Form990-PF

Department of the Treasury
Internal Revenue Service
Return of Private Foundation
or Section 4947(a)(1) Nonexempt Charitable Trust
Treated as a Private Foundation
Note. The foundation may be able to use a copy of this return to satisfy state reporting requirements.
OMB No. 1545-0052
2012
Open to Public Inspection
For calendar year 2012, or tax year beginning 10-01-2012 , and ending 09-30-2013
Name of foundation
JOHN & MARY PAPPAJOHN SCHOLARSHIP
FOUNDATION

Number and street (or P.O. box number if mail is not delivered to street address)666 WALNUT STREETROOM/SUITE 2116Room/suite
City or town, state, and ZIP code
DES MOINES, IA50309
A Employer identification number

42-1465551
B Telephone number (see instructions)

(515) 244-5746
C bullet
G Check all that apply:

D 1. bullet
2. bullet
H Check type of organization:
I Fair market value of all assets at end
of year (from Part II, col. (c),
line 16)bullet$929,216J Accounting method:
 
(Part I, column (d) must be on cash basis.)
E bullet
F bullet
Part I Analysis of Revenue and Expenses (The total of amounts in columns (b), (c), and (d) may not necessarily equal the amounts in column (a) (see instructions).) (a) Revenue and
expenses per
books 		(b) Net investment
income 		(c) Adjusted net
income 		(d) Disbursements
for charitable
purposes
(cash basis only)
Revenue 1 Contributions, gifts, grants, etc., received (attach schedule)  
2 Check bullet
3 Interest on savings and temporary cash investments 1 1  
4 Dividends and interest from securities...... 456 456  
5a Gross rents..............      
b Net rental income or (loss)  
6a Net gain or (loss) from sale of assets not on line 10 -160,750
b Gross sales price for all assets on line 6a 246,600
7 Capital gain net income (from Part IV, line 2)...  
8 Net short-term capital gain.........  
9 Income modifications...........  
10a Gross sales less returns and allowances  
b Less: Cost of goods sold....  
c Gross profit or (loss) (attach schedule).....    
11 Other income (attach schedule)....... Click to see attachment 9,772    
12 Total. Add lines 1 through 11........ -150,521 457  
Operating and Administrative Expenses 13 Compensation of officers, directors, trustees, etc.        
14 Other employee salaries and wages......        
15 Pension plans, employee benefits.......        
16a Legal fees (attach schedule).........        
b Accounting fees (attach schedule)....... Click to see attachment 1,985 992   993
c Other professional fees (attach schedule)....        
17 Interest...............        
18 Taxes (attach schedule) (see instructions)        
19 Depreciation (attach schedule) and depletion...      
20 Occupancy..............        
21 Travel, conferences, and meetings.......        
22 Printing and publications..........        
23 Other expenses (attach schedule)....... Click to see attachment 132 132    
24 Total operating and administrative expenses.
Add lines 13 through 23.......... 2,117 1,124   993
25 Contributions, gifts, grants paid........ 468,350 468,350
26 Total expenses and disbursements. Add lines 24 and 25 470,467 1,124   469,343
27 Subtract line 26 from line 12:
a Excess of revenue over expenses and disbursements -620,988
b Net investment income (if negative, enter -0-) 0
c Adjusted net income (if negative, enter -0-)...  
For Paperwork Reduction Act Notice, see instructions.
Cat. No. 11289X Form 990-PF (2012)
Form 990-PF (2012)
Page 2
Part II Balance Sheets Attached schedules and amounts in the description column
should be for end-of-year amounts only. (See instructions.)		 Beginning of year End of year
(a) Book Value (b) Book Value (c) Fair Market Value
Assets 1 Cash—non-interest-bearing............... 382,176 168,536 168,535
2 Savings and temporary cash investments..........      
3 Accounts receivable bullet  
Less: allowance for doubtful accounts bullet        
4 Pledges receivable bullet  
Less: allowance for doubtful accounts bullet        
5 Grants receivable.................      
6 Receivables due from officers, directors, trustees, and other
disqualified persons (attach schedule) (see page 15 of the
instructions)....................      
7 Other notes and loans receivable (attach schedule) bullet  
Less: allowance for doubtful accounts bullet        
8 Inventories for sale or use...............      
9 Prepaid expenses and deferred charges...........      
10a Investments—U.S. and state government obligations (attach schedule)      
b Investments—corporate stock (attach schedule)........ 1,385,216 Click to see attachment977,868 760,681
c Investments—corporate bonds (attach schedule)........      
11 Investments—land, buildings, and equipment: basis bullet  
Less: accumulated depreciation (attach schedule) bullet        
12 Investments—mortgage loans..............      
13 Investments—other (attach schedule)...........      
14 Land, buildings, and equipment: basis bullet  
Less: accumulated depreciation (attach schedule) bullet        
15 Other assets (describe bullet)      
16 Total assets (to be completed by all filers—see the
instructions. Also, see page 1, item I) 1,767,392 1,146,404 929,216
Liabilities 17 Accounts payable and accrued expenses..........    
18 Grants payable...................    
19 Deferred revenue..................    
20 Loans from officers, directors, trustees, and other disqualified persons    
21 Mortgages and other notes payable (attach schedule)......    
22 Other liabilities (describe bullet)    
23 Total liabilities (add lines 17 through 22)..........   0
Net Assets or Fund Balances bullet
and complete lines 24 through 26 and lines 30 and 31.
24 Unrestricted....................    
25 Temporarily restricted................    
26 Permanently restricted................    
bullet
and complete lines 27 through 31.
27 Capital stock, trust principal, or current funds.........    
28 Paid-in or capital surplus, or land, bldg., and equipment fund    
29 Retained earnings, accumulated income, endowment, or other funds 1,767,392 1,146,404
30 Total net assets or fund balances (see page 17 of the
instructions).................... 1,767,392 1,146,404
31 Total liabilities and net assets/fund balances (see page 17 of
the instructions).................. 1,767,392 1,146,404
Part III Analysis of Changes in Net Assets or Fund Balances
1 Total net assets or fund balances at beginning of year—Part II, column (a), line 30 (must agree
with end-of-year figure reported on prior year’s return)............... 1 1,767,392
2 Enter amount from Part I, line 27a..................... 2 -620,988
3 Other increases not included in line 2 (itemize) bullet 3  
4 Add lines 1, 2, and 3.......................... 4 1,146,404
5 Decreases not included in line 2 (itemize) bullet 5  
6 Total net assets or fund balances at end of year (line 4 minus line 5)—Part II, column (b), line 30. 6 1,146,404
Form 990-PF (2012)
Form 990-PF (2012)
Page 3
Part IV
Capital Gains and Losses for Tax on Investment Income
(a) List and describe the kind(s) of property sold (e.g., real estate,
2-story brick warehouse; or common stock, 200 shs. MLC Co.) 		(b) How acquired
P—Purchase
D—Donation 		(c) Date acquired
(mo., day, yr.) 		(d) Date sold
(mo., day, yr.)
1 a MISONIX, INC P 2005-11-17 2013-01-02
b MISONIX, INC P 2005-11-16 2013-01-02
c MISONIX, INC P 2005-11-15 2013-01-02
d MISONIX, INC P 2005-11-21 2013-01-03
e MISONIX, INC P 2005-11-18 2013-01-03
MISONIX, INC P 2005-11-17 2013-01-03
MISONIX, INC P 2005-11-23 2013-01-04
MISONIX, INC P 2005-11-21 2013-01-04
CYBERKINETICS NEUROTECHNOLOGY P 2004-12-01 2013-08-20
CYBERKINETICS NEUROTECHNOLOGY P 2004-11-30 2013-08-20
NEOSTEM, INC P 2007-04-11 2013-07-15
ULTRA FINANCIALS PROSHARES P 2008-07-23 2013-09-03
ULTRA FINANCIALS PROSHARES P 2008-05-15 2013-09-03
(e) Gross sales price (f) Depreciation allowed
(or allowable) 		(g) Cost or other basis
plus expense of sale 		(h) Gain or (loss)
(e) plus (f) minus (g)
a 362   213 149
b 64,131   37,961 26,170
c 18,910   11,201 7,709
d 14,201   8,968 5,233
e 2,313   1,454 859
18,935   11,872 7,063
4,804   3,424 1,380
31,126   22,176 8,950
    8,833 -8,833
    14,458 -14,458
4     4
45,907   120,870 -74,963
45,907   165,920 -120,013
Complete only for assets showing gain in column (h) and owned by the foundation on 12/31/69 (l) Gains (Col. (h) gain minus
col. (k), but not less than -0-) or
Losses (from col.(h))
(i) F.M.V. as of 12/31/69 (j) Adjusted basis
as of 12/31/69 		(k) Excess of col. (i)
over col. (j), if any
a       149
b       26,170
c       7,709
d       5,233
e       859
      7,063
      1,380
      8,950
      -8,833
      -14,458
      4
      -74,963
      -120,013
2 Capital gain net income or (net capital loss) Bracket If gain, also enter in Part I, line 7
If (loss), enter -0- in Part I, line 7		 Bracket 2 -160,750
3 Net short-term capital gain or (loss) as defined in sections 1222(5) and (6):
If gain, also enter in Part I, line 8, column (c) (see instructions). If (loss), enter -0-
in Part I, line 8 . . . . . . . . . . . . . . . . 		Bracket 3  
Part V
Qualification Under Section 4940(e) for Reduced Tax on Net Investment Income
(For optional use by domestic private foundations subject to the section 4940(a) tax on net investment income.)

If section 4940(d)(2) applies, leave this part blank.
Was the foundation liable for the section 4942 tax on the distributable amount of any year in the base period?
If “Yes,” the foundation does not qualify under section 4940(e). Do not complete this part.
1 Enter the appropriate amount in each column for each year; see page 18 of the instructions before making any entries.
(a)
Base period years Calendar
year (or tax year beginning in) 		(b)
Adjusted qualifying distributions 		(c)
Net value of noncharitable-use assets 		(d)
Distribution ratio
(col. (b) divided by col. (c))
2011 229,515 1,021,320 0.224724
2010 273,487 1,492,650 0.183222
2009 198,511 1,550,110 0.128063
2008 252,405 1,371,320 0.184060
2007 258,277 3,041,761 0.084910
2 Total of line 1, column (d) ...................... 2 0.804979
3 Average distribution ratio for the 5-year base period—divide the total on line 2 by 5, or by
the number of years the foundation has been in existence if less than 5 years. . . 		3 0.160996
4 Enter the net value of noncharitable-use assets for 2012 from Part X, line 5..... 4 947,034
5 Multiply line 4 by line 3....................... 5 152,469
6 Enter 1% of net investment income (1% of Part I, line 27b)........... 6  
7 Add lines 5 and 6......................... 7 152,469
8 Enter qualifying distributions from Part XII, line 4.............. 8 469,343
If line 8 is equal to or greater than line 7, check the box in Part VI, line 1b, and complete that part using a 1% tax rate. See
the Part VI instructions.
Form 990-PF (2012)
Form 990-PF (2012)
Page 4
Part VI
Excise Tax Based on Investment Income (Section 4940(a), 4940(b), 4940(e), or 4948—see page 18 of the instructions)
1a Bulletand enter “N/A” on line 1. Bracket
Date of ruling or determination letter:   (attach copy of letter if necessary–see instructions)
b 1 0
hereBulletand enter 1% of Part I, line 27b...................
c All other domestic foundations enter 2% of line 27b. Exempt foreign organizations enter 4% of Part I, line 12, col. (b)
2 Tax under section 511 (domestic section 4947(a)(1) trusts and taxable foundations only. Others enter -0-) 2  
3 Add lines 1 and 2............................ 3  
4 Subtitle A (income) tax (domestic section 4947(a)(1) trusts and taxable foundations only. Others enter -0-). 4  
5 Tax based on investment income. Subtract line 4 from line 3. If zero or less, enter -0- ..... 5  
6 Credits/Payments:
a 2012 estimated tax payments and 2011 overpayment credited to 2012 6a 994
b Exempt foreign organizations—tax withheld at source....... 6b
c Tax paid with application for extension of time to file (Form 8868) 6c  
d Backup withholding erroneously withheld ........... 6d  
7 Total credits and payments. Add lines 6a through 6d.............. 7 994
8 Enter any penalty for underpayment of estimated tax. if Form 2220 is attached. 8  
9 Tax due. If the total of lines 5 and 8 is more than line 7, enter amount owed.......Bullet 9  
10 Overpayment. If line 7 is more than the total of lines 5 and 8, enter the amount overpaid...Bullet 10 994
11 Enter the amount of line 10 to be: Credited to 2013 estimated taxBullet994 Refunded Bullet 11  
Part VII-A
Statements Regarding Activities
1a
During the tax year, did the foundation attempt to influence any national, state, or local legislation or did
Yes
No
it participate or intervene in any political campaign? ....................
1a
 
No
b
Did it spend more than $100 during the year (either directly or indirectly) for political purposes (see page 19 of
the instructions for definition)?............................
1b
 
No
If the answer is “Yes” to 1a or 1b, attach a detailed description of the activities and copies of any materials
published or distributed by the foundation in connection with the activities.
c
Did the foundation file Form 1120-POL for this year?.....................
1c
 
No
d
Enter the amount (if any) of tax on political expenditures (section 4955) imposed during the year:
(1) On the foundation. bullet$   (2) On foundation managers.bullet$  
e
Enter the reimbursement (if any) paid by the foundation during the year for political expenditure tax imposed
on foundation managers.bullet$  
2
Has the foundation engaged in any activities that have not previously been reported to the IRS?.......
2
 
No
If “Yes,” attach a detailed description of the activities.
3
Has the foundation made any changes, not previously reported to the IRS, in its governing instrument, articles
of incorporation, or bylaws, or other similar instruments? If “Yes,” attach a conformed copy of the changes....
3
 
No
4a
Did the foundation have unrelated business gross income of $1,000 or more during the year?........
4a
 
No
b
If “Yes,” has it filed a tax return on Form 990-T for this year?...................
4b
 
 
5
Was there a liquidation, termination, dissolution, or substantial contraction during the year?.........
5
 
No
If “Yes,” attach the statement required by General Instruction T.
6
Are the requirements of section 508(e) (relating to sections 4941 through 4945) satisfied either:
  • By language in the governing instrument, or
  • By state legislation that effectively amends the governing instrument so that no mandatory directions
    • that conflict with the state law remain in the governing instrument?................
    6
     
    No
    7
    Did the foundation have at least $5,000 in assets at any time during the year? If “Yes,” complete Part II, col. (c), and Part XV.
    7
    Yes
     
    8a
    Enter the states to which the foundation reports or with which it is registered (see instructions)
    bulletIA
    b
    If the answer is “Yes” to line 7, has the foundation furnished a copy of Form 990-PF to the Attorney
    General (or designate) of each state as required by General Instruction G? If “No,” attach explanation .
    8b
    Yes
     
    9
    Is the foundation claiming status as a private operating foundation within the meaning of section 4942(j)(3)
    or 4942(j)(5) for calendar year 2012 or the taxable year beginning in 2012 (see instructions for Part XIV)?
    If “Yes,” complete Part XIV.............................
    9
     
    No
    10
    Did any persons become substantial contributors during the tax year? If “Yes,” attach a schedule listing their names and addresses.
    10
     
    No
    11
    At any time during the year, did the foundation, directly or indirectly, own a controlled entity within the
    meaning of section 512(b)(13)? If "Yes," attach schedule. (see instructions) .............
    11
     
    No
    12
    Did the foundation make a distribution to a donor advised fund over which the foundation or a disqualified person had
    advisory privileges? If "Yes," attach statement (see instructions).................
    12
     
    No
    13
    Did the foundation comply with the public inspection requirements for its annual returns and exemption application?
    13
    Yes
     
    Website addressbulletN/A
    14
    The books are in care ofbulletMATT KINLEY Telephone no.bullet (515) 244-5746
    Located atbullet666 WALNUT STREET SUITE 2116DES MOINESIA ZIP+4bullet50309
    15
    Section 4947(a)(1) nonexempt charitable trusts filing Form 990-PF in lieu of Form 1041.........bullet
    and enter the amount of tax-exempt interest received or accrued during the year ......bullet
    15  
    16
    At any time during calendar year 2012, did the foundation have an interest in or a signature or other authority over
    a bank, securities, or other financial account in a foreign country? .................
    16
     
    No
    See instructions for exceptions and filing requirements for Form TD F 90-22.1. If "Yes", enter the name of the foreign country bullet  
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 5
    Part VII-B
    Statements Regarding Activities for Which Form 4720 May Be Required
    File Form 4720 if any item is checked in the “Yes” column, unless an exception applies.
    Yes
    No
    1a
    During the year did the foundation (either directly or indirectly):
    (1) Engage in the sale or exchange, or leasing of property with a disqualified person?
    (2) Borrow money from, lend money to, or otherwise extend credit to (or accept it from)
    a disqualified person?.........................
    (3) Furnish goods, services, or facilities to (or accept them from) a disqualified person?
    (4) Pay compensation to, or pay or reimburse the expenses of, a disqualified person?
    (5) Transfer any income or assets to a disqualified person (or make any of either available
    for the benefit or use of a disqualified person)?.................
    (6) Agree to pay money or property to a government official? (Exception. Check “No”
    if the foundation agreed to make a grant to or to employ the official for a period
    after termination of government service, if terminating within 90 days.).........
    b
    If any answer is “Yes” to 1a(1)–(6), did any of the acts fail to qualify under the exceptions described in Regulations
    section 53.4941(d)-3 or in a current notice regarding disaster assistance (see page 20 of the instructions)?...
    1b
     
     
    .........bullet
    c
    Did the foundation engage in a prior year in any of the acts described in 1a, other than excepted acts,
    that were not corrected before the first day of the tax year beginning in 2012?.............
    1c
     
     
    2
    Taxes on failure to distribute income (section 4942) (does not apply for years the foundation was a private
    operating foundation defined in section 4942(j)(3) or 4942(j)(5)):
    a
    At the end of tax year 2012, did the foundation have any undistributed income (lines 6d
    and 6e, Part XIII) for tax year(s) beginning before 2012?...............
    If “Yes,” list the years bullet20, 20, 20, 20
    b
    Are there any years listed in 2a for which the foundation is not applying the provisions of section 4942(a)(2)
    (relating to incorrect valuation of assets) to the year’s undistributed income? (If applying section 4942(a)(2)
    to all years listed, answer “No” and attach statement—see instructions.) ..............
    2b
     
     
    c
    If the provisions of section 4942(a)(2) are being applied to any of the years listed in 2a, list the years here.
    bullet20, 20, 20, 20
    3a
    Did the foundation hold more than a 2% direct or indirect interest in any business enterprise at
    any time during the year?.........................
    b
    If “Yes,” did it have excess business holdings in 2012 as a result of (1) any purchase by the foundation
    or disqualified persons after May 26, 1969; (2) the lapse of the 5-year period (or longer period approved
    by the Commissioner under section 4943(c)(7)) to dispose of holdings acquired by gift or bequest; or (3)
    the lapse of the 10-, 15-, or 20-year first phase holding period? (Use Schedule C, Form 4720, to determine
    if the foundation had excess business holdings in 2012.)....................
    3b
     
     
    4a
    Did the foundation invest during the year any amount in a manner that would jeopardize its charitable purposes?
    4a
     
    No
    b
    Did the foundation make any investment in a prior year (but after December 31, 1969) that could jeopardize its
    charitable purpose that had not been removed from jeopardy before the first day of the tax year beginning in 2012?
    4b
     
    No
    5a
    During the year did the foundation pay or incur any amount to:
    (1) Carry on propaganda, or otherwise attempt to influence legislation (section 4945(e))?
    (2) Influence the outcome of any specific public election (see section 4955); or to carry
    on, directly or indirectly, any voter registration drive?...............
    (3) Provide a grant to an individual for travel, study, or other similar purposes?
    (4) Provide a grant to an organization other than a charitable, etc., organization described
    in section 509(a)(1), (2), or (3), or section 4940(d)(2)? (see instructions)........
    (5) Provide for any purpose other than religious, charitable, scientific, literary, or
    educational purposes, or for the prevention of cruelty to children or animals?........
    b
    If any answer is “Yes” to 5a(1)–(5), did any of the transactions fail to qualify under the exceptions described in
    Regulations section 53.4945 or in a current notice regarding disaster assistance (see instructions)? ......
    5b
     
     
    .........bullet
    c
    If the answer is “Yes” to question 5a(4), does the foundation claim exemption from the
    tax because it maintained expenditure responsibility for the grant?............
    If “Yes,” attach the statement required by Regulations section 53.4945–5(d).
    6a
    Did the foundation, during the year, receive any funds, directly or indirectly, to pay premiums on
    a personal benefit contract?........................
    b
    Did the foundation, during the year, pay premiums, directly or indirectly, on a personal benefit contract?....
    6b
     
    No
    If “Yes” to 6b, file Form 8870.
    7a
    At any time during the tax year, was the foundation a party to a prohibited tax shelter transaction?
    b
    If yes, did the foundation receive any proceeds or have any net income attributable to the transaction? ....
    7b
     
     
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 6
    Part VIII
    Information About Officers, Directors, Trustees, Foundation Managers, Highly Paid Employees,
    and Contractors
    1 List all officers, directors, trustees, foundation managers and their compensation (see instructions).
    (a) Name and address (b) Title, and average
    hours per week
    devoted to position     		(c) Compensation
     (If not paid, enter
    -0-)     		(d) Contributions to
    employee benefit plans
    and deferred compensation     		(e) Expense account,
    other allowances
    JOHN PAPPAJOHNClick to see attachment DIRECTOR
    1.00     		0 0 0
    2116 FINANCIAL CENTER
    DES MOINES,IA50309
    MARY PAPPAJOHNClick to see attachment DIRECTOR
    1.00     		0 0 0
    24 FOSTER DRIVE
    DES MOINES,IA50312
    ANN VASSILIOUClick to see attachment DIRECTOR
    1.00     		0 0 0
    94 NATHAN HALE DRIVE
    STAMFORD,CT06902
    2 Compensation of five highest-paid employees (other than those included on line 1—see instructions). If none, enter “NONE.”
    (a) Name and address of each employee paid more than $50,000 (b) Title, and average
    hours per week
    devoted to position     		(c) Compensation (d) Contributions to
    employee benefit
    plans and deferred
    compensation     		(e) Expense account,
    other allowances
    NONE
    Total number of other employees paid over $50,000...................bullet  
    3 Five highest-paid independent contractors for professional services (see instructions). If none, enter "NONE".
    (a) Name and address of each person paid more than $50,000 (b) Type of service (c) Compensation
    NONE
    Total number of others receiving over $50,000 for professional services.............bullet  
    Part IX-A
    Summary of Direct Charitable Activities
    List the foundation’s four largest direct charitable activities during the tax year. Include relevant statistical information such as the number of organizations and other beneficiaries served, conferences convened, research papers produced, etc. Expenses
    1
     
    2  
    3  
    4  
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 7
    Part IX-B
    Summary of Program-Related Investments (see instructions)
    Describe the two largest program-related investments made by the foundation during the tax year on lines 1 and 2. Amount
    1 N/A  
    2  
    All other program-related investments. See page 24 of the instructions.
    3  
    Total. Add lines 1 through 3..........................bullet  
    Part X
    Minimum Investment Return (All domestic foundations must complete this part. Foreign foundations,
    see instructions.)
    1
    Fair market value of assets not used (or held for use) directly in carrying out charitable, etc.,
    purposes:
    a
    Average monthly fair market value of securities...................
    1a
    709,488
    b
    Average of monthly cash balances.......................
    1b
    251,968
    c
    Fair market value of all other assets (see instructions)................
    1c
    0
    d
    Total (add lines 1a, b, and c).........................
    1d
    961,456
    e
    Reduction claimed for blockage or other factors reported on lines 1a and
    1c (attach detailed explanation) .............
    1e
     
    2
    Acquisition indebtedness applicable to line 1 assets..................
    2
     
    3
    Subtract line 2 from line 1d.........................
    3
    961,456
    4
    Cash deemed held for charitable activities. Enter 1 1⁄2% of line 3 (for greater amount, see
    instructions) .............................
    4
    14,422
    5
    Net value of noncharitable-use assets. Subtract line 4 from line 3. Enter here and on Part V, line 4
    5
    947,034
    6
    Minimum investment return. Enter 5% of line 5..................
    6
    47,352
    Part XI
    Distributable Amount bullet and do not complete this part.)
    1
    Minimum investment return from Part X, line 6....................
    1
    47,352
    2a
    Tax on investment income for 2012 from Part VI, line 5......
    2a
     
    b
    Income tax for 2012. (This does not include the tax from Part VI.)...
    2b
     
    c
    Add lines 2a and 2b............................
    2c
     
    3
    Distributable amount before adjustments. Subtract line 2c from line 1............
    3
    47,352
    4
    Recoveries of amounts treated as qualifying distributions................
    4
     
    5
    Add lines 3 and 4............................
    5
    47,352
    6
    Deduction from distributable amount (see instructions).................
    6
     
    7
    Distributable amount as adjusted. Subtract line 6 from line 5. Enter here and on Part XIII,
    line 1................................
    7
    47,352
    Part XII
    Qualifying Distributions (see instructions)
    1
    Amounts paid (including administrative expenses) to accomplish charitable, etc., purposes:
    a
    Expenses, contributions, gifts, etc.—total from Part I, column (d), line 26 ..........
    1a
    469,343
    b
    Program-related investments—total from Part IX-B..................
    1b
     
    2
    Amounts paid to acquire assets used (or held for use) directly in carrying out charitable, etc.,
    purposes...............................
    2
     
    3
    Amounts set aside for specific charitable projects that satisfy the:
    a
    Suitability test (prior IRS approval required)....................
    3a
     
    b
    Cash distribution test (attach the required schedule) .................
    3b
     
    4
    Qualifying distributions. Add lines 1a through 3b. Enter here and on Part V, line 8, and Part XIII, line 4
    4
    469,343
    5
    Foundations that qualify under section 4940(e) for the reduced rate of tax on net investment
    income. Enter 1% of Part I, line 27b (see instructions).................
    5
     
    6
    Adjusted qualifying distributions. Subtract line 5 from line 4..............
    6
    469,343
    Note: The amount on line 6 will be used in Part V, column (b), in subsequent years when calculating whether the foundation qualifies for
    the section 4940(e) reduction of tax in those years.
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 8
    Part XIII
    Undistributed Income (see instructions)
    (a)
    Corpus     		(b)
    Years prior to 2011     		(c)
    2011     		(d)
    2012
    1 Distributable amount for 2012 from Part XI, line 7 47,352
    2 Undistributed income, if any, as of the end of 2012:
    a Enter amount for 2011 only.......  
    b Total for prior years:20, 20, 20  
    3 Excess distributions carryover, if any, to 2012:
    a From 2007....... 107,469
    b From 2008....... 180,459
    c From 2009....... 119,505
    d From 2010....... 199,576
    e From 2011....... 174,194
    fTotal of lines 3a through e......... 781,203
    4Qualifying distributions for 2012 from Part
    XII, line 4: bullet$ 469,343
    a Applied to 2011, but not more than line 2a  
    b Applied to undistributed income of prior years
    (Election required—see instructions)......     		 
    c Treated as distributions out of corpus (Election
    required—see instructions).........     		 
    d Applied to 2012 distributable amount..... 47,352
    e Remaining amount distributed out of corpus 421,991
    5 Excess distributions carryover applied to 2012.    
    (If an amount appears in column (d), the
    same amount must be shown in column (a).)
    6Enter the net total of each column as
    indicated below:
    a Corpus. Add lines 3f, 4c, and 4e. Subtract line 5 1,203,194
    b Prior years’ undistributed income. Subtract
    line 4b from line 2b ...........     		 
    c Enter the amount of prior years’ undistributed
    income for which a notice of deficiency has
    been issued, or on which the section 4942(a)
    tax has been previously assessed......     		 
    d Subtract line 6c from line 6b. Taxable amount
    —see instructions ...........     		 
    e Undistributed income for 2011. Subtract line
    4a from line 2a. Taxable amount—see
    instructions .............     		 
    f Undistributed income for 2012. Subtract
    lines 4d and 5 from line 1. This amount must
    be distributed in 2013 ..........     		0
    7 Amounts treated as distributions out of
    corpus to satisfy requirements imposed by
    section 170(b)(1)(F) or 4942(g)(3) (see
    instructions) .............     		 
    8Excess distributions carryover from 2007 not
    applied on line 5 or line 7 (see instructions) ...     		107,469
    9Excess distributions carryover to 2013.
    Subtract lines 7 and 8 from line 6a ......     		1,095,725
    10 Analysis of line 9:
    a Excess from 2008.... 180,459
    b Excess from 2009.... 119,505
    c Excess from 2010.... 199,576
    d Excess from 2011.... 174,194
    e Excess from 2012.... 421,991
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 9
    Part XIV
    Private Operating Foundations (see instructions and Part VII-A, question 9)
    1a If the foundation has received a ruling or determination letter that it is a private operating
    foundation, and the ruling is effective for 2012, enter the date of the ruling.......bullet
     
    b Check box to indicate whether the organization is a private operating foundation described in section or
    2a Enter the lesser of the adjusted net
    income from Part I or the minimum
    investment return from Part X for each
    year listed ..........     		Tax year Prior 3 years (e) Total
    (a) 2012 (b) 2011 (c) 2010 (d) 2009
             
    b 85% of line 2a .........          
    c Qualifying distributions from Part XII,
    line 4 for each year listed .....     		         
    d Amounts included in line 2c not used directly
    for active conduct of exempt activities ....     		         
    e Qualifying distributions made directly
    for active conduct of exempt activities.
    Subtract line 2d from line 2c ....     		         
    3 Complete 3a, b, or c for the
    alternative test relied upon:
    a “Assets” alternative test—enter:
    (1) Value of all assets ......          
    (2) Value of assets qualifying
    under section 4942(j)(3)(B)(i)    		          
    b “Endowment” alternative test— enter 2⁄3
    of minimum investment return shown in
    Part X, line 6 for each year listed...     		         
    c “Support” alternative test—enter:
    (1) Total support other than gross
    investment income (interest,
    dividends, rents, payments
    on securities loans (section
    512(a)(5)), or royalties) ....     		         
    (2) Support from general public
    and 5 or more exempt
    organizations as provided in
    section 4942(j)(3)(B)(iii)....     		         
    (3) Largest amount of support
    from an exempt organization    		          
    (4) Gross investment income          
    Part XV
    Supplementary Information (Complete this part only if the organization had $5,000 or more in
    assets at any time during the year—see instructions.)
    1Information Regarding Foundation Managers:
    aList any managers of the foundation who have contributed more than 2% of the total contributions received by the foundation
    before the close of any tax year (but only if they have contributed more than $5,000). (See section 507(d)(2).)
    bList any managers of the foundation who own 10% or more of the stock of a corporation (or an equally large portion of the
    ownership of a partnership or other entity) of which the foundation has a 10% or greater interest.
    2Information Regarding Contribution, Grant, Gift, Loan, Scholarship, etc., Programs:
    Check here bullet
    aThe name, address, and telephone number of the person to whom applications should be addressed:
    bThe form in which applications should be submitted and information and materials they should include:
    cAny submission deadlines:
    dAny restrictions or limitations on awards, such as by geographical areas, charitable fields, kinds of institutions, or other
    factors:
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 10
    Part XV
    Supplementary Information (continued)
    3 Grants and Contributions Paid During the Year or Approved for Future Payment
    Recipient If recipient is an individual,
    show any relationship to
    any foundation manager
    or substantial contributor
    		 Foundation
    status of
    recipient     		Purpose of grant or
    contribution     		Amount
    Name and address (home or business)
    aPaid during the year
    DRAKE UNIVERSITY
    2507 UNIVERSITY AVENUE
    DES MOINES,IA50311     		NONE PUBLIC CHARI EDUCATIONAL 9,000
    DES MOINES AREA COMMUNITY COLLEGE
    1100 7TH STREET
    DES MOINES,IA50314     		NONE PUBLIC CHARI EDUCATIONAL 7,500
    IOWA STATE UNIVERSITY
    300 C CARVER HALL
    AMES,IA50011     		NONE PUBLIC CHARI EDUCATIONAL 24,500
    AIB
    2500 FLEUR DRIVE
    DES MOINES,IA50321     		NONE PUBLIC CHARI EDUCATIONAL 1,500
    UNIVERSITY OF IOWA
    107 CALVIN HALL
    IOWA CITY,IA52242     		NONE PUBLIC CHARI EDUCATIONAL 142,500
    ARIZONA STATE UNIVERSITY
    PO BOX 870303
    TEMPE,AZ85287     		  PUBLIC CHARI EDUCATIONAL 3,000
    UNIVERSITY OF MISSOURI
    125 JESSE HALL
    COLOMBIA,MO65211     		NONE PUBLIC CHARI EDUCATIONAL 2,000
    UNIVERSITY OF MINNESOTA
    200 OAK STREET SE
    MINNEAPOLIS,MN55455     		NONE PUBLIC CHARI EDUCATIONAL 12,000
    UNIVERSITY OF NORTHERN IOWA
    1227 WEST 27TH STREET
    CEDAR FALLS,IA50614     		NONE PUBLIC CHARI EDUCATIONAL 11,000
    GRAND VIEW UNIVERSITY
    1200 GRANDVIEW AVENUE
    DES MOINES,IA50316     		NONE PUBLIC CHARI EDUCATIONAL 12,000
    RENSSELAER POLYTECHNIC INSTITUTE
    110 8TH STREET
    TROY,NY12180     		NONE PUBLIC CHARI EDUCATIONAL 1,000
    IOWA CENTRAL COMMUNITY COLLEGE
    1 TRITON CIRCLE
    FORT DODGE,IA50501     		NONE PUBLIC CHARI EDUCATIONAL 1,000
    CREIGHTON UNIVERSITY
    2500 CALIFORNIA PLAZA
    OMAHA,NE68102     		NONE PUBLIC CHARI EDUCATIONAL 500
    BUENA VISTA UNIVERSITY
    610 W 4TH STREET
    STORM LAKE,IA50588     		NONE PUBLIC CHARI EDUCATIONAL 1,000
    HELLENIC COLLEGE
    50 GODDARD AVE
    BROOKLINE,MA02445     		NONE PUBLIC CHARI EDUCATIONAL 1,000
    BAY COLONY SCHOLARSHIP FUND
    8700 BAY COLONY DRIVE
    NAPLES,FL34108     		NONE PUBLIC CHARI EDUCATIONAL 500
    GREEK AMERICAN FOUNDATION
    910 W VAN BUREN ST
    CHICAGO,IL60607     		NONE PUBLIC CHARI EDUCATIONAL 70,000
    PHI GAMMA DELTA FOUNDATION
    PO BOX 4599
    LEXINGTON,KY40544     		NONE PUBLIC CHARI EDUCATIONAL 10,000
    ANATOLIA COLLEGE
    130 BOWDOIN STREET
    BOSTON,MA02108     		NONE PUBLIC CHARI EDUCATIONAL 20,000
    HORATIO ALGER ASSOCIATION
    99 CANAL CENTER PLAZA
    ALEXANDRIA,VA22314     		NONE PUBLIC CHARI EDUCATIONAL 50,000
    IOWA AFRICAN AMERICAN HALL OF FAME
    C/O DIVISION OF STUDENT AFFAIRS ISU
    2350 BEARDSHEAR HALL
    AMES,IA50011     		NONE PUBLIC CHARI EDUCATIONAL 1,000
    HELLENIC TIMES SCHOLARSHIP FUND
    823 ELEVENTH AVENUE
    NEW YORK,NY10019     		NONE PUBLIC CHARI EDUCATIONAL 10,000
    HARDING LODGE 649
    304 1ST STREET SE
    MASON CITY,IA50401     		NONE PUBLIC CHARI EDUCATIONAL 100
    DES MOINES ART CENTER
    4700 GRAND AVENUE
    DES MOINES,IA50312     		NONE PUBLIC CHARI CHARITABLE 10,000
    PAN HELLENIC SCHOLARSHIP FOUNDATION
    17 NORTH WABASH AVE
    SUITE 600
    CHICAGO,IL60602     		NONE PUBLIC CHARI EDUCATIONAL 5,000
    JAMES B MORRIS SCHOLARSHIP FUND
    525 SW 5TH STREET
    DES MOINES,IA50309     		NONE PUBLIC CHARI EDUCATIONAL 2,500
    DES MOINES UNIVERSITY
    3200 GRAND AVENUE
    DES MOINES,IA50312     		NONE PUBLIC CHARI EDUCATIONAL 20,000
    PINE MANOR COLLEGE
    400 HEATH STREET
    CHESTNUT HILL,MA02467     		NONE PUBLIC CHARI EDUCATIONAL 5,000
    BETA GAMMA SIGMA
    125 WELDON PARKWAY
    MARYLAND HEIGHTS,MO63043     		NONE PUBLIC CHARI EDUCATIONAL 1,000
    NORTH IOWA AREA COMMUNITY COLLEGE
    500 COLLEGE AVENUE
    MASON CITY,IA50401     		NONE PUBLIC CHARI EDUCATIONAL 11,000
    MASON CITY EDUCATIONAL FOUNDATION
    C/O MASON CITY HIGH SCHOOL
    1700 FOURTH SE
    MASON CITY,IA50401     		NONE PUBLIC CHARI EDUCATIONAL 10,000
    MAYO MEDICAL SCHOOL
    200 1ST STREET SW
    ROCHESTER,MN55905     		NONE PUBLIC CHARI EDUCATIONAL 10,000
    WARTBURG COLLEGE
    100 WARTBURG BLVD
    WAVERLY,IA50677     		NONE PUBLIC CHARI EDUCATIONAL 1,000
    UPPER IOWA UNIVERSITY
    605 WASHINGTON STREET
    FAYETTE,IA52142     		NONE PUBLIC CHARI EDUCATIONAL 1,000
    IOWA COLLEGE FOUNDATION
    505 5TH AVENUE SUITE 1034
    DES MOINES,IA50309     		NONE PUBLIC CHARI EDUCATIONAL 750
    Total .................................bullet 3a 468,350
    bApproved for future payment
    Total .................................bullet 3b  
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 11
    Part XVI-A
    Analysis of Income-Producing Activities
    Enter gross amounts unless otherwise indicated. Unrelated business income Excluded by section 512, 513, or 514 (e)
    Related or exempt
    function income
    (See instructions.)
    1Program service revenue: (a)
    Business code     		(b)
    Amount     		(c)
    Exclusion code     		(d)
    Amount
    a
    b
    c
    d
    e
    f
    gFees and contracts from government agencies          
    2 Membership dues and assessments....          
    3Interest on savings and temporary cash investments     14 1  
    4 Dividends and interest from securities....     14 456  
    5 Net rental income or (loss) from real estate:
    aDebt-financed property......          
    bNot debt-financed property.....          
    6Net rental income or (loss) from personal property          
    7 Other investment income.....          
    8Gain or (loss) from sales of assets other than inventory     18 -160,750  
    9 Net income or (loss) from special events:          
    10 Gross profit or (loss) from sales of inventory..          
    11 Other revenue: aCLASS ACTION SETTLEMENTS     18 9,772  
    b
    c
    d
    e
    12 Subtotal. Add columns (b), (d), and (e)..   -150,521  
    13Total. Add line 12, columns (b), (d), and (e)..................
    13-150,521
    (See worksheet in line 13 instructions to verify calculations.)
    Part XVI-B
    Relationship of Activities to the Accomplishment of Exempt Purposes
    Line No.
    DownArrow     		Explain below how each activity for which income is reported in column (e) of Part XVI-A contributed importantly to
    the accomplishment of the foundation’s exempt purposes (other than by providing funds for such purposes). (See
    instructions.)
    Form 990-PF (2012)
    Form 990-PF (2012)
    Page 12
    Part XVII
    Information Regarding Transfers To and Transactions and Relationships With Noncharitable Exempt Organizations
    1
    Did the organization directly or indirectly engage in any of the following with any other organization described in section
    Yes
    No
    501(c) of the Code (other than section 501(c)(3) organizations) or in section 527, relating to political organizations?
    a
    Transfers from the reporting foundation to a noncharitable exempt organization of:
    (1) Cash...................................
    1a(1)
     
    No
    (2) Other assets.................................
    1a(2)
     
    No
    b
    Other transactions:
    (1) Sales of assets to a noncharitable exempt organization....................
    1b(1)
     
    No
    (2) Purchases of assets from a noncharitable exempt organization..................
    1b(2)
     
    No
    (3) Rental of facilities, equipment, or other assets.......................
    1b(3)
     
    No
    (4) Reimbursement arrangements...........................
    1b(4)
     
    No
    (5) Loans or loan guarantees.............................
    1b(5)
     
    No
    (6) Performance of services or membership or fundraising solicitations................
    1b(6)
     
    No
    c
    Sharing of facilities, equipment, mailing lists, other assets, or paid employees..............
    1c
     
    No
    d
    If the answer to any of the above is “Yes,” complete the following schedule. Column (b) should always show the fair market value
    of the goods, other assets, or services given by the reporting foundation. If the foundation received less than fair market value
    in any transaction or sharing arrangement, show in column (d) the value of the goods, other assets, or services received.
    (a) Line No. (b) Amount involved (c) Name of noncharitable exempt organization (d) Description of transfers, transactions, and sharing arrangements
    2a
    Is the foundation directly or indirectly affiliated with, or related to, one or more tax-exempt organizations
    described in section 501(c) of the Code (other than section 501(c)(3)) or in section 527?...........
    b
    If “Yes,” complete the following schedule.
    (a) Name of organization (b) Type of organization (c) Description of relationship
    Sign Here
    Under penalties of perjury, I declare that I have examined this return, including accompanying schedules and statements, and to the best of my knowledge and belief, it is true, correct, and complete. Declaration of preparer (other than taxpayer or fiduciary) is based on all information of which preparer has any knowledge.
    Bullet Bullet
    May the IRS discuss this return
    with the preparer shown below
    (see instr.)?
    Signature of officer or trustee Date Title
    Paid Preparer Use Only Print/Type preparer's name Preparer's Signature Date PTIN
    Firm's namebullet



    Firm's addressbullet







         		Firm's EINbullet
    Phone no.
    Form 990-PF (2012)
    Additional Data


    Software ID:  
    Software Version:  


    Form 990PF - Special Condition Description:
    Special Condition Description

    TY 2012 AccountingFeesSchedule
    Name:
    JOHN & MARY PAPPAJOHN SCHOLARSHIP
    FOUNDATION
    EIN: 42-1465551
    Category Amount Net Investment Income Adjusted Net Income Disbursements for Charitable Purposes
    ACCOUNTING FEES 1,985 992   993

    TY 2012 CompensationExplanation
    Name:
    JOHN & MARY PAPPAJOHN SCHOLARSHIP
    FOUNDATION
    EIN: 42-1465551
    Person Name Explanation
    JOHN PAPPAJOHN  
    MARY PAPPAJOHN  
    ANN VASSILIOU  

    TY 2012 InvestmentsCorpStockSchedule
    Name:
    JOHN & MARY PAPPAJOHN SCHOLARSHIP
    FOUNDATION
    EIN: 42-1465551
    Name of Stock End of Year Book Value End of Year Fair Market Value
    CYBERKINETICS NEUROTECHNOLOGY    
    HEALTHSOUTH 452,050 275,840
    MISONIC, INC    
    NEOSYSTEM INC 100,191 24,641
    PHARMATHENE, INC 172,013 231,000
    SIGA TECHNOLOGIES, INC 253,614 229,200
    ULTRA FINANCIAL PROSHARES    

    TY 2012 OtherExpensesSchedule
    Name:
    JOHN & MARY PAPPAJOHN SCHOLARSHIP
    FOUNDATION
    EIN: 42-1465551
    Description Revenue and Expenses per Books Net Investment Income Adjusted Net Income Disbursements for Charitable Purposes
    EXPENSES        
    BANK FEES 82 82    
    BROKER FEES 50 50    


    TY 2012 OtherIncomeSchedule2
    Name:
    JOHN & MARY PAPPAJOHN SCHOLARSHIP
    FOUNDATION
    EIN: 42-1465551
    Description Revenue And Expenses Per Books Net Investment Income Adjusted Net Income
    CLASS ACTION SETTLEMENTS 9,772