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"Barry! Barry! Barry!"
Giants 2, Cardinals 0
WP: Zito (3-0)
Save: Wilson (4)
Record: 10-7, 2nd in NL West, 1 game behind San Diego
For the first time in three years, the chant "Barry! Barry! Barry!" could be heard resonating throughout AT&T Park.
For the first time ever, the chant was for Barry Zito.
Zito continued his stellar April with the type of outing Giants fans have been dreaming about when he signed the largest contract in franchise history more than three years ago.
Zito pitched eight strong shutout innings, striking out 10 while walking three and giving up three hits in a 110-pitch outing.
And the Giants rewarded their veteran left-hander by plating two runs in the bottom of the ninth to beat the St. Louis Cardinals 2-0 on Saturday. It was the first series loss of the season for St. Louis.
Brian Wilson came in to pitch the ninth and finish off the Cardinals for his fourth save. It was the second time this season Wilson had saved a shutout that Zito had started.
So, again, the pitching was great. The offensive was good enough. But considering the Giants were facing the Cardinals' Adam Wainwright, the Giants' woes could be as much Wainwright's doing as the Giants' doing.
The Giants were again stung by the double-play ball, hitting into two more, giving them a major-league leading 24 for the season. After one double play, Giants announcer Duane Kuiper said "and after a Giants double play, we go to Amy G." referring to Giants on-field reporter Amy Gutierrez. Amy, surprised, just said "Awww, nooo." If Amy were quicker, she would have replied "What?!? Well, if that the case, I should get a raise!"
In the bottom of the eighth, Nate Schierholtz led off the inning with the hardest hit ball of the night off Wainwright, a shot down the right-field line for a double. Andres Torres was called to pinch-hit for Zito and bunt Schierholtz to third. But after failing to hit the ball fair in his first two attempts, Torres swung away and smacked the ball up the middle to center to score Schierholtz.
The Giants added a second run with a little help from the umps. After Eugenio Velez bunted Torres to second, Edgar Renteria hit a sharp grounder to short. Torres got caught to far off the bag and appeared to hung out diving back into second. But the umpire ruled him safe even though the throw clearly beat Torres. However, replays showed that Felipe Lopez's tag on Torres was high up his arm, allowing Torres to slip under and reach the bag safely.
Pablo Sandoval followed with a slow chopper to third, which the umpire ruled that Sandoval beat out at first. Replays show that he didn't, even though it was very close. That allowed Aubrey Huff to score Torres with a fly to left.

subset: commoncrawl


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Actress Sues Production Company After Disfiguring On-Set Injury
20-year-old actress Taylor Hickson is an up and coming actress who has appeared in Deadpool and Everything, Everything, but recently she was injured on the set of her latest film and she's now suing the company making it.
Taylor was filming the indie horror flick Ghostland when the director asked her to pound really hard on a glass pane of a door in an emotionally charged scene. She expressed concern but the director assured her it was safe.
The glass wound up shattering and her head and upper body went through the door and into shards that cut her so badly she needed 70 stitches to close her wounds. She was left with a permanent scar on her face.
She alleges that the injury caused her to lose income since she couldn't act while she was healing, and, according to the lawsuit, it's also caused her "mass amounts of insecurity." She said she is "conflicted, confused, hurt, angry, and sad that this was my last day on set and no precautions were taken."
Thankfully laser treatments and silicone treatments have helped Taylor's face.
Meanwhile, the artwork the film chose for their posters is interesting in the wake of Taylor's injury:
Ghostland has a premiere party next week in Paris but Hickson won't be there. She told Deadline, "I never worked so hard on a production in my life, and now it's a bittersweet way to end this piece of art that we worked so hard on."
Photo Credit: Mars Films


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Quickfind Code: 028471
192 in stock
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Eastman T185 MX is a 15" Double Cutaway Double cutaway, semi-hollow construction with Maple solid carved tops and Mahogany carved solid backs, solid 2" x 3" mahogany tone block the extends only under the stop tailpiece and fixed bridge to allow GREATER ACOUSTIC TONE & CLARITY to chord voicings than typical semi hollow models. This model features all Nickel Hardware, double Seymour Duncan Classic 57 humbucking pickups with 2 tone and 2 volume controls, nickel 3-way selector switch, stop tailpiece & fixed tunable bridge, and wooden maple binding on the body neck and headstock. 1 ¾" nut and 2 1/8" at 12th fret Very light weight a total weight of 5 pounds 9 ounces – the metal hardware alone weight 2 pounds and 10 ounces Suggested retail $2150. Please call for GnJ discounted price.
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We carry a huge selection of luthier carved archtops including and a large selection of Eastmans so that you can come in and pick out the one that is exactly right for you. We can also match archtops to your phone descriptions to help get you that perfect archtop if you cannot come to the shop. All purchases are on approval and fully returnable. Your full satisfaction is our goal! Call 908-403-3426 to make an appointment to visit our new Showroom in Summit, NJ. We are only 30 minutes from Manhattan by car; 2 blocks from the Summit train station - 35 minutes from NYC on the midtown direct!
To order an instrument, first CALL or FAX to confirm that the instrument is still available. Within the US we accept money orders, cashier's checks, certified checks, Mastercard, or Visa Amex, and Discover. Outside the US, please send US dollars on a US bank or bank transfer. Payment must include the purchase price plus shipping and insurance charges. Layaway plan voids approval period. A 25% non-refundable deposit will hold any instrument for 30 days. No COD's are accepted.
The customer pays all shipping, insurance, and bank charges including all charges for returned merchandise. All insurance claims are the responsibility of the customer. The original packaging and box must be saved. Shipping will be via UPS or Federal Express unless other arrangements are made.
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Signatures of Star Birth
The glowing, clumpy streams of material shown in these NASA Hubble Space Telescope images are the signposts of star birth.
Ejected episodically by young stars like salvos from a cannon, the blobby material zips along at more than 440,000 miles (770,000 kilometers) an hour. Called Herbig-Haro or HH objects, these speedy outflows have a bumpy ride through space.
When fast-moving blobs "rear-end" slower gas, bow shocks (the blue features) arise as the material heats up. Bow shocks are glowing waves of matter similar to waves produced by the bow of a ship plowing through water. In HH 2, at lower right, several bow shocks (the compact blue and white features) can be seen where fast-moving clumps bunch up like cars in a traffic jam. In HH 34, at lower left, a grouping of merged bow shocks reveals regions that brighten and fade over time as the heated material cools, shown in red, where the shocks intersect.
In HH 47, at top, a long jet of material has burst out of a dark cloud of gas and dust that hides the newly forming star. The blue, fan-shaped region at left is the edge of a cavity illuminated by the fledgling star. A massive clump of jet material collides with upstream gas, creating the white bow-shaped shock wave at right.
These images are part of a series of time-lapse movies astronomers have made showing the outflows' motion over time. The movies were stitched together from images taken over a 14-year period by Hubble's Wide Field Planetary Camera 2. Hubble followed the jets over three epochs. Observations of HH 2 were made from 1994, 1997, and 2007; HH 34 from 1994, 1998, and 2007; and HH 47 from 1994, 1999, and 2008.
The outflows are roughly 1,350 light-years from Earth. HH 34 and HH 2 reside near the Orion Nebula, in the northern sky. HH 47 is located in the southern constellation Vela.


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- Research article
- Open Access
Bayesian semiparametric regression models to characterize molecular evolution
- Saheli Datta1Email author,
- Abel Rodriguez2 and
- Raquel Prado2
© Datta et al.; licensee BioMed Central Ltd. 2012
- Received: 15 December 2011
- Accepted: 11 October 2012
- Published: 30 October 2012
Statistical models and methods that associate changes in the physicochemical properties of amino acids with natural selection at the molecular level typically do not take into account the correlations between such properties. We propose a Bayesian hierarchical regression model with a generalization of the Dirichlet process prior on the distribution of the regression coefficients that describes the relationship between the changes in amino acid distances and natural selection in protein-coding DNA sequence alignments.
The Bayesian semiparametric approach is illustrated with simulated data and the abalone lysin sperm data. Our method identifies groups of properties which, for this particular dataset, have a similar effect on evolution. The model also provides nonparametric site-specific estimates for the strength of conservation of these properties.
The model described here is distinguished by its ability to handle a large number of amino acid properties simultaneously, while taking into account that such data can be correlated. The multi-level clustering ability of the model allows for appealing interpretations of the results in terms of properties that are roughly equivalent from the standpoint of molecular evolution.
- Nonsynonymous Substitution
- Dirichlet Process
- Ancestral Sequence
- Nonsynonymous Change
- Truncation Level
The structural and functional role of a codon in a gene determines its ability to freely change. For example, nonsynonymous (amino acid altering) substitutions may not be tolerated at certain codon sites due to strong negative selection, while at other sites some nonsynonymous substitutions may be allowed if they do not affect key physicochemical properties associated with protein function[1]. Thus, at such preferentially changing sites, more frequent substitutions occur between physicochemically similar amino acids (or codons which lead to those amino acids) than dissimilar ones[2–4]. Methods which use changes in physicochemical amino acid properties have thus been proposed in the study of evolution. For example,[5–7] use distances to calculate deviations from neutrality for a particular amino acid property. Alternative approaches model the evolution of protein coding sequences as continuous-time Markov chains with rate matrices that distinguish between property-altering and property-conserving mutations as in[8] and[9]. More recently,[10] proposed a Bayesian hierarchical regression model that compares the observed amino acid distances to the expected distances under neutrality for a given set of amino acid properties and incorporates mixture priors for variable selection. The hierarchical mixture priors enable the model in[10] to identify neutral, conserved and radically changing sites, while automatically adjusting for multiple comparisons and borrowing information across properties and sites.
A common feature of all the methods listed above is the implicit assumption that properties are independent from each other in terms of their effect on evolution. A review of the amino acid index database (available for example at http://www.genome.jp/dbget/aaindex.html), which lists more than 500 amino acid properties, shows that a large number of them are highly correlated. Although the correlations we observe in the data can be different from those computed from the raw amino acid scores due to the influence of factors such as codon bias, by ignoring these correlations we are also ignoring the fact that correlated properties may affect a particular site in similar ways. Hence, approaches that do not take into account the correlations in the rates of mutations on different codons do not make use of key information about the relative importance of different physicochemical properties on molecular evolution.
A natural way to account for correlations in the data is by considering a factor structure, see for example[11]. However, selecting the number and order of the factors can be a difficult task in this type of factor models. In addition, the particular structure of the model in[11] makes it difficult to incorporate the effect of the factors on regions that are very strongly conserved. This paper extends the Bayesian hierarchical regression model in[10] by placing a nonparametric prior on the distribution of the regression coefficients describing the effect of properties on molecular evolution. The prior is an extension of the well known Dirichlet process prior[12, 13] to model separately exchangeable arrays[14, 15]. As in[10], the main goal of the model described in this paper is to identify sites that are either strongly conserved or radically changing. In order to account for correlations across properties, our model clusters properties with similar effects on evolution, and within each such group, clusters sites with similar regression coefficients and nonparametrically estimates their distribution. In addition to accounting for correlations across properties, this structure allows us to dramatically reduce the number of parameters in the model and generate interpretable insights about molecular evolution at the codon level.
Although the clusters of properties can in principle be considered nuisance parameters that are of no direct interest, in practice posterior inference on the clustering structure can provide interesting insights about the molecular evolution process of a given gene. Indeed, as will become clear in the following sections, our approach incorporates the effect of amino acid usage bias. Hence, any significant differences between the cluster structure estimated from the observed protein-coding sequence alignment and the correlation structure derived from the raw distances between the properties in such cluster can be interpreted a signal of extreme amino acid usage bias in that particular region of the genome.
The rest of the paper is organized as follows. A brief review of DP mixture models along with the details of our model is provided in the Methods section. This section also includes a review of some of the currently available methods for characterizing molecular evolution that take into account changes amino acid properties. The model is then evaluated via simulation studies and illustrated through a real data example. The simulated and real data analyses, as well as comparisons between the proposed semiparametric regression approach and other methods, are presented in Results and discussion. Finally, the Conclusions section provides our concluding remarks.
Dirichlet process mixture models
The Dirichlet process (DP) was formally introduced by[12] as a prior probability model for random distributions G. A DP(ρ, G0) prior for G is characterized by two parameters, a positive scalar parameter ρ, and a parametric base distribution (or centering distribution) G0. ρ can be interpreted as the precision parameter, with larger values of ρ resulting in realizations of G that are closer to the base distribution G0.
where denotes a point mass at ϕ l . The locations ϕ l are i.i.d. draws from G0, while the corresponding weights w l are generated using the following "stick-breaking" mechanism. Let w1=v1and define for l=2,3,…, where {v l :l=1,2,…} are i.i.d. draws from a Beta(1, ρ) distribution. Defining the weights in this way ensures. Furthermore, the sequences {v l :l=1,2,…} and {ϕ l :l=1,2,…} are independent.
One advantage of DP mixture models over other approaches to clustering and classification is that they allow us to automatically estimate the number of components in the mixture. Indeed, from the Pólya urn representation of the process it should be clear that, although the number of potential mixture components is infinite, the model implicitly places a prior on the number of components that, for moderate values of ρ, favors the data being generated by an effective number of components K∗=maxi≤n{ξ i }<n.
The model
Our data consist of observed and expected amino acid distances derived from a DNA sequence alignment, a specific phylogeny, a stochastic model of sequence evolution, and a predetermined set of physicochemical amino acid properties. In the analyses presented here, we disregard uncertainty in the alignment/phylogeny/ancestral sequence level since our main focus is the development and implementation of models that allow us to make inferences on the latent effects that several amino acid properties may have on molecular evolution for a given phylogeny and an underlying model of sequence evolution. Extensions of these analyses that take into account these uncertainties are briefly described in Conclusions. For further discussion on this issue, see also[10].
In order to calculate the observed distances, we first infer the ancestral sequences under a specific substitution model and a given phylogeny. In our applications, we use PAML version 3.15[20] and the codon substitution model of[21], which accounts for the possibility of multiple substitutions at a given site. Nonsynonymous substitutions are then counted by comparing DNA sequences between two neighboring nodes in the phylogeny. The observed mean distance, denoted as yi,j for site i and property j, is obtained as the mean absolute difference in the property scores due to all nonsynonymous substitutions at site i. Only those sites with at least one nonsynonymous change from the ancestral level are retained for further analysis.
We consider a hierarchical regression model that relates xi,j to yi,jand allows us to compare the expected and observed distances at the codon level for several properties simultaneously with the following rationale. If a given site i is neutral with respect to property j, then yi,j≈xi,j. If property j is conserved at site i, then yi,j<<xi,j and finally, if property j is radically changing at site i, then yi,j>>xi,j.
where is the observed number of nonsynonymous changes at a particular site i and βi,j and are the regression coefficient and variance parameter associated with site i and property j. The mixture model accounts for the fact that some of thes can be equal to zero as some nonsynonymous changes do not change the value of the property being measured (e.g., Aspargine, Aspartic acid, Glutamine, Glutamic acid all have the same hydropathy score).
To complete the model, we need to describe a model for the matrix of regression coefficients βi,j. There are a number of possible models for this type of data which utilize Bayesian nonparametric methods; some recent examples include the infinite relational model (IRM)[22, 23], the matrix stick breaking process (MSBP)[24], and the nested infinite relational model (NIRM)[14, 15].
is a random distribution such that, v k ∼Beta(1,ρ), and. Indeed, the discrete nature of F ensures that ties among the θ j happen with non-zero probability.
with, ul,k∼Beta(1,γ k ) for every k, and φl,k are independently drawn from the baseline measure G0,l,k.
whereInv-Ga(a κ ,b κ ), andInv-Ga. Here ϕl,k and respectively denote the unique values βi,jand can take, whereas λ is the prior probability that ϕl,khas the value zero (i.e., the properties associated with this cluster are strongly conserved at this cluster of sites).
Note that our model implies that both sites and properties are exchangeable a priori. If no additional prior information is available, this type of assumption seems reasonable. However, a posteriori, it is possible to have sites behave differently in different clusters.
To complete the model we place hyperpriors on all parameters of the resulting model. Conjugate priors are chosen for ease of computation. α k denotes the mean for the ϕl,ks that are different from zero belonging to a specific cluster of properties k and is assumed to have a N(m α ,C α ) prior for all k. The DP concentration parameters ρ and γ k are assumed to follow Ga(a ρ ,b ρ ) with mean a ρ /b ρ , and Ga(a γ ,b γ ) with mean a γ /b γ for all k, respectively. λ, which is the prior probability for the point mass at 0 in G0lk, follows a Beta(a λ ,b λ ). The specific choice of hyperparameters is discussed later as part of each data analysis. In general, we use Ga(1,1) priors for the DP concentration parameters and a N(1,C α ) prior for α k to correspond to our assumption of neutrality a priori for the properties.
Related work
We compare results from our proposed method with results from a few currently available methods that aim to characterize molecular evolution while also taking into account changes in amino acid properties, namely, the regression model in[10], TreeSAAP[25], and EvoRadical[9].
In[10], the first level of the model is the regression equation on as in equation (1), but it implicitly assumes independence among properties and independence among sites unlike our current model. The model in[10] is suitable for use when a few mostly independent amino acid properties are being analyzed whereas the new semiparametric model is better suited to the analysis of a large number of possibly correlated properties.
TreeSAAP uses the methods of[6] to classify nonsysnonymous substitutions into one of M categories, with higher numbered categories corresponding to sites showing radical changes and lower numbered categories used for sites showing conserved changes for a given property. For the analysis considered here, we used 8 categories where categories 6, 7, and 8 corresponded to sites showing radical changes, and categories 1 and 2 to sites showing conserved changes. Nonsynonymous changes are inferred from the ancestral reconstruction using the nucleotide substitution models in baseml implemented in PAML. We used a Bonferroni correction to correct for multiple comparisons.
EvoRadical implements the models of[9], which use partitions of amino acids to parameterize the rates of property-conserving and property-altering codon substitutions in a maximum likelihood framework. The model considers three types of substitutions: synonymous, property-conserving nonsynonymous and property-altering nonsynonymous which is a slight improvement from[8]. For analyses with multiple properties, one has to create different partitions for the different properties and run EvoRadical for each property.
Posterior simulation
Various algorithms exist for posterior inference of DP mixtures - some of the most popular ones use (i) the Pólya urn characterization to marginalize out the unknown distribution(s)[26, 27], (ii) a truncation approximation to the stick-breaking representation of the process which paves the way for the use of methods employed in finite mixture models[28, 29], (iii) reversible jump MCMC or split-merge methods[30, 31]. Some other recent approaches have also used variational methods[32] and slice samplers[33].
We use an extension of the finite mixture approximation discussed in[28] for its ease of implementation. Truncating F at a sufficiently large K, we write, with the weights Π k and locations generated as described earlier in this Section. Next we introduce configuration variables {ζ j } such that, for k=1,…,K, ζ j =k if and only if. Similarly for G k , we truncate at a sufficient level L, and introduce another set of configuration variables {ξi,k} where ξi,k=l, with l=1,…,L, if and only if. Additional details about the algorithm are provided in the Appendix.
To determine the truncation levels K and L, we follow[29]. In particular, note that conditional on ρ (the DP concentration parameter), the tail probability has expectation {ρ/(1 + ρ)}K−1. Using prior guesses for ρ and acceptable tolerance levels for the tail probability to be small, one can then solve for the truncation level K. In our analyses, we used K and L in the range of 25 to 35. These values are in line with those used in other applications (for example, see[34]).
Results and discussion
Empirical exploration via simulation studies
We present two simulation studies to check the performance of the model under different scenarios. Additional simulation scenarios that may be of interest are available as an Additional file1.
Simulation study 1
The setup for the first simulation is as follows. We generate values for the distinct regression coefficients (ϕl,k) from a N(1,0.25). The number of distinct regression coefficients depends on the particular clustering structure for the corresponding simulation. Once we obtain the regression coefficients, we generate observations yi,j from N(ϕl,kxi,j,σ2=0.001). The xi,js are obtained from the lysin data set described below with analyses for 32 properties, which implies J=32 and I=94.
We fitted the model in The Model subsection to thes ands, with the following modifications: (i) the NIRM is imposed on βi,j, so φl,k=ϕl,k and (ii) ϕl,k∼G0where G0∼N(α,τ2). We used K=25 and L=25 for the simulations. The MCMC algorithm was run with the following hyperpriors: ρ∼Ga(1,1), γ k ∼Ga(1,1) for all k, α∼N(1,0.25). σ2∼Inv-Ga(100, 10) and τ2∼Inv-Ga(2,4) were chosen such that the prior means corresponded to the true values for these hyperparameters. Results are based on 15000 iterations, with the first 5000 discarded as burn-in. Convergence was assessed by running two chains where each chain was initialized by randomly assigning the βi,js to different partitions. Posterior summaries based on the two chains were consistent with each other.
This scenario corresponds to the type of situation we expect on most real datasets: properties will cluster into groups and, within each group of properties, clusters of sites with similar responses can be clearly identified. Our results suggest that, as expected, the model is capable of identifying these multiple clusters with high accuracy and therefore accurately estimate the value of the regression coefficients. Other scenarios, including extreme cases where all properties belong to a common cluster while sites belong to one of several clusters, and cases where each property has a different effect on amino acid rates are available as Additional file1.
To investigate the effect of the truncation levels and the priors on our model, we performed sensitivity analysis by varying the truncation levels as well as the different hyperparameters. Increasing the truncation level to 35 did not affect the results and the estimated posterior means of the β s showed close agreement with the true values. The analyses was also fairly robust to the choice of the priors, since varying the hyperparameters had almost no effect on the results. Decreasing the prior variance of τ2 makes the results marginally better, i.e., posterior means of the βi,js,s, are slightly closer to the true values.
Simulation study 2 - data simulated from a biological model
In our second simulation study the model is evaluated in the context of biological sequences generated from an evolutionary model. In particular, a Markov model was used to generate 20 sequences of 90 codons each. For the first one-third of the sites (sites 1-30) we used transition probabilities obtained from the codon-substitution model of[21] with equal equilibrium probabilities for all 61 codons. For the second one-third of the sites (sites 31-60), we modified the transition probability matrix from the previous step by increasing the probabilities of transitions between codons that have small distances for volume and decreasing the probabilities of transitions between codons that have large distances for volume - this was done to encourage only those changes that conserve volume in this part of the sequences. Finally, for the last one-third of the sites (sites 61-90), we modified the original transition probability to encourage radical changes in hydropathy. Thus, we increased some transition probabilities between codons that have very different hydropathy scores and decreased a few of those that have similar hydropathy scores. Note that, since the equilibrium probabilities are either uniform or roughly uniform across all sites, the correlation structure across properties is retained in the expected distances, which simplifies the interpretation of the results.
Once we obtained the sequences, we generated ancestral sequences using PAML, version 3.15,[20] and calculated observed and expected distances yi,j and xi,j for five properties, namely, hydropathy (h), volume (M v ), polarity (p), isoelectric point (p H i ) and partial specific volume (V0). Of these, h and p are correlated and so are M v and V0.
Our model was fitted with K=25 and L=25 as truncation levels. The prior distributions were the same as the ones used for our previous simulation. Results are based on 15000 iterations, of which the first 5000 were burn-in. There did not seem to be any obvious problems with convergence, which was assessed by visual inspection of trace plots of some of the parameters.
Comparing results between models in [[10]] and the new semiparametric model, for the data simulated under a biological model
Parametric regression[10]
Semiparametric regression
30 sites with largest posterior mean for h
4, 5, 6, 10, 14, 18, 19, 21, 22, 23, 24, 33, 48, 52, 54, 59, 62, 64, 65, 67, 71, 74, 75, 77, 80, 81, 82, 84, 85, 89
4, 5, 14, 18, 19, 21, 24, 33, 37, 39, 48, 52, 54, 59, 62, 64, 65, 67, 71, 72, 74, 75, 77, 80, 81, 82, 84, 85, 86, 89
30 sites with lowest posterior mean for M v
5, 6, 7, 9, 16, 19, 24, 25, 26, 27, 28, 31, 32, 36, 44, 49, 51, 58, 59, 60, 61, 64, 65, 67, 79, 80, 82, 83, 85, 88
5, 6, 7, 9, 16, 18, 19, 24, 25, 26, 27, 28, 31, 32, 34, 36, 38, 49, 58, 59, 60, 61, 64, 65, 67, 79, 80, 83, 84, 88
Sites identified as significant by TreeSAAP for the different properties for the simulation study based on a biological model
Radically changing (1.645)
Radically changing (3.695)
Conserved (1.645)
Conserved (3.695)
5, 59, 65, 67, 71, 74, 81, 82, 89
36, 83
21, 24, 37, 64, 65, 67, 71, 74, 75, 81, 82, 89
7, 18, 36, 49, 55
M v
10, 33, 66
5, 18, 36, 49
10, 13, 33, 66
18, 36
p H i
39, 55, 72
11, 64, 72
Finally, we analyzed the sequences generated previously with EvoRadical using two different partitions[8] - one for p and the other for M v . We chose to run Evoradical with p instead of h, since a partition of the amino acids for polarity was already available in[8]. Additionally, given that h and p are correlated, we expect to see somewhat similar results for these two properties.
Sites that have high posterior probabilities (>0.95) of belonging to each site class for the different partitions for EvoRadical for the simulated data
ω≤1,γ ≤1
ω≤1,γ >1
ω>1,VVγ ≤1
ω>1,γ >1
1, 2, 5, 7, 10, 11, 12, 13, 14, 18, 19, 20, 26, 27, 30, 32, 33, 34, 36, 37, 42, 43, 47, 53, 57, 59, 61, 62, 63, 64, 66, 67, 68, 69, 72, 73, 74, 75, 77, 82, 83, 86, 87, 88, 90
M v
2, 7, 9, 18, 19, 20, 22, 27, 31, 32, 36, 38, 53, 55, 61, 62, 64, 67, 72, 74, 86
Illustration with Lysin data
Our proposed model was applied to the sperm lysin data set which consisted of cDNA from 25 abalone species with 135 codons in each sequence[35]. Sites with alignment gaps were removed from all sequences, which resulted in 122 codons for the analysis presented here. The phylogeny of[35] and the codon substitution model M8 in PAML, version 3.15,[20] was used to generate the ancestral sequences. The model M8 uses a discretized beta distribution to model ω values between zero and one with probability p0 and allows for an additional positive selection category with ω>1 and probability p1.
List of 32 amino acid properties used in the analysis
AAindex accession number (if available)
AAindex accession number (if available)
Helical contact area
C a
Molecular volume
M v
Isoelectric point
p H i
Surrounding hydrophobicity
H p
Long-range non-bonded energy
E l
p zim
Mean r.m.s. fluctuation displacement
Alpha-helical tendencies
P α
Molecular weight
M w
Normalized consensus hydrophobicity
H nc
Average number of surrounding residues
N s
Partial specific volume
Power to be at the C-terminal
α c
Polar requirement
P r
Power to be at the middle of alpha-helix
α m
Power to be at the N-terminal
α n
Equilibrium constant (ionization of COOH)
p K ′
Refractive index
Beta-structure tendencies
P β
Short and medium range non-bonded energy
E sm
B l
Solvent accessible reduction ratio
R a
B r
Thermodynamic transfer hydrophobicity
H t
Chromatographic index
Total non-bonded energy
E t
Coil tendencies
P c
Turn tendencies
Strongly conserved sites ( ) for lysin data for different clusters
Site number
2 and 3
22, 28, 35, 51, 111, 117, 128
11, 17, 18, 19, 24, 25, 27, 29, 33, 35, 42, 43, 47, 49, 51,
53, 58, 64, 66, 68, 69, 71, 73, 79, 81, 88, 94, 96, 98, 100,
101, 104, 105, 110, 111, 114, 115, 117, 121, 122, 129, 131
The results are fairly robust to the choice of different hyperparameter values. Note that the scale factor for ultimately affects the variation in the βi,jvalues, and it is advisable to choose it so that the prior variance for the unique βi,js is not too large.
In this paper, we present a Bayesian hierarchical regression model with a nested infinite relational model on the regression coefficients. The model is capable of identifying sites which show radical or conserved amino acid changes. The (almost sure) discreteness of the DP realizations induces clustering at the level of properties which is analogous to the factor model in[11], with the advantage being that the nonparametric method automatically determines the appropriate number of clusters. The multi-level clustering ability of the NIRM also induces clustering at the level of sites and allows us to capture skewness and heterogeneity in the distribution of the random effects distribution associated with each cluster of properties.
The main advantage of the models we have described is their ability to simultaneously handle multiple properties with potentially correlated effects on molecular evolution. Our simulations suggest that our models are flexible but robust, being capable of dealing with a range of situations including those where properties are perfectly correlated, as well as those where all properties are uncorrelated. Our semiparametric regression models also work well, particularly in comparison with the regression model in[10], TreeSAAP and EvoRadical, when applied to DNA sequence data generated from an evolutionary model. In addition, the analysis of the lysin data suggests that the model leads to reasonable results.
The NIRM that is the basis of our model defines a separately exchangeable prior on matrices. This means that the prior is invariant to the order in which properties and sites are included. This is due to the fact that the rows as well as the columns of the parameter of interest are independent draws from a DP. From the point of view of modeling multiple properties, this is a highly desirable property. However, assuming that DNA sites are exchangeable can be questionable. Although this is a potential limitation of our model, we should note that the assumption of independence across sites (which is a stronger assumption than exchangeability) underlies all the methods discussed in the Background section. If information about the 3-dimensional structure of the encoded protein or other sequence specific information that can guide the construction of the dependence model is available, our model could be easily extended to account for this feature. In the absence of such information, exchangeability across DNA sites seems to be a reasonable prior assumption. Indeed, in contrast to the most common independence assumption, our exchangeability assumption allows us to explain correlations at the level of sites.
In our applications, we have used codon substitution models for reconstructing ancestral sequences as we wished to compare our methods to other methods for detecting selective sites that also use codon substitution models, such as those implemented in PAML and EvoRadical. However, it is possible to perform the proposed Bayesian semiparametric analyses using amino acid substitution models instead of codon substitution models. Note that the substitution model is only used in the calculation of the observed distances. First, we infer the ancestral sequences under a specific substitution model and a given phylogeny. We then compute the observed distances for a given property and a given site as the mean absolute difference in property scores due to all nonsynonymous substitutions at that site, where the nonsynonymous substitutions are counted by comparing the DNA sequences between two neighboring nodes in the phylogeny. The reconstructed ancestral sequences, and therefore the observed distances in our model, may differ under different substitution models, but the method can be implemented under any substitution model, including amino acid substitution models. The gain in execution time from using amino acid substitution models instead of codon-based ones could potentially be significant if the uncertainty in the alignment/phylogeny/ancestral level is taken into account.
Finally, it is important to note that the "observed" distances are not really directly observed, but are instead constructed from ancestral sequences and, therefore, subject to error. A simple way to account for this additional level of uncertainty is to modify the computation of expected distances by incorporating the ideas of[37]. This approach was previously employed in[10], with little impact on the final results.
Appendix: details about the Gibbs sampler
with φl,k∼G0lkand Π k and wl,k being the appropriate stick breaking weights. Writing the model as in (5) helps in obtaining the forms of the full conditionals as below.
where is if ϕl,k=0 or is if ϕl,k is different from zero. Π k is sampled in two parts: first, by generating v k from a for k=1,…,K−1 and v K =1, where m k is the number of columns assigned to cluster k and then, by constructing.
The updated weights wl,k are sampled in a manner similar to the Π k , i.e., ul,k are generated from a for l=1,…,L−1 and u Lk =1, where nl,k is the number of βi,js assigned to atom l of cluster k and then, by constructing.
where is the number of unique row indicators ξi,k, for a specific cluster of columns k.
with the individual expressions obtained as follows.
where and.
Software availability
The R code implementing the models in the paper is freely available at http://www.ams.ucsc.edu/~raquel/software/.
RP and SD were supported by the NIH/NIGMS grant R01GM072003-02. AR was supported by the NIH/NIGMS grant R01GM090201-01.
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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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Research & Learning Librarian and Instruction Coordinator, U of Arizona | MLIS & MS in Instructional Design
February 6, 2013
Some brief thoughts on classroom management, techniques, and future lesson plans
The ERIAL Project has highlighted the issue of students with the lowest skill level in library research being the most confident about their abilities. I definitely notice this in the classes I teach, and particularly in this student success course. They seemed to feel very confident and like they didn't need me to show them anything (not the whole class, but the majority). In contrast, the students who were excelling and were doing more advanced research were the only ones asking questions and putting effort into the activity. I think an effective method in this case is to set them up for some struggle first and then show them that they could really use instruction. For example, have them search the database without direction, and then when they see they haven't found very useful results or too many results, demonstrating tactics and tricks can better capture their attention. That way when we say knowing how to do research effectively will actually save them time in the long run, they will believe it.
On the flipside, I went back to teach another session to freshmen football during their study table hours (this is part of my work in student retention), and it went amazingly well. The lead tutor who oversees their study table hours said my colleague and I are great at engaging a very difficult population (hooray!) and asked me to come back next month even though now we've covered all the sessions we agreed upon for the academic year (orientation, basic searching, evaluating sources, and citing/avoiding plagiarism).
With this group, I have been planning game-like activities to engage their competitive nature. Anytime they can go up against one another, they seem to get really into it. We planned a BINGO-style orientation session for them over the summer and they were hardcore about enforcing no answer sharing or explaining answers until the competition is over because they all wanted to win. At this latest session, we did plagiarism court and offered candy for answering correctly. I'm already plotting out our next session and think now that they have the basics, I'd love to teach them "research as conversation," and framing it that way should really help them understand the process better. I'm working on developing some things to illustrate this in a fun way and will share what I create along with the results. This is an exciting group to work with because I can try out a lot of different things and can make it fun.
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Blob Kids bean bag cover / Purple
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Main Index
Latest News
Browse the site choosing a game from the menu, here you'll find Story, Screenshots, Arenas, Props and Fighters of the game, each fighter page includes: A complete Spritesheet, Biography, Animations, Props, Movelist, Fatality Videos, Ending, Renders, Cut-Out Pictures, Wallpapers and more!
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The following sprites were ripped by Maggo:
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Happy Birthday MKW! Today marks the fifth anniversary of something that started as a hobby and has turned out to be one the things I've done that I'm most proud of. It's also time to thank all fellow MK fans and loyal visitors to the site, even if it sounds cliché at this point.
And now the formality, today's addition of Sektor's sprites has completed all of the sprites from MK3! And we're only 3 spritesheets away from completing every spritesheet from MK1 to MKT! Which is really exciting, as doing this has been the main goal of the site's since its conception 5 years ago.
As of now, there are no concrete future plans for the site after that goal is achieved, besides obviously further perfecting the site, since I know we're missing some Fatality movies, and a couple of sprites here and there, so I'll be sure to take care of that before doing any major changes to the site, after all, that's what makes this site one of the top-notch MK sites of the net!
Stay tuned, as there's more to come still!
67 responses to "MKW's 5th Birthday"
i have just found out that in mk4,noobsaibot can do the reiko thrust kick,and deep freeze uppercut fatalities!try em out!
nick_scryer Says:
July 31st, 2007 at 7:10 am
Yeah Kombat Pavillion took so long for update, i hope they will update Frost on Unmasked Section and either More Animations or Games like Updated version to Create A Fatality oh and Anyway MK Gold animations isn't in Kombat Pavillion? right Murdoink, Either i can do edit em' out
Can you guys palette swap a series of MK1 Ermac sprites? That would be like a dream come true
UltimateRyu, You can get those sprites from Nick_scryer and Kabal's MK Site But later i will have Free Webs that is :-)
Happy belated B-day MK Warehouse.
If you don't have any plans after getting all the MK1-MK:Trilogy sprites, maybe getting the MK:DA gameboy sprites might be a nice afterthough? Like the ones you got for Scorpion and Kenshi.
Is there's anybody can Rip the Mythologies Sprites?
Ahem! Remember that Kano_fan he ripped for those MK:SZ Sprites and stop asking for those MK3 Version of myself! I mean if you want MK3 Noob Sprites you must have Paint Shop Pro and Paint dot Net and Game Maker 7 (Sorry for i asking for Hydro in another way)
# Tetra_Vega Says:
August 2nd, 2007 at 7:43 am
MKW doesn't deal with custom sprites.
MKW does deal with custom sprites like black blood and Cut-our Pictures
Dude, where do you find all these things?
mkm:sz sprites needed! mkm:sz sprites needed! this problem will NOT go away, you must provide, or your life will gradually become more and more unbearable until you reach the point that you wish you had the oportunity to kill yourself
Happy 5 B-Day
Yall screwed this site up its sprites when you copy them theres black around em
its very hard with Noob Saibot
Also Happy B-day
soooooo,It doesnt matter the only way you are able to get the black off is if you save I dont want to save i just want to copy-paste
what do you do with sprites
you copy them
But theres black all around them
happy b-day mkw this is te best site ever my brithday is is this thrusday
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So how long did it take for them to ding you? I just checked my page and it just says Current File Status: Your application is complete...received on nov 17th and is being considered for early decision.I'd like to get my first ding out of the way...at least I assume that's what it'll be.
Wow! I guess being a resident v. a non-resident really does make a big difference!
Javert, are you an Angel fan?
Wow! I guess being a resident v. a non-resident really does make a big difference! They claim that it doesn't, but considering that yall were rejected with numbers higher than several of the people that were deferred (according to LSNumbers) I am inclined to think that it obviously does matter.
Quote from: LawSchoolDreams3 on November 28, 2004, 11:39:40 AMJavert, are you an Angel fan?Oops, missed this post. Not to threadjack, but it's a fairly good show. It has flaws, and about half of the 4th season was a complete trainwreck. It's not my favorite show, but it's a good one.


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When you remove stains from carpets, some can be easy and others can be hard. Blood is one stain that can be hard to remove. Blood is made of iron and proteins, which makes it difficult to remove. Carpet is not like a shirt or blouse that you can wash normally in the washing machine. It is something that you have to do by getting on your hands and knees. When you notice blood on the carpet, it can be tedious to remove if you do not instantly respond. Carpet cleaning can be expensive so before you call a professional here are some home solutions that you can try first.
• Get some cold tap water, pour it directly on the stain, and let it stand for fifteen seconds. Take a dry clean piece of cotton cloth and press into the stain. Do not sue wiping stroke but just dab the cloth on the stain. If the carpet appears to be drying, put some more cold tap water on the stain and repeat the dabbing with the cotton cloth. Once the cotton cloth has absorbed the stain as much as it can, dry it using a blow dryer
• Administer some oxidizing bleach specially made especially to remove stains from carpet but use it with care. When using this solution you could ruin your carpet so there is no chance of repair.
• Mix some water and fizzy soda together and put on the stain. Blot the stain with the mixture and soak up the stain with dry paper towels until the blood has been absorbed.
• Remove stains from carpet by making a mixture of talcum powder, cornmeal, and cornstarch with a little cold water to make a paste. Apply it to a fresh stain so it completely covers the stain. Leave it on for at least thirty minutes. Dip a sponge in cold water to gently remove the blood stain and paste.
• Put some salt onto the blood stain. Mix hydrogen peroxide and water in a ratio of 3:2, dip a piece of cloth in the solution, and dab it over the salted area. Next, clean the region with towel moistened with water.
• Make a paste of pre-wash laundry cleaner or laundry starch and water, put it on the stain with the back of a teaspoon or your fingers, and allow it to stand for at least thirty minutes. Use cold water and a sponge to remove stains from carpet. Do not use any type of brush as the bristles could damage the delicate carpet. Let it dry and then vacuum.
If these home remedies to remove stains from carpet that is blood you should call a professional carpet cleaning service.
Carpet Cleaning - Wet Vs Dry


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How are you all? I've been busy as usual doing a ton of fun projects, but I realized it's been forever since I've updated this blog!
Here are just a few of the things that have been keeping me so busy:
Tiffany, Stef and I are *nearly* all moved into the studio and we're almost ready to have you all over for some tea! In the meantime, be sure to check out our website because we have some uh-maze-ing workshops scheduled including:
- Shooting from the Heart, Expressive Photography with Shutter Sister Tracey Clark
- Layered Lines & Cardboard Wonders with Diana Fayt
- Inner Excavation with Liz Lamoreux & Vivienne McMaster
- The Joy of Intention: A Painting and Play Workshop with Alena Hennessey
OH! and PS: Did I mention that I'm writing a BOOK?! Nooo? Well, guess what...
I'm writing a book! Hooray!!!
I am thrilled to finally be able to completely spill the beans about this dream project -- and now you guys know the truth about what's been keeping me so busy!
I'm also in the midst of redesigning my website with an online shop, so for the sake of my sanity, I'm going to keep my etsy shoppe closed until the website launches this summer...
xox, mati


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Two People Run Over in Parking Lot After Jason Aldean and Luke Bryan Concert
Be careful in concert parking lots, people! On Thursday (Sept. 6), two concertgoers were run over by an SUV in the parking lot of the PNC Banks Arts Center in Holmdel, N.J. after taking in the Jason Aldean and Luke Bryan gig at the venue.
Police claimed that the parking lot was well illuminated and that two people who were laying down on the pavement were run over. The cops also said that alcohol was a factor in the incident, on the pedestrian's, as opposed to the driver's, part.
"Alcohol was definitely involved on the part of the pedestrians," said State Police spokesman Lt. Stephen Jones. He elected not to provide further or more specific details about the accident.
Four people were inside the SUV that ran over Jessica Hillman, 21. She suffered a broken pelvis, a broken leg and head trauma in the incident and had to be chartered to a local hospital via a MedEvac helicopter. Her condition is serious but stable. The other pedestrian, Charles Wright, 24, refused medical attention and suffered only minor injuries as a result.
The moral of the story? Don't lay down in active parking lots during concerts where there are thousands of vehicles. We hope Hillman has a speedy recovery.


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A Jacksonville man wanted to see Lil Wayne perform in Miami, but he wanted to get there as quickly and safely as possible with the help of a police escort.
Unfortunately for 20-year-old Michael Kruse, police escorts are generally reserved for politicians, celebrities and heads of state, but that didn't stop the rap enthusiast from calling 911 to request an escort or at least the use of a helicopter.
Kruse called 911 as he was heading south on I-95, requesting the escort.
"You want a police escort to take you to Miami?" the 911 dispatcher responded, according to WTLV.
"Or, you have a helicopter?" Kruse asked.
"We don't just send helicopters up for rappers," the dispatcher said.
Kruse said he was just trying to be cautious.
"Well, I'm driving there right now. I just wanted the fastest way to get there. I didn't want to get pulled over on the highway," Kruse said.
The dispatcher had Kruse pull off the highway where he was met by deputies and given an escort straight to jail, accused of misusing 911.
The best part is that Kruse had nearly been charged with misusing 911 less than 24 hours earlier, after he called the emergency number to say he was feeling sick.
During that call, the dispatcher began to suspect Kruse was high on something after his speech was slurred.
"Are you sure you haven't taken something sir?" the dispatcher asks. "Because you're not making a whole lot of sense."
"I've been smoking marijuana," Kruse tells the dispatcher.
"Do you want a deputy to come and take you to jail?" the dispatcher offers.
"Why?" says Kruse.
"You just told me on a taped line you just got done smoking marijuana," the dispatcher says.
"Awww. Are you serious?" Kruse asks.
Kruse was given a stern lecture after the first call but apparently hadn't learned his lesson.


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If you are interested in results from years before 2009, contact Linda Ambrose.


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Monday, May 11, 2009
Get Amarok 1.4 In Kubuntu 9.04
Almost everyone who loved the 1.4 Amarok hates the new Amarok 2. Even I didn't like the new buttons.
Unfortunately Kubuntu comes with Amarok 2 by default. However if you prefer Amarok 1.4 you can install it by follwing these instructions:
Add the PPA to your sources by creating a new file for the Amarok PPA:
gksu gedit /etc/apt/sources.list.d/amarok.list
Then in that new file add the following two lines:
deb http://ppa.launchpad.net/bogdanb/ppa/ubuntu jaunty main
deb-src http://ppa.launchpad.net/bogdanb/ppa/ubuntu jaunty main
Add the key for the PPA:
sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com \
Now update your sources, remove Amarok2 and install Amarok1.4:
sudo apt-get update
sudo apt-get remove amarok
sudo apt-get install amarok14
6 comments:
Very nice, worked like a charm!ReplyDelete
Love Jaunty (sorta) Hate Amarok 2
I believe the correct expression is: w00t!!ReplyDelete
thanks, can't believe they included Amarok 2.0.2 in Jaunty...was looking for another music player till I found this blog post! :D
I'm an Amarok developer and even I think selecting Amarok 2.0.2 was a mistake for Kubuntu.ReplyDelete
Amarok 2.1 is pretty awesome though! So another solution for some folks might be to add the backports repo.
I'm going to use these instructions on my girlfriends computer. She has a need to play these primitive plastic discs for some reason. :) (cd playing and ripping will be in Amarok 2.2).
I get the error:ReplyDelete
"E: Type 'sudo' is not known in line 4 in source list /etc/apt/sources.list.d/amarok.list"
Your instructions are great! I didn't like amarok 2.2 and missed 1.4 now I finally switched.
But I've got problem witch collection creating - after selecting base directory nothing happen, I've got selected SQLite as database maybe this is the problem?


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U.S. Department of Energy Smart Grid Privacy Workshop Summary Report
The U.S. Department of Energy Smart Grid Privacy Workshop sessions were led by professional facilitators, who guided participants in structured brainstorming and critical analysis to identify the most significant issues and build agreement on options and approaches to moving forward. The groups then reconvened and each breakout group provided a report on their groups discussions and results. This document provides a summary of the sessions and results.


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Lately I have noticed a lot of chatter going on about public tantrums. There seems to be two schools of thoughts: "Those parents need to learn how to control their kids" and "Leave the poor parents alone. They are probably doing the best that they can."
But those two schools of thought leave out two very important things. The first is that some people have a physical condition that makes the sound of a screaming toddler literally painful. And the second is that many people do not understand tantrums.
If you find the sound of a toddler screaming or a baby crying intensely upsetting, you may be one of millions of people who has a processing problem and is very sensitive to sound. Shrill sounds, in particular, are painful to be around.
The sound of a child screaming is supposed to be distressing. But for people who are very sound sensitive it is torture. I have known people who are tempted by the sound of a screaming child to beat their own heads against a wall just to distract themselves from the sound. What I find interesting about this kind of sound sensitivity is that it increases with age even though overall hearing declines.
If you are sound-sensitive and you find yourself becoming intensely emotional in response to a child's relentless screaming this does not make you a bad person. Your painful response to sound is no more your fault than something like ADHD or dyslexia would be.
However, the rules for public spaces should not be designed around us. You should just expect screaming any place where children are allowed. It is like poop in diapers: Not fun, but it comes with the territory.
Rather than blaming parents or children, I recommend using adaptive technology. Multiple pairs of good quality earplugs are practically a medical necessity. I carry a couple different pairs in a pill case attached to my key ring. I use a lightweight pair if I just need to cut the sound, like when I am in church. I use a thicker set if I need to not hear a baby. But by far the best adaptive technology is a good pair of ear buds and a "sounds of nature" application on your phone. I can put on my Bose ear buds and a recording of waves on a pebbly beach, and actually enjoy reading a book during a cross-country flight filled with screaming toddlers.
Now that we have covered why a few people are distressed by other people's tantrums, we need to talk about why it pisses off the rest of you. You assume that only bad parents who cannot control their children or rude people who don't give a crap about people around them would allow such an infernal noise to continue.
I understand where you are coming from. I would feel the same way if I hadn't attended some parenting classes. I insisted on them when my wife and I got engaged. I really wanted to be a good father, and I knew enough to know that I had no idea what I was doing when it came to raising kids. These classes did not make me an expert. But they gave me a working understanding that helped me be a good dad.
By far, the most important and valuable thing that I learned in those classes was what tantrums are. Once I understood them, dealing with them became much easier. Again, I am not a child-development expert. I am an engineer. And thinking about tantrums this way got me through a lot of tough years of parenting:
1) There are actually two kinds of tantrums: a shake-down and a melt-down.
2) A minority of tantrums are shake-down. It is a negotiation strategy. Unfortunately, little kids don't have a great sense of proportion, so they tend to start every negotiation by taking hostages. "I have your schedule, your sanity and your self-worth as a parent. If you want to be on time, get done what you planned and look at me without feeling guilty, you will give me that cookie NOW!"
3) Kids don't have a lot of power, so they enter every negotiation at a disadvantage. The one thing that they can bring to the table is "I will scream down the rafters." A kid who is taught other ways of negotiating will be less inclined to using the nuclear option.
4) The best response to a shake-down tantrum is to call the child's bluff. This is relatively easy to do in private, but harder to do in public because of people who try to shame parents into silencing their children.
5) When you say nasty things or glare at a parent while a child is having a shake-down tantrum, you are giving that kid more ammunition to use against the parent next time that they are in public. If you make a parent more uncomfortable letting a child scream, you are actually increasing the power a tantrum has thereby increasing the likelihood it will be employed. On behalf of those of us who do not enjoy shopping to the accompanying strains of "Screams of Rage in B Flat" I beg you, please do not harass the parents.
6) The majority of tantrums, even many that look like a shake-down, are actually a melt-down. Do not presume to know what is going on with another person's child.
7) Tantrums are not a bug. They aren't even an ordinary feature. They are a safety feature and you should never, ever disable a safety feature.
8) Tantrums are designed to be annoying or downright distressing. They are like smoke detectors. They are supposed to make you emotionally agitated. Safety features don't work if they don't strongly encourage people to change behavior.
9) Tantrums are designed to alert parents and other caregivers that a child has reached a melt-down state. Usually these melt-downs occur when the ability to process stimulus is exceeded by incoming stimulus. It is a deceptively simple formula because often we forget how much stimulus even normal environmental situations contain for young children.
10) Young brains are prone to melt-downs because they are very busy trying to figure out how the world works. To learn about the world, they are wired to be very sensitive to stimulus, but they do not have a corresponding increased capacity to process and deal with the stimulus.
To put it another way, they are running their little engines at maximum RPM all the time, but they have a very persnickety water pump.
11) Young children lack fundamental information and concepts necessary for processing all of the incoming data. To put it another way, being a toddler is like being dropped into a different foreign country every day. Everyone is speaking in a language that you don't know, and they make you go places and do things that you don't understand and that you cannot anticipate. You have no idea which colors, objects, and unfamiliar sounds are unimportant and which ones are required to keep you alive. Every day, you are doing very fast pattern-matching, trying to figure out what everything means. And some days, there is just so much stimulus to pattern-match that the wheels just come off your wagon.
12) Even shake-down tantrums are often rooted in this fundamental lack of understanding about how they world works. For example: a toddler may recognize a box in a store and remember that when their dad fills their bowl with stuff from that box, they really like it. So they may demand that the parent buy that particular box of cereal, and then launch into a full-scale tantrum when the parent says no. But they may not understand one or more of the following things:
- That stores restock their shelves regularly. They may think that all of the Sugar Smacks in all of the world sit on that shelf and that if you do not buy it, they will never again get to taste Sugar Smacks.
- They may not understand that when you say "No" today, this does not indicate a sweeping policy change for all future cereal acquisition.
- Their concept of time is Now and a Long, Long, Long time from now. So saying "We will get that the next time" is like your partner saying, "Not tonight dear, but we will definitely have sex eight years, six months and twenty-two days from now.
Let me bottom line this for those of you who are not have an issue with sound-sensitivity but hate to hear children screaming:
The world does not revolve around you. Other people have needs too. And young children, for a variety of reasons, need to throw tantrums. And parents of young children need to allow those tantrums to happen and not whisk them away every time that they start to scream.
You are an adult. You likely have more time than a parent does, so if you cannot stand to be in a store where a kid is screaming, then leave, and come back another time. And if all else fails, earplugs are cheap. Use them.
If you are just being judgmental: I think we all should listen to what you have to say about parenting and do exactly as you recommend - right after you turn the water into wine. Actually, make it a nice hard cider. I am really into those right now.
Pete Beisner is a father, husband and veteran who works in the field of information technology. He has a bachelor's degree, two master's degrees and hates writing.
More from The Good Men Project:


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Honda VTR250 Engine Accessories
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Find Your Perfect Home.
Parma Real Estate
Parma is located in Michigan. Parma, Michigan has a population of 760. Parma is more family-centric than the surrounding county with 42.75% of the households containing married families with children. The county average for households married with children is 27.36%.
The median household income in Parma, Michigan is $50,139. The median household income for the surrounding county is $45,452 compared to the national median of $53,482. The median age of people living in Parma is 33.3 years.
Parma Weather
The average high temperature in July is 82.2 degrees, with an average low temperature in January of 15.9 degrees. The average rainfall is approximately 34.6 inches per year, with inches of snow per year.
Parma Map
Real Estate Near Parma
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text: Some photos from the visit of Lochgilphead on Saturday. The 2002-03 age group enjoyed a couple of hours of 7 aside football on the All Weather Pitch in fine conditions with 5 teams competing. A good day was had by all and rounded off with excellent after match hospitality at The Hub - the association wish to say a big thank you for providing this service, great!


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Better late than never, I am *finally* getting around to posting some projects I worked on last year. Here we have Isabel's room. A sweet, fun space for a little girl and all her dreams, and ownership definitely suits her! As I was working in her room, Isabel would ask me each day "Is my room done yet?" to which I would say "Not quite yet, but soon." I finally declared the room finished to which she replied "I loooove my room!" It doesn't get better than that! A satisfied customer, a discerning one at that.
|It's Isabel's World
|The chest of drawers will eventually get pivoted to be on the same wall as the bed, but for now, we have a jumper, so it's as far away as possible to avoid head bonks and other disasters
|The color on the walls is a beautiful Lavender-Grey but really hard to capture on camera
Pom-Poms fill in an awkward space between curtain panels and window shades.
|Every little girl's room need a touch of glitter!
3 different shades of green and 4 different patterns and it all works together!
Chic little storage boxes for hair brushes and beads!
|I mean.....I want to work at this desk. So happy!
|Sophisticated and playful at the same time
|Newly painted desk and mirror hung at just the right height for an almost 5 year old. Step stool at the end of the desk aids in reaching items placed on top.
Paper pattern mash-up
|I created this Elephant artwork by tracing an Elephant silhouette onto some beautiful metallic wrapping paper and layering it with other papers to create a fun, colorful and vibrant accent in the room.
|Paint Power! Desk, tall bookcase and ottoman/stool ALL got makeovers with nothing more than paint (and a bit of new fabric on the ottoman)
|Mirror, Mirror.....
|Colorful, cozy corner


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An entity formed by owners of Boulder Indoor Soccer has acquired a property near the heart of Boulder Junction, and documents filed with the city indicate they're moving forward on a recreational sports complex for soccer and lacrosse.
BIS Holdings LLC paid $1.5 million for 3203 Pearl St., a more than 2.5-acre parcel of land that sits just east of the RTD station- and hotel-anchored Depot Square at Boulder Junction development, BIS Holdings officials said Tuesday.
Patrick Keane, a co-owner of Boulder Indoor Soccer and a partner of BIS Holdings, said in an interview Tuesday that the plans for the property have not been finalized. That decision could be made in the coming weeks, he said.
Coburn Development, on behalf of Boulder Indoor Soccer, filed a use review application with the city for Boulder Indoor Sports on Pearl, a 33,606-square-foot recreational sports complex that would include two indoor fields, office space, a spectator deck with a bar and cafe for refreshments, and one outdoor field to be added at a later time. The facility would be used for soccer and lacrosse, according to documents filed with the city.
"The Boulder Indoor Soccer team is committed towards providing a healthy and fun place for soccer enthusiasts to collaborate within the sport and help foster the development of players both young and old," officials wrote in the application. "The team is proposing to create a high-quality facility on the 3203 Pearl site that not only meshes well with surrounding uses, but also provides a new dynamic to the already diverse fabric of the Old Pearl District."
When asked about the Boulder Indoor Sports on Pearl facility, Keane declined to comment.
According to registration documents filed with the state, initial managers of BIS Holdings were Keane, Edwin E. Taylor, Simone Smead, Peter M. Ambrose and Patricia Agatha Ammann, who all are also co-owners of Boulder Indoor Soccer. Brendan Chatham, an attorney with Hutchinson Black and Cook LLC in Boulder, is the registered agent.
The land acquisition comes in a year of growth for Boulder Indoor Soccer, which has an 11,000-square-foot facility at 2845 29th St. in Boulder and is developing a 25,000-square-foot facility at 795 S. Sherman St. in Longmont.
The Longmont Indoor Soccer complex is scheduled to open by Sept. 30.
In an interview with the Daily Camera earlier this year, Boulder Indoor Soccer co-owner Ambrose said the company had its sights on land in Boulder for an expansion but declined to disclose details.
John R. Beaupré, a broker with Re/Max who represented property owner Boulder Pearl Ventures LLC in the transaction, and John Koval, who represented BIS Holdings, deferred comment to Keane and the principals of BIS Holdings.
Prior to its purchase, the 3203 Pearl property was eyed by a local businessman who aimed to build the Boulder Sporting Club, a facility with indoor fields for soccer, lacrosse and futsal — a Portuguese variation on soccer — in addition to an outdoor eight-vs-eight soccer field.
Rodrigo Garcia, owner of Boulder-based Anderson-Garcia Construction, filed a use review application in 2012 with the city of Boulder for the development of the Boulder Sporting Club. Earlier this year, Garcia said he was in discussions to purchase the property.
When reached Tuesday, Garcia said he does not have any future plans for the Boulder Sporting Club.


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A planter operator now has more real-time planting information with Precision Planting¹s new 20/20 SeedSense system. SeedSense lets the operator see on-the-go population, singulation, skips and multiples. It gives speed by row, down pressure and ground contact. As a result, a grower can see a problem as it happens and fix it in the field.
The new SeedSense is made up of a display, processor, row-unit module and downforce sensor. The system works with existing seed sensors and connections, so it installs quickly.
The base unit sells for $5,400 and includes three row-unit modules and downforce sensors with harness and mounts. Contact Precision Planting, Dept. FIN, 23207 Townline Rd., Tremont, IL 61568, 309/925-5050, www.precisionplanting.com.


text: The Obama Administration does not support blowing up planets. Nor did it expect federal employees to work the day before Christmas. It won't impeach President Obama or reallocate defense funds to NASA. But the White House will share its official home brew recipe – it's not classified. They'll share it. All you had to do was ask, and 12,240 people did, as part of the White House's We the People petition initiative. Launched in September 2011, the petition system lets users create petitions for just about anything they can dream up (though, of course, the petitions and site are tightly moderated). Then, after garnering an initial 150 electronic "signatures," the petitions are posted online. If, after 30 days, a petition has earned enough signatures, the White House promises to issue an official response. But there's a problem. The petition system has become too popular. The initial benchmark of 5,000 signatures was too easy to achieve, and was quintupled to 25,000 in October 2011. On Jan. 15, the White House again bumped up the threshold to 100,000, so only the most popular ideas would rise to the top. Now there's a petition to repeal that decision (signatures: ~700), and one asking to the administration to abolish what has become an "irritating sideshow" (signatures: 700+), and another asking the White House to please take the petitions seriously (signatures: 37,000+. Response: We're listening. Seriously.). Since September 2011, nearly 10 million signatures have been entered on the more than 141,000 petitions created. In the last two months of 2012 alone, 73,000 new petitions were created and 2.4 million people joined the system. As of Jan. 24, there are more than 285 petitions awaiting signatures. The most popular, by far, is the request to legally recognize the Westboro Baptist Church as a hate group (signatures: 325,000+). Many of the petitions are requesting some form of tax regulation or gun control, or a ban on gun control, or a pardon for a convicted criminal. But among the most recent petitions are some that relate to science and tech. Like, for example, the petition asking the administration to consider building a Death Star; 34,435 signatures later, it received the now-famous, fantastically space-nerdy, official, "No." In this gallery, we've collected some of our other favorite science-related petitions. And of course, included the White House homebrew recipe. Because if there's one thing we at Wired Science love as much as science, it's beer. White House Home Brew Ale to the Chief: White House recipes for Honey Ale and Honey Porter. White HouseShow Us the Aliens Petition Signatures: ~1,860 Roswell. Area 51. Beeping robotic spaceballs. Aliens with a bizarre interest in anal anatomy. It's a trend among petitioners: The plea for transparency about contact with extraterrestrials. This petition, filed Jan. 1, suggests that such disclosures will usher in "A golden age of peace, prosperity, health, and abundance for all humans [and non-humans] on Earth." Already, the White House has responded to similar requests. "The fact is we have no credible evidence of extraterrestrial presence here on Earth," an earlier response states. "Why continue the cover-up? The secrets? It is 2013. We know better. It is time to unite. We are all one," says the most recent petition, as if there's additional evidence yet to be disclosed. Believe us, people. We are just as eager as the rest of you to find out whether we are alone in the vast universe. But there is no proof yet. Patience. Image: NCReedplayer/Flickr First-Generation Starship Petition Signatures: ~7,200 "Few things could collectively inspire people on Earth more than seeing the Enterprise being built in space," reads this petition, filed December 22 by BuildtheEnterprise.org. The petition also claims that constructing a first-generation USS Enterprise-like starship falls within today's technological capability, and humbly suggests that the White House assign NASA to conduct a feasibility and design study. Though it would take 20 years to build, the interplanetary vessel would eventually "go on amazing missions" – and, we hope, avoid Tribbles. Note: This petition has been taken down after failing to attract enough signatures by the deadline. Screen grab is below. Image: jeffc5000/Flickr Protect Sasquatch! Petition Signatures: ~1,100 If the creators of this petition have their way, Bigfoot and his kin will be recognized as an indigenous species and "lawfully protected by laws." The laws would ban the hunting, trapping, or killing of these hairy ape-like creatures that mysteriously elude efforts by scientists to verify their existence. Except, of course, by a veterinarian at DNA Diagnostics who claims to have acquired and sequenced Sasquatch DNA. Image: Peachland Joe/Flickr Open-Access Publishing Petition Signatures: ~60,200 Free access to scientific journal articles arising from taxpayer-funded research is essential, argues this petition, filed in May 2012. "Requiring the published results of taxpayer-funded research to be posted on the Internet in human and machine readable form would provide access to patients and caregivers, students and their teachers, researchers, entrepreneurs, and other taxpayers who paid for the research," the petition says. Though this petition crossed the signature threshold in June, there doesn't appear to be an official White House response yet. The open-access debate has been raging between scientists and journal publishers for a while, and recently rose to greater visibility with the death of computer activist Aaron Swartz, a champion of open-access publishing. In September 2010, Swartz used MIT's network to download and liberate millions of journal articles that originally resided behind a paywall. After he was caught, Swartz was aggressively investigated and threatened with what many consider to be disproportional criminal repercussions. Coincidentally, there's also a petition to remove U.S. District Attorney Carmen Ortiz – blamed by many for the aggressive investigation of Aaron Swartz – from office (signatures: 43,000+). Image: Biblioteekje/Flickr Develop a Nuclear Space Rocket Petition Signatures: ~2,300 The six-word summary: Nuclear. Rocketship. To. Another. World. Now. "This is not new technology," says the petition, filed Jan. 3. "The physics and engineering are sound." Image: NASA Remove Congressman Paul Broun from the United States House Committee on Science, Space, and Technology Petition Signatures: ~8,700 "All that stuff I was taught about evolution and embryology, Big Bang theory -- all that is lies straight from the pit of hell," congressman Paul Broun (R-GA) said in October. He continued, "There are a lot of scientific data, that I've found out as a scientist [Broun holds an M.D.], that actually show that this is really a young Earth. I don't believe that's Earth's but about 9,000 years old." Filed Jan. 18, this petition suggests that Broun's preference for religious teachings affects the decisions he makes as a member of the House Committee on Science, Space, and Technology. That's right: Broun is a member of the congressional committee that oversees non-defense federal research at agencies like NASA, NOAA, NSF, and USGS. In 1958, congress created the committee's predecessor -- the House Committee on Science and Astronautics -- after the Soviets launched Sputnik 1. One of the committee's first acts was to create NASA. Over the years, its reach expanded to include environment, alternative energy sources, weather, and atomic energy research programs. Video: Bridge Project 21/YouTube Lose the Pounds Petition Signatures: ~35,400 The British Imperial System – which measures things in units of feet, miles, pounds, gallons, and more – is chaotic and convoluted, argues this petition, filed in December. "We [the U.S.] stubbornly still adhere to using the imprecise Imperial Unit -- despite the fact that practically every other country that we interact with uses Metric," it says. But the metric system – which measures things in units like kilograms, meters, and liters – isn't without its problems; perhaps most significantly, the standard kilogram isn't as standard as it ought to be. Maybe we ought to consider adopting the Potrzebie System of Weights and Measures, or measuring things in Sagans and Smoots. Image: Nils Geylen/Flickr Make a $1 Trillion Coin Petition Signatures: ~11,200 The idea of minting a single platinum coin worth one trillion dollars is "No more absurd than playing political football with the US -- and global -- economy at stake,"says this petition, filed Jan. 3. At Wired Science, we approached this suggestion from a more arithmetical point of view, and calculated the value of a platinum coin the size of a silver dollar -- about $1200. And though it's not what's being considered, a coin minted from $1 trillion worth of platinum would be too big to fit in any bank, too heavy for your average wallet: weighing almost 43 million pounds, the coin would be roughly 80 feet across and 6 feet thick. Image: Alchemist-hp/Wikimedia commons Make Distributed Denial of Service a Legal Form of Protest Petition Signatures: ~5,600 Submitted by hacktivist group Anonymous on Jan. 7, this petition asks the White House to consider decriminalizing the server-flooding tactic that knocks websites offline. DDoS maneuvers have been used on a number of targets, including U.S. and British government websites. The petition suggests that DDoS is not so much an "attack," but the Internet equivalent of a sit-in or the Occupy protests. "Instead of a group of people standing outside a building to occupy the area, they are having their computer occupy a website to slow (or deny) service of that particular website for a short time," the petition reads. Image: pameladrew2012/Flickr Dump Daylight Saving Time Petition signatures: ~5,700 First conceived by Benjamin Franklin, Daylight Saving Time is still a bone of contention. "Every year, 'Spring forward' causes clear and obvious loss of productivity: time required to adjust clocks, missed meetings, grumpy/confused/tired people, stressed parents...," says this petition, filed Jan. 12. We're not sure what kind of crazy-ass clock you guys are working with, but there are compelling arguments both for and against Daylight Saving Time. Regardless of which camp you align with, one thing is clear: It's damn confusing having some states on, some states off, some countries on, others off. And the recent switch in switching clocks doesn't help matters. Let's sort it out. Image: Wikimedia Commons


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We almost made it! We are almost there. Yes, the end of the semester is upon us. Before you enjoy your graduation or semester break, though, please enjoy the last 2012 offering of your favorite newsletter, The Pink Flamingo.
- Congratulations, December Graduates
- And More Congratulations…to University Award Winners
- And Even More Congratulations…to the Experimental Psych Poster Session Winners
- The Pink Flamingo Mailbag
- So…Enjoy Your Winter "Break"!