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LaTeX : From the mistakes I made 

Use label after caption so that reference to figure will come correctly
------------------------------------------------------------------------------------------------------------
correct
\begin{figure}[here]
\center
\includegraphics[width=0.5\textwidth]{../images/ex_circuit.png}
\caption{Connecting the output of the circuit to DSO}
\label{ex_circuit}
\end{figure}

Wrong
\begin{figure}[here]
\center
\includegraphics[width=0.5\textwidth]{../images/ex_circuit.png}
\label{ex_circuit}\caption{Connecting the output of the circuit to DSO}
\end{figure}
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Use \noindent if the text is not aligned to left

Using bibtex?
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You should do the compilation as follows (so that citations will come correctly)
pdflatex -> bibtex ->pdflatex -> pdflatex
Ref: http://tex.stackexchange.com/questions/204291/bibtex-latex-compiling
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Download IEEE BibTeX Bibliography Style file for IEEE Journals and Conferences
------------------------------------------------------------------------------------------------------------http://www.dlsi.ua.es/wemis09/styles/IEEEtran.bst
------------------------------------------------------------------------------------------------------------








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