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$collection = Mage::getModel('catalog/category')->getCollection();

$resource = Mage::getResourceModel('catalog/category');

// here get category collection

foreach($collection as $category) {
    $category->setStoreId(0);    // 0 for default scope (All Store Views)
    $category->setData('include_in_left_menu', 1);
    $resource->saveAttribute($category, 'include_in_left_menu');
}