The morality of problem selection in proteomics

The emerging power of new technologies in proteomics and the biological sciences to alter the human condition demands that scientists hold a new perspective on the social responsibilities of their research. Ethical theory can help scientists recognize not only those research projects that are harmful, but also those research paths that can create the greatest improvements in human health on a global scale. Whereas individual choices are important for the direction of scientific research, these choices may have limited social effects if they are not coordinated with larger institutional and inter-institutional structures. The perspective presented here calls for the Human Proteome Organization to recognize the ten most ethically significant proteomes to be characterized, with the hopes of rallying support and directing the research efforts of scientists in the proteomics community toward these goals.     

Classical detection theory and the cryo-EM particle selection problem

Particle selection is an essential but tedious step in the determination of macromolecular structures by single particle reconstruction. This paper presents an automatic, multi-reference particle detection scheme that is based on the classical matched filter principle. It makes use of a pre-whitening filter to standardize the noise, a reduced representation of the references by means of principal component analysis, and a statistic for distinguishing particles from image artifacts. Standardizing the noise allows the noise-induced false-positive frequency to be estimated, and also allows the distribution of the discrimination statistic to be calculated a priori. The method is demonstrated with an annotated dataset of cryo-EM images.     

The ties problem resulting from counting-based error estimators and its impact on gene selection algorithms

MOTIVATION: Feature selection approaches, such as filter and wrapper, have been applied to address the gene selection problem in the literature of microarray data analysis. In wrapper methods, the classification error is usually used as the evaluation criterion of feature subsets. Due to the nature of high dimensionality and small sample size of microarray data, however, counting-based error estimation may not necessarily be an ideal criterion for gene selection problem. RESULTS: Our study reveals that evaluating genes in terms of counting-based error estimators such as resubstitution error, leave-one-out error, cross-validation error and bootstrap error may encounter severe ties problem, i.e. two or more gene subsets score equally, and this in turn results in uncertainty in gene selection. Our analysis finds that the ties problem is caused by the discrete nature of counting-based error estimators and could be avoided by using continuous evaluation criteria instead. Experiment results show that continuous evaluation criteria such as generalised the absolute value of w2 measure for support vector machines and modified Relief's measure for k-nearest neighbors produce improved gene selection compared with counting-based error estimators. AVAILABILITY: The companion website is at http://www.ntu.edu.sg/home5/pg02776030/wrappers/ The website contains (1) the source code of all the gene selection algorithms and (2) the complete set of tables and figures of experiments.     

Dependence of release variables in the shot put

When the shot is released above a horizontal plane, range from this point depends on release height, speed and angle. Measured distance is the sum of this range and horizontal distance of the release point from the throwing circle edge. Optimal release conditions can be calculated only if the dependence of release velocity on other variables, due to thrower limitations, is known. Experiments on two shot-putters investigated the hypothesis that there are constraint relationships among these four release parameters. A variable scaling scheme, using measurement of impact point and the known magnitude of g, corrected 2D data from one camera for out-of-plane motion and yielded accurate estimates of release parameters. Multivariate regression analyses determined approximate constraint surfaces limiting performance. Achievable release speed decreases with increasing release angle at about 1.7(m/s)/rad and decreases with increasing release height at about 0.8(m/s)/m, with only small differences in sensitivities between the throwers. Horizontal release distance also decreases with increasing release angle at about 1.7m/rad and increases with increasing release height at about 1.3m/m, again with only small differences between the two throwers. Optimal release conditions producing maximum range for a particular athlete can be determined using similar constraints for that athlete.     

The cost of energy and cardiovascular expenditure in basketball players during a game

Energy expenditure was evaluated for 6 Basket players while exercising on a cyclergometer. Oxygen consumption (VO2), pulmonary ventilation (VE), heart rate (HR), respiratory quotient (QR) and other parameters were estimated at various levels of load (25 Watt each step of 3 minutes duration), till to submaximal load of 175 Watt. The same subjects participate to a regular Basket game and their heart rate was continuously stored on a tape recorder (Holter). Arterial blood pressure was also taken whenever possible (timeout, etc). From the laboratory and field data, estimates were made for the oxygen consumption together with energy cost of the game. This can be assume a net value of 0.1339 Kcal X Kg-1 X min-1.     

The effects of resistance training on explosive strength indicators in adolescent basketball players

ABSTRACT: Santos, EJAM and Janeira, MAAS. The effects of resistance training on explosive strength indicators in adolescent basketball players. J Strength Cond Res 26(10): 2641-2647, 2012-The purpose of this study was to assess the effects of a lower- and upper-body 10-week in-season resistance training program on explosive strength development in young basketball players. Twenty-five adolescent male athletes, aged 14-15 years old, were randomly assigned to an experimental group (EG; n = 15) and a control group (CG; n = 10). The subjects were assessed at baseline and after training for squat jump (SJ), countermovement jump (CMJ), Abalakov test, drop jump, and seated medicine ball throw (MBT). The EG showed significant increases (p < 0.05) in all the variable scores. Conversely, the CG significantly decreased (p < 0.05) in SJ, CMJ, and Abalakov test scores and significantly increased in the results of MBT test (p < 0.05). The groups were similar on pretest, but significant differences (p < 0.05) occurred on posttest in all the variables. The results of this study show that a 10-week in-season resistance training program with moderate volume and intensity loads increased vertical jump and MBT performance in adolescent male basketball players. Coaches should know that such a short resistance training program specifically designed for young basketball players induce increased explosivity levels, which are essential to a better basketball performance, with no extra overload on adolescents' skeletal muscle development.     

Detecting positive selection within genomes: the problem of biased gene conversion

The identification of loci influenced by positive selection is a major goal of evolutionary genetics. A popular approach is to perform scans of alignments on a genome-wide scale in order to find regions evolving at accelerated rates on a particular branch of a phylogenetic tree. However, positive selection is not the only process that can lead to accelerated evolution. Notably, GC-biased gene conversion (gBGC) is a recombination-associated process that results in the biased fixation of G and C nucleotides. This process can potentially generate bursts of nucleotide substitutions within hotspots of meiotic recombination. Here, we analyse the results of a scan for positive selection on genes on branches across the primate phylogeny. We show that genes identified as targets of positive selection have a significant tendency to exhibit the genomic signature of gBGC. Using a maximum-likelihood framework, we estimate that more than 20 per cent of cases of significantly elevated non-synonymous to synonymous substitution rates ratio (d_N/d_S), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high d_N/d_S (more than 2). Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection.     

The construct and longitudinal validity of the basketball exercise simulation test

The purpose of this study was to assess the validity of the recently developed Basketball Exercise Simulation Test (BEST). Ten semiprofessional (age, 22.7 ± 6.1 years; height, 189.6 ± 9.5 cm; weight, 86.5 ± 18.7 kg; % body fat, 14.7 ± 3.5%) and 10 recreational (age, 26.6 ± 4.0 years; height, 185.9 ± 7.9 cm; weight, 92.6 ± 8.4 kg; % body fat, 23.8 ± 6.3%) male basketball players volunteered for the study. The participants completed a Yo-Yo Intermittent Recovery Test (Yo-Yo IRT) and BEST trial midway through the playing season. Eight participants (semiprofessional, n = 4; recreational, n = 4) completed an additional Yo-Yo IRT and BEST trial at the end of the playing season. Performance measures from the BEST included sprint decrement (%), mean sprint and circuit time (seconds), and total distance covered (m). Construct validity was calculated using Student's unpaired t-tests to identify the differences in Yo-Yo IRT and BEST performances between playing levels. Longitudinal validity was determined based on the relationship between changes (%) in Yo-Yo IRT1 and BEST performances across the season. Semiprofessional players performed significantly (p < 0.01) better in the Yo-Yo IRT (1,283 ± 62 vs. 636 ± 297 m) and BEST (mean sprint time: 1.45 ± 0.01 vs. 1.65 ± 0.03 seconds; mean circuit time: 18.98 ± 1.79 vs. 22.72 ± 2.01 seconds; sprint decrement: 8.54 ± 0.15 vs. 15.38 ± 0.27%) compared with recreational players. For the group as a whole, a strong relationship was evident between the changes in BEST sprint decrement and changes in Yo-Yo IRT performance (R = -0.815, p = 0.014) across the season. In conclusion, the BEST displayed both discriminative and longitudinal validities and provides a novel match-specific fitness test for basketball players.