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Kerala's Muhammed Ajmal and Rince Joseph will compete in the 400m final on Wednesday.
Nayana took gold with an effort of 6.53m while Shaili settled for silver with 6.34.
Vithya, part of the Indian women's 4x400m relay squad that booked a Paris Olympics berth in Bahamas recently, pulled out immediately after the start of the women's 400m hurdles final race at the Kalinga Stadium.
Long Jumper Ancy Sojan and Triple Jumper Abdulla Aboobacker gave Kerala the gold medals on the final day of the meet in Ranchi.
Kerala's Maymon Poulose clocked 10.46 seconds men's 100m semifinals to enter the final.
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