Observed and predicted hydrogen bond motifs in crystal structures of hydantoins, dihydrouracils and uracils

A survey of crystal structures containing hydantoin, dihydrouracil and uracil derivatives in the Cambridge Structural Database revealed four main types of hydrogen bond motifs when derivatives with extra substituents able to interfere with the main motif are excluded. All these molecules contain two hydrogen bond donors and two hydrogen bond acceptors in the sequence of NH, C = O, NH, and C=O groups within a 5-membered ring (hydantoin) and two 6-membered rings (dihydrouracil and uracil). In all cases, both ring NH groups act as donors in the main hydrogen bond motif but there is an excess of hydrogen bond acceptors (two C=O able to accept twice each) and so two possibilities are found: (i) each carbonyl O atom may accept one hydrogen bond or (ii) one carbonyl O atom may accept two hydrogen bonds while the other does not participate in the hydrogen bonding. We observed different preferences in the type and symmetry of the motifs adopted by the different derivatives, and a good agreement is found between motifs observed experimentally and those predicted using computational methods. We identified certain molecular factors such as chirality, substituent size and the possibility of C-H⋯O interactions as important factors influencing the motif observation. © 2012 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.

Shannon, rényie and tsallis entropy analysis of DNA using phase plane

This paper analyzes DNA information using entropy and phase plane concepts. First, the DNA code is converted into a numerical format by means of histograms that capture DNA sequence length ranging from one up to ten bases. This strategy measures dynamical evolutions from 4 up to 410 signal states. The resulting histograms are analyzed using three distinct entropy formulations namely the Shannon, Rényie and Tsallis definitions. Charts of entropy versus sequence length are applied to a set of twenty four species, characterizing 486 chromosomes. The information is synthesized and visualized by adapting phase plane concepts leading to a categorical representation of chromosomes and species.

Generalization of Wertheim's theory for the assembly of various types of rings

We generalize Wertheim's first order perturbation theory to account for the effect in the thermodynamics of the self-assembly of rings characterized by two energy scales. The theory is applied to a lattice model of patchy particles and tested against Monte Carlo simulations on a fcc lattice. These particles have 2 patches of type A and 10 patches of type B, which may form bonds AA or AB that decrease the energy by epsilon(AA) and by epsilon(AB) = r epsilon(AA), respectively. The angle theta between the 2 A-patches on each particle is fixed at 601, 90 degrees or 120 degrees. For values of r below 1/2 and above a threshold r(th)(theta) the models exhibit a phase diagram with two critical points. Both theory and simulation predict that rth increases when theta decreases. We show that the mechanism that prevents phase separation for models with decreasing values of theta is related to the formation of loops containing AB bonds. Moreover, we show that by including the free energy of B-rings ( loops containing one AB bond), the theory describes the trends observed in the simulation results, but that for the lowest values of theta, the theoretical description deteriorates due to the increasing number of loops containing more than one AB bond.

Changes in Medical Management after Coronary CT Angiography

AbstractIntroduction:Coronary computed tomography angiography (CCTA) allows for non-invasive coronary artery disease (CAD) phenotyping. There are still some uncertainties regarding the impact this knowledge has on the clinical care of patients.Objective:To determine whether CAD phenotyping by CCTA influences clinical decision making by the prescription of cardiovascular drugs and their impact on non-LDL cholesterol (NLDLC) levels.Methods:We analysed consecutive patients from 2008 to 2011 submitted to CCTA without previous diagnosis of CAD that had two serial measures of NLDLC, one up to 3 months before CCTA and the second from 3 to 6 months after.Results:A total of 97 patients were included, of which 69% were men, mean age 64 ± 12 years. CCTA revealed that 18 (18%) patients had no CAD, 38 (39%) had non-obstructive (< 50%) lesions and 41 (42%) had at least one obstructive ≥ 50% lesion. NLDLC was similar at baseline between the grups (138 ± 52 mg/dL vs. 135 ± 42 mg/dL vs. 131 ± 44 mg/dL, respectively, p = 0.32). We found significative reduction in NLDLC among patients with obstrctive lesions (-18%, p = 0.001). We also found a positive relationship between clinical treatment intensification with aspirin and cholesterol reducing drugs and the severity of CAD.Conclusion:Our data suggest that CCTA results were used for cardiovascular clinical treatment titration, with especial intensification seen in patients with obstructive ≥50% CAD.

A cartography of the Van der Waals territory

The distribution of distances from atoms of a particular element E to a probe atom X (oxygen in most cases), both bonded and intermolecular non-bonded contacts, has been analyzed. In general, the distribution is characterized by a maximum at short EX distances corresponding to chemical bonds, followed by a range of unpopulated distances the van der Waals gap and a second maximum at longer distances the van der Waals peak superimposed on a random distribution function that roughly follows a d3 dependence. The analysis of more than five million interatomic"non-bonded" distances has led to the proposal of a consistent set of van der Waals radii for most naturally occurring elements, and its applicability to other element pairs has been tested for a set of more than three million data, all of them compared to over one million bond distances.

3D movement and muscle activity patterns in a violin bowing task

Objective: Overuse injuries in violinists are a problem that has been primarily analyzed through the use of questionnaires. Simultaneous 3D motion analysis and EMG to measure muscle activity has been suggested as a quantitative technique to explore this problem by identifying movement patterns and muscular demands which may predispose violinists to overuse injuries. This multi-disciplinary analysis technique has, so far, had limited use in the music world. The purpose of this study was to use it to characterize the demands of a violin bowing task. Subjects: Twelve injury-free violinists volunteered for the study. The subjects were assigned to a novice or expert group based on playing experience, as determined by questionnaire. Design and Settings: Muscle activity and movement patterns were assessed while violinists played five bowing cycles (one bowing cycle = one down-bow + one up-bow) on each string (G, D, A, E), at a pulse of 4 beats per bow and 100 beats per minute. Measurements: An upper extremity model created using coordinate data from markers placed on the right acromion process, lateral epicondyle of the humerus and ulnar styloid was used to determine minimum and maximum joint angles, ranges of motion (ROM) and angular velocities at the shoulder and elbow of the bowing arm. Muscle activity in right anterior deltoid, biceps brachii and triceps brachii was assessed during maximal voluntary contractions (MVC) and during the playing task. Data were analysed for significant differences across the strings and between experience groups. Results: Elbow flexion/extension ROM was similar across strings for both groups. Shoulder flexion/extension ROM increaslarger for the experts. Angular velocity changes mirrored changes in ROM. Deltoid was the most active of the muscles assessed (20% MVC) and displayed a pattern of constant activation to maintain shoulder abduction. Biceps and triceps were less active (4 - 12% MVC) and showed a more periodic 'on and off pattern. Novices' muscle activity was higher in all cases. Experts' muscle activity showed a consistent pattern across strings, whereas the novices were more irregular. The agonist-antagonist roles of biceps and triceps during the bowing motion were clearly defined in the expert group, but not as apparent in the novice group. Conclusions: Bowing movement appears to be controlled by the shoulder rather than the elbow as shoulder ROM changed across strings while elbow ROM remained the same. Shoulder injuries are probably due to repetition as the muscle activity required for the movement is small. Experts require a smaller amount of muscle activity to perform the movement, possibly due to more efficient muscle activation patterns as a result of practice. This quantitative multidisciplinary approach to analysing violinists' movements can contribute to fuller understanding of both playing demands and injury mechanisms .

É́tude sur la cinétique des défauts structuraux dans le silicium amorphe.

Cette thèse présente à la fois des résultats de simulations numériques en plus de ré- sultats expérimentaux obtenus en laboratoire sur le rôle joué par les défauts de structure dans le silicium amorphe. Nos travaux de simulation numérique furent réalisés avec une nouvelle méthode de simulation Monte-Carlo cinétique pour décrire l’évolution tempo- relle de modèles de silicium amorphe endommagés sur plusieurs échelles de temps jus- qu’à une seconde à la température pièce. Ces simulations montrent que les lacunes dans le silicium amorphe sont instables et ne diffusent pas sans être détruites. Nous montrons également que l’évolution d’un modèle de silicium amorphe endommagé par une colli- sion ionique lors d’un recuit peut être divisée en deux phases : la première est dominée exclusivement par la diffusion et la création/destruction de défauts de liaison, alors que la deuxième voit les créations/destructions de liens remplacées par des échanges de liens entre atomes parfaitement coordonnés. Les défauts ont aussi un effet sur la viscosité du silicium amorphe. Afin d’approfondir cette question, nous avons mesuré la viscosité du silicium amorphe et du silicium amorphe hydrogéné sous l’effet d’un faisceau d’ions. Nous montrons que la variation de la viscosité dans les deux matériaux est différente : le silicium amorphe hydrogéné a une viscosité constante en fonction de la fluence des ions alors que le silicium amorphe pur a une viscosité qui augmente de façon linéaire. Pour de faibles fluences, la viscosité du silicium hydrogéné est plus grande que la viscosité sans hydrogène. La présence d’hydrogène diminue également l’amplitude de la variation logarithmique de la contrainte observée lors de la relaxation à la température de la pièce.

Estudo preliminar das mastites bovinas nos rebanhos leiteiros da região de Ilha Solteira

Estudaram-se os resultados obtidos no exame clínico da glândula mamária de 3.191 vacas mestiças e no "California Mastitis Test" (CMT) em 12.764 amostras de leite colhidas destes animais, relacionando-os com o estádio de lactação, o número de partos e a localização das afecções. O exame clínico revelou que 50 quartos apresentavam mastite e 231 mostravam-se atrofiados ou afuncionais. A aplicação do CMT indicou alterações de secreção em 1.741 quartos. A localização das afecções nos quartos foi estatisticamente semelhante, o mesmo ocorrendo com a incidência de mastite clínica com relação ao estádio de lactação. Quanto ao número de partos, não houve diferença significativa em relação à incidência de mastite clínica, porém a ocorrência de casos subclínicos foi estatisticamente superior em animais de uma a seis crias. O percentual de quartos afuncionais foi significativamente maior nos animais, acima de quatro partos.

Controlling the formation of ionic-liquid-based aqueous biphasic systems by changing the hydrogen-bonding ability of polyethylene glycol end groups

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis and properties of cyclic gomesin and analogues

Gomesin (Gm) was the first antimicrobial peptide (AMP) isolated from the hemocytes of a spider, the Brazilian mygalomorph Acanthoscurria gomesiana. We have been studying the properties of this interesting AMP, which also displays anticancer, antimalarial, anticryptococcal and anti-Leishmania activities. In the present study, the total syntheses of backbone-cyclized analogues of Gm (two disulfide bonds), [Cys(Acm)2,15]-Gm (one disulfide bond) and [Thr2,6,11,15,d-Pro9]-Gm (no disulfide bonds) were accomplished, and the impact of cyclization on their properties was examined. The consequence of simultaneous deletion of pGlu1 and Arg16-Glu-Arg18-NH2 on Gm antimicrobial activity and structure was also analyzed. The results obtained showed that the synthetic route that includes peptide backbone cyclization on resin was advantageous and that a combination of 20% DMSO/NMP, EDC/HOBt, 60?degrees C and conventional heating appears to be particularly suitable for backbone cyclization of bioactive peptides. The biological properties of the Gm analogues clearly revealed that the N-terminal amino acid pGlu1 and the amidated C-terminal tripeptide Arg16-Glu-Arg18-NH2 play a major role in the interaction of Gm with the target membranes. Moreover, backbone cyclization practically did not affect the stability of the peptides in human serum; it also did not affect or enhanced hemolytic activity, but induced selectivity and, in some cases, discrete enhancements of antimicrobial activity and salt tolerance. Because of its high therapeutic index, easy synthesis and lower cost, the [Thr2,6,11,15,d-Pro9]-Gm analogue remains the best active Gm-derived AMP developed so far; nevertheless, its elevated instability in human serum may limit its therapeutic potential. Copyright (c) 2012 European Peptide Society and John Wiley & Sons, Ltd.

Eficácia e segurança da vacina brasileira contra hepatite B em recém-nascidos

OBJETIVO: Analisar a efi cácia e segurança de vacina recombinante contra hepatite B em recém-nascidos. MÉTODOS: O estudo foi conduzido em hospital geral do município de Guarulhos, SP, entre 2002 e 2005. A vacina recombinante contra hepatite B do Instituto Butantan (VrHB-IB) foi analisada em dois ensaios clínicos. Em ambos os ensaios, os recém-nascidos foram alocados aleatoriamente ao grupo experimental ou controle (vacina de referência). Os recém-nascidos receberam três doses das vacinas, uma em até 24 h após o nascimento e as subseqüentes 30 e 180 dias após. No primeiro ensaio 538 recém-nascidos completaram o protocolo e no segundo ensaio, 486. Considerou-se critério de equivalência a diferença na soroproteção inferior a 5%. RESULTADOS: A soroproteção no primeiro ensaio (anti HBs ≥ 10mUI/ml) foi de 92,5% (247/267) no grupo experimental, comparada a 98,5% (267/271) no grupo controle (p = 0,001). Com este resultado, a VrHB-IB não atingiu o critério de equivalência estabelecido. Após o aumento da concentração de antígeno na vacina para 25μg, a soroproteção no segundo ensaio foi de 100% no grupo experimental e 99,2% no grupo controle. Nenhum evento adverso grave foi registrado. CONCLUSÕES: A vacina VrHB-IB modifi cada foi considerada equivalente à vacina de referência e seu uso recomendado à vacinação de recém-nascidos.

Interacting quantum-dissipative tunnelling systems

Die Untersuchung von dissipativen Quantensystemen erm¨oglicht es, Quantenph¨anomene auch auf makroskopischen L¨angenskalen zu beobachten. Das in dieser Dissertation gew¨ahlte mikroskopische Modell erlaubt es, den bisher nur ph¨anomenologisch zug¨anglichen Effekt der Quantendissipation mathematisch und physikalisch herzuleiten und zu untersuchen. Bei dem betrachteten mikroskopischen Modell handelt es sich um eine 1-dimensionale Kette von harmonischen Freiheitsgraden, die sowohl untereinander als auch an r anharmonische Freiheitsgrade gekoppelt sind. Die F¨alle einer, respektive zwei anharmonischer Bindungen werden in dieser Arbeit explizit betrachtet. Hierf¨ur wird eine analytische Trennung der harmonischen von den anharmonischen Freiheitsgraden auf zwei verschiedenen Wegen durchgef¨uhrt. Das anharmonische Potential wird als symmetrisches Doppelmuldenpotential gew¨ahlt, welches mit Hilfe der Wick Rotation die Berechnung der ¨Uberg¨ange zwischen beiden Minima erlaubt. Das Eliminieren der harmonischen Freiheitsgrade erfolgt mit Hilfe des wohlbekannten Feynman-Vernon Pfadintegral-Formalismus [21]. In dieser Arbeit wird zuerst die Positionsabh¨angigkeit einer anharmonischen Bindung im Tunnelverhalten untersucht. F¨ur den Fall einer fernab von den R¨andern lokalisierten anharmonischen Bindung wird ein Ohmsches dissipatives Tunneln gefunden, was bei der Temperatur T = 0 zu einem Phasen¨ubergang in Abh¨angigkeit einer kritischen Kopplungskonstanten Ccrit f¨uhrt. Dieser Phasen¨ubergang wurde bereits in rein ph¨anomenologisches Modellen mit Ohmscher Dissipation durch das Abbilden des Systems auf das Ising-Modell [26] erkl¨art. Wenn die anharmonische Bindung jedoch an einem der R¨ander der makroskopisch grossen Kette liegt, tritt nach einer vom Abstand der beiden anharmonischen Bindungen abh¨angigen Zeit tD ein ¨Ubergang von Ohmscher zu super- Ohmscher Dissipation auf, welche im Kern KM(τ ) klar sichtbar ist. F¨ur zwei anharmonische Bindungen spielt deren indirekteWechselwirkung eine entscheidende Rolle. Es wird gezeigt, dass der Abstand D beider Bindungen und die Wahl des Anfangs- und Endzustandes die Dissipation bestimmt. Unter der Annahme, dass beide anharmonischen Bindung gleichzeitig tunneln, wird eine Tunnelwahrscheinlichkeit p(t) analog zu [14], jedoch f¨ur zwei anharmonische Bindungen, berechnet. Als Resultat erhalten wir entweder Ohmsche Dissipation f¨ur den Fall, dass beide anharmonischen Bindungen ihre Gesamtl¨ange ¨andern, oder super-Ohmsche Dissipation, wenn beide anharmonischen Bindungen durch das Tunneln ihre Gesamtl¨ange nicht ¨andern.

Distance education in transition

In his most recent publication, Against the Tide: Critics of Digitalisation, Otto Peters brings together some of the most formidable and critical voices and compelling perspectives on the potential hazards of digitalization. The viewpoints presented range from personal, anthropological, and pedagogical to more scientific and technical, and arise from multiple disciplines. Peters has long been a respected scholar in the field of distance education, and while Peters’ earlier work has advocated the affordances of digitalization, this latest book is an abrupt shift to the darker side of digitalization. The assembly of critics Peters has gathered come from around the world and different walks of life: journalists, educators, scientists, philosophers, lawyers, mathematicians, and computer scientists, to name a few. Their one shared bond is a deep-seated belief that digitalization will have a profound and lasting impact on humankind – and not only in positive ways. ...

Against the Tide

In his most recent publication, Against the Tide: Critics of Digitalisation, Otto Peters brings together some of the most formidable and critical voices and compelling perspectives on the potential hazards of digitalization. The viewpoints presented range from personal, anthropological, and pedagogical to more scientific and technical, and arise from multiple disciplines. Peters has long been a respected scholar in the field of distance education, and while Peters’ earlier work has advocated the affordances of digitalization, this latest book is an abrupt shift to the darker side of digitalization. The assembly of critics Peters has gathered come from around the world and different walks of life: journalists, educators, scientists, philosophers, lawyers, mathematicians, and computer scientists, to name a few. Their one shared bond is a deep-seated belief that digitalization will have a profound and lasting impact on humankind – and not only in positive ways. ...

Hypofibrinogenemia and liver disease: a new case of Aguadilla fibrinogen and review of the literature.

INTRODUCTION Fibrinogen storage disease (FSD) is characterized by hypofibrinogenemia and hepatic inclusions due to impaired release of mutant fibrinogen which accumulates and aggregates in the hepatocellular endoplasmic reticulum. Liver disease is variable. AIM We studied a new Swiss family with fibrinogen Aguadilla. In order to understand the molecular peculiarity of FSD mutations, fibrinogen Aguadilla and the three other causative mutations, all located in the γD domain, were modelled. METHOD The proband is a Swiss girl aged 4 investigated because of fatigue and elevated liver enzymes. Protein structure models were prepared using the Swiss-PdbViewer and POV-Ray software. RESULTS The proband was found to be heterozygous for fibrinogen Aguadilla: FGG Arg375Trp. Familial screening revealed that her mother and maternal grandmother were also affected and, in addition, respectively heterozygous and homozygous for the hereditary haemochromatosis mutation HFE C282Y. Models of backbone and side-chain interactions for fibrinogen Aguadilla in a 10-angstrom region revealed the loss of five H-bonds and the gain of one H-bond between structurally important amino acids. The structure predicted for fibrinogen Angers showed a novel helical structure in place of hole 'a' on the outer edge of γD likely to have a negative impact on fibrinogen assembly and secretion. CONCLUSION The mechanism by which FSD mutations generate hepatic intracellular inclusions is still not clearly established although the promotion of aberrant intermolecular strand insertions is emerging as a likely cause. Reporting new cases is essential in the light of novel opportunities of treatment offered by increasing knowledge of the degradation pathway and autophagy.