Get second minimum values per column in 2D array

Try this, in just one line:

[sorted(i)[1] for i in zip(*A)]

in action:

In [12]: A = [[72, 76, 44, 62, 81, 31], 
    ...:      [54 ,36 ,82 ,71 ,40, 45], 
    ...:      [63 ,59, 84, 36, 34 ,51], 
    ...:      [58, 53, 59, 22, 77 ,64], 
    ...:      [35 ,77, 60, 76, 57, 44]] 

In [18]: [sorted(i)[1] for i in zip(*A)]                                                                                                                                                                           
Out[18]: [54, 53, 59, 36, 40, 44]

zip(*A) will transpose your list of list so the columns become rows.

and if you have duplicate value, for example:

In [19]: A = [[72, 76, 44, 62, 81, 31], 
    ...:  [54 ,36 ,82 ,71 ,40, 45], 
    ...:  [63 ,59, 84, 36, 34 ,51], 
    ...:  [35, 53, 59, 22, 77 ,64],   # 35
    ...:  [35 ,77, 50, 76, 57, 44],]  # 35

If you need to skip both 35s, you can use set():

In [29]: [sorted(list(set(i)))[1] for i in zip(*A)]                                                                                                                                                                
Out[29]: [54, 53, 50, 36, 40, 44]

Operations on numpy arrays should be done with numpy functions, so look at this one:

np.sort(A, axis=0)[1, :]

Out[61]: array([54, 53, 59, 36, 40, 44])