text:
\section{Introduction}
A chromosome is a long sequence of double  helix  DNA made of base
pairing by an adenine-thymine($A=T$) pair or a
cytosine-guanine($C\equiv G$). Thus, one DNA strand decides the
sequence of its complementary strand. A segment of DNA sequence with
half length greater than or equal to a pre-specified length $L$ is
called a palindrome if one strand is identical to its complementary
one running at the reverse direction. It has been observed that DNA
palindromes are common candidates for searching genetic motifs
involved in different cellular processes, including gene
transcriptions, gene replications, and gene deletions. For example,
among nine octameres suggested to be transcription factor binding
sites, three are palindromes (FitzGerald et al, 2004). This might be
contributed by its potential to create the secondary genomic
structure (Leach, 1994).

Many studies have focused on investigating the occurrence rates of
palindromes in suspicious regions against random sequences. For
example, Lisnic and Svetec (2005) investigated the frequencies of
Palindromes in the yeast {\it Saccharmyces cerevisiae} genome
according to the length and contents of palindromes. Chew et al
(2005) proposed three score schemes, based on occurrence rates,
length or its likelihood, to quantify the palindromes and found the
association between the high score regions and the replication
origins. Lu et al (2007) reported that meaningful sites tend to have
higher palindrome scores by comparing the scores over the regions
including introns, exons, and upstream of transcription start sites
against simulated random sequences.

The performance of these comparison tests strongly depends on how
accurate the occurrence rate is estimated for the random sequence.
This rate is usually estimated by the average rate of palindromes on
the genome-wide sequence. Another approach is the iid model based
estimator which a formula has been derived when the DNA letter
frequencies are estimated (Chew, et al, 2005).  However, we observed
obvious discrepancies between these two estimates in various herpes
virus genomes. For an example on the BHV1CGEN(BoHV1) sequence,
average rate is 0.00166 and the iid model method estimate  the rate
as 0.00073. While the average rate might be bias due to hot spot
regions, the iid model might be too naive to describe the DNA
sequence. In this paper, we {provided} a formula to calculate the
occurrence rate under a Markov model, which the iid model would
become a special case.  For the BoHV1 case, our method estimates the
rate as 0.00098. Simulations are designed to check the performance
of the estimates on the null occurrence rate, including with and
without hot spot segments in the random sequences. The results show
 that our method performs better than the average rate in estimating the
 null occurrence rate against hot spot regions.

Chan and Zhang (2007) developed a method to approximate the p-value
of statistics for weighted Poisson process, which can be applied on
the DNA palindrome problems. In their approach, the analytic formula
for the moment generating function (MGF) of the palindrome score is
required. However, the distribution of the palindrome scores have
not been well studied except the length score under iid assumption.
Thus, we developed a method to derive the analytic formula for the
MGF on various scores under Markov model.
 Furthermore, this
analytic formula allows us to calculate an overshoot term in the
p-value approximation.

This paper is organized as follows.  In section 2, we show that
three commonly used scores proposed by Chew et. al. (2005) can be
derived by a likelihood approach firstly. Secondly, we show that the
occurrence rates can be calculated accurately under Markov model
through constructing a quasi transition matrix $T$. Thirdly, we
derive the moment generating function for various scores under the
Markov model. Last, we gave a p-value approximation with more
precise calculations on the overshoot term. In section 3, we show
the numerical study for both real data and simulated data. This
paper ends with a brief discussion.

\section{Method}

\subsection{Notations and Log Likelihood Ratio Statistics}

Let $N(t)$ be a counting process to describe the occurrence of
palindromes and let $N_w(t)=N(t+w)-N(t)$ denote the number of events
in the interval $(t, t+w]$. Leung et al (2005) proved that $N(t)$
can be approximated by a Poisson process under Markov Model. We let
$x_i$ be the score for the $i^{th}$ event along the genome sequence.
$S_{N_w(t)}$ is the summation of the Palindrome scores inside the
interval $(t, t+w]$, which can be expressed by equation (\ref{101}):
\begin{eqnarray}
S_{N_w(t)}=\sum_{i=N(t)+1}^{N(t+w)}x_i.\label{101}
\end{eqnarray}

To search the clusters of palindromes, Chew et al (2005) proposed 3
schemes on scoring palindromes for prediction of replication origins
in herpes viruses. They are palindrome count score(PCS), palindrome
length score(PLS), and base-pair weighted score of order m
($BWS_m$). PCS gives score one for each DNA palindrome; PLS gives
the score as the palindrome length divided by its minimum required
lenth; whereas $BWS_m$ gives the score as the minus log-likelihood
with Markov order $m$.

We would like to show that both $N_w(t)$ and $S_{N_w(t)}$ are
equivalent to some log-likelihood ratio statistics when the
alternative hypotheses are properly constructed. Under the Poisson
process model, $x_i$'s can be treated as iid with a density function
{$f_{\theta}(x)=f_0(x)\exp(\theta x - \phi(\theta))$, where $f_0(x)$
is an unknown distribution and $\phi(\theta)=\log \int e^{\theta
x}f_0(x)dx$.} The parameters for $N(t)$ and $x_i$ are $(\lambda_a,
\theta_a)$ for those events occurred in the interval $(t_a, t_a+w]$
and $(\lambda_0, \theta_0)$ otherwise; and the null hypothesis is
$\lambda_a=\lambda_0$ and $\theta_a=\theta_0$. When $t_a$ is known,
the likelihood ratio is
$f_{\lambda_a,\theta_a}(N_w(t_a),S_{N_w(t_a)})/
f_{\lambda_0,\theta_0}(N_w(t_a),S_{N_w(t_a)})$, where the likelihood
is as follows:
\begin{eqnarray}
&&f_{\lambda,\theta}(N_w(t),S_{N_w(t)})\nonumber\\
&=&f_{\lambda}(N_w(t))
f_{\theta}(S_{N_w(t)}|N_w(t))\nonumber\\
&=&{(\lambda w)^{N_w(t)}e^{-\lambda w}\over N_w(t)!}{\{\prod
f_0(x_i)\}}\exp(\theta
S_{N_w(t)}-N_w(t)\phi(\theta)).\nonumber\end{eqnarray}

Because $t_a$ is usually unknown, we search the maximum of the
statistic over all possible $t$.
\begin{itemize}
\item [Case 1.]
If the alternative hypothesis is constructed as $H_a:~$
$\lambda_a=\lambda_1>\lambda_0$ and $\theta_a=\theta_0$, then the
log-likelihood ratio statistic is equivalent to PCS in Chew et al
(2005), which is shown as follows
\begin{equation}\label{103}
\max_{t}l_t(\lambda_1,\theta_0)=\max_t\log\left({f_{\lambda_1,\theta_0}(N_w(t),S_{N_w(t)})
\over f_{\lambda_0,\theta_0}(N_w(t),S_{N_w(t)})}\right)=\max_t
N_w(t)\log({\lambda_1\over \lambda_0})-(\lambda_1-\lambda_0){w}.
\end{equation}

\item [Case 2.]
If the alternative hypothesis is constructed as $H_a:~$
$\lambda_a=\lambda_1>\lambda_0$ and $\theta_a=\theta_1>\theta_0$,
where $\lambda_1$ and $\theta_1$ are with the constraint
\begin{equation}\label{constraint}
\log({\lambda_1\over\lambda_0})- (\phi(\theta_1)-\phi(\theta_0))=0,
\end{equation}
the log-likelihood ratio statistic in formula (\ref{104}) can be
equivalent to PLS or $BWS_m$ proposed by Chew et al (2005),
depending on the definition of $x_i$'s.
\begin{eqnarray}\label{104}
\max_tl_t(\lambda_1,\theta_1)&=&\max_t\log\left({f_{\lambda_1,\theta_1}(N_w(t),S_{N_w(t)})
\over
f_{\lambda_0,\theta_0}(N_w(t),S_{N_w(t)})}\right)\nonumber\\
&=& {\max_t
\big\{-(\lambda_1-\lambda_0)w+(\theta_1-\theta_0)S_{N_w(t)} \big\}}
\end{eqnarray}
\end{itemize}

It can be observed that (\ref{103}) is equivalent to $\max_t N_w(t)$
and (\ref{104}) is equivalent to $\max_tS_{N_w(t)}$. While
(\ref{103}) only tests the Poisson parameter $\lambda$, (\ref{104})
tests both the Poisson parameter $\lambda$ and score parameter
$\theta$ with the constraint (\ref{constraint}). It may be helpful
to be reminded that $ N_w(t)$ can be treated as a special case of
$S_{N_w(t)}$ with $x_i=1$ for each $i$.

Chan and Zhang (2007) developed an approximation method to calculate
p-value of the scan statistics on a weighted Poisson process, which
can be applied to derive the threshold value of (\ref{101}) if the
MGF $\phi(\theta)$ of $x_i$ is properly formulated. Let $N(t)$ be a
Poisson process with mean $\lambda_0$ and moment generating function
(MGF) $x_i$'s are iid with {mean $\mu_0$}, then

\begin{eqnarray}\label{102}
&&\mathrm{P}_0(\max\limits_{0 <t< W}S_{N_w(t)} \geq b)\nonumber\\
&\sim& 1-exp\left(-(W-w) \nu_{\lambda_1,\theta_1}( b- \lambda_0
\mu_0)e^{-[b\theta_1-w(\lambda_1-\lambda_0)]} (2 \pi w \lambda_1
\phi''(\theta_1))^{-1/2}\right),
\end{eqnarray}
where $W$ is the total length of the sequence {and}
$\nu_{\lambda_1,\theta_1}$ is an overshoot correction term and
$\theta_1$ and $\lambda_1$ satisfy the equations:
\begin{eqnarray*}
&&\lambda_1\phi'(\theta_1)=b,\\
&&\log(\lambda_1/\lambda_0)={\phi(\theta_1)-\phi(\theta_0)}.
\end{eqnarray*}

Whether $ N_w(t)$ or $S_{N_w(t)}$ is used in testing the null
hypothesis, $\lambda_0$ always plays a crucial role.  If $\lambda_0$
is overestimated seriously, the test would be too conservative and
lose its power. Alternatively, if $\lambda_0$ is underestimated
seriously, the test would fail.

\subsection{Occurrence rate of DNA palindromes under Markov model}

The average rate is a commonly used estimator for the null parameter
of scan statistics. Yet, in various herpes virus genomes, it can be
observed that the average rate is positive bias affected by some hot
spot regions. On the other hand, the iid mode may not be a good
model to describe the DNA sequence well since it ignores the
correlation between adjacent DNA letters. Thus, we developed a
method to calculate the occurrence rate of the palindromes under a
Markov model. We constructed a matrix $T$, with
$T_{ij}=P_{a_ia_j}P_{\tilde{a}_j\tilde{a}_i}$ which groups together
the transition probabilities of symmetric complimentary pairs. For
example, AG  would conjugate with CT on its mirror site which leads
to define $T_{13}=P_{AG}P_{CT}$, and we call $T$ a quasi transition
matrix because its row does not sum to one.

\noindent{\bf Theorem 1} Assume that DNA letters along the genome
sequence follow a Markov model with transition probability $\{P_{a,
b}|a,b \in \{A,C,G,T\}\}$ and the letter frequency $P_0'=
(\pi_{A}~\pi_{C}~\pi_{G}~\pi_{T} )$, then the occurrence probability
of a palindrome given a starting position with half length greater
or equal to $L$ is
 \begin{equation}\label{201}
 \lambda_M\equiv P\left(\parallel I \parallel \ge L \right)
 = P'_0 T^{L-1} P_1
 \end{equation} {where $I$ describes the palindromic pattern given a starting position and $\| I\|$ denotes
 the corresponding maximum length},
 \begin{eqnarray}
P_1'&=& \left(P_{AT}~P_{CG}~P_{GC}~P_{TA} \right),\nonumber
\end{eqnarray} and
$$ T = \left(\begin{array}{cccc}
P_{AA}P_{TT} & P_{AC}P_{GT} & P_{AG}P_{CT} & P_{AT}P_{AT} \\
P_{CA}P_{TG} & P_{CC}P_{GG} & P_{CG}P_{CG} & P_{CT}P_{AG} \\
P_{GA}P_{TC} & P_{GC}P_{GC} & P_{GG}P_{CC} & P_{GT}P_{AC} \\
P_{TA}P_{TA} & P_{TC}P_{GA} & P_{TG}P_{CA} & P_{TT}P_{AA}
\\ \end{array} \right).$$

\noindent{\bf Proof:}  The set that a DNA palindrome with half
length greater or equal to $L$, is equivalent to the set that the
center $2L$ letters follows a palindrome pattern. Given a sequence
of length $2L$, it must satisfy that $a_{L+k}={\tilde a}_{L-k+1}$ to
become a palindrome, $\tilde{a}_{i}$ means the complementary letter
of $a_i$. Then, under a Markov model, we can sum the probability
over all possible the letters and get $\lambda_M$.

\begin{eqnarray}
\lambda_M=&& P\left(\parallel I \parallel \ge L
\right)\nonumber\\
&=&\sum_{\scriptstyle a_i\in{\{A,C,G,T\}} \atop \scriptstyle 1\le i
\le L}\pi_{a_{1}}P_{a_{1}a_{2}} \ldots
P_{a_{L-1}a_{L}}P_{a_{L}\tilde{a}_{L}}P_{\tilde{a}_{L}\tilde{a}_{L-1}}
P_{\tilde{a}_{L-1}\tilde{a}_{L-2}} \ldots
P_{\tilde{a}_{2}\tilde{a}_{1}}\nonumber\\
&=&\sum_{\scriptstyle a_i\in{\{A,C,G,T\}} \atop \scriptstyle 1\le i
\le L}\pi_{a_{1}}\left(P_{a_{1}a_{2}}
P_{\tilde{a}_{2}\tilde{a}_{1}}\right)\ldots
\left(P_{a_{L-1}a_{L}}P_{\tilde{a}_{L}\tilde{a}_{L-1}}\right)
P_{a_{L}\tilde{a}_{L}} \label{202}\\
 &=& P'_0 T^{L-1} P_1\nonumber
\end{eqnarray}

$P_{a_i,a_{i+1}}$ is the transition probability for letter $a_i$ to
letter $a_{i+1}$. $T$ is the matrix form of $(P_{a_{1}a_{2}}
P_{\tilde{a}_{2}\tilde{a}_{1}})$. $(\ref{202}$) can be viewed as a
matrix multiplication: a row vector multiplies a matrix to the power
of L and then multiplies with a column vector. This technique is
used repeatedly in this paper, including the proof for Theorem 3.

 \noindent{\bf Remark 1:} When the Markov model is
reduced to the iid model, $P_1'$ becomes
$$P_2'=\left(\begin{array}{cccc}
\pi_{T} & \pi_{G} & \pi_{C} & \pi_{A} \\
\end{array} \right),
$$ and $T$ becomes $P_2P_0'$. Thus,
{
\begin{equation}\label{203}
 \lambda_{\text{iid}}\equiv P\left(\parallel I \parallel
\ge L
\right)=P_0'(P_2P_0')^{L-1}P_2=(P_0'P_2)^L=\gamma^{L},
\end{equation}
} where $ \gamma = 2\left(\pi_{A}\pi_{T}+\pi_{C}\pi_{G}\right)$.
$(\ref{203})$ has been shown in
Leung et al(2005).\\

\noindent{\bf Theorem 2} With the same assumption in Theorem 1, the
PLS score for the $i^{th}$ palindrome is defined as $x_i=\|I_i\|/L$
conditional on $\|I_i\|\ge L$, where $L$ is the minimum half length
for the palindrome. Then, the MGF for $x_i$ is
\begin{equation}\label{204}
K_{PLS}(t)\equiv E\left(e^{x_it}|\|I_i\|\ge L\right)= {e^{t}\over
\lambda_M}P'_0T^{L-1}[I-e^{t/L}T]^{-1}[I-T]P_1
\end{equation}

\noindent{\bf Proof of Theorem 2}

\begin{eqnarray}
 &&E\left(e^{x_it}| \|I_i\|\geq L \right) \nonumber\\
 &=&\sum_{k=L}^{\infty}e^{kt/L}[P(\|I_i\|\ge k)-P(\|I_i\|\ge
 k+1)]/P(\|I_i\|\ge L)\nonumber\\
&=&P_0' \sum_{k=L}^{\infty}e^{kt/L}T^{k-1}(I-T)P_1/\lambda_M\nonumber\\
&=&{e^{t}\over \lambda_M}P'_0T^{L-1}[I-e^{t/L}T]^{-1}[I-T]P_1
\end{eqnarray}

 \noindent{\bf Remark 2:} When the Markov model is reduced to iid
model,
$$K_{PLS}(t)=\sum_{k=L}^{\infty}e^{kt/L}(\gamma^k-\gamma^{k+1})/\gamma^L
={e^t(1-\gamma)\over 1-e^{t/L}\gamma}.$$

\noindent{\bf Theorem 3} With the same assumption in Theorem 1, the
BWS score is defined as $x_i=-log( P(I_i))$ conditional on
$\|I_i\|\ge L$. Then, the MGF for $x_i$ is
\begin{eqnarray}\label{205}
K_{BWS}(t) \equiv \mathrm{E}[e^{x_it} | \|I_i\| \geq L] =
\frac{1}{\lambda_{M}}{\bf v'}(t)[I-Q(t)]^{-1}[Q(t)]^{L-1}{\bf u}(t),
\end{eqnarray}
where
 ${\bf v}(t)=(v_1(t)~v_2(t)~v_3(t)~v_4(t))'$ is defined as
${v}_i(t)=\big( [(I-T)P_0]_i\big)^{1-t}$; $Q(t)$ is defined as
$Q_{ij}(t) = (T_{ij})^{(1-t)}$; and ${\bf
u}(t)=(u_1(t)~u_2(t)~u_3(t)~u_4(t))'$ is defined as ${ u}_i(t)
=\left([P_1]_i\right)^{1-t}$ with $i=1,\cdots, 4$.

 \noindent{\bf Proof of Theorem 3}

\begin{eqnarray*} &&P(I_i=a_1\cdots
 a_k\tilde{a}_k\cdots\tilde{a}_1,
 \|I_i\|=k)\\
 &=&\big\{(\pi_{a_1}-\sum\limits_{a_0 \in \{A,C,G,T\}}
 \pi_{a_0}\mathrm{P}_{a_0a_1}\mathrm{P}_{\tilde{a}_1\tilde{a}_0})
 \mathrm{P}_{a_1a_2}\cdots\mathrm{P}_{a_{k-1}a_k}\mathrm{P}_{a_k\tilde{a}_k}
 \mathrm{P}_{\tilde{a}_k\tilde{a}_{k-1}}
 \cdots\mathrm{P}_{\tilde{a}_2\tilde{a}_1}\big\}.
 \end{eqnarray*}

 Thus, we have
\begin{eqnarray}\label{206}
&&K(t,k)\nonumber\\
&\equiv& \mathrm{E}[e^{x_it} ; \|I_i\|=k]=\mathrm{E}[\left(P\{I_i \text{~occurs}\}\right)^{-t} ; \|I_i\|=k]\nonumber\\
&=& \sum\limits_{a_j \in \{A,C,G,T\} \atop {1\leq j \leq k}}
\big\{(\pi_{a_1}-\sum\limits_{a_0 \in \{A,C,G,T\}}
\pi_{a_0}\mathrm{P}_{a_0a_1}\mathrm{P}_{\tilde{a}_1\tilde{a}_0})
\mathrm{P}_{a_1a_2}\cdots\mathrm{P}_{a_{k-1}a_k}\mathrm{P}_{a_k\tilde{a}_k}\mathrm{P}_{\tilde{a}_k\tilde{a}_{k-1}}
\cdots\mathrm{P}_{\tilde{a}_2\tilde{a}_1}\big\}^{(1-t)}\nonumber\\
&=& \sum\limits_{a_j \in \{A,C,G,T\} \atop {1\leq j \leq k}}
\big(\pi_{a_1}-\sum\limits_{a_0 \in \{A,C,G,T\}}
\pi_{a_0}\mathrm{P}_{a_0a_1}\mathrm{P}_{\tilde{a}_1\tilde{a}_0}\big)^{(1-t)}
\left(\mathrm{P}_{a_1a_2}\mathrm{P}_{\tilde{a}_2\tilde{a}_1}\right)^{(1-t)}
\times \cdots \nonumber\\
&&~~~~~~~~~~~~~~~~\times \left(\mathrm{P}_{a_{k-1}a_k}\mathrm{P}_{\tilde{a}_k\tilde{a}_{k-1}}\right)^{(1-t)}
\left(\mathrm{P}_{a_k\tilde{a}_k}\right)^{(1-t)}\nonumber\\
&=& {\bf v'}(t) [Q(t)]^{k-1}{\bf u}(t).
\end{eqnarray}

Then, taking the sum over $k=L$ to $\infty$ and dividing by
$\lambda_M$ lead to $(\ref{205})$.

\noindent{\bf Remark 3}\\
When the Markov model is reduced to iid model, (\ref{206}) becomes
$$K(t,k)=(1-\gamma)^{1-t}P'_0(t)(P_2(t)P'_0(t))^{k-1}P_2(t)
=(1-\gamma)^{1-t}(P'_0(t)P_2(t))^k=(1-\gamma)^{1-t}\gamma_t^k,$$
where $P'_0(t)=(\pi_A^{1-t}~\pi_C^{1-t}~\pi_G^{1-t}~\pi_T^{1-t})$,
$P'_2(t)=(\pi_T^{1-t}~\pi_G^{1-t}~\pi_C^{1-t}~\pi_A^{1-t})$, and
$\gamma_t=P'_0(t)P_2(t)=2[(\pi_A\pi_T)^{1-t}+(\pi_C\pi_G)^{1-t}]$.
So, for iid model,
\begin{equation}\label{207}
K(t)={(1-\gamma)^{1-t}\over
1-\gamma_t}\left({\gamma_t\over\gamma}\right)^L.
\end{equation}

\noindent{\bf Remark 4}\\
The conditional process involved in the overshoot term in the
p-value approximation can be approximated by a partial sum of iid
copies of $y =  (-\sum\limits^{N(\Delta)}_{k=1}x_k +
\sum\limits^{N^*(\Delta)}_{k=1}x^*_k)$, where $N(\cdot)$ and
$N^*(\cdot)$ are iid Poisson processes with rates $\lambda_0$ and
$\lambda_1$; $x_i$'s and $x_i^*$'s are independent random variables
with density functions $f_{\theta_0}$ and $f_{\theta_1}$. The
derivation is in the appendix. By the same method in Theorem 3 and
Theorem 4, the characteristic function of $y$ can be derived.
Applying Theorem 1 in Tu(2009), the overshoot term can be
calculated.

\section{Real Data Analyses and Simulations}

We studied 27 herpesvirus genome sequences from the database of EBI
Nucleotide Sequences. For each sequence, we estimated the transition
matrix and the stationary probabilities of DNA letters
$\{\text{A,C,G,T}\}$. {\bf Theorem 1} is applied  to estimate the
null occurrence rate for each sequence. These results are compared
with those estimated by their average rates in Figure \ref{f1}. The
average rates show higher values consistently.

\begin{center}
\smallskip
\begin{figure}
\includegraphics[width=0.8\textwidth]{gp.eps}
\caption{ \label{f1} 27 herpes virus genomic sequences were
downloaded from {the database of EBI Nucleotide Sequences}. Two
methods for estimating the null palindrome rates are presented,
including the average rate, and the Markov model based estimator. We
adopted the abbreviation for naming the genome sequences used in
Leung et al. (2005)}
\end{figure}
\end{center}

We also checked the accuracy performance of these two methods
through numerical simulation. While a real DNA sequence may contain
meaningful DNA codes which contribute to its non-randomness, random
sequences are generated to fit the null hypothesis.  All the
parameters involved in generating the random sequences, including
the stationary probabilities $\pi$ and the transition matrix $P$,
are estimated on the BoHV1 sequence. BoHV1 sequence, with sequence
ID BHV1CGEN, contains 135301 bases. The state probabilities are
estimated as
  $$\pi= ( 0.1354(A) ,   0.3588(C),    0.3654(G),   0.1404(T))$$ and the transition
probabilities are
$$P=\left(\begin{array}{ccccc} &A&C&G&T \\
A & 0.1854& 0.3288& 0.3556& 0.1303\\
C & 0.1258& 0.2932& 0.4347& 0.1463\\
G & 0.1343& 0.4512& 0.2994& 0.1151\\
T & 0.1141& 0.3151& 0.3695& 0.2012\\
\end{array} \right).$$

 The half length $L=6$ is adopted
to be the criterion as a palindrome event.  Palindrome events along
these random sequences could be well approximated by a homogeneous
Poisson process. It may be helpful to be reminded that, in this
case, the average rate $\bar{\lambda}$ is the maximum likelihood
estimator (MLE) for the occurrence rate. Our simulation shows that
both these two methods do the estimate well in the first numerical
row of Table 1.

\begin{table}
\centering
\begin{tabular}{|ccc|c|c|}
\hline $a_1$ & $a_2$ & $a_3$ & $\bar{\lambda}$ &  $\hat{\lambda}_M$ \\
\hline
 1&1&1        &.001078    &.001099\\ \hline
 10 & 10 & 10 &.001402    &.001110\\ \hline
 10 & 10 & 20 &.001515    &.001113\\ \hline
 10 & 20 & 20 &.001643   &.001117\\ \hline
 20 & 20 & 20 &.001739    &.001142\\ \hline
 30 & 30 & 30 &.002105   &.001135\\ \hline
\end{tabular}
\caption{ \label{t3} Tho methods for estimating the null occurrence
rate of palindrome sequences are compared when non-random clusters
exist. For each random sequence, three non-random clusters are
inserted with adjustable occurrence rates: $\lambda_i=a_i\lambda_0$,
$1\le i\le 3$. $\lambda_0=.00098$. The first row, with
$a_1=a_2=a_3=1$, means complete random sequence with no hot. }
\end{table}

The validity that the average rate can be a null parameter estimator
is based on the assumption that the number of events from non-random
clusters is much smaller than the total number of events. However,
this assumption may not work for a real DNA sequence. It has been
observed that meaningful sites in the sequence tends to have higher
palindrome rates. The average rate usually overestimates the null
occurrence rates. Here, we design a simulation experiment to check
the robustness of the estimates against  hot spot regions.

For each random sequence, we insert three hot spot segments with
length 1000 base pairs at different positions. The inserted segments
contain  palindromes  which are randomly resampled from the
palindrome bank.  The palindrome bank collects all the DNA
palindromes from BoHV1 sequences. We assigned three occurrence rates
for the three segments as $\lambda_i=a_i\lambda_0$, $1\le i\le 3$
and $\lambda_0=.00098$ is estimated by Markov model for BoHV1
sequence. $a_i$'s are to quantify the intensities of hot spots. The
simulation results for various components of $(\lambda_1, \lambda_2,
\lambda_3)$ based on 500 repeats are presented in Table \ref{t3}.
The estimators based on model calculation increase less than $8\%$
while the estimator based on the average rate almost doubles, when
the occurrence rates in the hot-spot regions  increase to 30 folds.

Overestimating the occurrence rate would increase the threshold
value for testing hypothesis and lead to power loss. The simulation
for power comparisons in Table 4 is designed as that of Table 3.
Table \ref{t4} shows the powers for detecting each of the three hot
spot regions of DNA palindromes.  We applied the PLS scores and BWS
scores with window size 1000 bp to scan the whole genome. The
calculation for threshold values follows Chan and Zhang (2007) on
weighted scan statistics, with modification on the overshoot term,
which is shown in the appendix of this paper. Here, power is defined
as the frequencies of detecting hot spot regions based on 500
replicates. Table \ref{t4} shows that $\hat{\lambda}_M$ can gain
powers more than 50$\%$ over $\bar{\lambda}$, when power is not
saturated.

\begin{table}
\centering
\begin{tabular}{|c|c|ccc|c|ccc|}
\hline PLS &\multicolumn{8}{c|}{ }\\
\hline \multirow{2}{*}{$(a_1,a_2,a_3)$}
&\multicolumn{4}{c|}{$\overline{\lambda}$}
&\multicolumn{4}{c|}{$\hat{\lambda}_M$}\\\cline{2-9} & Threshold
&\multicolumn{3}{c|}{Power} & Threshold &\multicolumn{3}{c|}{Power}
\\\hline (1,1,1)    &8.9063&0.0000 &0.0000 &0.0000 &9.0061 &0.0000
&0.0000 &0.0000      \\ \hline (7,7,7)    &9.6221&0.2100 &0.2025
&0.2275 &9.0399 &0.2975 &0.2900 &0.2900      \\ \hline (10,10,10)
&9.9477&0.4550 &0.5075 &0.4800 &9.0496 &0.5825 &0.6250 &0.6325
\\ \hline (10,10,20) &10.3013&0.4300 &0.5100 &0.9875 &9.0686 &0.5950
&0.6575 &0.9950      \\ \hline (10,20,20) &10.6435&0.3825 &0.9900
&0.9775 &9.0877 &0.6350 &0.9975 &0.9975      \\ \hline (20,20,20)
&11.0216&0.9675 &0.9850 &0.9850 &9.1014 &0.9900 &0.9925 &0.9975 \\
\hline
\hline BWS &\multicolumn{8}{c|}{ }\\
\hline \multirow{2}{*}{$(a_1,a_2,a_3)$}
&\multicolumn{4}{c|}{$\overline{\lambda}$}
&\multicolumn{4}{c|}{$\hat{\lambda}_M$}\\\cline{2-9} & Threshold
&\multicolumn{3}{c|}{Power} & Threshold &\multicolumn{3}{c|}{Power}
\\\hline (1,1,1)    &114.4505&0.0000 &0.0000 &0.0000 &115.7137
&0.0000 &0.0000 &0.0000      \\ \hline (7,7,7)    &123.2021&0.1950
&0.2425 &0.2625 &115.9571 &0.2700 &0.3250 &0.3200      \\ \hline
(10,10,10) &127.5283&0.5150 &0.5325 &0.5525 &116.0439 &0.6650
&0.6650 &0.6800      \\ \hline (10,10,20) &130.8699 &0.4575 &0.4625
&0.9800 &116.1847 &0.6425 &0.6325 &0.9925 \\ \hline (10,20,20)
&133.7581&0.4100 &0.9850 &0.9775 &116.1572 &0.6125 &1.0000 &0.9975
\\ \hline (20,20,20) &140.2448 &0.9825 &0.9825 &0.9750 &116.3187
&0.9950 &1.0000 &0.9925  \\ \hline
\end{tabular}
\caption{ \label{t4} Powers are compared  for using $\bar{\lambda}$
and $\hat{\lambda}_M$ to estimate the null occurrence rates of DNA
palindromes when hot spot regions are inserted. $\bar{\lambda}$
tends to be too conservative by overestimate the occurrence rates. }
\end{table}

\section{ Discussion}

Average rate is a popular method for estimating the null occurrence
rate of scan statistics. In this paper, we show  that it does not
always work through an example. Average rate can overestimate the
null occurrence rate twice the true number, in the herpesvirus
genome simulation.  We further proposed a model based estimator,
which avoids to directly count the number of events in hot spot
regions. Our method estimates the Markov parameters instead of
estimating the occurrence rate directly.

The hot spot regions have potential to contribute a large portion of
the number of events, especially when the null occurrence rate is
very low. On the other hand, when estimating the transition
probabilities for transition as well as the stationary state
probabilities under the Markov model, the hot spots have little
influence provided their size is much smaller than the total length
of the genomes. This explains why $\hat{\lambda}_M$ is not sensitive
to the hot spot effect. Our study suggests that average rate should
be carefully used for null parameter estimation, especially when the
process involves rare events with  hot spot regions, which are quite
common in epidemiology studies with rare diseases.

\section{ Appendix}

Chan and Zhang (2007) have provided a $p$-value approximation for
the scan statistics of marked Poisson processes. Here, we provide a
more general formula for calculating the overshoot term on various
distribution of $x_i$. Let $N$ be a Poisson process with constant
rate $\lambda_0
>0$ and let random variables
$x_1,\dots,x_n
 \stackrel{\mathrm{iid}}{ \sim} f_{\theta_0}(\cdot)$. Let
 $\lambda_1$ and $\theta_1$ satisfy two conditions : (a)
$\mbox{~}\lambda_1 \phi'(\theta_1)=b$. (b)
$\mbox{~}\log(\lambda_1/\lambda_0)-
(\phi(\theta_1)-\phi(\theta_0))=0$.  Then we have the following
theorem.

 \noindent{\bf Theorem 4} Let $W \rightarrow \infty$ as $w \rightarrow \infty$ such that
 $W-w \rightarrow \infty$. Then
\begin{eqnarray*}\label{A01}
&&\mathrm{P}_0(\max\limits_{0 <s< W}S_{N_w(s)} \geq b)  \approx
1-exp\bigg \{-(W-w) \nu_{\lambda_1,\theta_1}( b- \lambda_0
\mu_0)e^{-I(b)w} (2 \pi w \lambda_1 \phi''(\theta_1))^{-1/2} \bigg \},\\
&&\mbox{~with~~~~} \nu_{\lambda_1,\theta_1} = \frac{1-\mathrm{E}_0
e^{-S_{\tau_+}(\theta_1-\theta_0)}}{(1-e^{-(\theta_1-\theta_0)
})\mathrm{E}_0 S_{\tau_+}}.
\end{eqnarray*}
 \noindent{\bf Proof of Theorem 4}\\
Assume that the process is observed on the set $\{t_j|t_j=j\Delta,
0\le t_j\le W\}$, where $\Delta=o(w)$, then we have the inequality:

\begin{eqnarray*}
\mathrm{P}(\max_{0 \leq j\Delta \leq W}S_{N_w(j\Delta)} \ge b) \leq
\mathrm{P}( \max\limits_{0  \leq s \leq W} S_{N_w(s)} \ge b) \leq
\mathrm{P}(\max_{0 \leq j \Delta \leq W}S_{N_{w+\Delta}(j \Delta)}
\ge b).
\end{eqnarray*}
{ It can be shown that $ \mathrm{P}( \max\limits_{0  \leq s \leq W}
S_{N_w(s)} \ge b)$ converges when $w$ converges to a constant such
that $\lim_{\Delta\rightarrow 0}\mathrm{P}( \max\limits_{1 \leq i
\leq W/\Delta} S_{N_w(i\Delta)} \ge b)= \mathrm{P}( \max\limits_{0
\leq s \leq W} S_{N_w(s)} \ge b)$. In fact, in this study, if we let
$W$ be the total number of DNA base pairs, then $\Delta$ equals 1
instead of converging to 0.

First, we decompose the probability by the last time conditioning
$\tau_b=sup\{j|S_{N_w(j\Delta)}\ge b\}$ used in (Woodroofe, 1979)
\begin{eqnarray*}
&&\mathrm{P}\big(\max_{0 \leq j\Delta \leq W}S_{N_w(j\Delta)} \geq b\big)
=\sum_{0\leq j \leq \lfloor (W-w)/\Delta
\rfloor  }P(\tau_b=j)\\
&=& \sum\limits^{\lfloor (W-w)/\Delta
\rfloor}_{j=0}\mathrm{P}\bigg\{ \max\limits_{j< s \leq
\lfloor(W-w)/\Delta \rfloor} S_{N_w(s)} <b,
S_{N_w(j\Delta)}\geq b\bigg\}\\
&  \approx& \frac{(W-w)}{\Delta} \sum\limits^{\infty}_{k=0}
\mathrm{P}\bigg\{ \max\limits_{0< j \leq \infty} S_{N_w(j\Delta)}
<b, S_{N_w(0)}=b+k\bigg\}.
\end{eqnarray*}
}
 This approximation technique can be found in (Tu and Siegmund,
1999). We applied the new measure $\mathrm{Q}$ introduced in (Chan
and Zhang, 2007), which $\mathrm{Q}$ is defined as that $\mathrm{N}$
is nonuniform poisson with rate $\lambda_1$ on $(0,w]$ and rate
$\lambda_0$ on $(w,W]$; $x_i
\stackrel{\mathrm{ind.}}{\sim}f_{\theta_1}(\cdot) \mbox{~for~} 1\leq
i \leq N(w)$ and $x_i \stackrel{\mathrm{ind.}}{\sim}
f_{\theta_0}(\cdot) \mbox{~for~} N(w) \leq i \leq N(W)$. By (a) and
(b),
\begin{eqnarray*}
&&\frac{dQ}{dP}\{N,x_1,\dots\,x_{N(W)}\}\\
&=& \exp(S_{N_w(0)}(\theta_1-\theta_0)-(\lambda_1-\lambda_0)w).
\end{eqnarray*}
By change of measure, we have
\begin{eqnarray*}
&&\sum\limits^{\infty}_{k=0}\mathrm{P}(\max\limits_{0 < i \leq \infty }S_{N_w(i \Delta)} <b, S_{N_w(0)}=b+k)\\
&=&\sum\limits^{\infty}_{k=0}\mathrm{E}_{\mathrm{Q}}[
\frac{dP}{dQ}\textbf{1}\{\max\limits_{0 <i \leq \infty }S_{N_w(i \Delta)} <b, S_{N_w(0)}=b+k\}]\\
&=&\sum\limits^{\infty}_{k=0}e^{-I(b)w-k(\theta_1-\theta_0)}\mathrm{Q}(\max_{0<i
\leq \infty }S_{N_w(i\Delta)}-S_{N_w(0)} < -k |
S_{N_w{(0)}}=b+k)\mathrm{Q}(S_{N_w(0)}=b+k),
\end{eqnarray*}
where $I(b)=b(\theta_1-\theta_0)/w-(\lambda_1-\lambda_0) $.\\

By local CLT,
\[
\mathrm{Q}(S_{N_w(0)}=b+k) \approx [2\pi w \lambda_1
\phi''{\theta_1}]^{-1/2}.
\]
 Let $\{N^*(t),
x^*_1,\dots,x^*_{N^*(t)}\}$ be independent with $\{N(t),
x_1,\dots,x_{N(t)}\}$ and $N^*(t)$ be a poisson process with rate
$\lambda_1$ and $x^*$ is distributed from $f_{\theta_1}(\cdot)$; let
$w$ and $b$ be large enough such that
\begin{eqnarray*}
\mathrm{Q}(\max_{0<j \leq \infty}S_{N_w(j\Delta)}-S_{N_w(0)} < -k |
S_{N_w(0)}=b+k) \approx \mathrm{P}\bigg\{\min_{0<j \leq
\infty}(-\sum\limits^{N(j\Delta)}_{k=1}x_k +
\sum\limits^{N^*(j\Delta)}_{k=1}x^*_k)>k\bigg \}
\end{eqnarray*}
Let $y_1 =  (-\sum\limits^{N(\Delta)}_{k=1}x_k +
\sum\limits^{N^*(\Delta)}_{k=1}x^*_k)$, and $y_2$, $y_3, ~\cdots$
are iid copies of $y_1$. By (8.13) in Siegmund(1985), we have
\[ \mathrm{P}(\min\limits_{0<n\leq \infty}S_n
>k)=\frac{\mathrm{P}( S_{\tau_+} > k)\mathrm{E}_0y_1}{\mathrm{E}_0S_{\tau_+}},\mbox{~where~}S_n = \sum\limits^n_{i=1} y_i\mbox{~and~}\tau_+ = \inf\{n :
S_n>0\}.
\]
Since
$\sum\limits^\infty_{k=0}e^{-k(\theta_1-\theta_0)}\mathrm{P}(S_{\tau_+}>k)$
can be expressed as
$(1-\mathrm{E}e^{-S_{\tau_+}(\theta_1-\theta_0)})/(1-e^{-(\theta_1-\theta_0)})$,
we have
\[
\sum\limits^{\infty}_{k=0} \mathrm{P}\bigg\{ \max\limits_{0< s \leq
\infty} S_{N_w(s)} <b, S_{N_w(0)}=b+k\bigg\} \approx
v_{\lambda_1,\theta_1}(\mathrm{E} y_1)e^{-I(b)w} (2\pi w \lambda_1
\phi''(\theta_1))^{-1/2}.
\]
Therefore,
\[ \mathrm{P}(\max\limits_{0 <s< W}S_{N_w(s)} \geq b) \approx 1 - \exp \bigg\{ (W-w)v_{\lambda_1,\theta_1}( b- \lambda_0 \mu_0)e^{-I(b)w}
(2 \pi w \lambda_1 \phi''(\theta_1))^{-1/2} \bigg \}.
\]
 By Theorem 1 of (Tu, 2009), the overshoot
$v_{\lambda_1,\theta_1}$ can be calculated when the characteristic
function $\mathrm{E}e^{ity_1}$ is known. Let
$\mathrm{\phi}(t)=\mathrm{E}e^{itx_1}$. We have
\begin{eqnarray*}
\mathrm{E}[\exp\{-it\sum\limits^{N(\Delta)}_{j=1}x_j\}]
=\sum\limits^{\infty}_{k=0}\mathrm{K}^k(-t)\frac{e^{-\lambda_0\Delta}(\lambda_0\Delta)^k}{k!}
=e^{\lambda_0\Delta(\mathrm{\phi}(-t)-1)}
\end{eqnarray*}
and
\begin{eqnarray*}
\mathrm{E}[\exp\{it\sum\limits^{N^*(\Delta)}_{j=1}x^*_j\}]
=\mathrm{E_Q}[\exp\{it\sum\limits^{N(\Delta)}_{j=1}x_j\}]
=\mathrm{E}[\frac{dQ}{dP}\exp\{it\sum\limits^{N(\Delta)}_{j=1}x_j\}]
=e^{\{-\lambda_1\Delta+\lambda_0\Delta\mathrm{\phi}(t-(\theta_1-\theta_0)i)\}}.
\end{eqnarray*}
So $\mathrm{E}e^{ity_1}$ is derived.

redpajama_set_name: RedPajamaArXiv


From 75~Central exit west on Virginia Pkwy. Turn L on Stonebridge Drive. Turn L on Glen Oaks Drive. Turn L on Lake Creek Drive. House is on the left.
McKinney is located in Texas.
This content last refreshed on 4/19/2019 7:11 PM. Some properties which appear for sale on this web site may subsequently have sold or may no longer be available.
I am interested in 806 Lake Creek Drive, McKinney, TX 75072.


text:
Promises to Kids	
The Bishop's School Endowment	
$5 million to Wake Forest University
$5 million to San Diego State University
Manchester Plaza at Calloway School of Business at Wake Forest University
The Jenna Druck Foundation
Manchester Hall at Calloway School of Business at Wake Forest University
Manchester Athletic Facility at Wake Forest University
Manchester Executive Conference Center at University of San Diego
Manchester Child Development Center at University of San Diego
Manchester Village and Athletic Fields at University of San Diego
Nursing Scholarships to University of San Diego
Scripps Memorial Hospital Maternity Wing, San Diego
Academic Scholarships to The Bishop's School, La Jolla, CA
Cathedral Catholic High School Football Stadium, San Diego
San Diego Diocesan Ministries
Founding Chair of the Alexis de Tocqueville Society of United Way
Child Abuse Prevention Foundation
The Monarch School, San Diego
Preuss School Athletic Field, San Diego
YMCA Athletic Fields, La Jolla, CA
Boys & Girls Club of San Diego County
Manchester Ice & Event Centre, McCall, ID
National Conference of Christians and Jews
Billy Graham Crusade
U-T San Diego - Finish The Fight
The Vision of Children Foundation

redpajama_set_name: RedPajamaCommonCrawl


text:
Life-Sized LEGO X-wing Starfighter Makes Way to LEGOLAND California
June 11, 2013 / Allen "Tormentalous" Tran / 0 Comments
Last month, LEGO unveiled the life-size X-wing Starfighter in New York. The starfighter has traveled safely from New York and now resides at LEGOLAND California. In the video below, LEGO Master Model Builder, Gary McIntyre, shows the viewer around the ship and tells the back story of how it got from the East Coast all the way to California. Right now, it is safely stored away in a hanger area at the resort and will be open for the public to view on June 13th until the end of the year. To give some details on the ship, it contains 5,335,200 bricks and weighs 45,979.61 pounds. It stands at 11 feet tall and is 43 feet in length with a wingspan of 44 feet. 32 builders at the LEGO Model Shop in Kladno, Czech Republic spent 17,336 hours to construct the starfighter. It is made to look like set 9493 from a few years ago. The giant version of the ship is 42 times the size of the real LEGO set.
**Via CNN**
Marvel Comic Covers as LEGO Variants
LEGO Marvel Super Heroes Video Game E3 Gameplay Footage


text:
More news of Yale people
Yale junior Clemantine Wamariya, a survivor of the Rwandan genocide, was appointed in October by President Obama to the United States Holocaust Memorial Council, thegoverning board of the Holocaust Memorial Museum in Washington, DC. In 1994, at age six, Wamariya fled Rwanda with an older sister and lived in refugee camps in seven African countries before arriving in Chicago in 2000. She has spoken about her experience in Rwanda on the Oprah Winfrey show and at universities, high schools, and other organizations.
The members of the governing board of Yale–NUS College,the liberal arts college being created by Yale and the National University of Singapore, were announced in November. Yale and NUS each appoint five members of the board. Singaporean businesswoman Kay Kuok will chair the board, which also includes NUS president Tan Chorh Chuan, a deputy secretary of Singapore's Ministry of Education, and two other Asian businesspeople. Yale's appointees are President Richard Levin '74PhD, former Yale Corporation senior fellow Roland Betts '68, Vassar College president Catharine Bond Hill '85PhD,Yale vice president and secretary Linda Koch Lorimer '77JD,and former US ambassador to China Clark T. Randt Jr. '68.
Helen Jack '12 and Ronan Farrow '09JD are among the 32 recipients of this year's Rhodes Scholarships. Sophia Veltfort '12 is one of 36 Marshall Scholarship winners. The Rhodes and Marshall awards are given for study in the United Kingdom.
David Montgomery, the Farnam Professor Emeritus of History at Yale, died on December 2 in Philadelphia. He was 84. Montgomery, who worked as a machinist and a union organizer before going to graduate school, was a noted historian of the American labor movement and a pro-labor activist. He taught at Yale from 1979 to 1997.
Stepping Down
Vice president for development Inge Reichenbach announced in November that she will retire at the end of June. Reichenbach came to the university from Cornell in 2005 as Yale was preparing a capital campaign. Under her leadership, the campaign raised $3.88 billion, exceeding its $3.5 billion goal despite the 2008 recession.


text:
Posts Tagged 'water'
Perth to absorb 2 million more
Posted in Uncategorized, tagged $2 million, 40 years., absorb, analysis, Australian Bureau of Statistics, Bunbury, cars, city, city's education system, clogged, coastal hamlet of Lancelin, Curtin University, desalination plants, education, extra traffic, groans, hundreds of schools, Karrinyup, kilometres, Kwinana, l live, Mandurah, Morley, New York City, north to the Lakes, people, perth, perth hills, Perth is growing ., pockets, power generation, public transport, residents, roads, Rockingham, school, serious congestion, south, sprawl, stretch, Thousands, Treasurer, two million residents, water, Wayne Swan on March 31, 2010| Leave a Comment »
Perth will sprawl further than New York City, be clogged with cars and people will live in each other's pockets as the city groans under the weight of an extra two million residents over the next 40 years.
An analysis of how Perth is growing and will grow as more people call the city home also warns that more desalination plants, thousands of kilometres of roads and hundreds of schools will have to be built to cope with the surge in residents.
The Australian Bureau of Statistics is forecasting Perth's population to hit 3.8 million from its current 1.7 million by 2050.
For the first time the bureau has looked at what that will mean to Perth residents – and the picture is dominated by sprawling suburbs and long journeys to work.
Already the city covers 5423sq km but statistician Phil Smythe found that if the population reached 3.8 million, and even if housing density increased, Perth would sprawl over 12,000sq km.
New York City, home to 17.8 million people, covers 8700sq km.
Perth would stretch from the coastal hamlet of Lancelin in the north to the Lakes turn-off in the Perth Hills and south to a point midway between Mandurah and Bunbury.
The population density of Perth would increase to 710 people for every square kilometre, up from 319.
Mr Smythe said the number of vehicles would swell from 900,000 to almost two million.
Thousands of kilometres of roads would have to be built to cope with the extra traffic, and the use of public transport would have to increase dramatically.
Mr Smythe said fewer than 10 per cent of Perth residents used public transport now but that would have to increase to avoid serious congestion.
More desalination plants would be necessary to cope with the increased demand for water, and power generation would have to more than double to supply the energy demands.
There would be challenges for the city's education system, with the number of schools likely to more than double to 2300 with 600,000 students.
"This may mean stiff competition for school names," he said. "Already there are 73 schools named after saints, including 12 after St Joseph and nine after St Mary."
Professor of sustainability at Curtin University, Peter Newman, said the attitudes of Perth residents would change, as they were already in the US, with more people moving back towards the city centre rather than out to the suburban fringes.
He said there were huge costs associated with suburban growth, from transport to health, and it meant more people were now looking to higher density or inner-city life.
"You'll see places like Mandurah, Kwinana, Rockingham, Karrinyup and Morley fill up, especially as younger people start giving up their cars," he said.
Treasurer Wayne Swan said yesterday that people who demanded a cap on Australia's population were too narrowly focused in their complaints.
"It is all too easy to speak of the costs of an increased population, and forget the benefits," he said. "This is a mistake too often made." "You'll see places like Mandurah, Kwinana, Rockingham, Karrinyup and Morley fill up, especially as younger people start giving up their cars," he said.
"It is all too easy to speak of the costs of an increased population, and forget the benefits," he said. "This is a mistake too often made."Source : www.thewest.com.au
Bushfire threatens homes, locals told to flee
Posted in Local News, tagged 15000 hectares, 18km, 25, airconditioners., beach., blackened, blaze, Broome, bushfire, close all doors, coast, Coconut Wells, defend, drive, evaporative, FESA, fire, Fire and Emergency Services Authority, firefighters, food, home, Homes, houses, involved, Lullfitz., Morrel Park, operation, prepare, rescue service, residents, Road closures, service, slowly, sun protection, threatens, turn off, two brigades, volunteer, WA, WA Kimberly, water, windows on October 14, 2009| Leave a Comment »
A BUSHFIRE is threatening homes near the WA Kimberly coast town of Broome and residents have been told to head for the beach.
The blaze has so far blackened some 15,000 hectares and houses in Coconut Wells, about 18km from Broome, are now at risk, says the Fire and Emergency Services Authority (FESA) says.
Residents who abandoned their homes were advised to go to the beach as the blaze has also begun to close in on Morrel Park and Lullfitz.
"It may be hours before it is safe to return home so take water, food and sun protection," FESA said in a statement.
"People who have decided to stay and defend their home should prepare for the fire."
Residents have been told to close all doors and windows and turn off evaporative airconditioners.
The FESA says 25 volunteer fire and rescue service and bushfire service firefighters from two brigades are involved in the operation.
They saved six homes yesterday and extra crews are being flown in.
Road closures are in place and motorists have been urged to drive slowly.
Source : www.news.com.au
Winter sprinkler bans to become permanent
Posted in Living in Perth, Local News, tagged 2.2 billion, 880, a year, August, averages, ban, ban in winter, bans, billion, catchments, Collie, dams, during July and August, east, equivalent, Esperance, fall, figures, filling, Graham, Graham Jacobs, historical, Jacobs, july, Kalbarri, Kalgoorlie-Boulder, litres, litres of water, Manjimup, Minister, move, Olympic-sized, permanent, permanent ban, perth, pool, pools, rain., rainfall, residents, saved, sprinkler, supply, supplying Perth, supported the move, towns, trial sprinkler ban., two-month trial ban, WA, water, Water Corporation, Water Minister, winter, year, year-to-date. on September 10, 2009| Leave a Comment »
Sprinklers will be permanently switched off during winter from next year after the State Government today to retain this year's trial sprinkler ban.
Yesterday's decision follows a two-month trial ban during July and August, which Water Minister Graham Jacobs said saved about 2.2 billion litres of water, equivalent to filling 880 Olympic-sized pools and enough to supply towns the size of Manjimup or Collie for a year.
The permanent ban will apply from June 1 to August 31.
The trial ban – for most scheme users south of Kalbarri – was introduced after water usage earlier this winter was running at 800 million litres a day, 300 million litres above average.
Dr Jacobs said today that the ban saved 50 million litres a day, while an independent survey last month indicated 93 per cent of residents supported the move.
"This is an outstanding community achievement because while there has been reasonably consistent rain, we are still well below the long-term annual rainfall average," Dr Jacobs said
Dams were now at 45.5 per cent of capacity, their second-highest level this decade. They are holding 19 per cent more water than the same time last year.
Water Corporation figures show rainfall in all but one of the catchments for dams supplying Perth are below their historical averages for the year-to-date.
Dr Jacobs said the exact area of the permanent ban, and any adverse impact for industry and local government users would still have to be worked out.
This would occur "soon", and some areas that took part in the trial ban – which ran from Kalbarri to Esperance and east to Kalgoorlie-Boulder – could have a case to be excluded.
These users were asked to voluntarily stop using bores during the two-month ban period, while garden bore users were allowed to turn them on for maintenance reasons.
"A lot of people say garden bores are not pulling on the scheme, but we all realise our underground water resources are all related," Dr Jacobs said last month.
Source : www.watoday.com.au
Immigration plan brings Australia's needs to the fore
Posted in Immigration News, tagged 50 year migration plan, 50-year vision, Andrew Metcalfe, approach, asylum, asylum seekers, Australia's, Australian, … A long-term, brings, Canberra, Christmas Island, climate change, conducting, conference, consider, contribute, demographic, department, Department of Immigration and Citizenship, Economic, environmental goals., fore, framework, global, global environment, globe, high level of education, immigration, Immigration plan, intakes, island, kevin rudd, language proficiency, long-term, long-term economic, long-term issues, mainland, migration, Migration Occupations in Demand List, MODL, nation's, national security, new policy, New Zealand School of Government, objectives, officials, other skills, plan, planning, policy, range, rounded, rudd, seekers, skilled migrants, skilled migration program., to Australia's, visionary, water, water needs, well-planned on September 6, 2009| Leave a Comment »
IMMIGRATION officials are preparing a 50-year migration plan to ensure that intakes consider a range of long-term issues such as climate change, water needs and national security.
The Secretary of the Department of Immigration and Citizenship, Andrew Metcalfe, said yesterday the department was conducting a review of the nation's migration needs to ensure a more rounded and visionary approach.
"In terms of the future, we are trying to lift ourselves away from year-to-year decisions to a 50-year vision," he told the Australian and New Zealand School of Government conference in Canberra.
"We are trying to move away from an immigration department that is responsive to one that can help the government achieve long-term objectives … A long-term planning framework … is something whose time has come."
Mr Metcalfe said a well-planned skilled migration program could contribute to Australia's long-term economic, demographic and environmental goals.
"We want to ensure our skilled migration programs are responding to longer-term skill needs which cannot be addressed through domestic training and skills development," he said.
"The question then is how we can best address shorter-term labour market requirements … It will be important that the skilled migrants we choose are not only young and healthy but also have a high level of education, language proficiency and other skills. This will ensure that skilled migration contributes both to labour force growth and to the productivity of our labour force."
Mr Metcalfe said the review will include an examination of the points system used to select skilled migrants, known as the Migration Occupations in Demand List.
"The MODL is not as flexible as we would like to address a rapidly changing and uncertain global environment. In my view, one of themes of this century will be the increased mobility of people around the globe, and we need to manage this adroitly."
But the Government has denied it has adopted a new policy towards asylum seekers in the wake of a decision this week to process a group of 10 Afghan children on the mainland rather than on Christmas Island.
"These are 10 unaccompanied minors and therefore what's happened is that they've been transferred from Christmas Island to the mainland on September 2," he said
Asked whether there had been a change of policy, the Prime Minister, Kevin Rudd, said: "Absolutely not."
He told 3AW yesterday the group of 10 children had been transferred to the mainland because unaccompanied minors were given priority in processing.
"That's what's happening in the case of these minors," he said. "That's why they're treated separately."
Source : www.smh.com.au
Explosion rips through Newport Marina
Posted in ALL news, tagged afternoon, Australia, blazing, blazing boats, boats, burning, burning craft, Central Coast, Damage, dragged, dragged out, drifted, east coast, engulfed, engulfed by flames, explosion, extinguished, fire, fire boats, fires, fires out, five luxury boats, flames, floating, further, Gosford, injured, luxury, luxury boats, Marina in Sydney, moored., nearby, Newport, Newport Marina, Norm Buckley, NSW, NSW Fire Brigades, open water, Plumes of smoke, pose any danger, prevent, reportedly, rips, Rural Fire Service's, sand flats, scene, Sirsi Marina, smoke, smoke inhalation, spokesman, Sydney, the bay, this afternoon, treated, water, wharf on July 22, 2009| Leave a Comment »
THREE people have been injured and five luxury boats engulfed by flames after an explosion at Newport Marina in Sydney this afternoon.
One person was seriously injured, while another two were treated at the scene following smoke inhalation.
The fire started when one boat caught alight while moored. The flames quickly spreading to two other boats which were moored nearby.
Two of the burning craft were dragged to nearby sand flats and extinguished, but one drifted to nearby Sirsi Marina, and set another two boats alight.
NSW Fire Brigades spokesman Norm Buckley said the boats were dragged out into open water to prevent further damage.
"We pushed those crafts that were actually on fire out into the water so they don't pose any danger to the actual wharf itself or any part of the structures or indeed any of the other boats," he said.
"We're also using one of the Rural Fire Service's fire boats, and they'll be putting those fires out on those boats that are floating in the bay."
Plumes of smoke from the blazing boats have reportedly been seen from as far away as Gosford on the Central Coast.
Heavy rain, thunderstorms lash Perth and South-West
Posted in weather, tagged (SES), 100km/h tore, 109km/h., 115km/h, across, Beaufort St, blowing, Bunbury, Busselton, cancelled, Cape Leeuwin, Cape Naturalist, Capel., caused, ceiling, city, City Beach., coastal suburbs, cold fronts, collapsing, Collie, damage to homes, darkness., Doubleview, fallen trees, ferry services, flights, flooding, granny flat, gust of 107km/h, gusts, havoc, Homes, house, isolated, Joondalup, Kwinana ports, midday, minor, Ocean Reef, operations, overnight, parts, perth, perth hills, Perth's international terminal, plunging, port, ports of Fremantle, power, rain., rainfall, recorded, reports, ripping, Riverside Drive., Rockingham, roof off, roofs, rottnest, State, State and Emergency Services, storm, suburbs, suspended, Swan River were lapping around peak hour traffic on the Kwinana Freeway, tearing, travelling, trees, Two Rocks, uprooting, WA, WA Bureau of Meteorology, WA Water Corporation, Walpole, water, weather, weather forecast, wettest day of the year., wild, wind, wind gusts, windows, winds on June 29, 2009| 1 Comment »
WILD weather has caused havoc across Perth, uprooting trees, tearing off roofs and plunging homes into darkness.
Winds travelling at more than 100km/h tore through the city overnight, ripping the roof off a granny flat in Doubleview, collapsing a ceiling in Joondalup and blowing in the windows of a house in City Beach.
More than 17,000 are believed to be without power because of the storm, mostly in the Perth hills.
State and Emergency Services (SES) have recorded 70 calls for help since 7am, with a total of 125 incidents logged since 6pm last night and 240 properties impacted.
Damage has been reported in coastal suburbs from Two Rocks to Rockingham and all SES units in the metropolitan area have been activated with volunteers in Northam called in for backup.
A series of cold fronts have been lashing the city since Friday, with Rottnest, Ocean Reef, Mandurah and Bickley some of the worst hit areas.
Ocean Reef recorded a wind gust of 107km/h and gusts of 115km/h were recorded at Rottnest, where ferry services have been cancelled.
The ports of Fremantle and Kwinana ports have suspended operations until midday.
Across the state, Cape Naturalist and Cape Leeuwin recorded wind gusts of up to 109km/h. There have been reports of fallen trees and minor damage to homes in Bunbury, Busselton and Capel.
The WA Bureau of Meteorology says it is the wettest day of the year.
Flights from Perth's international terminal are running half an hour behind schedule, and Main Roads are urging motorists to slow down and take care in the inclement weather.
Near the city, waves from the Swan River were lapping around peak hour traffic on the Kwinana Freeway this morning, while Riverside Drive and parts of Beaufort St have isolated flooding.
Traffic lights are out on the intersection of Great Eastern Highway and Stoneville Rd in Mundaring and at the junction of Kalamunda Rd and Gooseberry Hill Rd.
WA Bureau of Meteorology climate information officer John Relf says 23.2mm of rain has fallen overnight taking Perth much closer to the 177mm average with 147.8mm of rain recorded this month.
"We have exceeded last year's June rainfall of 142mm," he said.
Heavy rain has been reported from Collie to Walpole.
WA Water Corporation spokeswoman Clare Lugar says dams should have now started benefiting from the all rainfall.
"Up until Friday the streams hadn't started to flow," Ms Lugar said. "But we are expecting it to have begun flowing over the weekend."
The wild weather is expected to ease up later tonight with fine weather forecast by Thursday.
Winter storms batter WA
Posted in weather, tagged Abnormally, area, Australian, batter, beach., Beaufort Street, blacked out., Boat owners, boats, Bolton Road, border, brace, Bureau of Meteorology, Burswood., Canning Highway, causing, city, citybound., clocked, coastal areas., cold fronts, damaging, destructive, destructive winds, drains, Emergency, erosion, flooding, forecast, gale, Great Eastern Highway, gusts, hail storms., heading, heavy conditions, heavy showers, high tides, Inglewood, intersection, issued, Kalbarri, Kwinana Freeway, low-lying, moored., north, overnight, perth, Perth Airport, Perth metropolitan, potentially, powerlines, rain., Riverside Drive., Rottnest Island, securely, service, severe, shelter, Showers, slammed, south, speeds, State, State Emergency Service, storm, storms, streams, Surfers, Swan River, Thunderstorms, Traffic lights, trees, WA, warning, washing, water, weather, wind gust, winter on June 29, 2009| Leave a Comment »
The latest in a series of destructive cold fronts slammed into WA overnight, causing destructive winds, rain and hail storms.
The Bureau of Meteorology issued a severe weather warning at 6.45am, following similar warnings issued throughout the weekend.
Waves from the Swan River are washing onto the Kwinana Freeway north of Canning Highway citybound. There is also flooding on Beaufort Street in Inglewood heading into the city and on Riverside Drive.
Traffic lights are blacked out at the Great Eastern Highway and Bolton Road intersection in Burswood.
The front is the most severe of a series that have descended on WA over the past few days.
A wind gust of 115kmh was recorded at Rottnest Island about 6am today, and the Bureau is warning people to expect winds up to 100kmh with potentially damaging gusts reaching 125kmh this morning.
Alex Krisman from WeatherZone said Cape Naturaliste (109kmh) and Cape Leeuwin (104kmh) also recorded heavy gusts of wind – which coincided with a line of lightning flashes- at the same time as Rottnest Island.
Winds at Perth Airport hit 83kmh while the Perth metropolitan area clocked speeds up to 72kmh at 5.50am.
Rainfall was heavy, particularly across the south west. So far, Bridgetown has had 32mm from 9am yesterday morning.
Thunderstorms and heavy showers are forecast for today, particularly over the Lower West, South-West and South Coastal districts.
Abnormally high tides are set to cause flooding in low-lying coastal areas.
A gale warning has been issued from Kalbarri right through to the South Australian border.
Surfers are being warned to brace for heavy conditions, which are likely to cause significant beach erosion.
The State Emergency Service has warned people to secure loose objects, move vehicles under cover and stay inside away from windows.
People caught outdoors should find shelter away from trees, powerlines, storm water drains and streams. Boat owners should make sure their boats are securely moored.
$236 Million Northbridge Link Project
Posted in Local News, tagged $236, $236 million, $470, $470 million, 350 job opportunities, 600 passengers, additional, announce, approximately, attract, bus services, business, business sectors, central, central open, city, city precinct, commence, commencing, commercial, committing, concluded, connect, construction, contribution, cost, create, creatings, development, each day, employment, entertainment., estimated, Federal, federal government, formally, government, greatest transformation, important, include, integration, jobs, kevin, kevin rudd, later, link, Local News, million, network, northbridge, Northbridge Link project., opportunities, perth, Prime Minister, project, public, public transport network, rail, residential, result, rudd, sectors, sitework, space area, start, Tendering, Transform, transformation, transport, transpot, underground, water, waterfront, year, years time, yesterday on May 23, 2009| Leave a Comment »
Prime Minister Kevin Rudd was in Perth yesterday to formally announce the federal government committing $236 million for the Northbridge Link project.
The underground construction is estimated to cost about $470 million, with the sitework set to start later this year.
The construction will be commencing in approximately a years time.
The transformation of the the city precinct will include commercial, residential and entertainment opportunities, which would transform the city.
Added will be a waterfront development which will be the greatest transformation of the city of Perth.
This will connect the city with Northbridge and will result in a better integration of rail and bus services.
Mr Rudd said the project would create about 350 job opportunities for the construction and business sectors and attract an additional 600 passengers on the public transport network each day.
Tendering will be concluded later this year and construction due to commence next year.
This is an important contribution to employment as well.
Petrol tanker explodes in Perth suburb
Posted in Local News, tagged 40000-litre tanker, 500-metre radius, A Fire, A petrol, AAP, ask, authorities, building, businesses, Caltex station, clear, confident, contaminated, destroyed, drained, ervices, evacuated., exploded, explosion, fire, Firemen, focus, forecourt, friday, Homes, ignite., investigation, irefighters., Local News, Maddington., majority, massive, mergency, nder control, night, parts, perth, petrol, petrol tanker, quickly, recover, roof, safe, Saturday, scene, shop front., shopping centre, sokesman, starting, station, suburb, suburban, tanker, the spokesman, through, unleaded petrol., vehicle, water, work on May 15, 2009| Leave a Comment »
Firemen will work through the night to clear petrol from the scene of a massive explosion at a petrol station in the Perth suburb of Maddington.
A petrol tanker exploded at the Caltex station, starting a fire that destroyed parts of the vehicle, the roof of the forecourt and the shop front.
A Fire and Emergency Services Authority spokesman told AAP the fire was brought quickly under control by firefighters.
"The focus is now on making the scene safe, which is a very important task," the spokesman said.
"There was a fair bit of damage to the majority of the building."
Petrol still left in the 40,000-litre tanker will be drained into another tanker, while specialists work to recover any water that may have been contaminated by the unleaded petrol.
About a quarter of the petrol in the tanker burnt in the fire.
Homes and businesses, including a suburban shopping centre, within a 500-metre radius of the station have been evacuated.
Residents will not be allowed to return until authorities are confident the area is safe and there is no petrol left to ignite.
That is likely to be sometime late on Friday night, the spokesman said.
No one was injured in the incident.
"It is great news. Fire authorities were called very quickly, and they got to the scene in a good time, meaning there were no injuries.
"There were people on the forecourt, in the shop, and of course the tanker driver," the spokesman said.
The truck will not be removed until Saturday, while the investigation into why the fire started will continue for a few days.
www.news.ninemsn.com.au article
www.watoday.com.au Ben White photo


This truly is a rare opportunity to have a significant role in changing the face of child recruitment services. Are you hoping to build your web resume? Need to show "real" work and could benefit from a reference from a national nonprofit? We would love to partner with you, and benefit both of us. We are looking to invest in someone that we can assist in their growth, and they will make a commitment to work with us for a year. Does not need to be located at our office, can be done from anywhere.We are very committed to how technology could change the lives of many children living in foster care and engage volunteers outside of our local area. Are you looking too?
If you are looking for a role that will get you real hands on matching experience, this is the role for you. We offer hands on training on searching and matching families with waiting children. This is a unique, real career opportunity, and potential growth opportunity within the organization.
Work hand-in-hand with you in a role that is very much like an Adoption Worker for the family.
Read the family's biography and provide suggestions for changes. Read the family's home study, provide child recruitment updates when requested by the family, and provide assistance and guidance to their families as needed.
Responsible for checking in with assigned families on a regular basis.
Support your family through their adoption journey. Stay in contact with your families regularly, at least twice a month.
Read the family's biography and provide suggestions to make it stronger.
Read the family's home study and make sure it matches what the family has written in their family profile.
Be available to help answer questions about the adoption process including promotion, submission, selection, and placement.
Help the family become their own advocate during the process.
Help find caseworker's contact information and when requested, update the family on children they have.


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'iPhone City' lockdown finally ends: How much it cost Apple and all other details
Luminous to build India's first green solar panel factory in Uttarakhand
India plans to classify clean activities, technologies under a new policy
The last week or so has been tough for Apple and Foxconn — its biggest manufacturing partner — in China. Zhengzhou — better known as iPhone City — has been under strict Covid-19 lockdown and that has dealt a severe blow to Apple's iPhone sales. According to a report by CNN, the five-day lockdown in Zhengzhou has finally been lifted. The news will come as a massive relief to Foxconn and Apple.
Protests, lockdowns and more
Zhengzhou has seen a massive unrest in the last few days. It was reported that over 20,000 workers had left the city. Then there were reports about violent protests over wages and the lockdown rules.
Multiple reports also suggested that workers had been isolated and were forced to live and work on-site with limited food and supplies to prevent further outbreaks. It was also reported that Foxconn offered to pay the protesting workers extra money to quit their jobs. A report by CNN revealed that Foxconn had offered to pay workers CNY 10,000 (approximately Rs 1,14,000) to quit and leave the iPhone factory. The sum is reported to be workers' one or two months of wages.
$1 billion and counting: Estimated loss for Apple
According to the CNN report, Daniel Ives, managing director of equity research at Wedbush Securities, estimates that Apple lost close to $1 billion in sales in a week because of the protests, lockdowns and general unrest in iPhone City.
Another analyst — Ming-Chi Kuo — suggests that Apple 14 Pro and iPhone 14 Pro Max have suffered massively. As per Kuo, the production estimates for iPhone in the fourth quarter have been slashed by by 20 per cent. Kuo believes Apple will ship close to 80 million iPhone units in this quarter. Further, Kuo expects iPhone 14 Pro models' shipments to drop by 15 million to 20 million units.
Follow Gadgets Now on Facebook and Twitter. For the latest news, tech news, breaking news headlines and live updates checkout Gadgetsnow.com


Our furnace has not worked for years. Some of the furnaces in big motor homes take 15 amps of DC power. While ours is smaller at 7 amps; it is still a lot of battery power to run all night long and is just not a practical thing to run on solar power unless you can spend a lot of money on it. We use a propane heater without a fan instead, which actually uses half the propane that a furnace would. Those furnaces are very inefficient; great for heating the great outdoors but not so good at keeping the heat inside. Of course we keep a vent open when we have it on (common sense). Yes, burning propane produces a lot of water vapor plus carbon dioxide but adequate venting takes care of it without reducing the efficiency to anywhere as low as the average RV furnace. IMHO, the best heater is the Empire ceramic tile or "brick". These are made in the US. I believe all the others are Chinese, but some are prettier than the Empire (and of course cheaper). In particular the Legacy was pretty (no longer available), but I think you need to balance that with quality and what sending our dollars to China is doing to our economy. The portable base for an Empire is steel and stable, while the base for the others is a couple of wimpy pieces of plastic. (One of our friends knocked their Legacy over and the tiles broke.) The grill is chrome plated, not a painted piece of expanded metal that will rust. These are radiant heaters like a catalytic but you can get them with a thermostat, something lacking on the Olympian catalytic.
The only time I had a problem with an Empire heater the factory air expressed a new pilot & thermo-couple assembly to me at no charge without a proof of purchase, just a phone conversation. This is a good company. We had a smaller 10,000 BTU single brick one in our first trailer back in 2000. We bought a second one & found it wasn't enough for our bigger & leaky fifth wheel. We now use the bigger 18,000 BTU 3 brick unit with a thermostat. It is now 7 or 8 years old, it works perfectly and we love it. We know somebody who prefers the three brick without the thermostat because you can switch it so that you have one, two or three bricks lit. He claims it is nicer to have even heat, not the on & off of all the heat at once that the thermostat does. We like the thermostat so that we can leave it on low at night, keeping us at about 50 degrees. I wish they made it with both features, I have been thinking about doing some modifying.
We're not dead yet, so don't believe those people who tell you that it is dangerous to leave a heater going at night. Right now in Montana this heater is going 24/7. The warning page that comes with the catalytic heater convinced us to never buy a second one when the first failed after only 2 years. According to the factory, pet hair & dust both corrupt the pads. I quote what they said when I complained: "You don't keep it covered?" Egad no…. We use it!


Table Cafe is a great little spot tucked away in Larkspur, a town just 10 or 20 minutes north of the Golden Gate bridge. A perfect place for lunch, Table Cafe offers gluten free dosas with a number of tasty fillings along with fresh salads, soups and homemade spritzers. All of their produce is local or organic, and their meats come from sustainable farms like Niman Ranch, Marin Sun Farms, and Prather Ranch. The cafe's seasonal menu includes more than 10 different dosas, and an enticing lineup of daily specials. We ordered up two dosas, one stuffed with fresh asparagus and gruyere cheese, the other filled with curried cauliflower, pickled veggies, and wilted greens. I'm pleased to say, both were fantastic.
Most of the menu is gluten free, however there are some items that do have wheat (brownies, lamb meatballs). Be sure to have their friendly waitstaff confirm that your order is safe.
I just wanted to leave you a note to check out The Inspired Cookie. Their brownie is amazing!!!


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Song Fight! Board index Song Fight! Complaints and Suggestions
Cool Song Fight! related stuff people should make
Use this forum for title suggestions, bitching at moderators, whining about phpBB, and grand ideas that will solve all of Song Fight's problems.
Post by Lunkhead » Fri Feb 15, 2013 4:23 pm
A thread for brainstorming whatever things occur to people that they think would be cool for somebody to build, related to Song Fight!
This is probably mostly around apps or Web sites or other software, but hey, if you have hardware/building/event/etc. ideas put 'em here too!
Re: Cool Song Fight! related stuff people should make
Post by fluffy » Fri Feb 15, 2013 5:03 pm
I've been wanting to build a Pandora-esque thing where people can vote on whether they like a song or not, and which would coalesce songs into clusters based on taste-similarity. Pandora's algorithms are both secret and require a lot of "tagging" work but I have ideas on how it could be done without that sort of approach.
Caravan Ray
Instruments: Penis
Submitting as: Caravan Ray,G.O.R.T.E.C,Lyricburglar,The Thugs from the Scallop Industry
Location: Toowoomba, Queensland
Contact Caravan Ray
Post by Caravan Ray » Fri Feb 15, 2013 6:48 pm
fluffy wrote: I've been wanting to build a Pandora-esque thing where people can vote on whether they like a song or not, and which would coalesce songs into clusters based on taste-similarity. Pandora's algorithms are both secret and require a lot of "tagging" work but I have ideas on how it could be done without that sort of approach.
Pull my finger!
http://www.caravanray.com
Billy's Little Trip
Odie
Instruments: Guitar, Bass, Vocals, Drums, Skin Flute
Recording Method: analog to digital via Presonus FireBox, Cubase and a porn machine
Submitting as: Billy's Little Trip, Billy and the Psychotics
Location: Cali fucking ornia
Post by Billy's Little Trip » Mon Feb 18, 2013 9:40 am
That is a good idea, fluffy. There are so many genre style here, it would be a nicer experience for people to listen in their genre of interest.
I mean, it's good to be exposed to a large range of genres, but it's pretty annoying to me when I'm listening to some great indie blues rock and then hit with rap on the next song.
How I thought, wrote and played in my 20s
Post by fluffy » Mon Feb 18, 2013 10:01 am
What I'm thinking of wouldn't cause clusters based on genre (personally I think that "genre" is a pretty arbitrary and pointless criterion to classify things based on), it would cause clusters based on the mindset that likes them.
The basic idea (in case someone else wants to implement it - I don't have much free time these days, and I also might have some legal issues with my employer if I do it myself) is that every song and user are considered to be "particles" in a large multidimensional space (the number of dimensions doesn't matter, as long as it's at least 2, but the more the better; I'd probably start with 5). A "love" is an attractive force, and a "hate" is a repulsive force. So, whenever someone likes a song, the user and the song get drawn closer to each other, and whenever someone hates a song, the user and the song get pushed apart. Then, multiple users can also be compared based on their respective love and hate lists, and based on how similar they were, they'd attract or repel each other too. Beyond the initial impulse there would also be an ongoing process that occasionally pushes stuff around based on past data.
What I'd expect from this is that users with similar tastes will eventually move towards each other, and songs which a lot of people love will get concentrated in little bundles that are close to the users who like them, far from the users who hate them, and hopefully relatively near each other as well. Songs which are universally hated would end up getting scattered outwards. Presumably there'd also be a natural gravitational attraction between songs as well, to help the clustering along (although I wouldn't want to start that up until there's a lot of user data to work with).
I'd also expect to get some pretty pictures, at the very least, and a lot of data which could be used to train other algorithms as well.
Post by Billy's Little Trip » Fri Feb 22, 2013 8:32 am
Let me see if I get what you're saying. Instead of bundling music in genres so that people can listen to what they want when they are in the mood for a certain type of music, you want to segregate people into cliques based on the music they like. Is that the gist?
Jim of Seattle
Instruments: Keyboards
Recording Method: Sonar X3, Adobe Audition, Windows pc, Roland synth, EastWest orchestra
Submitting as: Jim of Seattle, Ants (Invisible), Madi Singer/Songwriter, Restless Events
Contact Jim of Seattle
Post by Jim of Seattle » Fri Feb 22, 2013 9:18 am
The difference between Pandora and something like this is that there is an extra dimension here that Pandora doesn't have to worry about, and that is the basic quality of the track. Pandora assumes that as long as it's got the right attributes, a given song can make someone's playlist. But if I told SFandora I wanted to hear a specific kind of music, it would do so regardless of the actual quality of a song. I mean, right?
Is there any reason you haven't bought my album yet? "We Are All Famous", on iTunes, CD Baby, and Green Monkey Records. Also available in unlimited edition "free" version:
Yes! I want to hear Jim's album without paying for it!
roymond
Instruments: Guitars, Bass, Vocals, Logic
Recording Method: Logic X, MacBookPro, Guitar Rig 5, Rig Kontrol 3, Focusrite Scarlett 2i2, iPad3, Apogee Jam
Submitting as: roymond, Dangerous Croutons, Intentionally Left Bank
Contact roymond
Post by roymond » Fri Feb 22, 2013 2:14 pm
Jim of Seattle wrote: The difference between Pandora and something like this is that there is an extra dimension here that Pandora doesn't have to worry about, and that is the basic quality of the track. Pandora assumes that as long as it's got the right attributes, a given song can make someone's playlist. But if I told SFandora I wanted to hear a specific kind of music, it would do so regardless of the actual quality of a song. I mean, right?
Yup. So if one of the attributes was "sucks" and you made a playlist for songs that "don't suck" that should work. Problem is that "sucks" is entirely subjective, which is why I'd like a pandora type radio feature that let's me define additional filters based on artist, specific tracks, etc. If it's playing and I encounter a track I despise, I'd like to say "NEVER PLAY THAT FUCKING TRACK AGAIN" and feel confident I will never hear it in any of my playlists ever again. Pandora allows you to ban a track, but only from the current playlist, so there is no such guarentee.
roymond.com | songfights | covers
"Congratulatons, roymond; you finally managed to write a song I don't really care for." - Märk
Post by Jim of Seattle » Fri Feb 22, 2013 2:23 pm
So then for any individual user there would be an enormous ramp-up while they continued to have sucky songs pop up that they then have to blacklist. I mean, we're at 10,000 songs now. I'm willing to bet that 5,000 or them I don't ever want to hear again. A user should also be allowed to say "Don't ever play anything by <sucky band> again".
Truth is, most artists that usually suck catch lightning at least once. Without naming names, I am thinking of a few off the top of my head that I would be tempted to blacklist, EXCEPT for one particular song.
Roy, what would you think of a rating scheme with five ratings:
block, dislike, neutral, like, favorite
Post by ken » Fri Feb 22, 2013 4:26 pm
That is a really good idea. I was thinking you could let most people have a 3 tier rating of Good, ok, bad, but give some special people a 5 tier rating that allows them some extra points when needed. This is even better.
I was thinking either five icons in a row, you can select/highlight only one, or maybe instead a slider to dial in your enjoyment/hatred of a song?
This could be applied to artists, too. Allowing for exceptions for certain songs of an artist would be tricky though.
Lunkhead wrote: Roy, what would you think of a rating scheme with five ratings:
Are you talking about a personal play list where you can rank like that - with some sort of smart software that would suggest the favourites of other people who had made similar rankings?
If so - then that sounds good
I'm thinking of something Pandora like, but super basic. The main mode is you'd get a stream of random songs from the archive, and you could rate them along that scale, if you wanted to, and FB like/share, Tweet, plus on G+, if you wanted to. It wouldn't do suggestions, at least not at first. I'd also like to have so you can see your ratings, and maybe also let you listen to only liked/favorited songs/artists instead of the full "firehose". I think with disliked songs/artists it would reduce the likelihood that the song/artist would show up in the random stream, and with blocked songs/artists they'd be completely removed from the random stream. If I were try to add suggestions, it would just be super simple stuff along the lines of "people who liked that song/artist also liked: suggestion1, suggestion2, etc.". I don't think I'd want to give a lot of visibility to other peoples' ratings, except in that kind of anonymized and general way. Although, it would be cool to listen to somebody else's liked/favorited stream, or maybe the firehose as perceived by someone else, but without spelling out what they've blocked/disliked/liked/favorited, etc.
Jim of Seattle wrote: So then for any individual user there would be an enormous ramp-up while they continued to have sucky songs pop up that they then have to blacklist. I mean, we're at 10,000 songs now. I'm willing to bet that 5,000 or them I don't ever want to hear again. A user should also be allowed to say "Don't ever play anything by <sucky band> again".
I was totally thinking about banning bands outright. If I listen to a fight, I'd want the whole thing I suppose. But in radio mode I'd be happy never to hear <sucky band> at all.
It does bring up the challenge of recognizing how bands develop or change styles, but damn there are a number of show stoppers where I simply don't care. There are thousands of awesome songs, I don't care if they did one good (meaning tolerable) song. On the other hand, if I do hear that one good song when listening to a fight or something, I could revisit my ratings, right? Perhaps if the "ban this band" option banned all their current songs (rather than all songs now and in the future) then they'd reemerge in future fights.
Sorry, this maybe should be in the fugkinh drunk thread. Wine is flowing freely...
Unstructured similarity clouds (what I described earlier) would hopefully provide SOME sort of genre-awareness while also providing suckiness as something that pushes things away from the clouds. I think (based on the thought experiments behind the algorithm) that you'd end up with a galaxy of music where the core has stuff that everyone likes, little nodules bud off of the center with genre-biased clusters, and stuff that's universally reviled gets cast off to the inter-galactic aether. (Stuff like pricklypears which require a certain mindset to appreciate would be in a little bud off to the side that is outside of the central core but would still roughly stick together.)
The main problem I can see with it is that there needs to be a way of weighting stuff such that people who love or hate everything only affect the outliers, rather than affecting things based on consensus. I suppose that every song would end up needing a mean and standard deviation, and the ratings "push" should be based on statistical significance, but that gets outside of my algorithmic expertise. (I've only done this stuff where things are equally weighted within its domain space; similar stuff was the basis of some of the work I did on automatic document conversion for Kindle back in the day. Thus, potential legal issues.)
Post by Jim of Seattle » Sat Feb 23, 2013 9:23 am
While I'm not as excited about this idea as others here seem to be - it seems too ambitious - I think that the need it is trying to answer to is the most critical need on Song Fight, and that is that there need to be some street signs to easier navigate the enormous archive.
How about having a site where people can upload home grown playlists, and anyone can access them, such as "Dexter's 10 Best Songs About Food" or "Best of the One-Submission Wonders" or whatever. It would be more usable than if someone posted a list of links on the BB, because it would be a functional playlist like on the SF Jukebox. Having this site usable on a smartphone would be even better. Just like the "user lists" feature down the right column at IMDB.com. I plan to offer something like that in my in-progress Song Fight Hall of Fame blog.
Post by glennny » Sat Feb 23, 2013 10:06 am
I want to make an annual deck of trading cards with the 52 most prominent acts of that year. A picture of them on the front. Then stats for them up to that year with a little bio blurb and/or quote. You know like star wars cards or baseball cards. E.g.
Frankie Big Face
2 time Nur Ein champ
Best known for Crinkle Binkle
Xx entries, xx wins
"what we need, is exactly what we have"
Post by Jim of Seattle » Sat Feb 23, 2013 10:27 am
"I'll trade you 6 Catknife Horsebombs for your Brother Machine rookie card."
Instruments: Piano, Guitar, Harmonica, Mandolin, Accordion, Bass
Recording Method: Cubase 5AI, Cubase 6
Submitting as: Jon Eric, Hunky
Location: Pittsburgh, PA
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Post by Generic » Sat Feb 23, 2013 4:12 pm
Jim of Seattle wrote: "I'll trade you 6 Catknife Horsebombs for your Brother Machine rookie card."
Worst. Trade. Ever.
"Warren Zevon would be proud." -Reve Mosquito
Jon Eric - Get your feel on.
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Circle of Titles!!!!!!
jast
Instruments: Vocals, guitar
Recording Method: REAPER, Steinberg UR44
Submitting as: Jan Krueger
Location: near Aachen, Germany
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Post by jast » Fri Mar 01, 2013 6:01 pm
Just saw this thread now.
fluffy wrote: The basic idea [...] is that every song and user are considered to be "particles" in a large multidimensional space (the number of dimensions doesn't matter, as long as it's at least 2, but the more the better; I'd probably start with 5). A "love" is an attractive force, and a "hate" is a repulsive force. So, whenever someone likes a song, the user and the song get drawn closer to each other, and whenever someone hates a song, the user and the song get pushed apart. Then, multiple users can also be compared based on their respective love and hate lists, and based on how similar they were, they'd attract or repel each other too. Beyond the initial impulse there would also be an ongoing process that occasionally pushes stuff around based on past data.
Out of my experience with data analysis, the assumption "the more the better" is rather optimistic. Data analysts talk about the "curse of dimensionality" in this context: the more dimensions you have, the longer the distances between points get, and so the less meaningful the distances are.
So, one integral part of anything like this is actually reducing the number of dimensions, and then you're left with the usual big challenge: figuring out a good compromise between model complexity (roughly equivalent to number of dimensions), too much of which makes the model too specific, and simplification, too much of which makes the model inaccurate.
On implementation details: this seems to invite a clustering-style algorithm, or more probably the k-NN algorithm. k-NN often performs surprisingly well, but if it doesn't, there's no real way to fix it (at least in my experience). Since we're essentially trying to combine multiple distributions of the same points (songs) -- the opinions of different users -- there's a whole layer of extra computations we need to do on top of that. I kind of doubt it could be computed online, so there might be some significant delays involved.
Another interesting idea, perhaps: generate a GMM for each user's song preferences and calculate the pairwise divergence of users' models... though I have no concrete ideas about how to do that if the number of GMM components differs between users.
No, I'm not volunteering to implement it.
most of my music
Song Fight-related stuff I host: ZIP archives // Circle of Titles
Post by fluffy » Fri Mar 01, 2013 7:05 pm
I'm just thinking that a casual relaxation approach would be good enough for starters, and if we want to actually form specific clusters of things that you can just do a QT filter afterwards. But the point was just that things that people like about the same tend to move towards each other, and things that they don't like move away from each other, and it could just make recommendations based on where in the space songs are in relation to the listener.
Basically I was just seeing it as something slightly better than a global good/bad/neutral rating scheme, without requiring a lot of input from individuals.
The great thing is that if we do accumulate preferential data from people then we can try all sorts of crazy algorithms on it and see what works well and what doesn't and so on. The data set is small enough (a few hundred users, a few thousand songs) that something naive could possibly generate something interesting, but large and subjective enough that it would be infeasible to use the usual choices in algorithm.
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Compensation for Trip at Work
In September 2003 Margaret tripped and fell forward, striking her chin on the ground. She sustained a laceration to her chin and attended her local A&E department. She complained of jaw pain and nausea. No x-rays were ordered and no referral was made to a senior A&E doctor or to the maxillofacial team. Margaret's chin wound was cleaned and closed, and she was discharged without further advice or follow up.
Over the next few days Margaret continued to suffer pain, but as the pain lessened she became aware her teeth did not feel normal. She attended her dentist on 5th November 2003, and x-rays were taken which confirmed she had an undiagnosed fracture of the condyles on both sides of her jaw.
The hospital admitted that the fracture should have been diagnosed in A&E. Margaret's medical expert confirmed that if her fractures had been diagnosed at that time, she would have had a period of jaw immobilisation and she would have made a satisfactory recovery. However, instead the fractures healed in their displaced positions, such that her teeth no longer meet. This causes her pain on both sides of her jaw, there is a grinding sensation when she moves her jaw, and she is only able to eat a soft diet due to her inability to chew properly. There is, however, further dental treatment available which might improve the contact between her teeth.
Margaret's personal injury claim was successful and she received a five-figure settlement.
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This weekend, the World Congress of Families (WCF) meets in Moldova for their annual conference. The conference will include panels on gender identity, faith and politics, motherhood, anti-abortion efforts, and George Soros, among others. The intermarriage between far-right politics and religious positions is obvious and unsurprising. What may be less obvious is how this brings together Christian fundamentalists, alt-right activists, and Russian interests.
Start with the Southern Poverty Law Center's background on the WCF. It was founded between American Allan Carlson and Russians Anatoly Antonov and Viktor Medkov. The group came together when Carlson, a former history professor at a conservative Christian college, published writings asserting that feminism and sexual liberation were causing "demographic decline," which reached Antonov and Medkov, Russian sociologists. The three would come together to fight the causes, as they saw them, including: divorce, homosexuality, and women joining the workforce, among others.
The WCF was formed in 1997 and has spent two decades publishing propaganda that opposes women's rights and LGBTQ rights. A documentary they produced in 2007 names a list of causes they blame for population decline, including higher education for women, access to birth control, and prosperity, which the group says leads to families having fewer children and investing more money in each child.
More than twenty years in, the influence of the network, which has created international connections, including giving Russian operatives access to American political activists and religious leaders, continues to forge an influence. In the era of President Donald Trump, these connections are of particular concern. Over the last few years, America has watched Russia reach out to influence the 2016 Presidential election, and subsequently witnessed the new president frantically work to cover up those influences.
I have never promised to be the president of the gays, they should have elected their own president.
Where this connects to current American politics and religion is in the speakers and attendees. They include, according to a list procured by the SPLC, Americans with influence in politics, religion, and education such as Stephen Baskerville and Tim Rarick.
Baskerville is a professor at Patrick Henry College, a conservative Christian college in Virginia, who has blamed the fight for LGBT rights for the rise of the Nazi party.
Rarick is a professor at Brigham Young University Idaho. If the name doesn't give it away, the college is run by the Church of Latter-Day Saints. Rarick has a documented history of opposing transgender rights.
In addition to American influencers, speakers include activists from Nigeria, Russia, France, and Latin America, with histories that include fighting to criminalize homosexuality, pushing to decriminalize domestic violence, running an organization to "prepare white French youth for a civil war against people of color, Muslims and immigrants," and similar activism. They include politicians, Bishops of the Catholic Church, leaders in other churches, educators, and leaders of political activist organizations.
In 2015, the Human Rights Campaign released a warning about the group as they planned a conference in Utah, noting that many influential anti-LGBT activists from the U.S. and other countries would be attending.
Think Progress warned this week that the prominence of the network has promoted connections between Russian oligarchs and American political operations. Multiple Russian oligarchs currently under sanctions from the U.S. are reported to be sponsors of the conference.
The WCF reportedly hopes to promote Vladimir Putin's leadership as a model for the United States to follow. While this organization has existed for decades, for most of that time America wasn't under the rule of President Trump.
Donald Trump openly and publicly praises Putin's leadership and intelligence. He has promoted policies matching the values the WCF espouses, using a military ban to attempts to push transgender individuals out of one aspect of public life, opposing immigration and women's freedom to prevent or end a pregnancy, and, through his Justice Department, and arguing in favor of the right to discriminate on the basis of sexuality.
While the 'values' that the World Congress of Families promotes may be damaging at any time, there's currently a clear opening in the United States for them to access politics at the highest level, and this year's panels, especially focusing on the intermingling of politics and religious extremism, should be a concern for anyone who is a member of the resistance against Donald Trump.


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Russian nitrate threatens UKs
IMPORTS of Russian ammonium nitrate are threatening the UK fertiliser market.
So says the Fertiliser Manufacturers Association, which has called on the EU to review its minimum import price system.
The current set-up, claims FMAs Barry Higgs, is not having the intended anti-dumping effect, leaving the UK in an "unsustainable position". "Excessively cheap imports put the UK industry at risk, while also displacing the established Russian trade."
The cheapest Russian product is available at up to a £30/t discount on domestic fertiliser, putting on-farm prices at just over £100/t in some cases.
Prices have fallen not only because of varying "interpretations" of the minimum import price rules, says ICIs Andy Yates, but also because of sterlings strength.
With the minimum import price set in ecus, recent currency movements have seen this fall by over £10/t, says Mr Yates.
Tim Relf
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