The Physicist's Guide to the Orchestra

An experimental study of strings, woodwinds (organ pipe, flute, clarinet, saxophone and recorder), and the voice was undertaken to illustrate the basic principles of sound production in music instruments. The setup used is simple and consists of common laboratory equipment. Although the canonical examples (standing wave on a string, in an open and closed pipe) are easily reproduced, they fail to explain the majority of the measurements. The reasons for these deviations are outlined and discussed.Comment: 11 pages, 10 figures (jpg files). Submitted to European Journal of Physic

Fair Mixing: the Case of Dichotomous Preferences

We consider a setting in which agents vote to choose a fair mixture of public outcomes. The agents have dichotomous preferences: each outcome is liked or disliked by an agent. We discuss three outstanding voting rules. The Conditional Utilitarian rule, a variant of the random dictator, is strategyproof and guarantees to any group of like-minded agents an influence proportional to its size. It is easier to compute and more efficient than the familiar Random Priority rule. Its worst case (resp. average) inefficiency is provably (resp. in numerical experiments) low if the number of agents is low. The efficient Egalitarian rule protects individual agents but not coalitions. It is excludable strategyproof: I do not want to lie if I cannot consume outcomes I claim to dislike. The efficient Nash Max Product rule offers the strongest welfare guarantees to coalitions, who can force any outcome with a probability proportional to their size. But it even fails the excludable form of strategyproofness

Intonation and Compensation of Fretted String Instruments

In this paper we present mathematical and physical models to be used in the analysis of the problem of intonation of musical instruments such as guitars, mandolins and the like, i.e., we study how to improve the tuning on these instruments. This analysis begins by designing the placement of frets on the fingerboard according to mathematical rules and the assumption of an ideal string, but becomes more complicated when one includes the effects of deformation of the string and inharmonicity due to other string characteristics. As a consequence of these factors, perfect intonation of all the notes on the instrument can never be achieved, but complex compensation procedures are introduced and studied to minimize the problem. To test the validity of these compensation procedures, we have performed extensive measurements using standard monochord sonometers and other basic acoustical devices, confirming the correctness of our theoretical models. In particular, these experimental activities can be easily integrated into standard acoustics courses and labs, and can become a more advanced version of basic experiments with monochords and sonometers.Comment: Improved version, with minor changes. 25 pages, including 6 figures and 2 tables. Accepted for publication in the American Journal of Physics (AJP

Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution

Models of protein evolution currently come in two flavors: generalist and specialist. Generalist models (e.g. PAM, JTT, WAG) adopt a one-size-fits-all approach, where a single model is estimated from a number of different protein alignments. Specialist models (e.g. mtREV, rtREV, HIVbetween) can be estimated when a large quantity of data are available for a single organism or gene, and are intended for use on that organism or gene only. Unsurprisingly, specialist models outperform generalist models, but in most instances there simply are not enough data available to estimate them. We propose a method for estimating alignment-specific models of protein evolution in which the complexity of the model is adapted to suit the richness of the data. Our method uses non-negative matrix factorization (NNMF) to learn a set of basis matrices from a general dataset containing a large number of alignments of different proteins, thus capturing the dimensions of important variation. It then learns a set of weights that are specific to the organism or gene of interest and for which only a smaller dataset is available. Thus the alignment-specific model is obtained as a weighted sum of the basis matrices. Having been constrained to vary along only as many dimensions as the data justify, the model has far fewer parameters than would be required to estimate a specialist model. We show that our NNMF procedure produces models that outperform existing methods on all but one of 50 test alignments. The basis matrices we obtain confirm the expectation that amino acid properties tend to be conserved, and allow us to quantify, on specific alignments, how the strength of conservation varies across different properties. We also apply our new models to phylogeny inference and show that the resulting phylogenies are different from, and have improved likelihood over, those inferred under standard models

Caracterização da qualidade acústica de salas de aula para prática e ensino musical

Resumo O músico necessita perceber adequadamente o som nos recintos destinados ao estudo e prática musical, o que é possível quando estes locais estão acusticamente preparados e permitem o desenvolvimento e aprimoramento da percepção sonora musical. Neste trabalho três salas de estudo e três salas de aula coletiva, destinadas ao ensino e prática de Música de uma universidade, foram caracterizadas acusticamente através da opinião dos músicos usuários e de medições da sua resposta impulsiva. As salas descritas pelos músicos como secas tiveram, nas bandas de frequência de oitava de 500 a 1000 Hz, um Tempo de Reverberação em torno de 0,3 segundos, entre 14 e 22 dB de Clareza e entre 88% a 96% de Definição. As salas caracterizadas como reverberantes tiveram um tempo ao redor de 1,5 segundos, Clareza de 1 dB e Definição de 40%. A opinião dos músicos permitiu compreender as preferências da qualidade acústica das salas e as informações fornecidas pelos músicos se mostraram coerentes com os dados das medições

Lipid metabolism in myocardial ischaemia: Correlation between tissue and mitochondrial free fatty acid (FFA) contents and mitochondrial oxidative phosphorylation

[No abstract available

Mitochondrial oxidative phosphorylation in low-flow hypoxia: Role of free fatty acids

The mechanism of mitochondrial damage was investigated in hypoxic hearts, perfused at low pressure without exogenous substrate, as a model of myocardial ischaemia. Mitochondrial and tissue free fatty acid (FFA) contents were determined in control hearts (perfused aerobically at a higher pressure, without exogenous substrate), and in the hypoxic hearts; the functional capacities of mitochondria isolated from the two types of tissue were also compared. Mitochondrial FFA contents were found to be evaluated, relative to the controls, after 20 min of low-flow hypoxic perfusion. However, mitochondrial FFA contents were not different in control and hypoxic hearts after 70 min of perfusion. Low-flow hypoxic perfusion for 70 min caused a significant elevation of tissue C16:0, C18:1 FFA fractions, while total FFA and triglyceride contents were also increased. Accumulation of FFA in whole tissue was accompanied by a depression in mitochondrial function. Thus, after 20 min, both tissue FFA contents and ADP/O and RCI values of mitochondria isolated from control and hypoxic hearts were not different, whereas after 70 min, tissue FFA levels were significantly elevated in hypoxic hearts, with an equally significant depression in the function of isolated mitochondria.Articl

Mouse mammary tumor virus proviral sequences congenital to c3h/sm mice are differentially hypomethylated in chemically induced, virus-induced, and spontaneous mammary tumors.

C3H/Sm mice have lost the exogenous milk-borne mouse mammary tumor virus (MMTV) characteristic of the C3H strain and have a very low (1.5%) incidence of spontaneous mammary tumors, yet they are highly susceptible to mammary carcinogenesis by either chemical carcinogens or infection with the milk-borne virus. We have analyzed the MMTV proviral DNA content of normal tissues and of spontaneous, virus-induced, and chemically induced mammary tumors by restriction endonuclease digestion and Southern blot analysis. Although the results clearly showed additional MMTV sequences in the virus-induced tumor which are not present in normal liver DNA, none of the spontaneous or chemically induced tumors could be shown to contain either newly acquired exogenous or amplified endogenous MMTV sequences. Interestingly, mammary tumors arising in C3H/Sm mice treated simultaneously with infectious MMTV (C3H) and dimethylbenz[a]anthracene (DMBA) possessed new exogenous MMTV DNA even though no quantitative change in tumor production was observed when these mice were compared with C3H/Sm mice treated with DMBA alone (Smith et al., Int. J. Cancer 26:373-379, 1980). Our data indicate that the endogenous MMTV proviral units are extensively methylated in normal tissues, such as livers and normal nonlactating mammary glands. In the absence of MMTV (C3H), we found that in the rare, spontaneously occurring C3H/Sm mammary tumors, certain endogenous MMTV sequences were specifically hypomethylated. Hypomethylation of endogenous MMTV sequences was also noted in the chemically induced mammary tumors, even though radioimmune competition assays for MMTV gp52 and p28 are negative (Smith et al., Int. J. Cancer 27:81-86, 1981). Our results support the conclusion that amplification of endogenous MMTV sequences is not intrinsic to C3H/Sm mouse mammary tumors arising spontaneously or after induction by chemicals. On the other hand, integration of exogenous MMTV DNA into the genome was a constant feature of mammary tumors developing in MMTV (C3H)-infected C3H/Sm mice, even when DMBA was used as the carcinogen. Hypomethylation of some endogenous MMTV sequences is characteristic of C3H/Sm mammary tumors, whether spontaneous or induced by chemicals, which suggests that these sequences are located in actively transcribing regions of the tumor cell genome