Comprehensive functional specifications and design for IT support of clinical research at an academic medical center

We present a framework for understanding and developing an Information Technology (IT) infrastructure for human subject research. First, we review the process of clinical research in an academic medical center. Next,we describe the entities,roles,and functional relationships within the clinical research enterprise to define a conceptual data model. Finally, we address design and implementation issues for an IT infrastructure that can be adapted to the local needs of research institutions.

Vibrational transition moment angles in isolated biomolecules: a structural tool

Infrared spectroscopy is used extensively in the study of isolated biomolecules, but it becomes less useful as it is applied to systems of increasing complexity. Even if the individual vibrational bands can be resolved spectroscopically, their assignment becomes problematic when they are more closely spaced than can be determined using ab initio methods. We describe a method that helps to alleviate this difficulty by measuring the direction of the vibrational transition moment for each vibrational band. The molecules of interest (adenine and cytosine) are cooled to 0.37 kelvin in liquid helium nanodroplets and oriented in a large dc electric field. A polarized infrared laser is then used to determine the directions of the infrared transition moments relative to the permanent dipole moment. Comparisons with ab initio calculations provide detailed structural information, including experimental evidence for nonplanarity of adenine and three tautomers of cytosine.

4-1BB-specific monoclonal antibody promotes the generation of tumor-specific immune responses by direct activation of CD8 T cells in a CD40-dependent manner

4-1BB (CD137) is a member of the TNFR superfamily (TNFRSF9). T cell expression of 4-1BB is restricted to activated cells, and cross-linking has been shown to deliver a costimulatory signal. Here we have shown that treatment of tumor-bearing mice with agonistic 4-1BB-specific Abs can lead to T cell-mediated tumor rejection. In vivo mAb depletion experiments demonstrated that this rejection requires CD8(+) cells but not CD4(+) or NK cells. Both IFN-gamma- and CD40-mediated signals were also required, because no benefit was observed on treatment with 4-1BB mAb in mice in which the genes for these molecules had been knocked out. Interestingly, 4-1BB-mediated stimulation of immune responses in CD40L(-/-) mice is effective (although at a reduced level), and may suggest the existence of an alternative ligand for CD40. Additional experiments in IL-15(-/-) mice indicate that IL-15 is not required for either the generation of the primary tumor-specific immune response or the maintenance of the memory immune response. In contrast, the presence of CD4 cells during the primary immune response appears to play a significant role in the maintenance of effective antitumor memory. Finally, in mice in which the number of dendritic cells had been expanded by Fms-like tyrosine kinase3 ligand treatment, the antitumor effects of 4-1BB ligation were enhanced.

Coupled atomistic and discrete dislocation plasticity

A computational method for multiscale modeling of plasticity is presented wherein each dislocation is treated as either an atomistic or continuum entity within a single computational framework. The method divides space into atomistic and continuum regions that communicate across a coherent boundary, detects dislocations as they approach the boundary, and seamlessly converts them from one description to another. The method permits the study of problems that are too large for fully atomistic simulation while preserving accurate atomistic details where necessary, but is currently limited to a 2D implementation. A validation test is performed by comparing the method against full atomistic simulations for a 2D nanoindentation problem.

Spiers Memorial Lecture. Comparative studies of cluster dynamics in the gas and condensed phases

Although an overview of the field of cluster dynamics is impossible to give in this Introductory Lecture, several important themes have emerged that can provide a backdrop for this Faraday Discussion. As a result, the first part of this paper introduces some of these themes, using results from the literature to illustrate some of the important issues. Although much of the work on clusters is being carried out in the gas phase (usually in free jet expansions and molecular beams), new approaches have recently been developed that permit the study of the same complexes in or on nanoscale clusters. In particular, recent developments in the field of superfluid helium droplet spectroscopy (SHEDS) permit high-resolution studies of atoms, molecules and clusters in this exotic quantum fluid. After introducing this new field, the author will discuss experiments from his own laboratory to illustrate some of the capabilities of the technique.

Cyclosporin A effects during primary and secondary activation of human umbilical cord blood T lymphocytes

OBJECTIVE

Cyclosporin A (CsA), effective in prophylaxis and treatment of graft-vs-host disease (GVHD) after human allogeneic transplantation, blunts T-cell responses by inhibiting nuclear factor of activated T cells-1 (NFAT1) activation. This laboratory has shown that NFAT1 protein expression is severely reduced in human UCB (umbilical cord blood) T cells. Since UCB is increasingly used as a hematopoietic stem cell source in allogeneic transplantation, it is important to determine whether CsA sensitivity in UCB differs from that of adult T cells.

METHODS

Surface flow cytometric analysis, intracellular cytokine staining, flow cytometric analysis of cell death, and thymidine incorporation were used in this study to determine T-cell activation and effector functions during primary and secondary stimulation in the presence of CsA.

RESULTS

Although we observed differential CsA sensitivity of T-cell activation marker (CD69, CD45RO, CD25) upregulation comparing UCB and adult, we did not observe any significant difference in CsA sensitivity of T-cell effector functions. Importantly, we observed reduced IFN-gamma and TNF-alpha expression in UCB T cells both in primary and secondary stimulation, as well as increased rates of activation-induced cell death (AICD).

CONCLUSION

Thus, our studies do not support the previous hypothesis that reduced GVHD observed after UCB transplantation is attributable to increased CsA sensitivity of UCB T cells. Rather, reduced UCB T-cell cytokine production and increased AICD may be important cellular mechanisms underlying these favorable rates of GVHD in UCB transplant recipients.

Quantitative detection of aromatic compounds in single aerosol particle mass spectrometry

Most laser-based aerosol mass spectrometers rely on a single ultraviolet laser to both ablate and ionize the aerosol particle. This technique produces complex and fragmented mass spectra, especially for organic compounds. The approach presented here achieves a more robust and quantitative analysis using a CO2 laser to evaporate the aerosol particle and a vacuum ultraviolet laser to ionize the vapor plume. Vacuum ultraviolet laser ionization produces little fragmentation in the mass spectra, making the identification of an aerosol particle's constituents more straightforward. An analysis of simple, three-component mixtures of aniline, benzyl alcohol, and m-nitrotoluene shows that the technique also provides a quantitative analysis for all the components of the mixture. Furthermore, the detection of predominantly parent ion signal from anthracene particles demonstrates the utility of the technique in the analysis of lower vapor pressure, solid-phase aerosols. Finally, we discuss the potential and limitations of this technique in analyzing organic atmospheric aerosols.

Probing the structure of metal cluster-adsorbate systems with high-resolution infrared spectroscopy

High-resolution infrared laser spectroscopy was used to obtain rotationally resolved infrared spectra of adsorbate-metal complexes. The method involves forming the bare metal clusters in helium nanodroplets and then adding a molecular adsorbate (HCN) and recording the infrared spectrum associated with the C-H stretching vibration. Rotationally resolved spectra were obtained for HCN-Mg(n) (n = 1 to 4). The results suggest a qualitative change in the adsorbate-metal cluster bonding with cluster size.

Noncontact quantitative spatial mapping of stress and flexural rigidity in thin membranes using a picosecond transient grating photoacoustic technique

This paper describes a purely optical technique for measuring and spatially mapping out stress and rigidity in thin membranes. Its application to a membrane of aluminum nitride that has significant spatial nonuniformities in its elastic properties demonstrates the method. The attractive features of this technique--fast, noncontacting measurement, good spatial resolution, ability to quantify in-plane anisotropy--make it potentially useful for characterizing elements of microelectromechanical structures, masks for advanced lithography systems, acoustic filters, and other devices in which the mechanical properties of membranes are important.

Infrared Optothermal Spectroscopy of N(2)- and OC-DCCH: The C-H Stretching Region

High-resolution optothermal laser spectroscopy is reported for the C-H stretching vibrations of the binary complexes formed between monodeuterated acetylene and carbon monoxide and nitrogen. In contrast with a previous study of the corresponding C(2)H(2) complexes, where the C-H fundamental spectra were highly perturbed [R. D. Beck, A. G. Maki, S.-H. Tseng, and R. O. Watts, J. Mol. Spectrosc. 158, 306-317 (1993)], the present spectra are well described by a simple linear-rotor Hamiltonian. This is presumed to result from the fact that the C-H vibration in the monodeuterated complexes is decoupled from the intermolecular degrees of freedom. Copyright 2000 Academic Press.

Clinical presentation and antiviral therapy for poxvirus infection in pudu (Pudu puda)

A severe poxvirus infection occurred in three pudu (Pudu puda), resulting in two fatalities. Cutaneous ulcers with mucopurulent exudate were present around the eyes and nose, at the lip margins, coronary bands, and teats. Mucosal ulcers were present in the oral cavity, esophagus, and forestomachs. In the two fatalities, a secondary disseminated fungal infection also occurred. Affected animals were leukopenic, hypocalcemic, and hyperphosphatemic and had elevated serum alkaline phosphatase, alanine aminotransferase, and aspartate aminotransferase levels. Electron microscopic examination of affected skin confirmed the presence of a poxvirus. Neutralizing antibody titers to this virus were present in the two pudu tested. One case was treated with cidofovir, 5 mg/kg i.v. q7d for four treatments. Complete recovery occurred in the treated animal. This is the second report of poxvirus infection in pudu and the first report describing clinical presentation, presence of secondary disseminated fungal infection, and successful treatment.

Quantitative determination of dipalmitoylphosphatidylcholine and palmitic acid in porcine lung surfactants used in the treatment of respiratory distress syndrome

A high-performance liquid chromatography (HPLC) method was developed that can separate and quantify dipalmitoylphosphatidylcholine and its degradation product, palmitic acid from various phospholipids contained in a porcine lung surfactant used in the treatment of respiratory distress syndrome, which was recently approved for use by the FDA. The method used a C8 reversed-phase HPLC column with a (50:45:10) acetonitrile/methanol/acetic acid mobile phase, and refractive index detection. The active component of the lung surfactant, dipalmitoylphosphatidylcholine (DPPC) and palmitic acid (PA), could be quantified following a liquid-liquid extraction procedure along with an internal standard, dimyristoylphosphatidylcholine (DMPC). The assay was validated for linearity, accuracy, precision, reproducibility and ruggedness. Column stability was measured by performing the assay over time and monitoring the system suitability parameters. The extraction procedure has a 90% recovery and the assay is linear over a range of 5 microg/ml to 300 microg/ml. The assay is used to release commercial product and monitor stability of existing lots of material.

Synthesis and antimalarial activity of sixteen dispiro-1,2,4, 5-tetraoxanes: alkyl-substituted 7,8,15,16-tetraoxadispiro[5.2.5. 2]hexadecanes

Sixteen alkyl-substituted dispiro-1,2,4,5-tetraoxanes (7,8,15, 16-tetraoxadispiro[5.2.5.2]hexadecanes) were synthesized to explore dispiro-1,2,4,5-tetraoxane SAR and to identify tetraoxanes with better oral antimalarial activity than prototype tetraoxane 1 (WR 148999). The tetraoxanes were prepared either by peroxidation of the corresponding cyclohexanone derivatives in H(2)SO(4)/CH(3)CN or by ozonolysis of the corresponding cyclohexanone methyl oximes. Those tetraoxanes with alkyl substituents at the 1 and 10 positions were formed as single stereoisomers, whereas the five tetraoxanes formed without the stereochemical control provided by alkyl groups at the 1 and 10 positions were isolated as mixtures of diastereomers. Three of the sixteen tetraoxanes were inactive (IC(50)'s > 1000 nM), but five (2, 6, 10, 11, 12) had IC(50)'s between 10 and 30 nM against the chloroquine-sensitive D6 and chloroquine-resistant W2 clones of Plasmodium falciparum compared to corresponding IC(50)'s of 55 and 32 nM for 1 and 8.4 and 7.3 nM for artemisinin. We suggest that tetraoxanes 13, 16, and 17 were inactive and tetraoxanes 4 and 7 were weakly active due to steric effects preventing or hindering peroxide bond access to parasite heme. Tetraoxanes 1, 10, 11, and 14, along with artemisinin and arteether as controls, were administered po b.i.d. (128 mg/kg/day) to P. berghei-infected mice on days 3, 4, and 5 post-infection. At this dose, tetraoxanes 10, 11, and 14 cured between 40% and 60% of the infected animals. In comparison, artemisinin and tetraoxane 1 produced no cures, whereas arteether cured 100% of the infected animals. There was no apparent relationship between tetraoxane structure and in vitro neurotoxicity, nor was there any correlation between antimalarial activity and neurotoxicity for these seventeen tetraoxanes.

Mice lacking flt3 ligand have deficient hematopoiesis affecting hematopoietic progenitor cells, dendritic cells, and natural killer cells

The ligand for the receptor tyrosine kinase fms-like tyrosine kinase 3 (flt3), also referred to as fetal liver kinase-2 (flk-2), has an important role in hematopoiesis. The flt3 ligand (flt3L) is a growth factor for hematopoietic progenitors and induces hematopoietic progenitor and stem cell mobilization in vivo. In addition, when mice are treated with flt3L immature B cells, natural killer (NK) cells and dendritic cells (DC) are expanded in vivo. To further elucidate the role of flt3L in hematopoiesis, mice lacking flt3L (flt3L-/-) were generated by targeted gene disruption. Leukocyte cellularity was reduced in the bone marrow, peripheral blood, lymph nodes (LN), and spleen. Thymic cellularity, blood hematocrit, and platelet numbers were not affected. Significantly reduced numbers of myeloid and B-lymphoid progenitors were noted in the BM of flt3L-/- mice. In addition a marked deficiency of NK cells in the spleen was noted. DC numbers were also reduced in the spleen, LN, and thymus. Both myeloid-related (CD11c(++) CD8alpha(-)) and lymphoid-related (CD11c(++) CD8alpha(+)) DC numbers were affected. We conclude that flt3L has an important role in the expansion of early hematopoietic progenitors and in the generation of mature peripheral leukocytes.

Formation of cyclic water hexamer in liquid helium: the smallest piece of Ice

The cyclic water hexamer, a higher energy isomer than the cage structure previously characterized in the gas phase, was formed in liquid helium droplets and studied with infrared spectroscopy. This isomer is formed selectively as a result of unique cluster growth processes in liquid helium. The experimental results indicate that the cyclic hexamer is formed by insertion of water molecules into smaller preformed cyclic complexes and that the rapid quenching provided by the liquid helium inhibits its rearrangement to the more stable cage structure.

Reduced NFAT1 protein expression in human umbilical cord blood T lymphocytes

Umbilical cord blood (UCB) stem cells from related and unrelated allogeneic donors have emerged as novel treatment for patients with hematologic malignancies. The incidence and severity of acute graft-versus-host disease (GVHD) after UCB transplantation compares favorably with that observed in recipients of matched unrelated donor allogeneic grafts, but remains a major cause of morbidity and mortality. It has been shown that stimulated lymphocytes from UCB have reduced production of cytokines including interferon-gamma (IFN-gamma) and tumor necrosis factor-alpha (TNF-alpha), which play a role in GVHD pathophysiology. We investigated the molecular mechanisms underlying this reduced cytokine production by analyzing expression of nuclear factor of activated T cells-1 (NFAT1) in UCB T cells. We detected no constitutive expression of NFAT1 protein in unstimulated UCB T cells compared with adult T cells. Moreover, although NFAT1 expression in UCB T cells was upregulated after prolonged (40 hours) T-cell stimulation, it was only partially upregulated when compared with adult controls. Our observation of minimal NFAT1 expression after stimulation correlated with reduced cytoplasmic IFN-gamma and TNF-alpha production in UCB T cells studied simultaneously. Reduced NFAT1 expression may blunt amplification of donor UCB T-cell alloresponsiveness against recipient antigens, thereby potentially limiting GVHD incidence and severity after allogeneic UCB transplantation.

Synergistic Action of fms-Like Tyrosine Kinase 3 Ligand and CD40 Ligand in the Induction of Dendritic Cells and Generation of Antitumor Immunity In Vivo

Daily treatment of mice with fms-like tyrosine kinase 3 ligand (Flt3L) leads to a significant increase in the number of dendritic cells and induces antitumor immunity. Here, we show that Flt3L and CD40 ligand (CD40L) synergize in the generation of immune responses against two poorly immunogenic tumors, leading to complete tumor rejection in a high proportion of mice. Rechallenge of the Flt3L + CD40L-treated mice with the immunizing tumor resulted in complete inhibition of tumor growth, indicating that these animals had developed long-lasting antitumor immunity. In addition, we demonstrate that endogenous CD40L plays a critical role in antitumor immunity, since blockade of CD40-CD40L interactions in vivo prevents the generation of antitumor immunity in therapeutic and vaccination protocols. Dendritic cells generated in mice treated with Flt3L alone or in combination with CD40L were equally potent in stimulating allogeneic T cells and expressed similar levels of MHC class II, CD80, and CD86. However, mice treated with Flt3L + CD40L had significantly more dendritic cells than mice treated with either of the cytokines alone, suggesting that CD40L promotes the proliferation and/or survival of dendritic cells generated by Flt3L treatment. Dendritic cells generated in this manner are likely to be involved in the priming of antitumor immune responses.

Synergistic action of fms-like tyrosine kinase 3 ligand and CD40 ligand in the induction of dendritic cells and generation of antitumor immunity in vivo

Daily treatment of mice with fms-like tyrosine kinase 3 ligand (Flt3L) leads to a significant increase in the number of dendritic cells and induces antitumor immunity. Here, we show that Flt3L and CD40 ligand (CD40L) synergize in the generation of immune responses against two poorly immunogenic tumors, leading to complete tumor rejection in a high proportion of mice. Rechallenge of the Flt3L + CD40L-treated mice with the immunizing tumor resulted in complete inhibition of tumor growth, indicating that these animals had developed long-lasting antitumor immunity. In addition, we demonstrate that endogenous CD40L plays a critical role in antitumor immunity, since blockade of CD40-CD40L interactions in vivo prevents the generation of antitumor immunity in therapeutic and vaccination protocols. Dendritic cells generated in mice treated with Flt3L alone or in combination with CD40L were equally potent in stimulating allogeneic T cells and expressed similar levels of MHC class II, CD80, and CD86. However, mice treated with Flt3L + CD40L had significantly more dendritic cells than mice treated with either of the cytokines alone, suggesting that CD40L promotes the proliferation and/or survival of dendritic cells generated by Flt3L treatment. Dendritic cells generated in this manner are likely to be involved in the priming of antitumor immune responses.