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Preheat oven to 375 degrees. Place liners in muffin pan and set aside.
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In a medium bowl, whisk flour, pumpkin pie spice, baking soda and salt until well-combined. Set aside.
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In a large bowl, whisk together pumpkin, sugar and brown sugar.
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Beat in eggs, vegetable oil and vanilla extract. Slowly whisk in the flour mixture until there are no lumps. Fill muffin tins ¾ full.
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In a medium bowl, beat cream cheese until smooth. Add in sugar, egg yolk, and vanilla extract and beat until well-combined.
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Top each muffin with 1 tablespoon of cream cheese mixture and use a toothpick to swirl it into the batter.
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Bake muffins for 18-20 minutes, or until a toothpick inserted in the center comes out clean.