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Cook penne in a large pot of slightly salted boiling water until al dente, firm but tender.
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Drain well.
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Meanwhile, heat 1 tablespoon oil in a large skillet over medium-high heat.
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Add mushrooms; sauté 8 minutes or until tender.
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Remove from skillet.
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Heat remaining oil in skillet.
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Add onion; sauté 5 minutes.
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Add garlic; sauté 2 minutes.
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Whisk together flour and milk in a small bowl.
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Add to skillet.
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Bring to boiling, stirring occasionally.
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Reduce heat to low; add salt and nutmeg and simmer 5 minutes.
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Heat oven to 400°F
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Lightly grease a 13 x 9 x 2-inch shallow baking dish.
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In same pot used to cook penne, toss penne with sauce, mushrooms, lemon juice, and pepper.
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Combine all the cheese in a bowl; set aside ¼ cup.
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Add remaining cheese to penne mixture, stirring gently.
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Spoon into prepared baking dish.
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Sprinkle with reserved cheese.
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Bake, uncovered, 20 to 30 minutes or until browned and bubbly.