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Work is negative when a system does work, which means that it expands. If you do work, you lose energy, so it is negative. On the other hand, work is being done on the system when it is compressed. Think of it as the system can expand by itself, but you have to do something to the system to compress it.
Work = -(pressure)(FinalVolume - InitialVolume). Therefore, if your final volume is greater than your initial volume (gas expands) then your change in volume will be positive, so this is why work will be negative. Additionally if your initial volume is greater than your final volume (gas is compressed), then your change in volume will be negative, so work will be positive.
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