both radiobiology and molecular physics. While radiobiology is interested in the damage inflicted on the molecule upon irradiation, molecular physics exploits these studies to obtain infor-mation about the physical properties of the molecule and the quantum me-chanical processes involved in the interaction. This thesis work investigated how a small change in the structure or composition of a biomolecule changes the response of the molecule to ioniz-ing radiation. Altogether eight different biomolecules were studied: nucleo-sides uridine, 5-methyluridine and thymidine; amino acids alanine, cysteine and serine; and halogenated acetic acids chloro- and bromoacetic acids. The effect of ionizing radiation on these molecules was studied on molecular level, investigating the samples in gas phase. Synchrotron radiation of VUV or soft x-ray range was used to ionize sample molecules, and the subsequent fragmentation processes were investigated with ion mass spectroscopy and ion-ion-electron coincidence spectroscopy. The comparison between the three nucleosides revealed that adding or removing a single functional group can affect not only the bonds from which the molecule ruptures upon ionization but also the charge localiza-tion in the formed fragments. Studies on amino acids and halogenated acetic acids indicated that one simple substitution in the molecule can dramatical-ly change the extent of fragmentation. This thesis work also demonstrates that in order to steer the radiation-induced fragmentation of the molecules, it is not always necessary to alter the amount of energy deposited on the molecules but selecting a suitable substitution may suffice.

The role of molecular, clinical and socioeconomic factors in the long-term survival of axillary node negative breast cancer patients

The overall objective of this study was to investigate factors associated with long-term survival in axillary node negative (ANN) breast cancer patients. Clinical and biological factors included stage, histopathologic grade, p53 mutation, Her-2/neu amplification, estrogen receptor status (ER), progesterone receptor status (PR) and vascular invasion. Census derived socioeconomic (SES) indicators included median individual and household income, proportions of university educated individuals, housing type, "incidence" of low income and an indicator of living in an affluent neighbourhood. The effects of these measures on breast cancer-specific survival and competing cause survival were investigated. A cohort study examining survival among axillary node negative (ANN) breast cancer patients in the greater Toronto area commenced in 1 989. Patients were followed up until death, lost-to-follow up or study termination in 2004. Data were collected from several sources measuring patient demographics, clinical factors, treatment, recurrence of disease and survival. Census level SES data were collected using census geo-coding of patient addresses' at the time of diagnosis. Additional survival data were acquired from the Ontario Cancer Registry to enhance and extend the observation period of the study. Survival patterns were examined using KaplanMeier and life table procedures. Associations were examined using log-rank and Wilcoxon tests of univariate significance. Multivariate survival analyses were perfonned using Cox proportional hazards models. Analyses were stratified into less than and greater than 5 year survival periods to observe whether known markers of short-tenn survival were also associated with reductions in long-tenn survival among breast cancer patients. The 15 year survival probabilities in this cohort were: for breast cancerspecific survival 0.88, competing causes survival 0.89 and for overall survival 0.78. Estrogen receptor (ER) and progesterone receptor (PR) status (Hazard Ratio (HR) ERIPR- versus ER+/PR+, 8.15,95% CI, 4.74, 14.00), p53 mutation (HR, 3.88, 95% CI, 2.00, 7.53) and Her-2 amplification (HR, 2.66, 95% CI, 1.36, 5.19) were associated with significant reductions in short-tenn breast cancer-specific survival «5 years following diagnosis), however, not with long-term survival in univariate analyses. Stage, histopathologic grade and ERiPR status were the clinicallbiologieal factors that were associated with short-term breast cancer specific survival in multivariate results. Living in an affluent neighbourhood (top quintile of median household income compared to the rest of the population) was associated with the largest significant increase in long-tenn breast cancer-specific survival after adjustment for stage, histopathologic grade and treatment (HR, 0.36, 95% CI, 0.12, 0.89).

Similarity of Options and the Measurement of Diversity

This paper analyzes the measurement of the diversity of sets based on the dissimilarity of the objects contained in the set. We discuss axiomatic approaches to diversity measurement and examine the considerations underlying the application of specific measures. Our focus is on descriptive issues: rather than assuming a specific ethical position or restricting attention to properties that are appealing in specific applications, we address the foundations of the measurement issue as such in the context of diversity.