Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example

Alzheimer`s disease is an ultimately fatal neurodegenerative disease, and BACE-1 has become an attractive validated target for its therapy, with more than a hundred crystal structures deposited in the PDB. In the present study, we present a new methodology that integrates ligand-based methods with structural information derived from the receptor. 128 BACE-1 inhibitors recently disclosed by GlaxoSmithKline R&D were selected specifically because the crystal structures of 9 of these compounds complexed to BACE-1, as well as five closely related analogs, have been made available. A new fragment-guided approach was designed to incorporate this wealth of structural information into a CoMFA study, and the methodology was systematically compared to other popular approaches, such as docking, for generating a molecular alignment. The influence of the partial charges calculation method was also analyzed. Several consistent and predictive models are reported, including one with r (2) = 0.88, q (2) = 0.69 and r (pred) (2) = 0.72. The models obtained with the new methodology performed consistently better than those obtained by other methodologies, particularly in terms of external predictive power. The visual analyses of the contour maps in the context of the enzyme drew attention to a number of possible opportunities for the development of analogs with improved potency. These results suggest that 3D-QSAR studies may benefit from the additional structural information added by the presented methodology.

Stability of periodic travelling shallow-water waves determined by Newton`s equation

We study the existence and stability of periodic travelling-wave solutions for generalized Benjamin-Bona-Mahony and Camassa-Holm equations. To prove orbital stability, we use the abstract results of Grillakis-Shatah-Strauss and the Floquet theory for periodic eigenvalue problems.

Experiencing Science in Action: The Use of Exhibition Techniques in Guided Tours to a Scientific Laboratory

The current paper presents a study conducted at CERN, Switzerland, to investigate visitors' and tour guides' use and appreciation of existing panels at visit itinerary points. The results were used to develop a set of recommendations for constructing optimal panels to assist the guides' explanation.

Nonstationary feature extraction techniques for automatic classification of impact acoustic signals

Condition monitoring of wooden railway sleepers applications are generallycarried out by visual inspection and if necessary some impact acoustic examination iscarried out intuitively by skilled personnel. In this work, a pattern recognition solutionhas been proposed to automate the process for the achievement of robust results. Thestudy presents a comparison of several pattern recognition techniques together withvarious nonstationary feature extraction techniques for classification of impactacoustic emissions. Pattern classifiers such as multilayer perceptron, learning cectorquantization and gaussian mixture models, are combined with nonstationary featureextraction techniques such as Short Time Fourier Transform, Continuous WaveletTransform, Discrete Wavelet Transform and Wigner-Ville Distribution. Due to thepresence of several different feature extraction and classification technqies, datafusion has been investigated. Data fusion in the current case has mainly beeninvestigated on two levels, feature level and classifier level respectively. Fusion at thefeature level demonstrated best results with an overall accuracy of 82% whencompared to the human operator.

Acoustic Design in Urban Development : analysis of urban soundscapes and acoustic ecology research in New York City

The world is urbanizing rapidly with more than half of the global population now living in cities. Improving urban environments for the well-being of the increasing number of urban citizens is becoming one of the most important challenges of the 21st century. Even though it is common that city planners have visions of a ’good urban milieu’, those visions are concerning visual aesthetics or practical matters. The qualitative perspective of sound, such as sonic diversity and acoustic ecology are neglected aspects in architectural design. Urban planners and politicians are therefore largely unaware of the importance of sounds for the intrinsic quality of a place. Whenever environmental acoustics is on the agenda, the topic is noise abatement or noise legislation – a quantitative attenuation of sounds. Some architects may involve acoustical aspects in their work but sound design or acoustic design has yet to develop to a distinct discipline and be incorporated in urban planning.My aim was to investigate to what extent the urban soundscape is likely to improve if modern architectural techniques merge with principles of acoustics. This is an important, yet unexplored, research area. My study explores and analyses the acoustical aspects in urban development and includes interviews with practitioners in the field of urban acoustics, situated in New York City. My conclusion is that to achieve a better understanding of the human living conditions in mega-cities, there is a need to include sonic components into the holistic sense of urban development.

Acoustic Variability in the Production of English Vowels by Native and Non-Native Speakers

The features of non-native speech which distinguish it from native speech are often difficult to pin down. It is possible to be a native speaker of any of a vast number of varieties of English. These varieties each have their phonetic characteristics which allow them to be identified by speakers of the varieties in question and by others. The phonetic differences between the accents represented by these varieties are very great. It is impossible to indicate any particular configuration of vowels in the acoustic vowel space or set of consonant articulations which all native-speaker varieties of English have in common and which non-native speakers do not share. This study considers the vowel quality in a single word by native and non-native speakers.

Reflection of matter waves in potential structures

In this paper the behavior of matter waves in suddenly terminated potential structures is investigated numerically. It is shown that there is no difference between a fully quantum mechanical treatment and a semiclassical one with regards to energy redistribution. For the quantum case it is demonstrated that there can be substantial reflection at the termination. The neglect of backscattering by the semiclassical method brings about major differences in the case of low kinetic energies. A simple phenomenological model is shown to partially explain the observed backscattering using dynamics of reduced dimensionality.

Single-mode acceleration of matter waves in circular waveguides

Ultracold gases in ring geometries hold promise for significant improvements of gyroscopic sensitivity. Recent experiments have realized atomic and molecular storage rings with radii in the centimeter range, sizes whose practical use in inertial sensors requires velocities significantly in excess of typical recoil velocities. We use a combination of analytical and numerical techniques to study the coherent acceleration of matter waves in circular waveguides, with particular emphasis on its impact on single-mode propagation. In the simplest case we find that single-mode propagation is best maintained by the application of time-dependent acceleration force with the temporal profile of a Blackmann pulse. We also assess the impact of classical noise on the acceleration process.

New challenges for international economic law teaching and research in México: Mexico’s outstanding waves of reforms

This position paper argues that at this time of Mexico’s ongoing big transformation, legal educators and researchers in Mexico need to pay greater attention to international economic law, and that a renewal and perhaps some re-orientation of the approach to teaching international economic law, could provide significant contributions to and shape and support both the objectives and outcomes of reform in Mexico. International Economic Law courses and research can be made more useful, not only for students themselves, but also for their contribution towards the role that academics, lawyers, and other epistemic communities need to play in the political, economic and social evolution that is accelerating in Mexico.

Characterization of heat waves affecting mortality rates of broilers between 29 days and market age

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

Efficacy of linear and convex transducers for ultrasound-guided transvaginal follicle aspiration

A new device was developed to hold linear transducers for transvaginal follicle aspiration. Efficacy of follicle aspiration was compared using a linear 6 MHz and a convex 5 MHz transducer. Fifty-five cows were submitted to follicle aspiration at random days of the estrous cycle. Aspirations were conducted with linear (n = 28) and convex (n = 38) transducers with 18 G needles at a negative pressure corresponding to 13 ml H2O/min. A greater number of follicles were aspirated using convex than to linear probe (12.4 versus 7.8, respectively, P < 0.05). Mean number of oocytes and recovery rates were similar for convex (5.4 and 48.6%) and linear (4.6 and 59.3%) transducers. Limited space between the linear transducer and needle guide restricted access to some portions of the ovary, reducing the number of follicles aspirated using a linear transducer. The newly developed adaptor allowed greater stability, holding the ovaries firmly against the linear transducer. This diminished mobility permitted a similar number of oocytes to be recovered with both transducers. In conclusion, this new adaptor provided a low cost alternative for routine follicle aspiration and oocyte recovery in cattle. (C) 2002 Elsevier B.V. All rights reserved.

Relationship between follicle size and ultrasound-guided transvaginal oocyte recovery

We evaluated the relationship between follicle size and oocyte recovery (OR) using ultrasound-guided follicle aspiration. Thirty Holstein cows were subjected to OR without gonadotrophic therapy. Oocytes were recovered two to four times from each cow in a total of 67 aspiration sessions, Ovarian follicles with diameters less than or equal to4 mm and >4 mm were aspirated in separated groups. Recovered oocytes from each group were kept separate and submitted to in vitro maturation, fertilization, and culture to the blastocyst stage. A total of 430 follicles were aspirated, of which 154 (35.8%) were from follicles >4 mm and 276 (64.2%) were from follicles less than or equal to4 mm. Seventy-seven oocytes (50%) were recovered from follicles >4 mm and 200 (72.2%) were from follicles less than or equal to4 mm. Nineteen blastocysts were obtained from follicles >4 mm, whereas 45 blastocysts were obtained from follicles less than or equal to4 mm. Recovery rate was greater (P < 0.01) in follicles less than or equal to4 mm, Oocyte quality, cleavage rate and blastocyst development did not differ between different follicle sizes. Routine aspiration of small follicles (less than or equal to4 mm) could increase the number of oocytes available for in vitro development. (C) 2001 Elsevier B.V. B.V. All rights reserved.