Rapid data-driven model reduction of nonlinear dynamical systems including chemical reaction networks using ℓ1-regularization.

Large-scale nonlinear dynamical systems, such as models of atmospheric hydrodynamics, chemical reaction networks, and electronic circuits, often involve thousands or more interacting components. In order to identify key components in the complex dynamical system as well as to accelerate simulations, model reduction is often desirable. In this work, we develop a new data-driven method utilizing ℓ1-regularization for model reduction of nonlinear dynamical systems, which involves minimal parameterization and has polynomial-time complexity, allowing it to easily handle large-scale systems with as many as thousands of components in a matter of minutes. A primary objective of our model reduction method is interpretability, that is to identify key components of the dynamical system that contribute to behaviors of interest, rather than just finding an efficient projection of the dynamical system onto lower dimensions. Our method produces a family of reduced models that exhibit a trade-off between model complexity and estimation error. We find empirically that our method chooses reduced models with good extrapolation properties, an important consideration in practical applications. The reduction and extrapolation performance of our method are illustrated by applications to the Lorenz model and chemical reaction rate equations, where performance is found to be competitive with or better than state-of-the-art approaches.

Plasmodium genetic loci linked to host cytokine and chemokine responses.

Both host and parasite factors contribute to disease severity of malaria infection; however, the molecular mechanisms responsible for the disease and the host-parasite interactions involved remain largely unresolved. To investigate the effects of parasite factors on host immune responses and pathogenesis, we measured levels of plasma cytokines/chemokines (CCs) and growth rates in mice infected with two Plasmodium yoelii strains having different virulence phenotypes and in progeny from a genetic cross of the two parasites. Quantitative trait loci (QTL) analysis linked levels of many CCs, particularly IL-1ß, IP-10, IFN-γ, MCP-1 and MIG, and early parasite growth rate to loci on multiple parasite chromosomes, including chromosomes 7, 9, 10, 12 and 13. Comparison of the genome sequences spanning the mapped loci revealed various candidate genes. The loci on chromosomes 7 and 13 had significant (P<0.005) additive effects on IL-1ß, IL-5 and IP-10 responses, and the chromosome 9 and 12 loci had significant (P=0.017) interaction. Infection of knockout mice showed critical roles of MCP-1 and IL-10 in parasitemia control and host mortality. These results provide important information for a better understanding of malaria pathogenesis and can be used to examine the role of these factors in human malaria infection.

New candidate vaccines against blood-stage Plasmodium falciparum malaria: prime-boost immunization regimens incorporating human and simian adenoviral vectors and poxviral vectors expressing an optimized antigen based on merozoite surface protein 1.

Although merozoite surface protein 1 (MSP-1) is a leading candidate vaccine antigen for blood-stage malaria, its efficacy in clinical trials has been limited in part by antigenic polymorphism and potentially by the inability of protein-in-adjuvant vaccines to induce strong cellular immunity. Here we report the design of novel vectored Plasmodium falciparum vaccines capable of overcoming such limitations. We optimized an antigenic insert comprising the four conserved blocks of MSP-1 fused to tandemly arranged sequences that represent both allelic forms of the dimorphic 42-kDa C-terminal region. Inserts were expressed by adenoviral and poxviral vectors and employed in heterologous prime-boost regimens. Simian adenoviral vectors were used in an effort to circumvent preexisting immunity to human adenoviruses. In preclinical studies these vaccines induced potent cellular immune responses and high-titer antibodies directed against MSP-1. The antibodies induced were found to have growth-inhibitory activity against dimorphic allelic families of P. falciparum. These vectored vaccines should allow assessment in humans of the safety and efficacy of inducing strong cellular as well as cross-strain humoral immunity to P. falciparum MSP-1.

Role of self-carriers in the immune response and tolerance. I. B-cell unresponsiveness and cytotoxic T-cell immunity induced by haptenated syngeneic lymphoid cells.

Normal spleen cells cultured with TNP-modified syngeneic spleen cells fail to mount an anti-TNP PFC response to TNP-ficoll or TNP-red blood cells,but go on to generate cytotoxic T cells directed at hapten-modified H-2.These results suggest that hapten-modifeid spleen cells may differentially induce B-cell tolerance and T- (Ly 2,3) cell immunity. The differential response to modified self by lymphocyte subpopulations is discussed.

Inhibitory activity of tea polyphenol and Candida ernobii against Diplodia natalensis infections.

AIMS: To investigate the effect of tea polyphenol (TP) and Candida ernobii alone or in combination against postharvest disease (Diplodia natalensis) in citrus fruit and to evaluate the possible mechanisms involved. METHODS AND RESULTS: TP at concentrations of 0.1%, 0.5% and 1.0% alone, or in combination with C. ernobii (1x10(6) CFU ml(-1)), showed a lower infection rate of stem-end rot. TP at the concentration of 0.5% or above significantly inhibited the spore germination of D. natalensis. TP at the concentration of 1.0% showed inhibitary ability on mycelium growth of D. natalensis. The addition of TP did not affect the growth of C. ernobii in vitro and significantly increased the population of C. ernobii in vivo. CONCLUSIONS: TP exhibited an inhibitory effect against D. natalensis and improved the biocontrol efficacy of C. ernobii. It was direct because of the inhibitory effects of TP on spore germination and mycelial growth of D. natalensis in vitro and indirect because of the increased populations of C. ernobii in vivo. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggested that TP alone or in combination with biocontrol agents has great potential in commercial management of postharvest diseases in fruits.

Inhibitory activity of tea polyphenol and Hanseniaspora uvarum against Botrytis cinerea infections.

AIMS: To investigate the effect of tea polyphenol (TP) and Hanseniaspora uvarum alone or in combination against Botrytis cinerea in grapes and to evaluate the possible mechanisms involved. METHODS AND RESULTS: TP alone was effective in controlling grey mould in grape at all concentrations. TP at 0.5 and 1.0% in combination with H. uvarum (1 x 10(6) CFU ml(-1)) showed a lower infection rate of grey mould. TP at 0.01% or above significantly inhibited the spore germination of B. cinerea. TP at 0.1% showed inhibition ability on mycelium growth of B. cinerea. The addition of TP did not affect the growth of H. uvarum in vitro and significantly increased the population of H. uvarum in vivo. CONCLUSIONS: TP exhibited an inhibitory effect against B. cinerea and improved the biocontrol efficacy of H. uvarum. The inhibitory effects of spore germination and mycelial growth of B. cinerea and the increased populations of H. uvarum in vivo may be some of the important mechanisms of TP. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggested that TP alone or in combination with biocontrol agents has great potential in the commercial management of postharvest diseases of fruits.

Taxol arrests the development of blood-stage Plasmodium falciparum in vitro and Plasmodium chabaudi adami in malaria-infected mice.

Taxol, a natural product used to treat a variety of human cancers, is shown here to be extremely effective against chloroquine- and pyrimethamine-resistant malaria parasites. Addition of Taxol (1.0 microM) for one cycle to cultures of human erythrocytes infected with Plasmodium falciparum prevents the establishment of new infections. Blood parasitemia is eliminated in mice infected with Plasmodium chabaudi adami when they are given a single intraperitoneal injection of Taxol at 150 mg/m2. The majority of the animals treated immediately preceding parasite schizogony remain free of infection after eight replication cycles. The impressive antimalarial activity of Taxol, at a dosage that has been tolerated in humans, establishes its potential utility for treatment of severe, drug-resistant human malaria.

Immunity to blood stages of malaria.

Those developmental stages of malaria parasites that infect erythrocytes are responsible for the severe morbidity and mortality associated with this disease. The nature and specificity of the slowly acquired immunity seen in endemic populations remain to be defined, but significant progress has been made recently in identifying specific blood-stage proteins, characterizing immune responses to them, and exploring the dynamics of non-specific host responses to infection.

Dose-intensive vinorelbine with concurrent granulocyte colony-stimulating factor support in paclitaxel-refractory metastatic breast cancer.

PURPOSE: We evaluated weekly single-agent intravenous (IV) vinorelbine as salvage therapy for metastatic breast cancer. After the first five patients, all received elective growth factor support with granulocyte colony-stimulating factor (G-CSF; filgrastim) in an attempt to maximize delivered dose-intensity (DDI). Objective tumor response, DDI, and toxicity were assessed, as well as time to progression (TTP) and survival. PATIENTS AND METHODS: This single-center nonrandomized trial enrolled 40 patients. Anthracycline exposure and subsequent progression were common to all patients, and 38 of 40 were paclitaxel-refractory. Vinorelbine was given initially at 30 mg/m2/wk, then at 35 mg/m2/wk in a phase I/II design, which involved first intermittent (6 days of 7) and then continuous (daily) administration of G-CSF at 5 micrograms/kg. RESULTS: The maximum-tolerated starting dose was 35 mg/m2/wk with continuous G-CSF support. The mean DDI was 27.7 mg/m2/wk for all patients. There were two complete responses (CRs) and eight partial responses (PRs) in 40 assessable patients for an overall response rate of 25% (95% confidence interval [CI], 13% to 41%). The median TTP was 13 weeks and median survival time 33 weeks. The dose-limiting toxicity was neutropenia, with dose delay or reduction required in 14 of 27 patients entered at 35 mg/m2. Febrile neutropenia that required hospitalization was unusual (three of 40 patients, 8%). There were no treatment-related deaths. Grade 3/4 thrombocytopenia occurred in nine patients (23%) and 26 patients (65%) required RBC transfusions for anemia. Seven patients (18%) had reversible grade 3/4 nonhematologic complications, primarily related to neurotoxicity. Grade > or = 3 mucositis was absent. CONCLUSION: Concurrent administration of weekly vinoralbine and daily G-CSF is feasible and permits an increase in DDI for vinorelbine of 43% to 76% over that reported in series without growth factor support. The response rate, TTP, and survival data are encouraging for therapy given to heavily pretreated patients with metastatic breast cancer. Vinorelbine is not cross-resistant with paclitaxel and should be considered for further trials in the dose-intensified mode made possible by G-CSF, alone or combined with other agents.

Sequence of the gene encoding the N-terminal portion of the Plasmodium yoelii yoelii 17XL merozoite surface protein-1 (MSP-1).

The nucleotide (nt) sequence of the 5' portion of the gene encoding the Plasmodium yoelii yoelii (Pyy) 17XL merozite surface protein-1 (MSP-1) was determined by direct sequencing of both strands of the polymerase chain reaction (PCR) product. This report completes the entire coding region of the Pyy 17XL MSP-1 gene which we have found to be identical to the nt sequence of the Pyy YM MSP-1 [Lewis, Mol. Biochem. Parasitol. 36 (1989) 271-282], despite independent selection of parasite clones, passages and replications in mice over many years.

Sequence heterogeneity of the C-terminal, Cys-rich region of the merozoite surface protein-1 (MSP-1) in field samples of Plasmodium falciparum.

Recent results with primate plasmodia and rodent models of infection have focused attention on the C-terminal region of the merozoite surface protein-1 (MSP-1) as one of the leading candidates for vaccination against the erythrocytic stages of malaria. However, sequence heterogeneity of this region may compromise its use as a vaccine candidate. While the C-terminal region of MSP-1 from the two prototypic alleles of P. falciparum has been shown to be relatively conserved in laboratory-maintained strains, little data exist on sequence heterogeneity of this region in field isolates from diverse geographic areas. To address this question, DNA encoding the C-terminal, Cys-rich region of P. falciparum MSP-1 from field samples was analyzed by a polymerase chain reaction (PCR)-direct sequencing method. Sequence data were consistent with those obtained from laboratory-maintained strains. In 15 isolates from Africa, Asia and Latin America, only a few nucleotide changes were found leading to amino-acid alterations at four positions out of 102 residues. All the variations corresponded to the predicted amino-acid sequence of the other prototype, suggesting that these changes were possibly due to allelic recombinations. The four changes were E-->Q at position 1644 and TSR-->KNG, or KNG-->TSR at positions 1691, 1700 and 1701. Thus, only three patterns of the C-terminal, Cys-rich region of MSP-1, E-TSR, Q-KNG and Q-TSR, were detected. All the Cys residues were conserved. These results support the potential utility of the C-terminal region of MSP-1 as a vaccine candidate.

Interaction between two domains of the P. yoelii MSP-1 protein detected using the yeast two-hybrid system.

Several model systems of plasmodia have demonstrated the potential of the merozoite surface protein, MSP-1, to induce protective immunity. However, little is known about the function of this protein or its interaction with other surface molecules that may also serve as immunological targets. To identify potentially significant inter- and intra-molecular interactions involving MSP-1, we have utilized the yeast two-hybrid system. A cDNA activation domain library was constructed from the erythrocytic stages of the murine malarial parasite Plasmodium yoelii yoelii 17XL. A 795 bp region of Py17XL MSP-1 (bait), homologous to the Plasmodium falciparum MSP1(33) fragment, was inserted into a Gal4p DNA binding domain vector and used to screen the activation domain library (target). Several randomly selected clones that demonstrated bait-target interaction were found to express overlapping regions of Py17XL MSP-1. Deletion constructs further localized the peptide fragments retaining interaction indicating that a region within the MSP-1(38) fragment interacts with the MSP-1 bait domain. Subsequent studies confirmed this interaction, as both peptides were co-precipitated from cell lysate by a peptide tag-specific antibody. It was observed that the interaction of these two fragments significantly increased the half-life of the MSP-1(38) within yeast cells. The specific interaction described here demonstrates the potential of this approach to elucidate additional inter- or intra-molecular interactions of Py17XL MSP1 and other malarial proteins.

Accuracy and precision of low-dose insulin administration.

OBJECTIVE: To determine the lowest dose of concentrated (U100) insulin that can be reproducibly delivered. METHODS: A telephone survey was used to determine current practices in major pediatric hospitals regarding the administration of low doses of concentrated insulin. A sensitive gravitometric technique was used to determine the error in measurement of low doses of U100 insulin by pediatric nurses and parents of diabetic children. RESULTS: A telephone survey revealed that doses as low as 0.5 or 1.0 U (5 to 10 microL) are routinely administered in pediatric hospitals. In our study of pediatric nurses, attempts to deliver 0.5, 1.0, and 2.0 U resulted in delivered doses of 0.975 +/- 0.315, 1.638 +/- 0.376, and 2.153 +/- 0.435 U (mean +/- standard deviation of the mean), respectively. The use of 0.3-mL syringes compared to 0.5-mL syringes did not improve accuracy or precision. Taken as a group, parents of children with diabetes were more accurate (mean delivered dose of 1.063 +/- 0.276 for the 1-U dose), but the individual means ranged from 0.641 to 1.300 and coefficients of variation ranged from 5% to 33%. Only three of the seven parents could deliver 1.0 U with acceptable precision and accuracy. CONCLUSIONS: When currently available syringes are used, insulin injections of less than 20 microL (2 U of U100) have an unacceptably large error. It is recommended that, in the inpatient setting, diluted insulin be used if the prescribed dose is less than 2.0 U.

Protective efficacy against malaria of a combination sporozoite and erythrocytic stage vaccine.

Most malariologists believe that optimal malaria vaccines will induce protective immune responses against different stages of the parasite's life cycle. A multiple antigen peptide (MAP) vaccine based on the Plasmodium yoelii circumsporozoite protein (PyCSP) protects mice against sporozoite challenge by inducing antibodies that prevent sporozoites from invading hepatocytes. A purified recombinant protein vaccine based on the P. yoelii merozoite surface protein-1 (PyMSP-1) protects mice against challenge with infected erythrocytes, presumably by inducing antibodies against the erythrocytic stage of the parasite. We now report studies designed to determine if the PyMSP-1 vaccine protects against challenge with sporozoites, the stage encountered in the field, and if immunization with a combination of the PyCSP and PyMSP-1 vaccines provides additive or synergistic protection against sporozoite challenge. In two experiments, using TiterMax or Ribi R-700 as adjuvant, 3 of 19 mice immunized with the PyMSP-1 vaccine were completely protected against sporozoite challenge. The remaining mice had significantly delayed onset and lower levels of peak parasitemia than did control mice (11.1 +/- 2.8% vs. 36.7 +/- 1.6% in experiment #2, P < 0.01). Immunization with the combination vaccine reduced by approximately 50% the level of antibodies induced to PyCSP and PyMSP-1, as compared to that induced by the individual components. However, in two experiments, there was evidence of additive protection. Six of 19 (31.6%) immunized with the PyCSP vaccine, 3 of 19 (15.8%) immunized with the PyMSP-1 vaccine, and 10 of 19 (52.6%) immunized with the combination were completely protected against sporozoit challenge. This modest increase in protection in the combination group may be a reflection of additive anti-PyCSP and anti-PyMSP-1 immunity, since mice in the combination group had diminished levels of antibodies to each components. These studies indicate that considerable work may be required to optimize the construction, delivery, and assessment of multi-stage malaria vaccines.

Effects of L-triiodothyronine and the thyromimetic L-94901 on serum lipoprotein levels and hepatic low-density lipoprotein receptor, 3-hydroxy-3-methylglutaryl coenzyme A reductase, and apo A-I gene expression.

The mechanisms by which thyroid hormone (triiodothyronine (T3)) and a thyromimetic, 2-amino-3-(3,5-dibromo-4-[4-hydroxy-3-(6-oxo-1,6-dihydro-pyridazin -3-ylmethyl)-phenoxyl]-phenyl)propionic acid (L-94901), lower plasma low density lipoprotein (LDL) cholesterol and raise plasma high density lipoprotein (HDL) cholesterol levels was investigated in thyroidectomized and sham-operated rats. Thyroidectomy resulted in a 77% increase in plasma LDL cholesterol, a 60% decrease in plasma triglycerides, and a modest reduction in HDL cholesterol. Daily oral dosing with T3 (10-170 nmol/kg) or L94901 (100-1000 nmol/kg) for 7 days decreased plasma LDL cholesterol in thyroidectomized rats by 60-80%, respectively. This reduction in LDL cholesterol was accompanied by a dose-dependent increase in HDL cholesterol levels of up to 60%. Thus, the ratio of LDL to HDL was decreased from 1.01 to 0.12 after treatment with L-94901 and to 0.25 after dosing with T3. In sham-operated animals, T3 and L-94901 lowered LDL cholesterol by 61 and 46%, respectively, and increased HDL cholesterol by 25 and 53%, respectively. Immunoblotting analysis of liver membranes prepared from thyroidectomized or sham-operated rats demonstrated that LDL receptor protein levels were increased by up to eight-fold. Northern blotting analysis revealed similar large increases in hepatic LDL receptor mRNA levels that accounted for the increases in LDL receptor protein levels. Hepatic 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase mRNA, protein, and activity were increased 2- to 3-fold. The T3- and L-94901-mediated increases in serum HDL levels were associated with 2- to 3-fold increases in apo A-I mRNA levels. In contrast with most other hypocholesterolemic agents, T3 and L-94901 significantly increase HDL cholesterol levels in addition to decreasing LDL cholesterol levels due to induction of hepatic apo A-I and LDL receptor gene expression.

Frequent detection of tumor cells in hematopoietic grafts in neuroblastoma and Ewing's sarcoma.

Many poor-risk neuroblastomas and tumours of the Ewing's sarcoma family (ET) recur despite autologous transplants. Recurrence may be due to tumor cells contained in the BM harvests or PBSC harvests. The objectives of this prospective study were to: (1) determine the incidence and degree of tumor cell contamination in paired BM and PBSC harvests; and (2) determine the efficacy of tumor cell purging by immunomagnetic CD34+ cell selection. 198 samples from 11 consecutive patients with neuroblastoma or Ewing's sarcoma were analyzed. We assayed tumor contamination by RT-PCR assay for PGP 9.5, plus immunohistochemistry for neuroblastoma-specific antigens (the latter in neuroblastoma only). None of these patients had tumor cells detected in their BM by clinical histology immediately before BM or PBSC harvests. However, 82% of PBSC and 89% of backup BM harvests were contaminated with tumor by RT-PCR and/or immunocytochemistry assays. Unselected PBSC and BM harvests contained similar quantities of tumor cells (median, approximately 200000 cells). Cyclophosphamide plus G-CSF mobilization did not affect the incidence or level of contamination in PBSC harvests, as compared to blood obtained before mobilization. Immunomagnetic CD34+ cell selection depleted tumor cells by a median of 3.0 logs for PBSC, and 2.6 logs for BM harvests.

Immunity to erythrocytic stages of malarial parasites.

In those individuals who live in endemic areas, immunity to malaria is slow to develop and stage-specific. The nature and antigenic specificity of this response, which may involve components of both cell-mediated and humoral immunity, is not well understood. Rodent models provide useful systems to explore the spectrum of host responses that may contribute to resolution of erythrocytic-stage infection or possibly to pathogenesis. Moreover, these models allow identification of plasmodial molecules that can induce different types of host responses. Two different mouse model systems, Plasmodium yoelii yoelii and P. chabaudi adami are presented. These have been selected because resolution of infection by P. yoelii yoelii has been shown to require B cell-dependent mechanisms, while control of acute P. chabaudi adami infection can be achieved by T cell-dependent mechanisms. A monoclonal antibody that provides passive protection to P. yoelii challenge infection has been shown to recognize the cysteine-rich, carboxyl-terminal region of the merozoite surface protein-1. This region, obtained in an appropriate configuration from recombinant Escherichia coli, can induce significant protective immune responses in naive mice. In contrast, cell-mediated immune mechanisms make a major contribution to resolution of asexual-stage P. chabaudi adami infection. An empirical approach using continuous flow electrophoresis has identified several low molecular weight plasmodial proteins that can induce partial protective responses in susceptible hosts. These observations are briefly discussed with respect to human malaria.

Drug discovery, development and deployment: a report from the 28th Joint Conference of the U.S.-Japan Parasitic Diseases Panels, Baltimore, Maryland, July 1993.

The 28th Joint Conference of the Parasitic Diseases Panels of the U.S.-Japan Cooperative Medical Sciences Program held in Baltimore, Maryland focused on current research within both countries on antiparasitic chemotherapy. This meeting report summarizes presentations of work in progress on antiparasitic drugs currently in use and drugs under development or in clinical trials, as well as reports on potentially unique parasite characteristics that may provide targets for development of future therapeutics.

Elevated luteinizing hormone on the day of human chorionic gonadotropin administration does not reduce cycle fecundity in a low-dose flare-up in vitro fertilization protocol.

OBJECTIVE: To determine if elevated LH at the time of hCG administration occurs and adversely affects success in a low-dose gonadotropin-releasing hormone analogue (GnRH-a) flare-up protocol in hMG-stimulated IVF cycles. DESIGN: Pearson correlation matrix analysis of hormonal, gamete, and clinical data derived from 203 consecutive IVF cycles was performed. All patients were treated with low-dose GnRH-a (250 micrograms SC leuprolide acetate) and hMG. In 203 consecutive IVF cases, serum was obtained on the day of hCG administration and assayed for E2, LH, and P. These data were correlated with peak E2, number of follicles, oocytes, embryos, and conceptions. Additionally, patients with elevated LH were compared with the nonelevated LH group. RESULTS: Twenty six women had LH > 35 mIU/mL (mean +/- SEM; 51.1 +/- 1.9) and five pregnancies (cycle fecundity 19.2% per retrieval). One hundred seventy-seven patients had LH < 35 mIU/mL (16.3 +/- 0.5) and 25 pregnancies (cycle fecundity 14.1%). There were no differences in the mean P (1.0 +/- 0.1 ng/mL, conversion factor to SI unit, 3.81) and E2 (1,672 +/- 144 pg/mL, conversion factor to SI unit, 3.671) of the former group compared with the P (1.1 +/- 0.07 ng/mL) and E2 (1,456 +/- 69 pg/mL) of the latter group. There was no correlation with the number of follicles, oocytes, embryos, pregnancies, E2, or P to LH concentration (rmax = 0.132). CONCLUSION: In a low-dose, GnRH-suppression, IVF induction protocol, elevated LH occurs in a small subset (13%) of women at the time of hCG administration. This event does not appear to alter cycle fecundity nor induce premature luteinization.