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For several years, the FDA has requested that sponsors submit clinical trial data in CDISC SDTM format. Recently, the FDA has begun requiring submissions of other forms of data to be in standardized CDISC formats, for example, CDISC ADaM for analysis data, and CDISC SEND for animal toxicology studies. While commercial tools have been available to validate CDISC SDTM data since the beginning of this standardsadoption process, they have not been freely available to everybody. OpenCDISC. org was initiated in 2008 as an open source community dedicated to the creation of extensible tools for the implementation of CDISC standards, with an initial focus on data validation. The OpenCDISC Validator is built using Java and is configurable so that it can check not only various versions of CDISC data, but can also be tailored to meet the specific needs of a particular submission or a particular setting within a pharmaceutical company. The tool is configured using XML files, which can be modified or created us...

Voltage-dependent K+ channels like Shaker use an intracellular gate to control ion flow through the pore. When the membrane voltage becomes more positive, these channels traverse a series of closed conformations before the final opening transition. Does the intracellular gate undergo conformational changes before channel opening? To answer this question we introduced cysteines into the intracellular end of the pore and studied their chemical modification in conditions favoring each of three distinct states, the open state, the resting closed state, and the activated-not-open state (the closed state adjacent to the open state). We used two independent ways to isolate the channels in the activated-not-open state. First, we used mutations in S4 (ILT; Smith-Maxwell, C.J., J.L. Ledwell, and R.W. Aldrich. 1998. J. Gen. Physiol. 111:421–439; Ledwell, J.L., and R.W. Aldrich. 1999. J. Gen. Physiol. 113:389–414) that separate the final opening step from earlier charge-movement steps. Second, we used the open channel blocker 4-aminopyridine (4-AP), which has been proposed to promote closure of the intracellular gate and thus specifically to stabilize the activated-not-open state of the channels. Supporting this proposed mechanism, we found that 4-AP enters channels only after opening, remaining trapped in closed channels, and that in the open state it competes with tetraethylammonium for binding. Using these tools, we found that in the activated-not-open state, a cysteine located at a position considered to form part of the gate (Shaker 478) showed higher reactivity than in either the open or the resting closed states. Additionally, we have found that in this activated state the intracellular gate continued to prevent access to the pore by molecules as small as Cd2+ ions. Our results suggest that the intracellular opening to the pore undergoes some rearrangements in the transition from the resting closed state to the activated-not-open state, but throughout this process the intracellular gate remains an effective barrier to the movement of potassium ions through the pore.

The best-known Shaker allele of Drosophila with a novel gating phenotype, Sh5, differs from the wild-type potassium channel by a point mutation in the fifth membrane-spanning segment (S5) (Gautam, M., and M.A. Tanouye. 1990. Neuron. 5:67–73; Lichtinghagen, R., M. Stocker, R. Wittka, G. Boheim, W. Stühmer, A. Ferrus, and O. Pongs. 1990. EMBO [Eur. Mol. Biol. Organ.] J. 9:4399–4407) and causes a decrease in the apparent voltage dependence of opening. A kinetic study of Sh5 revealed that changes in the deactivation rate could account for the altered gating behavior (Zagotta, W.N., and R.W. Aldrich. 1990. J. Neurosci. 10:1799–1810), but the presence of intact fast inactivation precluded observation of the closing kinetics and steady state activation. We studied the Sh5 mutation (F401I) in ShB channels in which fast N-type inactivation was removed, directly confirming this conclusion. Replacement of other phenylalanines in S5 did not result in substantial alterations in voltage-dependent gating. At position 401, valine and alanine substitutions, like F401I, produce currents with decreased apparent voltage dependence of the open probability and of the deactivation rates, as well as accelerated kinetics of opening and closing. A leucine residue is the exception among aliphatic mutants, with the F401L channels having a steep voltage dependence of opening and slow closing kinetics. The analysis of sigmoidal delay in channel opening, and of gating current kinetics, indicates that wild-type and F401L mutant channels possess a form of cooperativity in the gating mechanism that the F401A channels lack. The wild-type and F401L channels' entering the open state gives rise to slow decay of the OFF gating current. In F401A, rapid gating charge return persists after channels open, confirming that this mutation disrupts stabilization of the open state. We present a kinetic model that can account for these properties by postulating that the four subunits independently undergo two sequential voltage-sensitive transitions each, followed by a final concerted opening step. These channels differ primarily in the final concerted transition, which is biased in favor of the open state in F401L and the wild type, and in the opposite direction in F401A. These results are consistent with an activation scheme whereby bulky aromatic or aliphatic side chains at position 401 in S5 cooperatively stabilize the open state, possibly by interacting with residues in other helices.

The cardiopulmonary bypass (CPB) circuit is designed to perform four major functions: (1) oxygenation and carbon dioxide elimination, (2) circulation of blood, (3) systemic cooling and rewarming, and (4) diversion of blood from the heart to provide a bloodless surgical field. Typically, venous blood is drained by gravity from the right side of the heart into a reservoir that serves as a large mixing chamber for all blood return, additional fluids, and drugs. Because (in most instances) negative pressure is not employed, the amount of venous drainage is determined by the central venous pressure, the column height between the patient and reservoir, and resistance to flow in the venous circuitry. Venous return may be decreased deliberately (as is done when restoring the patient’s blood volume before coming off bypass) by application of a venous clamp. From the reservoir, blood is pumped to an oxygenator and heat exchanger unit before passing through an arterial filter and returning to the patient. Additional components Goals and Mechanics of Cardiopulmonary Bypass