B+ in a bunch of major and minor courses: does it matter?

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I'm a current sophomore math major(minor STAT+CS) intending to apply for applied math/stat/cs phd(particularly in probability, machine learning, dynamical systems, data mining, algorithms). However, my last quarter GPA wasn't that satisfactory. How much will B+s in point-set topology, statistics, intro to c++ hurt my applications? Is it ok to make it up by getting ok grades in advanced level major/minor courses in the coming semester and junior year?

P.S. Sorry for typing English only here folks - school computer has no Chinese input.

补充内容 (2016-1-27 12:25):
P.S. 现在overall cumulative GPA = 3.7+/4.3, major GPA = 4.11-4.12/4.3
暑假之前在Berkeley summer上过两门upper div math, 4.0/4.0 - 这个结果能抵消这个学期下滑吗?
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