text:
\documentclass{article}
\usepackage{a4}
\usepackage{url}
\usepackage{moreverb}
% graphicx package, useful for including eps and pdf graphics
% include graphics with the command \includegraphics
\usepackage{graphicx}
\usepackage{tabularx}
\begin{document}

\newcommand{\PALMA}{{\sl PALMA}}
\newcommand{\PALMapper}{{\sl PALMapper}}
\newcommand{\GM}{{\sl GenomeMapper}}
\newcommand{\Galaxy}{{\sl Galaxy}}
\newcommand{\mGene}{{\sl mGene}}
\newcommand{\ASP}{{\sl ASP}}
\newcommand{\evaluationToolbox}{{\sl evaluationToolbox}}
\newcommand{\QP}{{\sl QPALMA}}
\newcommand{\QPA}{{\sl QPALMA alignment algorithm }}
\newcommand{\QPH}{{\sl QPALMA approximation }}
\newcommand{\QPP}{{\sl QPALMA pipeline }}
\newcommand{\qparam}[1]{{\bf #1}}

\setlength{\parindent}{0cm}

\title{PALMapper Documentation}
\author{G\'eraldine Jean}
\date{December 2010}

\maketitle
%
%
%

\section{Overview}
\label{sec:overview}

\PALMapper{}~\cite{Palmapper} is the fusion of the short read mapper
\GM{}~\cite{GenomeMapper} and the short read aligner
\QP{}~\cite{DeBona08}. This is an easy-to-use and flexible tool
to accurately and efficiently align both transcriptome reads (spliced
and unspliced) from RNA-Seq experiments against a reference
genome. \PALMapper{} is able to take advantage of read-quality
information by using the efficient training algorithm of \QP{}. It is
additionally able to benefit from computational splice-site
predictions which can be computed via
\mGene{}~\cite{Schweikertetal09,Schweikertetal09b} or
\ASP{}~\cite{Sonnenburgetal07} to improve the alignment accuracy.\\
This documentation describes how to install \PALMapper{} and how to
use it on the command-line based on (a) the reference genome, (b) a
set of RNA-seq reads and (c) a \QP{} parameter file (obtained by
training \QP{}). \PALMapper{} can also be used through a Web service,
which is a customized version of the Galaxy
framework~\cite{Galaxy1,Galaxy2,Galaxy3}. For further detail, a
comprehensive tutorial~\cite{Palmapper} about
training \QP{}, aligning with \PALMapper{}, evaluating and visualizing
the resulting alignments is available in Current Protocols in
Bioinformatics.

For further information, you may contact:
\begin{center}
Gunnar R\"atsch (Gunnar.Raetsch@tuebingen.mpg.de)\\
G\'eraldine Jean (gjean@tuebingen.mpg.de)
\end{center}

\section{Installation}
\label{sec:installation}

\subsection{Dependencies}
\label{sec:dependencies}
\PALMapper{} is designed to run on \emph{Linux}/UNIX or \emph{Mac OS X} platforms and
can be downloaded at this address:\\
\url{http://ftp.tuebingen.mpg.de/pub/fml/raetsch-lab/software}.\\
This package is distributed under the GNU Public License (GPL). Read
the license before installation. The programs are distributed as C++
source. The memory requirement of \PALMapper{} depends on which kind of index is used:
\begin{itemize}
\item GenomeMapper index: it needs about seven times the genome size
  of main memory (four times for the index, about two times for
  splice-site predictions, and one time the genome size as working
  memory). In this case, \PALMapper{} requires about 21 GB of memory
  for the human genome.
\item Burrows-Wheeler transform (bwt)-based index. %TODO
\end{itemize}
The machine's architecture does not significantly influence the memory requirement for
these program.\\

The software package has the following dependencies on other packages:
\begin{itemize}
\item C++ compiler, for instance GNU C/C++ Compiler gcc/g++
(http://www.gnu.org). For other compilers, the compiler flags may need to be
adapted in the Makefile file.
\item Standard programs, such as \texttt{wget}, \texttt{make}, etc.
\item SAMtools for manipulating alignments in the SAM format
(http://samtools.sourceforge.net/).
\end{itemize}

\subsection{Step by step installation guide}
\label{sec:installguide}

\begin{enumerate}
\item Go to \url{http://ftp.tuebingen.mpg.de/pub/fml/raetsch-lab/software/}
    and download the package \texttt{palmapper/palmapper-0.4.tar.gz}
    to the home directory.

\item Extract the tar-gzipped file in your home directory as follows:
\begin{verbatim}user:~$ cd
user:~$ tar zxvf palmapper-0.4.tar.gz\end{verbatim}
This command decompresses and unpacks the different files contained in
the archive to a directory named \texttt{palmapper-0.4}.

\item Compile \PALMapper{} by typing:
\begin{verbatim}user:~$ cd palmapper-0.4
user:~/palmapper-0.4$ make\end{verbatim}
Two binary files are created in the working directory: \texttt{palmapper} (the
mapping program) and \texttt{pmindex} (genome array-based index
builder). An other binary file named \texttt{bwa} is created under
\texttt{src/bwa/} and is used for building a genome bwt-based index.
\end{enumerate}

\section{Generating alignments with PALMapper}
\label{sec:aligning}

This section shows how to use \PALMapper{} for generating both unspliced
and spliced alignments for a set of RNA-Seq reads on the
command-line with the consideration that \QP{}~\cite{DeBona08} has
been already trained and optionally splice sites have been predicted
(see section~\ref{sec:inputfile} about input files) for the organism
of interest. Finally, this section describes a testcase suite included in
the package that checks whether \PALMapper{} gives the expected
results. The Galaxy version of \PALMapper{} is briefly described in
section~\ref{sec:aligninggal}.

\subsection{Input files}
\label{sec:inputfile}
Aligning with \PALMapper{} needs the following files:
\begin{itemize}
\item Genome sequence in FASTA format
\item Read data to align in Sanger FASTQ format (see section
  \ref{sec:readfile} for Sanger FASTQ format).
\item Genome annotation in GFF3 format (optional).
\item Donor and acceptor splice-site predictions in SPF format and
corresponding binary files (optional; see section
\ref{sec:splicescoresfile} for BSPF format). There are two ways for
obtaining these files: splice site predictions can be computed for a
given genome via an appropriate tool (see
\mGene{}~\cite{Schweikertetal09,Schweikertetal09b} or
\ASP{}~\cite{Sonnenburgetal07} for example). It can be done using the
Galaxy system (\url{http://galaxy.tuebingen.mpg.de/}) and then
downloaded for local use. Alternatively, the user can directly
download precomputed splice site predictions for a growing list of
organisms at
\url{http://ftp.tuebingen.mpg.de/pub/fml/raetsch-lab/predictions/splice}. In
this case, the splice site predictions have to be used together
with the corresponding version of genome sequence. Splice-site
predictions and the corresponding version of the genome can be easily
downloaded by running the command:
\begin{verbatim}
user:~/palmapper-0.4/splice_predictions$ make <organism>
\end{verbatim}
where \texttt{<organism>} is the name of the organism of interest.\\
The user may also disable the use of splice site predictions by using
\texttt{-no-ss-pred} parameter in the way explained in step 2 below.
\item \QP{} parameter file (see
  Figure~\ref{fig:qp_parameter_file}). This file is obtained by
  training \QP{} (for more information, consult the comprehensive tutorial
  paper about \PALMapper{}~\cite{Palmapper}). Pretrained \QP{}
  parameter files for use with \PALMapper{} are located
in: \texttt{~/palmapper-0.4/qpalma\_parameters}. Be sure to read the
README file in the same directory for more information.
\end{itemize}

\begin{figure}[h!]
\begin{center}
\includegraphics[width=\textwidth]{QPALMAFile.jpg}
\end{center}
\caption{Example of a \QP{} parameter file generated during the training
  phase of \QP{}. The first lines starting with $\#\#$ characters
  describe the parameters used for generating this file. The following
  lines represent the piece-wise linear functions for intron length (h),
  donor splice sites (d), acceptor splice sites (a) and edit operations
  for match/mismatch/gap on read (q). Each piece-wise linear function is
  defined by the range of possible x-values (length for h, splice site
  predictions for d and a, quality for q) which is followed by the
  values for all support points (first, x-values separated by commas
  then, after a space, y-values separated by commas
  too). \texttt{mmatrix} defines fixed scores for a gap on DNA according
  to possible aligned base in read. Finally, \texttt{prb\_offset} is the
  quality offset for determining the quality value from the ASCII
  quality character.}
\label{fig:qp_parameter_file}
\end{figure}

\subsection{Aligning with PALMapper on the command-line}
\label{sec:aligningcl}

\begin{enumerate}
\item Create an index of the reference genome:\\
\PALMapper{} offers the possibility to use two different kinds of
index for the reference genome: array-based and bwt-based indexes. The
first one uses more space but provides a better runtime especially for
small genomes. We advise the user to
use array-based index for genomes of small size (\emph{C. Elegans} for
instance) and the bwt-based index for large genomes as \emph{Human}.
\begin{itemize}
\item[a.] Create an array-based index:
\begin{verbatim}
user:~$ cd palmapper-0.4/
user:~/palmapper-0.4$ ./pmindex -i <genome_file> -s <index_size> -v
\end{verbatim}
where \texttt{<index\_size>} is the seed length used during indexing
(e.g., 13). This creates 4 files the prefix of which is
\texttt{<genome\_file>}:
\begin{itemize}
\item \texttt{<genome\_file>.cid}: chromosome index file
\item \texttt{<genome\_file>.mta}: meta index file
\item \texttt{<genome\_file>.mfd}: forward index file
\item \texttt{<genome\_file>.mrc}: reverse index file
\end{itemize}

\item [b.] Create a bwt-based index:
\begin{verbatim}
user:~$ cd palmapper-0.4/src/bwa
user:~/palmapper-0.4/src/bwa$ ./bwa index <genome_file>
\end{verbatim}
This creates 4 files the prefix of which is \texttt{<genome\_file>}:
\begin{itemize}
\item \texttt{<genome\_file>.bwt}: forward index file
\item \texttt{<genome\_file>.rbwt}: reverse index file
\item \texttt{<genome\_file>.sa}: suffix array for forward index
\item \texttt{<genome\_file>.rsa}: reversed suffix array for reverse
  index file
\end{itemize}
\end{itemize}

\item Use the command below to run \PALMapper{} within the working directory. The
command provided here is a generic one for computing both unspliced and spliced
alignments (spliced via \texttt{-S} option), and the user should
revise the options described in section~\ref{sec:settings} for best results.
\begin{verbatim}
user:~/palmapper-0.4$ ./palmapper -i <genome_file> -q <read_file> \
[OPTIONS_PALMAPPER] -S -qpalma <qpalma_param_file> \
-acc <acc_pred_file> -don <don_acc_file> -o <out_mapped_file> \
-u <out_unmapped_file> [OPTIONS_QPALMA]
\end{verbatim}

where:
\begin{itemize}
\item \texttt{<genome\_file>} is the path to the genome sequence file.
\item \texttt{<read\_file>} is the path to the genome read data file.
\item \texttt{<qpalma\_param\_file>} is the path to the \QP{} parameter file.
\item \texttt{<acc\_pred\_file>}, \texttt{<don\_pred\_file>} are the paths to acceptor and
donor splice-site prediction files. Replace both of these parameters
by \texttt{-no-ss-pred} option if you want to disable the use of splice
site predictions during the alignment process. In this case, use a
\QP{} parameter file obtained by training \QP{} without using splice
site predictions.
\item \texttt{<out\_mapped\_file>}, \texttt{<out\_unmapped\_file>}
are the paths to the alignment output and the unmapped reads files.
See section~\ref{sec:settings} for detail about
\texttt{[OPTIONS\_PALMAPPER]} and \texttt{[OPTIONS\_QPALMA]}.
\end{itemize}
By default, the array-based index is used to generate alignments. To
switch to bwt-based index, the user should add the option \texttt{-bwa
  <seed\_length>} (i.e. with 12 for seed length) in the command-line.
\item Two output files are generated and are located according to the specified paths
\texttt{<out\_mapped\_file>}, and \texttt{<out\_unmapped\_file>}:
\begin{itemize}
\item An alignment file, which stores all alignments of reads for which an alignment
satisfying the specified criteria has been found.
\item An unmapped read file, which stores all reads for which no alignment has been
found. The \texttt{-u} option is optional.
\end{itemize}
By default, the alignment file is encoded in a SAM format but the user can alternatively
choose between BED, an extended BED format (BEDx), SHORE, and SAM formats using
the option \texttt{-f}. The unmapped reads are written in FASTQ
format. See sections~\ref{sec:readfile} and \ref{sec:samfile} for
specifications of FASTQ and SAM formats, respectively.

\item \emph{Optional}: Convert alignment files in SAM format into
  wiggle VariableStep format by running the following commands:
\begin{verbatim}
user:~/palmapper-0.4$ cd tools/
user:~/palmapper-0.4/tools/$ python sam2wig.py --input=<alignment_file> \
--ref-file=<genome_file> --output=<wiggle_file> --expName=<exp_name> \
\end{verbatim}

where \texttt{<alignment\_file>} is the path to alignment file
obtained in step 3, \texttt{<genome\_file>} is the path to the
sequence file of reference genome, \texttt{<wiggle\_file>} is the path
to output wiggle VariableStep file, and \texttt{<exp\_name>} is the
name the user wants to give to his experiment (e.g., Experiment
SRX001872). Alternatively, one may use the
\texttt{-report-coverage-wig} option to generate the coverage wiggle
file directly. Wiggle VariableStep files are necessary if you want to
visualize the resulting alignments using a genome browser (GBrowse for
instance) or Galaxy Trackster.
\end{enumerate}

\subsection{Aligning with PALMapper on an example}
\label{sec:example}

\begin{enumerate}
\item Open a new shell window and go to \texttt{testcase} directory by
  typing:
\begin{verbatim}
user:~$ cd palmapper-0.4/testcase/
\end{verbatim}
The user can easily test different options of \PALMapper{} on an
example from \emph{C. elegans} that is ready to run in the
\texttt{testcase} directory of \PALMapper{} package.
\item Run testcase by typing:
\begin{verbatim}
user:~/palmapper-0.4/testcase$ make all
\end{verbatim}
This command first downloads splice-site predictions and the
\emph{C. elegans WS209} reference sequence, and builds array-based and
bwt-based indexes. Then, for each type of index, it runs \PALMapper{}
for testing the following options. Each testcase can be run separately:
\begin{itemize}
\item \texttt{make [bwa]map}: test typical usage of \PALMapper{} with
  the following detailed command:
\begin{verbatim}
../palmapper -i data/c_elegans.WS209.dna.fa -q data/split_1m.000 \
-acc data/C_elegans_SpliceSitePred_WS209/acc_pred.bspf/contig_%i%c \
-don data/C_elegans_SpliceSitePred_WS209/don_pred.bspf/contig_%i%c \
-o data/map/split_1m.000.sam -u data/map/split_1m.000.unmapped \
-S -f sam -report-coverage-wig data/map/split_1m.000.wiggle -qpalma \
data/parameters.qpalma -threads 1 -rlim 10000\
-M 4 -G 1 -E 4 -l 20 -L 35 -K 12 -C 55 -z 1 \
-seed-hit-cancel-threshold 1000
\end{verbatim}
\item \texttt{make [bwa]mapUnspliced}: test \PALMapper{} without
  spliced mapping.
\item \texttt{make [bwa]mapPolytrim}: test \texttt{-polytrim} option
  of \PALMapper{}.
\item \texttt{make [bwa]mapRtrim}: test \texttt{-rtrim} option
  of \PALMapper{}.
\item \texttt{make [bwa]mapNoss}: test \PALMapper{} without splice
  site predictions (option \texttt{-no-ss-pred}).
\item \texttt{make [bwa]mapBedx}: test bedx output of \PALMapper{}
  (option \texttt{-f bedx}).
\item \texttt{make [bwa]mapall}: test all cases for a particular index
  (array-based by default, and bwt-based if \texttt{bwa} is provided
  in target name).
\end{itemize}

The output files (alignment file, unmapped reads file and coverage
file) are stored in \texttt{./palmapper-0.4/testcase/data/}. Finally,
the program checks whether \PALMapper{} has correctly run by comparing
obtained results with precomputed results on the same data set. For
each testcase, the user should see the following information
confirming that produced results are those expected appear in the
shell window:

\begin{verbatim}
split 1m.000.sam: OK
split 1m.000.unmapped: OK
split 1m.000.wiggle: OK
\end{verbatim}

At the end, a summary is printed out and should look like to the
following one if everything ran well:

\begin{verbatim}
--------------------------------------------------------
Test summary (12 testcases):
   Test Failed: 0
   Test Passed: 12
      mapBedx (bwt-based index): OK
      mapNoss (bwt-based index): OK
      mapPolytrim (bwt-based index): OK
      mapRtrim (bwt-based index): OK
      map (bwt-based index): OK
      mapUnspliced (bwt-based index): OK
      mapBedx (array-based index): OK
      mapNoss (array-based index): OK
      mapPolytrim (array-based index): OK
      mapRtrim (array-based index): OK
      map (array-based index): OK
      mapUnspliced (array-based index): OK
\end{verbatim}
\end{enumerate}

\section{Aligning with PALMapper using Galaxy tools}
\label{sec:aligninggal}
\PALMapper{} can also be used via a Web service
(\url{http://galaxy.fml.mpg.de/}), which is a customized version of
the Galaxy frameworks~\cite{Galaxy1,Galaxy2,Galaxy3}. There are no
difference between these two ways of using \PALMapper{} except that using
galaxy saves the user from installing the software. Moreover, it is
preferable to align with \PALMapper{} via galaxy if the rest of the study is
carried out with galaxy as well. For further details about how to
align with \PALMapper{} using Galaxy tools, please read \PALMapper{}
tutorial \cite{Palmapper}.

\section{File Formats / Specifications}
\label{sec:formats}
This section introduces all formats and conventions to be used when
aligning with \PALMapper{}.

\subsection{The read file}
\label{sec:readfile}

The read file is encoded in Sanger FASTQ format. A FASTQ file normally
uses four lines per sequence. The first line begins with a '@'
character and is followed by the read identifier and an optional
description. The second line is the nucleotide sequence of the
read. The third line begins with a '+' character and is optionally
followed by the same identifier (and any description) again than in
line 1. The last line encodes the quality values for the sequence in
line 2, and must contain the same number of symbols as letters in the
sequence. Sanger format encodes a quality score from 0 to 93 using ASCII
33 to 126. For a more detailed description of the FASTQ format consult:
\url{http://en.wikipedia.org/wiki/FASTQ_format}. Figure~\ref{fig:fastq}
is an example of a Sanger FASTQ file.

\begin{figure}[h!]
\begin{center}
\includegraphics[width=0.5\textwidth]{ReadFile.jpg}
\end{center}
\caption{Example of a Sanger FASTQ file for input read data.}
\label{fig:fastq}
\end{figure}

\subsection{Splice Scores}
\label{sec:splicescoresfile}

As mentioned before, the splice site scores can be generated using an
appropriate tool such that
mGene~\cite{Schweikertetal09,Schweikertetal09b} or
ASP~\cite{Sonnenburgetal07}. If you would like to use your own splice
site predictions you can create files according to the Binary Signal
Prediction Format (BSPF) described below:

For each canonical acceptor ($AG$) and donor site ($GT$/$GC$)
\PALMapper{} expects a score. The data is organized in files for each
signal (acc/don) for each strand (+/-). The information on positions of
canonical splice sites and the corresponding scores lies in separate
files. Every chromosome or contig leads then to $8$ files (acc/don, +/-
and pos/score). The position and score files are raw binary files
containing the ordered positions and the scores. The positions are
stored as unsigned values and the scores as floats. Note that you have
to be careful when working in an inhomogeneous cluster environment
(endianness, data type size). The positions are 1-based and the
assignment of positions and their scores is as follows: The acceptor
score positions are the positions right after the $AG$ and the donor
score positions are the positions right on the $G$ of the $GT$ or
$GC$. For example:
\begin{center}
\begin{tabular}{ccccccccccc}
... & 3 & 4 & 5 & 6 & 7 & 8 & 9 & 10 & 11 & ... \\
... & w & g & t & x & y & z & a & g  & v  & ... \\
... &   & 0.2&  &   &   &   &   &    & 0.3 & ...
\end{tabular}
\end{center}

\subsection{Alignment file}
\label{sec:samfile}
By default, the alignment file is encoded in a SAM format but the user
can alternatively choose between BED, an extended BED format (BEDx),
SHORE, and SAM formats using the option \texttt{-f}.

The SAM format used by \PALMapper{} is described below. For
complementary information, you should refer to
\url{http://samtools.sourceforge.net/}. Each row in SAM file describes
an alignment with the following fields:
\begin{enumerate}
\item \textbf{qname} - Query name (read id)
\item \textbf{flag} - Bitwise flag
\item \textbf{rname} - Reference sequence name (chromosome id)
\item \textbf{pos} - 1-based leftmost position/coordinate of the
  clipped sequence
\item \textbf{mapq} - Mapping Quality (phred-scaled posterior probability that the mapping
position of this read is incorrect). Field MAPQ considers pairing in
calculation if the read is paired. Providing MAPQ is recommended. If
such a calculation is difficult, 255 should be applied, indicating the
mapping quality is not available.
\item \textbf{cigar} -extended CIGAR string
\item \textbf{mrnm} - Mate reference sequence name; "=" if the same as
  RNAME (set to * if no paired information)
\item \textbf{mpos} - 1-based leftmost Mate position of the clipped
  sequence (set to 0 if no paired information)
\item \textbf{isize} - inferred Insert SIZE (set to 0 if no paired information)
\item \textbf{seq} - query sequence
\item \textbf{qual} - query quality; ASCII-33 gives the Phred base quality
\item \textbf{tag} - Tag
\item \textbf{vtype} - Value type
\item \textbf{value} - match vtype (space allowed)
\end{enumerate}

The fields \texttt{tag}, \texttt{vtype} and \texttt{value} are
concatenated and separated by a ":''. The possible tags
encountered in the output of \PALMapper{} are the following:\\

\begin{tabular}{|c|c|p{12cm}|}
\hline
{\bf Tag}&{\bf Type}&{\bf Description}\\
\hline
NM&i&Number of nucleotide differences (i.e. edit distance to the reference sequence)\\
\hline
H0&i&Number of perfect hits\\
\hline
XS&A&Strand information (for spliced alignments only)\\
\hline
Xe&i&Minimal exon length\\
\hline
XI&i&Maximal intron length\\
\hline
Xi&i&Minimal intron length\\
\hline
XC&Z&Non consensus splice site sequence in case of a spliced alignment
with a non-consensus splice site (with option \texttt{-non-consensus-search}) \\
\hline
XQ&i&Sum of mismatch qualities\\
\hline
XN&i&Number of exon(s)\\
\hline
ZS&f&\QP{} score for the alignment\\
\hline
AS&i&Alignment score generated by aligner (for \PALMapper{}, it
corresponds to \QP{} score multiplied by 100)\\
\hline
HI&i&Query hit index, indicating the alignment record is the i-th one stored in SAM\\
\hline
XD&f& \QP{} score difference between the alignment with the best
\QP{} score and the given one for the same query\\
\hline
Xd&i&Difference in terms of edit operations between the given
alignment and the alignment with the minimum number of edit operations
for the same query\\
\hline
\end{tabular}

\section{General settings}
\label{sec:settings}

\PALMapper{} offers a large set of parameters to run \GM{} and \QP{}
(see Tables~\ref{tab:palmapper_param} and~\ref{tab:qpalma_param}) and
running this tool with default parameters may lead to suboptimal
results. It is therefore important to monitor the alignment quality
using the provided evaluation and visualization tools before they are
used for further analysis.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PALMapper options
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{table}[h!]
\begin{tabular}{p{3cm}p{6cm}cp{2cm}}
\hline
Option/Flag&Description&Default&Range\\
\hline
\texttt{-f}& output format&sam& [shore, bed, bedx, sam]\\
\texttt{-o}& output filename & stdout& STRING\\
\texttt{-u}& unmapped reads filename&/dev/null& STRING\\
\texttt{-z}& report a number of top scoring alignments&10&INT\\
\texttt{-a}& report all alignments as good as the best one&&\\
\texttt{-ar}& report a limited number of best alignments&0(all)&INT\\
\texttt{-r}& disable reverse alignment &&\\
\texttt{-h}& always perform alignment on entire read (implied for
spliced alignments)&&\\
\texttt{-d}& align gaps most right (most left) (ignored for spliced alignments)&&\\
\texttt{-w}& allow more gaps for best hit (ignored for spliced
alignments)&&\\
\texttt{-l}& seed length & index size & INT\\
\texttt{-threads}&maximal number of threads &4&INT\\
\texttt{-seed-hit -cancel-threshold}& number of hits of a seed that
lead to its ignoration &&INT\\
\texttt{-index-precache}& linearly read index file to fill caches&&\\
\texttt{-rtrim}&shortens the read until a hit is found or the minimal length is reached&&INT\\
\texttt{-polytrim}& trims polyA or polyT ends until a hit is found or
the minimal length is reached&&INT\\
\texttt{-rlim}& limit the number of reads for alignment&&INT\\
\texttt{-M}& max number of mismatches&3&INT\\
\texttt{-G}& max number of gaps&1&INT\\
\texttt{-E}& max edit operations&3&INT\\
\texttt{-m}& mismatch penalty&4&DOUBLE\\
\texttt{-g}& gap penalty &5&DOUBLE\\
\texttt{-v}& verbose &silent&\\
\hline
\end{tabular}
\caption{Description of the options that influence the general
  behaviour of \PALMapper{} (mostly for unspliced alignments).}
\label{tab:palmapper_param}
\end{table}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% QPALMA options for alignment
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{table}[h!]
\begin{tabular}{p{3cm}p{6cm}clc}
  \hline
  Option/Flag&Description&Default&Range&Optional?\\
  \hline
\texttt{-S}& report spliced alignments (detailed options below)&&No\\
  \texttt{-qpalma}&file name with qpalma parameters&&STRING&No\\
  \texttt{-acc}&path name to acceptor splice site predictions&&STRING&No\\
  \texttt{-don}&path name to donor splice site predictions&&STRING&No\\
  \texttt{-no-ss-pred}&indicates that no splice site predictions should
  be used&&&Yes\\
  \texttt{-filter-splice -sites-top -perc}&trigger spliced alignments, if
  best read alignment covers putative splice site with score in the given top percentile &&[0-1],Float&Yes\\
  \texttt{-filter-max -mismatches}&trigger spliced alignment, if
  unspliced alignment has at least this many mismatches &0&INT&Yes\\
  \texttt{-filter-max-gaps}&trigger spliced alignment, if unspliced
  alignment has at least this many gaps&0&INT&Yes\\
  \texttt{-C}& min combined length&Auto&INT&Yes\\
  \texttt{-L}& min length of long hit&Auto&INT&Yes\\
  \texttt{-K}& min length of short hit&Auto&INT&Yes\\
  \texttt{-I}& longest intron length&Auto&INT&Yes\\
  \texttt{-EL}&Minimum segment length in spliced alignments&Auto&INT&Yes\\
  \texttt{-SA}& maximum number of spliced alignments per read &10&INT&Yes\\
  \texttt{-NI}& maximum number of introns in spliced alignments &Auto&INT&Yes\\
  \texttt{-CT}& distance to tolerate between hit and existing hit cluster&10&INT&Yes\\
  \texttt{-QMM}&number of matches required for identifying a splice site&5&INT&Yes\\
  \texttt{-qpalma-use-map -max-len}& limit the map extension up- and
  downstream to the given length &$10000$&INT&Yes\\
  \texttt{-report}& file for map reporting&&STRING&Yes\\
\texttt{-report-coverage -wig}&Output read coverage track in wriggle
format&&STRING&Yes\\
\texttt{-report-splice -sites}&Report splice sites with confidence not less than a threshold&&  FLOAT& Yes\\
\texttt{-report-splice -sites-top-perc}&Report splice sites with
confidence in top percentile&&[0-1], FLOAT& Yes\\
 \texttt{-report-gff-init}& initialize map with exons from GFF file&&STRING&Yes\\
  \hline
\end{tabular}
\caption{Description of the parameters influencing the spliced
  alignments in \PALMapper{} (only needed when option \texttt{-S} is given).}
\label{tab:qpalma_param}
\end{table}

\subsection{Influencing the General Behaviour}
The most important parameters that influence the sensitivity and
specificity of \PALMapper{} are \texttt{-M}, \texttt{-G} and
\texttt{-E} for specifying the maximal number of mismatches, gaps and
edit operations (mismatch or gaps) allowed in a reported alignment. We
often allow 4-6 mismatches for sequences of length 76 nt with at most
2 gaps.  However, reasonable results can already be obtained with just
1-2 mismatches and no gap (depending on the sequence quality and the
technology). Moreover, the options \texttt{-z}, \texttt{-a} and
\texttt{-ar} determine which alignments should be written into the
result files. In most cases, the setting \texttt{-z 1} will be
sufficient, where only the best alignment is determined and written to
the output file.

\subsection{Spliced Alignments}
There exist a few parameters that influence spliced alignments. First
of all, there are parameters, which influence when a spliced alignment
is triggered. This decision is made based on the number of mismatches
and gaps, the presence of strong splice site predictions for the best
unspliced alignment (options \texttt{-filter-max- mismatches},
\texttt{-filter-max-gaps}, and
\texttt{-filter-splice-site-top-perc}). Once the spliced alignment
routine is  triggered, the seed hits are analyzed and a full alignment
is performed for regions that are longer than a given length (option
\texttt{-L}). This parameter should be set smaller than half of the
read length. The options \texttt{-I} and \texttt{-NI} determine the
maximal intron length and number that is allowed in spliced
alignments.

\subsection{Using Report Maps to Improve Alignments}
\PALMapper{} implements a mechanism to exploit information from
existing annotations or from previous alignments to increase the
sensitivity of alignments. For instance, the option \texttt{-report-gff-init}
allows the user to specify a GFF file with known exons to guide and
improve spliced alignments. Similarly, the option
\texttt{-report-map-read} enables storing information of previously
mapped reads to improve the recognition of exonic regions in following
spliced alignments. This option is often used in conjunction with
option \texttt{-report}, which specifies a file name to which the
mapping information is saved, and a two-step alignment approach: 1)
the reads are preliminarily aligned (for instance, unspliced or with
other stringent settings to increase the speed), and 2) a map file is
generated. This map file is used in the second step for a refined
spliced alignment. Finally, the options \texttt{-report-splice-sites} (and
\texttt{-report-splice-sites-top-perc}) can be used to exploit
computational splice site predictions to identify genomic regions to
which the reads should be aligned.

\subsection{Settings for Faster Alignments}
The following strategies will help to limit the computing time needed
for the alignment:
\begin{itemize}
\item For very repetitive or large genomes the option
  \texttt{-seed-hit-cancel-threshold 1000} can help to reduce the
  alignment time, by ignoring seed hits which occur too often (more
  than 1,000 times) in the genome.
\item To reduce the number of spliced alignments performed
for one read, one may use the option \texttt{-SA} (e.g., \texttt{-SA 2}).
\item The seed length (option \texttt{-s} specified during index
  creation with pmindex) also determines the speed of the alignment:
  larger seeds have fewer hits in the genome and, hence, lead to
  faster alignment, but also to less sensitive results.
\item Reducing the maximal intron length (\texttt{-I}) will
also lead to quicker alignments.
\item To limit the size of the regions that are used for alignment
  that are inferred from the report maps (see above), there is a
  parameter: \texttt{-qpalma-use-map-max-len}. This parameter
  crucially influences the alignment speed, when the large parts of
  the genome are covered with reads or are annotated as exonic (set
  it, for instance, to 5000 to limit the alignment sequence length to
  2X5000 nt).
\end{itemize}

It is useful to use the parameter \texttt{-rlim} to perform the
alignment first on a small subset of the reads, for instance, 10,000,
to estimate the time needed for aligning the reads.

\section{Internet Resources}
\url{http://www.fml.mpg.de/raetsch/suppl/palmapper}\\
\emph{\PALMapper{} project web-page.}\\
\url{http://www.fml.mpg.de/raetsch/suppl/palmapper/tutorial}\\
\emph{\PALMapper{} tutorial web-page.}\\
\url{http://www.fml.mpg.de/raetsch/suppl/qpalma}\\
\emph{\QP{} project web-page.}\\
\url{http://www.fml.mpg.de/raetsch/suppl/mgene}\\
\emph{\mGene{} project web-page.}\\
\url{http://www.fml.mpg.de/raetsch/suppl/splice}\\
\emph{\ASP{} project web-page.}\\
\url{http://ftp.tuebingen.mpg.de/pub/fml/raetsch-lab/software/}\\
\emph{http server for downloading \QP{}.}\\
\url{http://galaxy.fml.mpg.de/}\\
\emph{\Galaxy{} server.}\\

%
% Bibliography
%

\begin{thebibliography}{1}

\bibitem[1]{DeBona08}
  \newblock F.~De~Bona, S.~Ossowski, K.~Schneeberger, and G.~R{\"a}tsch.
  \newblock Optimal Spliced Alignment of Short Sequence Reads.
  \newblock {\em Bioinformatics}, 24(16):i174-i180, 2008.

\bibitem[2]{Palmapper}
  \newblock G.~Jean, A.~Kahles, V.T.~Sreedharan, F.~De~Bona, and G.~R\"atsch.
  \newblock RNA-Seq Read Alignments with PALMapper.
  \newblock {\em Curr. Protoc. Bioinformatics}, 32:11.6.1-11.6.38, 2010.

\bibitem[3]{GenomeMapper}
  \newblock K.~Schneeberger, J.~Hagmann, S.~Ossowski, N.~Warthmann,
  S.~Gesing, O.~Kohlbacher, and D.~Weigel.
  \newblock Simultaneous alignment of short reads against multiple genomes.
  \newblock {\em Genome Biology}, 10(9):R98, 2009.

\bibitem[4]{Tsochantaridis04}
  \newblock I.~Tsochantaridis, T.~Hofmann, T.~Joachims and Y.~Altun.
  \newblock Support Vector Machine Learning for Interdependent and Structured Output Spaces.
  \newblock {\em Proceedings of the 16th International Conference on Machine Learning}, 2004.

\bibitem[5]{Schweikertetal09}
  \newblock G.~Schweikert, G.~Zeller, A.~Zien, J.~Behr, C.-S.~Ong, P.~Philips,
  A.~Bohlen, S.~Sonnenburg, and G.~R\"atsch.
  \newblock {mGene}: {A} Novel Discriminative Gene Finding System.
  \newblock {\em Genome Research}, 19:2133-2143, 2009.

\bibitem[6]{Schweikertetal09b}
  \newblock G.~Schweikert, J.~Behr, A.~Zien, G.~Zeller, S.~Sonnenburg, and G.~R\"atsch.
  \newblock mGene.web: a web service for accurate computational gene
  finding.
  \newblock {\em Nucleic Acids Research}, 37(Suppl. 2):W312–W316, 2009.

\bibitem[7]{Sonnenburgetal07}
  \newblock S.~Sonnenburg, G.~Schweikert, P.~Philips, J.~Behr, and
  G.~R{\"a}tsch.
  \newblock Accurate splice site prediction using support vector machines.
  \newblock {\em BMC Bioinformatics}, 8(Suppl 10):S7, 2007.

\bibitem[8]{Galaxy1}
  \newblock D.~Blankenberg, J.~Taylor, I.~Schenck, J.~ He, Y.~Zhang,
  M.~Ghent, N.~Veeraraghavan, I.~Albert, W.~Miller, K.~Makova, R.~Hardison, and A.~Nekrutenko.
  \newblock A framework for collaborative analysis of ENCODE data: making largescale analyses biologist-friendly.
  \newblock {\em  Genome Research}, 17(6):960–964, 2007.

\bibitem[9]{Galaxy2}
  \newblock J.~Taylor, I.~Schenck, D.~Blankenberg, and A.~Nekrutenko.
  \newblock Using galaxy to perform large-scale interactive data
  analyses.
  \newblock {\em Curr. Protoc. Bioinformatics}, 19:10.5.1-10.5.25, 2007.

\bibitem[10]{Galaxy3}
  \newblock D.~Blankenberg, G.~Von~Kuster, N.~Coraor, G.~Ananda,
  R.~Lazarus, M.~Mangan, A.~Nekrutenko, J.~Taylor.
  \newblock Galaxy: A WebBased Genome Analysis Tool for Experimentalists.
  \newblock {\em Curr. Protoc. Molecular Biology}, 89:19.10.1-19.10.21, 2010.

\end{thebibliography}
%
%
%
\end{document}

redpajama_set_name: RedPajamaGithub


This here is my favorite breakfast in cupcake form. I eat my pancakes with peanut butter and maple syrup. It's how I've always done it since I was a child, learned from my mother, who also ate it this way as a child.
I usually get a weird look when I pull out the peanut butter jar from people who have never tried it, but don't knock it 'til you try it! Pancakes, peanut butter and syrup were meant to be together. It's also excellent with sunflower seed butter if you have a peanut allergy.
The cupcake alone is just a basic buttermilk pancake batter. You wouldn't want to eat it plain but you can make real pancakes with it if you wish. I added chocolate chips to sweeten the deal, topped them with silky peanut butter frosting and then drenched them in maple syrup while they were still slightly warm from the oven. All that's missing is the bacon!
Cupcakes that taste like pancakes topped with a creamy peanut butter frosting, chocolate chips and maple syrup!
Preheat oven to 350ºF and line muffin tin with cupcake liners. Set aside.
In a separate bowl, beat butter, egg and buttermilk until well combined. Add to dry ingredients and mix until just combined. Fold in chocolate chips. Pour into prepared pan. Bake for 18-20 minutes or until a toothpick inserted in center comes out clean. Cool completely.
For the frosting, mix all ingredients except the cream in a stand mixer or with handheld beaters. Add the cream a tablespoon at a time and beat on high speed until light and silky. Pipe onto cupcakes, top with extra chocolate chips and drizzle with maple syrup.
Wow, that looks dangerously delicious! Pretty much anything peanut butter I love.
Agree! And I love that point when PB starts to get a little melty…Mmm!


HERE IS YOUR HOME, I HOPE YOU HAVE FUN HERE AND MAKE PLENTY OF MEMORIES. DO NOT FORGET TO THROWS PARTIES AND INVITE YOUR FAMILY OVER, ALRIGHT? LOVE YOU, FROM BIG TAE XOXO.
How did I get someone so handsome?
/Whispers softly while I pull my mouth away from you slowly and slowly pushes myself upwards.
Yes my love you can please do.
@kang jihyun /Uses my large hands to press them against your thighs, softly squeezing them and pushes then down while my kisses trailed to your line. I took the waistband between my teeth and stated at you while I pulled them down your legs with my teeth, my breath hitting against sensitive areas of your thighs and legs while your came off.
Is there any doubt dear god my love you are a natural it feel amazing.
I think i like these a lot, shows that I am yours.
@kang jihyun /Smirks slightly against your chest, continuing to abuse them with my soft mouth, using my hand to bring your long, beautiful legs up to wrap them around my waist, gripping your small waist with my large hands and lifting my head to look at you, grinning from down below.
@kang jihyun /Breathes a shaky sigh as my body presses against yours, feeling the heat radiating from your skin to mine and I cup your cheeks again, capturing your lips in another slow, but slightly rough kiss, then slides my hand down towards one of your s and gently cups it in my hand, giving it a few squeezes while using my other hand to slide it down between our bodies and to the string of your bedtime shorts, loosening them quickly.
You are so beautiful Jihyun, every single inch of you.
All of this is your my love, I am yours.
@kang jihyun /Breathes softly against your skin and takes in the beautiful sight of your upper half, smiling to myself and moving my lips to kiss yours, gently sliding my arms around your back and fiddling with the back of your bra before unhooking it slowly.
I love you the most...my baby girl..
/Hums softly while kissing your shoulders as I slid the straps down your arms, then slowly slid off your bra and put it to the side, hesitantly opening my eyes to gaze down at your chest, my face flushed and hot from the beautiful sight.
@kang jihyun /Breaks my kiss from you for a moment, staring at you with so much love and affection, soon smiling to myself before I sat up on my knees and over on your lap, bringing my shirt up and above my head before tossing it to the ground.
/I whisper softly while slowly leaning back and pressing my head closer to your stomach, using my fingers to pull up your shirt close to your chest and my lips leave a trail of soft kisses up your skin slowly while your shirt moves more a over your head, trying to take it off your body.
@ten I will love you even after I die.
@kang jihyun I love you too baby girl, I love you till I die.
/Grins widely and kisses you back, placing my hand on the back of your neck and tilting my head while I slightly deepen the kiss.
I love you so much so much. I am the luckiest girl in the world to have found someone so perfect.
I dont think I will get pregnant it is not the right time for that.
@kang jihyun /Chuckles at you looking around the room, giving my head a small shake and gently turning your chin to look at me, staring at you as you asked that important question.
I- the question is would we be ready for a kid? I would be ok with it.
@kang jihyun /Slowly smiles and bites my lip slowly, grinning a bright smile and sits up slowly, bringing you up with me and hugging you close to my body.
Baby, I'll make sure you feel great.
/Murmurs softly and presses a more deeper and tender kiss to your shoulder while wrapping my arms around your waist.
/Fiddles with my words, trying to say I didn't have any use of protection with me.
I am more than sure my love. We have been together for a while and I want to love all of you and want you to have a chance to love all of me.
@kang jihyun /Goes to say something, but is silenced by your lips against mine, I sighed through my nose gently, then slowly opens eyes and looks at you, slowly parting my lips at your words.
/Mumbles to you softly, gesturing towards the more mature side of me.
when you got those few hours of sleep what?
@kang jihyun /Gently pulls my head back and glances down at you.
What got me so excited?
/Tilts head with a small smile and bites my lip slowly.
I guess its just been something I've been thinking about all day, and when I got those few hours of sleep.


1Cover is an online travel insurance specialist and have been established for almost 7 years. 1Cover sell travel insurance direct to the consumer so you don't have to go through your Travel Agent. This means you don't have to pay your Travel Agent any commissions.


text:
Trignani v. R. – Child Support and Tax Deductibility of Legal Fees
Mr. Trignani, a Child Support payor, challenged the Canada Revenue Agency's refusal to allow him to deduct his Child Support related legal fees.
Up until this decision, the common consensus among family law practitioners was that only Child Support recipients (and thus not Child Support payors) could deduct their Child Support related legal fees when filing their income tax returns.
Mr. Trignani was successful in his appeal. This means that a payor of Child Support was permitted to deduct the Child Support related portion of his legal fees from his income. This does not mean that all Child Support payors are now allowed to do the same. This case appears to state that Child Support payors may only deduct their legal fees incurred to resolve the issue of Child Support where:
they made a claim for Child Support,
this claim was not frivolous,
this claim had reasonable chance of success, and
this claim was not abandoned prior to incurring the legal fees in question.
Whether the payor must have joint custody of the children in order to claim this deduction is unclear. Mr. Trignani did have joint custody in this case, so this may also be a requirement for tax deductibility of Child Support related legal fees for payor spouses.

redpajama_set_name: RedPajamaCommonCrawl


INFLUENCES OF FOOD AND WINE TO BRIDGE THE GREAT GAP IN IDEOLOGY.
INTERLOPER, A MERE PRIME MINISTER AND ONE FROM SYDNEY AT THAT.
PRIME MINISTERS COME AND PRIME MINISTERS GO BUT YOU GO ON FOREVER.
THINK YOU MIGHT EVEN COME TO ENJOY IT.
WITH MINE, WE CAN WORK TOGETHER.
BEEN ACTIVE IN FORMING AMONG57THEMSELVES A ', ESTERN ; REGIONS COMMISSION.
REACHING OUR GOAL OF OVERCOMING THE BACKLOG IN SEWERAGE BY 1980.
OF THE VAST MAJORITY OF OUR PEOPLE.
EXHILARATING FOR US ALL AS AUSTRALIANS.


Ube Cake – unusual purple chiffon cake made with ube (Filipino name for purple yam/sweet potato) and coconut.
This cake recipe was on my to-do list for over 6 years. The reason I didn't make it sooner is because I couldn't find truly purple sweet potatoes / yams. On more occasions I would buy sweet potatoes with purple skin, but when I peeled them it turned out their flash was white. They tasted like chestnuts, were very sweet and suitable for desserts, but they did not have that deep purple color necessary for "ube" desserts. When I finally saw purple yams in my shop a few days ago I knew immediately what I'm going to use them for.
In the Philippines, purple yam (Dioscorea alata) is known as ube and is used used in a variety of desserts like cakes, ice cream, Swiss rolls, tarts, cookies, and other pastries.
I first found the recipe on lindyscakes.co.uk, but I made some changes to it. The original cake is filled with macapuno – coconut preserves. Since it is not sold in our shops, I had to come up with some other way of doing it. I decided to make a filling/icing with mascarpone cheese and coconut milk. It is lighter then buttercream frosting, but still has slight taste of coconut like macapuno. In case you dislike coconut taste, you can use whipping cream instead of coconut milk. If you didn't know, coconut milk can be whipped into cream in the same way as whipping cream. It is just necessary to chill it in the fridge for at least 8 hours prior to whipping.
This chiffon cake is intended to be baked in 3 cake pans, 9 inch diameter. I poured 1/4 of the batter into an 8-inch iron pan and the rest into a large sheet pan. After baking, I used the iron pan as a stencil to cut out 2 more circles out of the dough. I placed remaining dough into a food processor to make purple crumbs which I used to decorate the cake together with some coconut cookies. You certainly don't need to make this additional step.
I do not use to food coloring in my recipes, except in some special occasions like red velvet cake recipes. If using powdered food coloring, I suggest you dissolve it in liquid prior to adding to flour.
Anyway, if you like to try out new, unusual or even exotic recipes like me, maybe Ube Cake is the right thing for you.
Mix 7 egg yolks with 3/4 cup caster sugar. Add mashed ube, milk, vanilla, oil and food coloring (if using). Add flour mixture and beat until smooth.
Whisk egg white with lemon juice until foamy. Slowly add 3/4 cup caster sugar until stiff peaks form. Carefuly fold beaten egg whites into the batter using spoon or spatula (do not use mixer for this step).
Pour the batter into 3 9-inch cake pans lined with baking paper. Bake at 175 C (350 F) for about 30 minutes.
Immediately after baking, take cakes out of their pans, turn them upside down on a wire rack and let cool.
ICING: Open the can of chilled coconut milk and scoop out the cream. Mix it cream with vanilla extract and a sugar until fluffy. Mix in the mascarpone cheese. Use this mixture as both a filling and frosting for the cake.
Optional step: decorate the cake with purple cake crumbs and coconut cookies.


The gas division welcomes members of the BFA who are interested in gas ballooning. Join the division to today to access information about gas ballooning in the members only area. This area has announcements, a newsletter and technical archive for those interested in learning more about gas balloons used for Lighter Than Air Flights.
What is the Gas Division and why should I join?
The BFA Gas Division is a growing segment of the Balloon Federation of America. It is made up of pilots and crew members interested keeping the oldest part of our sport relevant and growing. Flying a gas balloon is complex, challenging, and extreme. It provides a significantly different perspective on lighter than air sports.
It forces pilots to deal with issues that are much easier to control or avoid when flying a hot air balloon. You will experience longer flights, must deal with weather, airspace and interact with air traffic control. Gas balloons fly differently and perform well in high winds and difficult weather. It provide pilots and crews a great learning opportunity typically not experienced when flying hot air balloons.
You can join the gas division for $10.00 per year as an associate member. Voting members must hold a free balloon rating and they are charged $25.00 per year.
The gas division produces its own newsletter for the membership as a part of your dues. We invite everyone who has an interest to join the group.


text:
Chiang Mai Citylife > Articles > Long distance charity cyclists in Chiang Mai
Long distance charity cyclists in Chiang Mai
by Citylife
Aurelie and Marco are 36 years old, married, and passionate about cycling. She's French and he's half English and half İtalian. Together they have decided to live their lifelong dream; to cycle across the globe. Their chosen path will lead them from Helsinki to Singapore.
421Adventure is the name of this jorney; 4 wheels, 2 hearts, 1 world.
From April 2018 to March 2020 they will cross countries, cultures and languages very different one from another but all the same very enriching. Finland, Russia, Poland, Bulgaria, Turkey, İran, Uzbekıstan, Nepal, Bhurma or Laos are just some examples of the 26 countries through which this route will take them. Check out the complete itinerary here; www.421adventure.wordpress.com/2018/03/18/the-way/
This international couple has created a platform to allow anyone to follow them, www.421adventure.wordpress.com and on which they will regularly relate their experiences. You can also find them on Facebook, Instagram and Youtube; @421adventure
Furthermore, they have also decided to associate this adventure to a fundraiser for two charitable association whose work is related to bıcycles. The first one, Wheels For Wellbeing, is London based and helps disabled people to discover the benefits of cycling through the use of adapted bıcycles which allow them to become more independent and improve their mental and physical health. Isabelle Clement, the founder, is a wheelchair user and works closely with authorities on a national scale to improve the accessibility to inclusive cycling. Her work is an example and a source of inspiration for many cities around the world.
The second association is called 88bikes and supplies bikes to young girls who have been victims of human trafficking in underdevelopped countries such as Thailand, Uganda or Peru. Thanks to the bıcycle these girls can more easily access education or find a job. They have already donated thousands of bikes in the last 8 years empowering girls and young women to become future doctors, teachers, etc.
The pair arrived in Chiang Mai on Sunday and plan to spend a week here.
You can help them reach their objectıve of 5.000€ by making a donation here; www.421adventure.wordpress.com/donate/ where 100% of the proceeds will go to these admirable causes.
www.421adventure.wordpress.com
Facebook / Instagram / Youtube @421adventure


Electricity demand and supply can fluctuate greatly. And sometimes, one utility might become overwhelmed. To prevent this from occurring, a utility can enter into a Power Pool with other utilities. A Power Pool is a compilation of terms in which multiple utilities agree to share energy and resources. This can decrease operating costs and enable more reliability. However, pool agreements can be complex and might lead to some friction between different utilities.


7.00 pm 10.00 pm Normal duplicate with the field split into an Open and Novice section. This allows the Open Section to run smoothly and the Novice Section the ability to debrief as each hand is completed.
Wednesday evenings there are toasted sandwiches available at a cost of $2 per sandwich.
We break for lunch on Monday, Wednesday and Friday am sessions - lunches can be ordered at the club (unless it is a public holiday) or you may prefer to bring your own.
It would be appreciated if you could arrive at least 15 minutes prior to session start times.
Could Wednesday and Friday morning players please not use the upper car park.
Players can come to any Monday to Friday, morning or afternoon session without a partner - we guarantee one.


Being a member of Scribes Rugby Club has so many benefits and it's easy to join.
NEW MEMBERS CAN REGISTER ONLINE BY CLICKING HERE.
Spring & Summer Season dues for the remained of the 2018/2019 season are just $280 for adult players.


text:
Q: HttpHandler with Flash file upload question I have a flash file uploader that allows uploading multiple files in one shot.
Now on one click how many times will the hanlder is supposed to be called?
I am seeing that the ProcessRequest() of the HttpHandler is getting called for each of the files I upload. If I upload 5 files, then the Process request gets called 5 times.
This seems odd. I would expect the handler to be called just once where I will loop the
Can anyone confirm this behavior or I am missing something?

A: The Flash uploader and the ASP.Net HTTPHandler are not related.  If the Flash uploader calls the HTTPHandler 5 times, you will see ProcessRequest() called 5 times.
If the Flash uploader serializes the data, and passes the entire string to the HTTPHandler for deserialization and processing, you will see ProcessRequest() called once.

redpajama_set_name: RedPajamaStackExchange


Blaine takes on Ferndale at 7:15 p.m. Tuesday, Jan. 27, at home.
Port Townsend: Dances 7, Ralls 14, Adkins 8, Sua 3, Kelsall 6, Easley 0, Hill 2, Charlton 4, Mason 4, Partcher 5. Totals: no information provided.
Blaine: Charlie Baldwin 11, Johnny Starcer 0, Anthony Ball 9, Jalen Kortlever 6, Ben Hodgin 1, Aaron Shaw 8, Michael Baldwin 0, Carson Knutzen 4, Marcus Potts 5, Shaq Woods 15, Jon Fakkema 6, Kier Munzanreder 2. Totals: no information provided.
3-point field goals — Port Townsend: 7 (Ralls 3); Blaine: 6 (C. Baldwin 3). Rebounds — no information provided. Assists — no information provided. Fouls — Port Townsend: 14; Blaine: 11. Turnovers — no information provided.


Here at Luxury Lodges Wales we pride ourselves on our exclusive and bespoke luxury short break holiday destination for all of our guests.
All of our authentic Alpine holiday lodges are individual, while maintaining the same standard of luxury facilities and accommodation that you would expect from a Five Star self-catering holiday destination.
Each has its own outlook over the surrounding countryside towards the Severn Valley and Cambrian Mountains here in the county of Powys. You can choose which type of aspect you'd like in the full knowledge of the privacy you'd expect.
They're also accessible to local walks and just a short walk from a local village pub serving home cooked meals and local ales.
Each lodge includes all of the facilities mentioned and are privately located, positioned to offer different aspects of the local Welsh countryside. Many of our returning visitors often like to try a different one each time.
A hot-tub on the front veranda, (sheltered it can be used in all weather).
A 32" flat screen TV in the main living room, and two further TVs all with Sky (All Freeview).


text:
Congress, Privacy Groups Question Amazon's Echo Dot for Kids
Amazon's Echo Dot smart speaker.Amazon
Nitasha Tiku
The groups are concerned that Amazon's new services aimed at children promote dependence on technology and may jeopardize kids' privacy.
Lawmakers, child development experts, and privacy advocates are expressing concerns about two new Amazon products targeting children, questioning whether they prod kids to be too dependent on technology and potentially jeopardize their privacy.
In a letter to Amazon CEO Jeff Bezos on Friday, two members of the bipartisan Congressional Privacy Caucus raised concerns about Amazon's smart speaker Echo Dot Kids and a companion service called FreeTime Unlimited that lets kids access a children's version of Alexa, Amazon's voice-controlled digital assistant.
"While these types of artificial intelligence and voice recognition technology offer potentially new educational and entertainment opportunities, Americans' privacy, particularly children's privacy, must be paramount," wrote Senator Ed Markey (D-Massachusetts) and Representative Joe Barton (R-Texas), both cofounders of the privacy caucus.
The letter includes a dozen questions, including requests for details about how audio of children's interactions is recorded and saved, parental control over deleting recordings, a list of third parties with access to the data, whether data will be used for marketing purposes, and Amazon's intentions on maintaining a profile on kids who use these products.
In a statement, Amazon said it "takes privacy and security seriously." The company said "Echo Dot Kids Edition uses on-device software to detect the wake word and only the wake word. Only once the wake word is detected does it start streaming to the cloud, and it will present a visual indication (the light ring at the top of the device turns blue) to show that it is streaming to the cloud."
Echo Dot Kids is the latest in a wave of products from dominant tech players targeting children, including Facebook's communications app Messenger Kids and Google's YouTube Kids, both of which have been criticized by child health experts concerned about privacy and developmental issues.
Like Amazon, toy manufacturers are also interested in developing smart speakers that would live in a child's room. In September, Mattel pulled Aristotle, a smart speaker and digital assistant aimed at children, after a similar letter from Markey and Barton, as well as a petition that garnered more than 15,000 signatures.
One of the organizers of the petition, the nonprofit group Campaign for a Commercial Free Childhood, is now spearheading a similar effort against Amazon. In a press release Friday, timed to the letter from Congress, a group of child development and privacy advocates urged parents not to purchase Echo Dot Kids because the device and companion voice service pose a threat to children's privacy and well-being.
"Amazon wants kids to be dependent on its data-gathering device from the moment they wake up until they go to bed at night," said the group's executive director Josh Golin. "The Echo Dot Kids is another unnecessary 'must-have' gadget, and it's also potentially harmful. AI devices raise a host of privacy concerns and interfere with the face-to-face interactions and self-driven play that children need to thrive."
FreeTime on Alexa includes content targeted at children, like kids' books and Alexa skills from Disney, Nickelodeon, and National Geographic. It also features parental controls, such as song filtering, bedtime limits, disabled voice purchasing, and positive reinforcement for using the word "please."
Despite such controls, the child health experts warning against Echo Dot Kids wrote, "Ultimately, though, the device is designed to make kids dependent on Alexa for information and entertainment. Amazon even encourages kids to tell the device 'Alexa, I'm bored,' to which Alexa will respond with branded games and content."
In Amazon's April press release announcing Echo Dot Kids, the company quoted one representative from a nonprofit group focused on children that supported the product, Stephen Balkam, founder and CEO of the Family Online Safety Institute. Balkam referenced a report from his institute, which found that the majority of parents were comfortable with their child using a smart speaker. Although it was not noted in the press release, Amazon is a member of FOSI and has an executive on the board.
In a statement to WIRED, Amazon said, "We believe one of the core benefits of FreeTime and FreeTime Unlimited is that the services provide parents the tools they need to help manage the interactions between their child and Alexa as they see fit." Amazon said parents can review and listen to their children's voice recordings in the Alexa app, review FreeTime Unlimited activity via the Parent Dashboard, set bedtime limits or pause the device whenever they'd like.
Balkam said his institute disclosed Amazon's funding of its research on its website and the cover of its report. Amazon did not initiate the study. Balkam said the institute annually proposes a research project, and reaches out to its members, a group that also includes Facebook, Google, and Microsoft, who pay an annual stipend of $30,000. "Amazon stepped up and we worked with them. They gave us editorial control and we obviously gave them recognition for the financial support," he said.
Balkam says Echo Dot Kids addresses concerns from parents about excessive screen time. "It's screen-less, it's very interactive, it's kid friendly," he said, pointing out Alexa skills that encourage kids to go outside.
In its review of the product, BuzzFeed wrote, "Unless your parents purge it, your Alexa will hold on to every bit of data you have ever given it, all the way back to the first things you shouted at it as a 2-year-old."
Far From Sesame Street
Facebook funded most of the experts who vetted its Messenger Kids, an app for children as young as 6.
Child-health advocates asked Facebook to discontinue Messenger Kids, claiming it will undermine childhood development.
In a complaint to the FTC, child health and privacy groups allege that YouTube is violating a law that protects children online.
Nitasha Tiku is a senior writer for WIRED in San Francisco, covering people and power in Silicon Valley and the tech industry's impact on politics and culture. Before coming to WIRED she worked as a senior writer for BuzzFeed News. Tiku received her bachelor's degree from Columbia University and a... Read more
TopicsAmazonAlexachildren
How to Control What Alexa and Google Assistant Do With Your Voice Data
Virtual assistants like Google Home and Amazon Alexa can be amazing but what are they doing with all of your questions? Here's how to control all of that data.
The Spawn of ChatGPT Will Try to Sell You Things
Companies are exploring how to adapt powerful new chatbot technology to negotiate with customer service—and to persuade humans to buy stuff.
Will Knight
Mastodon Is Hurtling Toward a Tipping Point
As the niche, decentralized social networking platform rises in popularity, it faces rising costs, culture shifts—and potential legal risks.
Big Tech Laid Off Thousands. Here's Who Wants Them Next
Governments, nonprofits, and small startups hope to scoop up people let go by the likes of Meta and Amazon. It's their big chance to lure top-tier talent.
Why the US Is Primed for Radicalization
A confluence of factors is leading people in the nation to gravitate toward extremist views.
Thor Benson
The company's founders pioneered putting employees first and said they'd never bow down to Wall Street. How things have changed.


text:
Matt Hancock gives update on when he expects lockdown 3 to end
The lockdown regulations are in place until the end of March
Health Secretary Matt Hancock is in the House of Commons for a debate on the third national lockdown.
He told MPs he does not expect regulations enabling a national lockdown to be fully in place until the end of March.
Conservative Sir Graham Brady, chairman of the party's backbench 1922 Committee, asked in the Commons: "Approving these regulations today would allow for lockdown for three months until the end of March."
Sir Graham said Prime Minister Boris Johnson had assured him he did not expect MPs to have to "wait that long" for an opportunity to decide whether or not to end the regulations.
Sir Graham added: "Will he go further and give a commitment to a further vote at the end of January and end of February, so this House will have control over what is happening?"
Mr Hancock replied: "While these regulations do provide for new restrictions until the end of March, it is not because we expect the full national lockdown to continue until then but to allow the steady, controlled and evidence-led move down through the tiers on a local basis.
"Those tier changes do require a vote in Parliament. The restrictions will therefore be kept under continuous review, there's a statutory requirement to review every two weeks and a legal obligation to remove them if they're no longer deemed necessary to limit the transmission of the virus."
UK & World NewsMorrisons customer reveals how she got £15 worth of groceries for just £3The savvy shopper grabbed some bargain fruit and vegetables using a clever hack


This report was developed based on submissions from International Research network for Low Carbon Society (LCS-RNet) members, presented during their 9th conference hosted by UKERC in 2017, and includes contributions from 28 authors from around the world.
LCS-RNet is a community of researchers and research organisations contributing directly to policymaking and implementing processes, along with other like-minded stakeholders including policymakers, business and financial entities and civil society. Together they facilitate the formulation and implementation of science-based policies for low carbon development in the world.
Currently 16 research organisations work to develop the LCS-RNet, with Japan, Germany, France, UK playing a core role in cooperation with Brazil, China, India and Korea.
As national priorities are shifting inwards, and as the global sense of unity in face of the threat of climate change is being questioned, now is an opportune time to reaffirm the benefits of a decarbonized economy.
The transition to a low-carbon society through the decarbonisation of energy systems can bring social and economic benefits and foster countries' economic competitiveness. Research shows that decarbonisation of energy systems is not only beneficial to both those issues, but it also impacts other Sustainable Development Goals (SDGs) through co-benefits and synergies (see Chapter 1).
Climate finance needs to be made available to match the levels pledged in the Paris Agreement and to support developing countries on their low-carbon journey. To facilitate this, governments can provide innovative policy support and radically change the way greenhouse gas (GHG) emissions are priced (see Chapter 2).
The economic performance of industry is tightly linked to energy systems and energy price fluctuation. Governments can facilitate the transition of this sector by adopting industrial policies that encourage long-term decarbonisation. Appropriate policies can help maintain the economic competitiveness of the industrial sector while undertaking this transition, whilst also fostering innovation and resource productivity within wider society (see Chapter 3).
Finally, decarbonisation of energy systems is no longer a theoretical matter. Many examples exist around the world of successful cases, from emerging economies to multinational companies. These cases provide solid evidence of the existence of effective solutions for a transition to a low-carbon society (see Chapter 4).
In order to move the implementation of the Paris Agreement forwards, governments need to adopt long-term visions that integrate several policies, particularly industrial policy, energy policy and trade policy.
The transition to a low-carbon society needs to be paved by innovative financial mechanisms and ambitious carbon pricing. Further research is needed to quantify the social benefits of low-carbon investments.
Energy access is one of the key challenges of this century, notably in developing regions such as Africa. It is crucial for related issues such as climate change mitigation and poverty reduction. The related financial, technological and social barriers need to be addressed through innovative policies to facilitate energy access for a wide range of vulnerable populations and to raise awareness of the problem in developed countries.
Green growth plans, industrial strategies, product regulations and standards should be further developed, taking into account long-term innovation and circular economy patterns.


To honor those who have helped make the firm what it is today, we established the RSM Hall of Fame in 2016. We are proud to recognize the many people who have shaped our rich past and prepared us for the bright future that lies ahead.
In 2016, RSM's past and present came together to celebrate the firm's 90th anniversary and the inaugural Hall of Fame induction. Attendees traveled from across the country to Cedar Rapids, Iowa, where the firm originated in 1926.


text:
Becoming A Belieber
A couple months ago, when I first saw the preview of "Never Say Never," I laughed out loud. I could hardly believe that a movie was being made about Justin Bieber. He looked like a twelve-year old kid who just happened to have awesome hair and the heart of just about every tween girl, and suddenly he was the star of a movie about his rise to stardom.
At this point, I was definitely NOT a Belieber.
I didn't know much about Justin Bieber, but I assumed he was just like every other teen heart-throb – fairly talented, good-looking, famous for a few years, and then mostly forgotten. I didn't think there was anything too special about him, and I honestly thought he was twelve years old.
It was my best friend Laura who convinced me to go see the movie. She started showing me videos of Justin on YouTube, and I had to admit – this kid really could sing and his dance moves weren't too bad either. She also informed me that, much to my surprise, he was actually sixteen. I wasn't exactly a Belieber yet, but I knew that I definitely wanted to see Justin's movie. So, a couple days later, Laura and I went to Carmike Cinemas on Stimulus Tuesday and saw "Never Say Never."
I caught what they call the "Bieber Fever."
The movie opens with Justin's most famous YouTube video – his cover of Chris Brown's hit "With You," and it follows his fast-paced rise to fame. Born to a teenage mom, Bieber developed a love for music early in life; the film shows home videos of a pint-sized Justin playing drums with perfect rhythm in his garage and singing on the steps of a local theater. In 2008, a talent manager named Scooter Braun stumbled upon one of Bieber's YouTube videos, and he quickly made contact with Justin's mother – and the rest is history.
Dispersed throughout the movie are songs from Justin's concerts, such as "One Less Lonely Girl," in which he always sings to one lucky female fan in the audience who gets to join him on stage. His faster-paced songs showed off his impressive dance skills. The kid has moves! He works the stage like a performer twice his age and with twice his experience.
And then, there was the glorious hair flip.
There's nothing like a slow-motion, 3D hair flip done by the wonderful head of golden, shiny hair that belongs to Justin Bieber to make someone catch the Bieber Fever.
Honestly, the movie portrays Justin as a down-to-earth, respectable young man who truly cares about his fans and is pretty much your average teenage boy. He plays basketball with his friends, Twitters constantly, and even has to cancel a show due to sickness.
So, needless to say, this movie made me a Belieber. I don't know how it happened exactly. Maybe it was his sweet voice or his warm personality – or maybe it was the slow-motion hair flip. Whatever it was, I now have a new respect for this sixteen (not twelve) year old boy and hope to see his success continue for many years to come.
Merry Christmas From The High Post Staff!
The Disney Magic Never Dies For Any Age
An Inside Look On The Fall Play "Love…No Barriers"
Teens and Their Pets – Josh Skok


text:
Opinion | Pride Shabbat Is a Step Toward Equality
noipornpan / iStock / Getty Images Plus
On a recent Friday night, I wore a black T-shirt with "Proud Mom" in rainbow letters, and had a (temporary) glitter tattoo on my arm that read "Love is Kosher." My 14-year-old son wore a rainbow T-shirt and had a rainbow sweatband on his wrist.
We weren't participating in Pride festivities downtown; we were at my synagogue's first Pride Shabbat.
My son — who came out as gay in elementary school — said the service made him feel more welcome in the community. That feeling is one of the reasons why our synagogue, Temple Emanuel of South Hills in Pittsburgh, created a LGBTQ+ task force; the goal is to ensure that our community is truly inclusive.
This same feeling is why I became active in youth group at the local and regional level when I was in high school. Organizers and peers ensured that my deafness didn't preclude me from feeling a part of the group. I wanted my son to experience this, too, so when I found out that Keshet — an organization that works for the full equality of LGBTQ Jews and families in Jewish life — was hosting an East Coast Shabbaton for LGBTQ and ally Jewish teens, I encouraged him to go.
But what teenage boy listens to his mother?
Luckily, mine does … sometimes! I continued to bring up the Shabbaton occasionally, each time saying it would be good for him and to please think about it. Just before the deadline, he acquiesced, saying he knew he had to push himself.
Last March, he traveled to where it was held, knowing no one. The first day, he was shy. The following morning, he tried to break out of his shell. Spoiler alert: He started having fun. In recounting the weekend afterward, he shared two meaningful experiences that included a friendship circle.
Throughout the weekend, the kids broke out into the same small groups to check in with each other and have a safe space to talk. Shy teenagers befriended outgoing ones, and made sure others were included.
The true measure of success was when my son said he wants to go back next year. He's also keeping in touch with Keshet friends on social media.
I knew this wouldn't be enough. It shouldn't be enough. No one should have to go somewhere else to find community.
A cursory check of local congregations finds LGBTQ inclusion woefully lacking. As Rabbi Ruti Regan said in a recent webinar on inclusion and pride, you can't build a Jewish community without acknowledging LGBTQ Jews and Jews with disabilities. In valuing all our people as much as God does, our community needs to act like LGBTQ Jews, disabled Jews and LGBTQ Jews with disabilities are part of the Jewish people. We all bring something important to the conversation, she said.
In the year since the LGBTQ+ task force was created, Temple Emanuel has added a LGBTQ+ Safe Zone widget on its website, posted Safe Space stickers in the building, purchased Keshet posters like one that outlines seven Jewish values for an inclusive Jewish community to hang on the walls, purchased LGBTQ books for the temple library, added Temple Emanuel to Keshet's Equality Guide, converted a bathroom to be gender neutral, hosted a conversation with Evan Wolfson (founder and president of Freedom to Marry) on "Making More Progress for Gay & Transgender People in our Community, Pennsylvania, the U.S. and the World: What Can We Do?" and held our first Pride Shabbat.
My son declared that Pride Shabbat, which had a great turnout, was "perfect." The task force made rainbow Shabbat candles and put together a service that included kids and teenagers reading the seven Jewish values. We modified some prayers to make them more inclusive, like changing a word from "brothers" to kulanu, meaning all.
Task force members read material from various sources, and the Temple Emanuel Band performed songs like an adapted version of "If We Only Have Love" with the lyrics, "If we only have love/Then Jerusalem stands/And then death has no shadow/There are no foreign lands…"
Our work is far from done, but in just one year, we've made a lot of progress.
As Rabbi Regan said, the Jewish community has always been the only safe place from anti-Semitism.
"If we discriminate against LGBTQ+ and disabled Jews, they have no place to be safe and valued. If we are not for ourselves, who will be for us?" she asked.
We must match our words and deeds as we demonstrate our faith. Words read during our Pride Shabbat were never more poignant: "Beneath our uniqueness, we are all bound together by our common humanity."
Lisa A. Goldstein is a freelance journalist who lives in Pittsburgh.
Previous articleReflections From 12 Years After a Spouse's Death
Next articleCamp Stories | After Two Synagogue Shootings, a Look at Camp Security
Panelists Discuss Being Trans in the Jewish Community
Opinion | How an Uninvited Shabbat Guest Put Everything Into Perspective
Opinion | #ShowUpForShabbat: Gather, Remember and Act


text:
Hundreds feared dead after migrant boat capsizes off Egypt
Less than half the estimated 450 migrants believed to be on a boat that capsized off the Egyptian coast have been rescued, the country's military said, according to CNN.
The vessel had set off from Egypt and was heading for Italy when it was found 12 nautical miles northeast of the town of Rashid -- also known as Rosetta -- in El Beheira Governorate on Wednesday, September 21 afternoon, the Egyptian military said in a statement.
The statement added that 163 people had been rescued, while 43 bodies were recovered. Initial estimates put the number of people on board the boat at 600.
Mahmoud Aly spent Wednesday going between hospitals along the coast. His brother and cousin were on board the boat that capsized.
He told CNN his cousin was rescued but his 24-year-old brother is missing. "The boat had more people than it could take. It's a wooden boat," he said.
He said his family would spend the night on the beach waiting for boats to resume the search and rescue efforts at daylight. "We saw the last boat after sunset. Seven people were on board."
Photo: Stringer/AFP/ Getty Images


text:
from neutronclient.i18n import _
from neutronclient.neutron import v2_0 as neutronV20

def _format_timestamp(component):
    try:
        return component['heartbeat_timestamp'].split(".", 2)[0]
    except (TypeError, KeyError):
        return ''

class ListAgent(neutronV20.ListCommand):
    """List agents."""

    resource = 'agent'
    list_columns = ['id', 'agent_type', 'host', 'alive', 'admin_state_up',
                    'binary']
    _formatters = {'heartbeat_timestamp': _format_timestamp}
    sorting_support = True

    def extend_list(self, data, parsed_args):
        for agent in data:
            if 'alive' in agent:
                agent['alive'] = ":-)" if agent['alive'] else 'xxx'

class ShowAgent(neutronV20.ShowCommand):
    """Show information of a given agent."""

    resource = 'agent'
    allow_names = False
    json_indent = 5

class DeleteAgent(neutronV20.DeleteCommand):
    """Delete a given agent."""

    resource = 'agent'
    allow_names = False

class UpdateAgent(neutronV20.UpdateCommand):
    """Updates the admin status and description for a specified agent."""

    resource = 'agent'
    allow_names = False

    def add_known_arguments(self, parser):
        parser.add_argument(
            '--admin-state-down',
            dest='admin_state',
            action='store_false',
            help=_('Set admin state up of the agent to false.'))
        parser.add_argument(
            '--description',
            help=_('Description for the agent.'))

    def args2body(self, parsed_args):
        body = {
            self.resource: {
                'admin_state_up': parsed_args.admin_state, }, }
        neutronV20.update_dict(parsed_args, body[self.resource],
                               ['description'])
        return body


text:
Home Mystery Booms Mystery loud boom in Bradford, Vermont related to a US army jet...
Sonic Booms
Mystery loud boom in Bradford, Vermont related to a US army jet sonic boom – February 24 2013
Not many people knew what the loud boom was that rattled stores and homes Thursday. But the Massachusetts Air National Guard had to take the blame. One of their jets broke the sound barrier. The big bang was an F-15 fighter jet from the Massachusetts Air National Guard of the 104th Fighter Wing. It broke the sound barrier, traveling near seven hundred mph and creating a sonic boom. The boom was not appropriate it made a lot of people nervous. The Massachusetts Air National Guard shouldn't have broken the sound barrier in the area. In a statement they released they said "We will continue to work hard to prepare our pilots to fulfill our mission of air superiority, and our commitment to the community's safety is always paramount, never intending to cause undue concern."
FOX44 – Burlington / Plattsburgh News, Weather
Here a few resident reports of the sonic boom:
"I heard a boom", "It sounded like ten elephants or something had landed on the roof", "I haven't heard anything like that in a long time", "It literally moved the whole building", "They were leaving trails in the sky. It was pretty blue, a nice sunny day and it turned out sure enough that's what it was".
Mysterious booms continue rattling hundreds of people in the US, Canada and the UK, leaving officials speechless
Mysterious booms shake Haiti and Nebraska, baffling residents and officials
Mysterious booms and rumblings, and unexplained strange sounds baffle residents across the world, but the mystery remains!


Loud noise continued for several minutes. Never heard a sound like this around here in the almost year I've lived here. Btw it's not a plane.
a haarp station may be located in columbia and spartanburg sc. you can see the action on weather maps.


My mum received a Christmas card from an old friend a few years back with a brief update on family news, including this plaintive summary: 'The kids are both doing jobs I don't understand.' And who can blame her. For centuries how people described what they did in the working day was fairly consistent, but suddenly there's a whole new crop of jobs that your granny wouldn't recognize: futurologist, digital prophet, head of analytics, genius (thanks Apple), back-end developer (which always makes me snigger), positioning expert. Positioning expert is how Mark Levy of Levy Innovations LLC, this week's guest in The Extraordinary Business Book Club, describes himself. And the results are dramatic: he claims the firm's clients, experts in their fields, typically consultants, increase their fees by up to 2000% through positioning themselves in the right way online and off. A key part of this involves writing a book that positions the expert as a thought leader, and so Mark has effectively also become a book coach (it was one of his clients, Robbie Kellman Baxter, who recommended I speak to him for the podcast). Experts who want to be successful authors and publishers share a common focus: pleasing the reader. Many of the people Mark works with spend a significant amount of time and money finding out what people want, just as publishers pore over book sales data and run focus groups to identify what's working and generate some more of it. Which is great, of course. But Mark suggests that it's not the place to start. When he works with his clients, he asks them first to create what he calls a 'meaning and fascination pile': the experiences, stories, ideas, facts, images and so on that have stuck with them, that shape how they view their topic and the world. Only then does he encourage them to look out to the target reader and think about how this might apply to them. 'I tell [my clients], "You need to write a book. If you want to be a thought leader, just looking to your audience is bad because if you look to your audience first, they're only going to tell you what's already been out there."' For many authors, this will mean drawing together threads from different areas of their life, and that cross-pollination can sometimes in itself create an enlightening shift in perception or a helpful new metaphor. He also encourages his authors to see the writing itself as means of discovering the meaning and creating something original: 'Robert Frost said, "No surprise for the writer, no surprise for the reader." That's a real design parameter to me. If you just sit there and… you're trying to write down exactly what it is you do, you're going to be so bored and that boredom's going to come through to the reader. You need to use the writing itself as a discovery process.' For publishers, I think there are two challenges implied here.
1) How well are we supporting our authors to do that original thinking?
Balancing the clarity of the proposal and the decisions we need to make about the commerciality of a book against the opportunity to create something really original but more uncertain is tough, and requires the publisher to offer both support and challenge to the author. If your author's thoughts are developing away from the original proposal as he or she writes, how will you know and how can you be involved in that process?
2) How good are we at recognizing the 'irrelevant' aspects of our authors' biographies and how these might inform the book they're writing?
The unexpected insights and perspectives that they bring from their wider experience of life could be the magic that transforms their book from an also-ran to a runaway success, and the better we get to know our authors, the more likely it is that we can spot and nurture those opportunities. Until publishers rise to those challenges, authors will continue to look elsewhere – to positioning experts, coaches and publishing services providers – to find that support, and that could bring an even more intractable challenge to the industry in the long term. Alison Jones (@bookstothesky) is a publishing partner for businesses and organizations writing world-changing books. She also provides executive coaching, consultancy and training services to publishers. www.alisonjones.com.
Written by Mollie Broad on November 16, 2015 . Posted in Academic, Articles, Blog, Marketing, Marketing and publicity, Publicity, Traditional Marketing.
This is a guest post by Mollie Broad. Mollie is a PR Assistant at SAGE Publications, a leading independent publisher of journals, books and digital media. The publishing industry encompasses hundreds of different roles within countless disciplines and subjects. Across the industry, PR works to draw attention to the respective publishing programme. However, when generating publicity for books, it is in the approach where the differences between academic and trade publishing lie.
This is a guest post by Phoebe Morgan. Phoebe works as an Editor at Octopus Publishing Group across a range of non-fiction titles. She blogs about her favourite books here.
Written by Sam Coleman on January 5, 2011 . Posted in Articles, Business, Careers, How-To.
At the last BookMachine event we were pleased to meet Sam Coleman from Atwood Tate. He's certainly a man in the know if you're looking for a job, as he speaks to recruiters in the industry every day. Here he shares some tips for finding work. Times have certainly changed since I started work as a Production Assistant for a distinguished publishing house only a decade ago. Now, rather than massaging strained biceps from carrying piles of carefully packaged proofs from desk to desk, we harp on about carpel tunnel syndrome and ponder deep thoughts about metadata. The era of Digital publishing is upon us and, like a towering Galactus it's going nowhere.


Causley Fresh ship to Australian addresses only.
Shipping is a flat rate of $10 for all orders under $100. Orders over $100 are shipped free of charge. Shipping is added automatically at the checkout.
We aim to have orders processed and dispatched within 2 business days of receipt.
Causley Fresh offers an "Express Post" option at the checkout. Express Post is a flat rate of $20 independent of order value.
Express Post; orders are dispatched the same day if received by 1pm or the following day if received after 1 pm. We choose the courier that we believe will provide the fastest service. If, for any reason, we cannot meet these goals you will be contacted immediately.
Once shipped you will be notified by email and provided a tracking number if applicable.
Causley Fresh will endeavour to ensure that all goods ordered by you are dispatched within 2 business days of receipt of your order. If an item is out of stock you will be contacted within that period advising you of any potential delay in the delivery of your order. If you find the delay unacceptable we can offer alternative, comparable products or a refund of the out of stock item or a refund of the entire order.
We strive to process orders quickly. If you wish to cancel or change an order you should contact us immediately. If your order has not yet been dispatched we will try to accommodate your request.
If a product is received in a damaged condition or does not match what was described on our web site please contact us via email within 24 hours of receiving your goods and provide a brief description of the issue and a photo for verification.
You will be contacted by phone or email regarding the best solution to the problem which may include a refund, dispatch of replacement products or alternative products.
Causley Fresh does not accept returns due to a change of mind.


text:
Alice Bradshaw
Alice Bradshaw was born on January 24, 1922 in Brooklyn, NY. Raised in New Rochelle, NY, her father was an architect who worked in New York City. Alice attended Parson's School of Design from 1941 through 1942 but ultimately left school to work with her father. Alice served as an Air Raid Warden and also […]
Alice Bradshaw was born on January 24, 1922 in Brooklyn, NY. Raised in New Rochelle, NY, her father was an architect who worked in New York City. Alice attended Parson's School of Design from 1941 through 1942 but ultimately left school to work with her father. Alice served as an Air Raid Warden and also worked for the Red Cross during the war. She has two brothers, one of which worked in an airplane factory during the war and the other was assigned to study at MIT by the Navy. After the war, Alice continued work as an architect and married a World War II Veteran, Winn Bradshaw. Alice, now 96, has two children and a number of grandchildren and great-grandchildren whom she enjoys seeing.
In this interview, Mrs. Bradshaw shares her Home Front experiences from World War II. Alice remembers everyone pulling together behind the country and making sacrifices. She recalled working as an Air Raid Warden late at night and shared a complimentary letter she received from the Red Cross for her work designing a poster for them. Mrs. Bradshaw also discusses rationing, victory gardens, USO Dances and her late husband's time in the Navy.
http://nationalhomefrontproject.org/wp-content/uploads/2018/07/BradshawAlice_HFL-OH_070318_story-01_editsIR.mp3
Reactions to Pearl Harbor
I was in college, and what do you say when you hear your country's been attacked? You just absolutely shut down. So I think the amazing thing about what happened to the country almost overnight is that everybody came upright and said, "What do we do to win this conflict?" And so overnight we didn't have all the food we thought we were entitled to, we didn't have oil in our homes, we didn't have gasoline. I mean, zip! Now can you picture yourself without a car? But it was a different world. It was quite different and nobody complained. We just wanted to do the very best we could. And I was in school, and the men all of a sudden disappeared from school. And so then, the women started disappearing because they were starting to take the jobs the young men would have been moving into, so everything changed.
Material Rationing
Well, there wasn't any building. There was absolutely no house building at all. That was stopped. Every building material went towards the war effort, and I mean everything. I mean we saved the fat from our cooking, we saved our tin cans. They had to be flattened. That metal was used. The railroad down at the end of our street which was a local wasn't being used as much so they stopped the railroad, they tore up the tracks and that all went into the war effort. So that meant this wonderful easy access into New York City now was no longer available. I mean, I don't think you kids can possibly understand what it was like. I would go out during my lunch time, I would go out and stand in line to see if there were any eggs on the market.
http://nationalhomefrontproject.org/wp-content/uploads/2018/07/BradshawAlice_HFL-OH_070318_story-03_final.mp3
Dances and War Contributions
There were so many things we did if you knew how to dance. It's important to know how to dance because everybody danced. Everybody was giving what we called tea dances, and the service people were invited wherever they were stationed. In the Hotel Commodore, they used to have a beautiful tea dance for the enlisted men, no officers. And then they would invite women to come and be there as hostesses. And you weren't supposed to give your name. But, you know, we did everything we could. We wrote letters. We wrote letters to everybody, all our friends. And just to hold a letter in your hand from somebody helps. Because we went to dancing school, we learned to dance from our parents and so on. And if you knew how to dance, you could come together in a group not knowing a soul and have a marvelous time. And it kept you out of trouble. You didn't go in any bars back then to meet a girl. No, you had hostesses around, you had a wonderful time and always there was some eats of some simple food of some kind. And they would have the dances for non-commissioned, and so I went to a lot of them. So, if you knew how to dance, and most of the boys knew how to dance, you could have a wonderful time. You didn't have to talk, just smile and jiggle. And I think dancing today—if the kids today would let go of their little tools and dance, it'd be wonderful for you. It's exercise too. So you learned to dance with any boy who asked you to dance. You learned you'll quickly get his vibrations, and you can dance. Fortunately, my husband was a marvelous dancer.
An MIT Education for Free
Oh, then my younger brother, he had a lucky break because when he graduated from high school, he went on over to the Navy recruitment office and signed up. Well, he was a very smart kid and worked very hard in school, and the next thing he knew, his assignment was to go up to MIT. So he did MIT in three years, and they really worked him! And then by the time he got out, the war was over. So he got his education thanks to Uncle Sam. But then many of the service people coming home too under the GI Bill [got an education]. That was a wonderful thing, unbelievable. I mean, you can't imagine what that meant to people, changing their lives. And construction was open; it was just amazing.
A not so Victorious Victory Garden
Oh, my father dug up the front lawn. He said, "I'm going to have [a victory garden]," and he was not a gardener. He didn't have the tools or anything but he tried, and he came in with his crop. I think he had three string beans or something. (laughting) But, no, victory gardens were big if you had the property.
Air Raid Warden
Oh yeah, we were all air raid wardens. And, of course, being lights out, no lights showing at all, period. Everyone knew it, night had to be darkened. So the air raid wardens, (I have my little certificate that I'm approved an air raid warden) we went out with our metal hats and our cane. I have the cane because there were no lights. You try to walk around the campus without any lights. I dare you to. But Long Island, they were in darkness all over because the German subs are out there bombarding all of our supply ships as they came out of New York Harbor or Boston Harbor. So, we lost a lot of shipping because of the subs out there. Someone was out there every single night to check that everybody's house was darkened. You didn't have to stay out every night but you want to be sure everybody had dark shades or something.
I remember I was writing to someone who was up in Greenland which seemed like the end of the world to me. And I guess he was so touched by the letters that I got a bouquet from him on Valentine's Day or something. But, you know, it's nice because it made him feel good. We were just friends but I can't explain just how important letters were then. I think anybody you talk to, I should think would mention that.
Narrator Alice Bradshaw with the cane she was issued as an Air Raid Warden (Photo Credit: Patricia Rana)
From left to right: Narrator Alice Bradshaw shares stories of her high school with Ethan O'Malley (Photo Credit: Isaiah Reese)
From left to right: Patricia Rana, Narrator Alice Bradshaw and Ethan O'Malley (Photo Credit: Isaiah Reese)
The narrator's husband, Win Bradshaw in a portrait for the United States Navy (Courtesy of Alice Bradshaw)
Alice Bradshaw's certificate of identity for her volunteer job as an Air-raid warden (Courtesy of Alice Bradshaw)
The front cover of a World War II ration book with the narrator's name (Courtesy of Alice Bradshaw)
The inside of the narrator's ration book with leftover coupons due to the end of World War II (Courtesy of Alice Bradshaw)
A group photo of the narrator's husband (Win Bradshaw) along with his Naval crew and officers in the city of Olongapo in the Philippines (Courtesy of Alice Bradshaw)
"U.S.S. YMS-54 with her officers and crew" Olongapo, Subic Bay, Luzon, Philippines April 23, 1946 (Courtesy of Alice Bradshaw)
From top to bottom: The narrator's mail received from the American Red Cross and the letter contained inside regarding her award of merit. (Courtesy of Alice Bradshaw)
A newspaper clipping of Alice Bradshaw's service during World War II as a waitress (Courtesy of Alice Bradshaw)
Conducted July 3rd, 2018
Interviewers: Patricia Rana, Ethan O'Malley, and Isaiah J. Reese