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PubMed1998

Ecological determinants for germination and growth of some Aspergillus and Penicillium spp. from maize grain.

This study compared the effect of temperature (5-45 degrees C), water availability (water activity, aw; 0.995-0.75) and their interactions on the temporal rates of germination and mycelial growth of three mycotoxigenic strains of Aspergillus ochraceus and one isolate each of A. flavus, A. niger, Penicillium aurantiogriseum and P. hordei in vitro on a maize extract medium. Germination was very rapid at > 0.90 aw with an almost linear increase with time for all species. However, at < 0.90 aw, the germination rates of A. flavus and P. hordei were slower. The aw minima for germination were usually lower than for growth and varied with temperature. The effect of aw x temperature interactions on the lag phases (h), prior to germination, and on the germination rates (h(-1)), were predicted for the first time for these fungi using the Gompertz model modified by Zwietering. This showed that A. flavus, A. niger and the two Penicillium spp. had very short lag times between 0.995-0.95 aw over a wide temperature range. At marginal temperatures, these were significantly higher, especially at < 10 degrees C for Aspergillus spp. and > 30 degrees C for Penicillium spp. There were also statistically significant differences between lag phases and germination rates for three different isolates of A. ochraceus. The Aspergillus spp. also germinated faster than the Penicillium spp. The temperature x aw profiles for mycelial growth varied considerably between species, both in terms of rates (mm d(-1)) and tolerances. Predictions of the effects of important environmental factors such as temperature, aw and their interactions on lag times to germination, germination rates and mycelial growth are important in the development of hurdle technology approaches to predicting fungal spoilage in agricultural and food products.

Aspergillus↗
PubMedDate not supplied

Cost-effectiveness of enoxaparin versus low-dose heparin for prophylaxis against venous thrombosis after major trauma.

We attempted to determine health and economic outcomes from the perspective of an integrated health system of administering enoxaparin 30 mg twice/day versus heparin 5000 U twice/day for prophylaxis against venous thrombosis after major trauma. A decision-analytic model was developed from best literature evidence, institutional data, and expert opinion. We assumed that 40% of proximal deep vein thromboses (DVTs) and 5% of distal DVTs are diagnosed and confirmed with initial or repeat duplex scanning; 50% of undiagnosed proximal DVTs result in pulmonary embolism; 2% and 1% of undiagnosed proximal DVTs will lead to readmission for DVT and pulmonary embolism, respectively, and pulmonary embolism-related mortality rates range from 8-30%. Length of hospital stay data and 1996 institutional drug use and acquisition cost data were used to estimate the cost of enoxaparin and heparin therapy. Diagnosis and treatment costs for DVT and pulmonary embolism were derived from institutional charge data using cost:charge ratios. A second analysis of patients with lower extremity fractures was completed. One-way and multiway sensitivity analyses were performed. For 1000 mixed trauma patients receiving enoxaparin versus heparin, our model showed that 62.2 (95% CI -113 to -12) DVTs or pulmonary emboli would be avoided, resulting in 67.6 (8 to 130) life-years saved at a net cost increase of $104,764 (-$329,300 to $159,600). Enoxaparin versus heparin resulted in a cost of $1684 (-$3600 to $9800) for each DVT or pulmonary embolus avoided and a discounted cost/life-year saved of $2303 (-$8100 to $19,000). For 1000 patients with lower extremity fractures, enoxaparin versus heparin resulted in a cost of $751 (-$4200 to $3300) for each DVT or pulmonary embolus avoided and a discounted cost/life-year saved of $1017 (-$10,200 to $6300). Although enoxaparin increases overall health care costs, it is associated with a cost/additional life-year saved of only $2300, which is generally lower than the commonly used hurdle rate of $30,000/life-year saved. The cost-effectiveness ratio is more favorable in patients with lower extremity fractures than in the general mixed trauma population.

Anticoagulants↗
PubMed2006

Using endophenotypes for pathway clusters to map complex disease genes.

Nature determines the complexity of disease etiology and the likelihood of revealing disease genes. While culprit genes for many monogenic diseases have been successfully unraveled, efforts to map major complex disease genes have not been as productive as hoped. The conceptual framework currently adopted to deal with the heterogeneous nature of complex diseases focuses on using homogeneous internal features of the disease phenotype for mapping. However, phenotypic homogeneity does not equal genotypic homogeneity. In this report, we advocate working with well-measured phenotypes portrayed by amounts of transcripts and activities of gene products or their metabolites, which are pertinent to relatively small pathway clusters. Reliable and controlled measures for oligogenic traits resulting from proper dissection efforts may enhance statistical power. The large amounts of information obtained on gene and protein expression from technological advances can add to the power of gene finding, particularly for diseases with unclear etiology. Data-mining tools for dimension reduction can assist biologists to reveal novel molecular endophenotypes. However, there are still hurdles to overcome, including high cost, relatively poor reproducibility and comparability among platforms, the cross-sectional nature of the information, and the accessibility of human tissues. Concerted efforts are required to carry out large-scale prospective studies that are integrated at the levels of phenotype characterization, high throughput experimental techniques, data analyses, and beyond.

Chromosome Mapping↗
PubMed2003

Cytokines and antitumor immunity.

Currently, the notion of immunosurveillance against tumors is enjoying something of a renaissance. Even if we still refuse to accept that tumors arising in the normal host are unable to trigger an immune response because of the lack of initiation ("danger") signals, there is no doubt that the immune system can be manipulated experimentally and by implication therapeutically to exert anti-tumor effects. For this activity to be successful, the appropriate cytokine milieu has to be provided, making cytokine manipulation central to immunotherapy. On the other hand, the major hurdle currently preventing successful immunotherapy is the ability of tumors to evolve resistant variants under the pressure of immune selection. Here, too, the cytokine milieu plays an essential role. The purpose of this brief review is to consider the current status of the application of cytokines in facilitating antitumor immunity, as well their role in inhibiting responses to tumors. Clearly, encouraging the former but preventing the latter will be the key to the effective clinical application of cancer immunotherapy.

Animals↗
PubMed2005

Response of Escherichia coli O157:H7, Listeria monocytogenes, Salmonella typhimurium, and Staphylococcus aureus to the thermal stress occurring in model manufactures of Grana Padano cheese.

The purpose of this research was to investigate the effect of temperature in the technology of production of Grana cheese against Escherichia coli O157:H7, Listeria monocytogenes, Salmonella Typhimurium, and Staphylococcus aureus. According to the technology of production, the cheese curds are cooked at 55 degrees C and then cooled at room temperature (25 degrees C). A curd-cooling model was developed to estimate the temperature variation across the curd during cooling, and the thermal stress was applied to the pathogens according to the model in model-scale productions of Grana cheese artificially contaminated with approximately 10(4) cfu/mL of the selected pathogens. According to the numerical results, the initial temperature inside the cheese is kept at almost the initial value (above 50 degrees C) for at least 4 h during cooling, whereas the crust of the curd cools rapidly to 30 degrees C in the first hour. The best case was that of the core of the cheese where the high temperature was able to efficiently eliminate the contaminating pathogens. Moreover, the worst case was where the external ring of the curd in which a more rapid cooling allowed bacterial survival. Therefore, the thermal stress in the technology of production of Grana cheese can be only partially effective in the control of the selected pathogens. However, the whole technology of production includes other hurdles that can affect the survival of the pathogens and that need to be taken into account as a whole to evaluate the safety of Grana Padano cheese.

Cheese↗
PubMed2006

Gene therapy progress and prospects: Duchenne muscular dystrophy.

Duchenne muscular dystrophy (DMD) is a severe muscle wasting disorder affecting 1/3500 male births. There is currently no effective treatment, but gene therapy approaches are offering viable avenues for treatment development. The last 10 years have seen the development of a number of strategies and tools for muscle gene therapy. However, the major hurdle has been the inability to deliver vectors at high enough efficiency via a systemic route. The last 2-3 years (reviewed here) have seen unrivalled progress in efficient systemic delivery of viral and non-viral gene transfer agents and antisense oligonucleotides. This progress, coupled with the successful completion of the first gene therapy clinical trial for DMD, has led to three more clinical trials planned for the immediate future.

Animals↗
PubMed2006

Atom-by-atom substitution of Mn in GaAs and visualization of their hole-mediated interactions.

The discovery of ferromagnetism in Mn-doped GaAs has ignited interest in the development of semiconductor technologies based on electron spin and has led to several proof-of-concept spintronic devices. A major hurdle for realistic applications of Ga(1-x)Mn(x)As, or other dilute magnetic semiconductors, remains that their ferromagnetic transition temperature is below room temperature. Enhancing ferromagnetism in semiconductors requires us to understand the mechanisms for interaction between magnetic dopants, such as Mn, and identify the circumstances in which ferromagnetic interactions are maximized. Here we describe an atom-by-atom substitution technique using a scanning tunnelling microscope (STM) and apply it to perform a controlled study at the atomic scale of the interactions between isolated Mn acceptors, which are mediated by holes in GaAs. High-resolution STM measurements are used to visualize the GaAs electronic states that participate in the Mn-Mn interaction and to quantify the interaction strengths as a function of relative position and orientation. Our experimental findings, which can be explained using tight-binding model calculations, reveal a strong dependence of ferromagnetic interaction on crystallographic orientation. This anisotropic interaction can potentially be exploited by growing oriented Ga(1-x)Mn(x)As structures to enhance the ferromagnetic transition temperature beyond that achieved in randomly doped samples.

Journal Article↗
PubMed2003

Some notes on crystallizing fibrinogen and fibrin fragments.

We have recently determined the structure of a native fibrinogen at 2.7-A resolution. Not the least of the hurdles during the many years of this project was growing X-ray-grade crystals from suitably purified proteins. Small, synthetic peptides based on the parts of fibrinogen exposed by the action of thrombin contributed greatly to these experiments. In addition, trimethylamine oxide (TMAO) was found to improve the diffraction of fibrinogen crystals. The history of my interest in fibrinogen and its crystallization can be traced back in part to some early interactions with John Edsall.

Animals↗
PubMed2025

vcfsim: flexible simulation of all-sites VCFs with missing data.

BACKGROUND |: VCFs are the most widely used data format for encoding genetic variation. By design, standard VCFs do not include data from sites where all individuals are homozygous for the reference allele ("invariant sites") and thus do not differentiate these from sites where data are completely missing. However, missing data are a key feature of biological datasets across all domains of genomics, and many recent studies have shown that missing data can introduce a variety of statistical biases in the estimation of key population genetic parameters. A solution to this limitation is to include invariant sites in a standard VCF, creating an "all-sites VCF", exposing missing and invariant sites explicitly. One hurdle to the wider adoption of all-sites VCFs is a reliable parameterized simulation framework for generating biologically realistic all-sites VCFs. RESULTS |: Here, we introduce an open-source command line tool, vcfsim, that interfaces with the popular coalescent simulation platform msprime and provides convenience functions for simulating all-sites VCFs with variable levels of ploidy and missing data. We show that the post-processed VCFs generated using vcfsim align precisely with population genetic expectations (i.e. are statistically identical to raw msprime output), accurately introduce missing data, and permit the simulation of data with varying ploidy levels, including the simulation of intraindividual ploidy variation (e.g. heterogametic sex chromosomes) and population structures. CONCLUSIONS |: Our results vcfsim is a useful and easy-to-use tool for the benchmarking of new software tools, performing population genetic inference, training of machine learning models, and the exploration of the effects of missing data in genomics data sets.

Benchmarking↗
PubMed2002

Patient safety and health policy: a history and review.

Policy initiatives on many fronts have converged to improve patient safety. A major tension that characterizes this process is the attempt to achieve a balance between learning and control in complex systems with technical, social, and organizational components. Efforts to improve learning are marked by better information flow, discovery, flexibility in thinking, embracing of failures as learning opportunities, and core incentives to promote voluntary participation of all stakeholders in the process. Efforts to improve accountability are traditionally marked by public disclosure, meeting of certain widely disseminated standards, availability of performance measures, exposure to legal liability, and compliance with mandated directives (statutes, regulations, accreditation requirements). In some sense, these directions are mutually exclusive. Although a more collaborative regulatory-improvement model would be helpful in creating an industrywide safety culture, it is likely that learning and accountability functions will follow separate tracks. An exception would be policy that stimulates organizations to comply with regulation by showing how well and by what methods they are learning and how others can profit from these experiences. Any approach to improving patient safety should, at a minimum, include a nonpunitive in-depth mechanism for reporting incidents, postincident evaluations for identification of system changes to prevent subsequent occurrences, and state-guaranteed legislative protection from discovery for all aspects of information gathered to improve patient safety. Nonpunitive approaches have yielded useful results in other industries [43]. State and federal courts, state licensing boards, and accrediting bodies such as JCAHO all function to maintain accountability and standards; however, the very fear of existing legal liability or its misapplication are the greatest hurdles to pioneering patient-safety efforts. The health care system needs to transform the existing culture of blame and punishment that suppresses information about errors and adverse events into a culture of safety that focuses on openness and information sharing to improve health care and prevent adverse outcomes. Education and leadership will be most important to creating and sustaining a strong safety culture and arguably the most important defense against preventable harms. Safety culture cannot be legislated, just as the old adage states that it is easier to pull rather than push a piece of spaghetti. Given the imbalances and inefficiencies of market forces in health care, perverse incentives that have strengthened resistance to change, and secrecy when it comes to adverse event information, however, it is likely that policy initiatives will continue to play an important role in the transformation of the industry to more highly reliable, safer levels of care.

Delivery of Health Care↗
PubMed2005

Object-oriented biological system integration: a SARS coronavirus example.

MOTIVATION: The importance of studying biology at the system level has been well recognized, yet there is no well-defined process or consistent methodology to integrate and represent biological information at this level. To overcome this hurdle, a blending of disciplines such as computer science and biology is necessary. RESULTS: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. The scalability of this object-oriented software engineering approach indicates that we can apply this technology for the integration of large complex biological systems. AVAILABILITY: A navigable web-based version of the system is freely available at http://people.musc.edu/~zhengw/SARS/Software-Process.htm

Animals↗
PubMedDate not supplied

An economic approach to clinical trial design and research priority-setting.

Whilst significant advances have been made in persuading clinical researchers of the value of conducting economic evaluation alongside clinical trials, a number of problems remain. The most fundamental is the fact that economic principles are almost entirely ignored in the traditional approach to trial design. For example, in the selection of an optimal sample size no consideration is given to the marginal costs or benefits of sample information. In the traditional approach this can lead to either unbounded or arbitrary sample sizes. This paper presents a decision-analytic approach to trial design which takes explicit account of the costs of sampling, the benefits of sample information and the decision rules of cost-effectiveness analysis. It also provides a consistent framework for setting priorities in research funding and establishes a set of screens (or hurdles) to evaluate the potential cost-effectiveness of research proposals. The framework permits research priority setting based explicitly on the budget constraint faced by clinical practitioners and on the information available prior to prospective research. It demonstrates the link between the value of clinical research and the budgetary restrictions on service provision, and it provides practical tools to establish the optimal allocation of resources between areas of clinical research or between service provision and research.

Bayes Theorem↗
PubMed2005

Considerations when using the significance analysis of microarrays (SAM) algorithm.

BACKGROUND: Users of microarray technology typically strive to use universally acceptable data analysis strategies to determine significant expression changes in their experiments. One of the most frequently utilised methods for gene expression data analysis is SAM (significance analysis of microarrays). The impact of selection thresholds, on the output from SAM, may critically alter the conclusion of a study, yet this consideration has not been systematically evaluated in any publication. RESULTS: We have examined the effect of discrete data selection criteria (qualification criteria for inclusion) and response thresholds (out-put filtering) on the number of significant genes reported by SAM. The use of a reduced data set by applying arbitrary restrictions vis-à-vis abundance calls (e.g. from D-chip) or application of the fold change (FC) option within SAM (named the FC hurdle hereafter), can substantially alter the significant gene list when running SAM in Microsoft Excel. We determined that for a given final FC criteria (e.g. 1.5 fold change) the FC hurdle applied within Microsoft Excel SAM alters the number of reported genes above the final FC criteria. The reason is that the FC hurdle changes the composition of the control data set, such that a different significance level (q-value) is obtained for any given gene. This effect can be so large that it changes subsequent post hoc analysis interpretation, such as ontology overrepresentation analysis. CONCLUSION: Our results argue for caution when using SAM. All data sets analysed with SAM could be reanalysed taking into account the potential impact of the use of arbitrary thresholds to trim data sets before significance testing.

Adult↗
PubMed2001

The future of human gene therapy.

Human gene therapy (HGT) is defined as the transfer of nucleic acids (DNA) to somatic cells of a patient which results in a therapeutic effect, by either correcting genetic defects or by overexpressing proteins that are therapeutically useful. In the past, both the professional and the lay community had high (sometimes unreasonably high) expectations from HGT because of the early promise of treating or preventing diseases effectively and safely by this new technology. Although the theoretical advantages of HGT are undisputable, so far HGT has not delivered the promised results: convincing clinical efficacy could not be demonstrated yet in most of the trials conducted so far, while safety concerns were raised recently as the consequence of the "Gelsinger Case" in Philadelphia. This situation resulted from the by now well-recognized disparity between theory and practice. In other words, the existing technologies could not meet the practical needs of clinically successful HGT so far. However, over the past years, significant progress was made in various enabling technologies, in the molecular understanding of diseases and the manufacturing of vectors. HGT is a complex process, involving multiple steps in the human body (delivery to organs, tissue targeting, cellular trafficking, regulation of gene expression level and duration, biological activity of therapeutic protein, safety of the vector and gene product, to name just a few) most of which are not completely understood. The prerequisite of successful HGT include therapeutically suitable genes (with a proven role in pathophysiology of the disease), appropriate gene delivery systems (e.g., viral and non-viral vectors), proof of principle of efficacy and safety in appropriate preclinical models and suitable manufacturing and analytical processes to provide well-defined HGT products for clinical investigations. The most promising areas for gene therapy today are hemophilias, for monogenic diseases, and cardiovascular diseases (more specifically, therapeutic angiogenesis for myocardial ischemia and peripheral vascular disease, restenosis, stent stenosis and bypass graft failure) among multigenic diseases. This is based on the relative ease of access of blood vessels for HGT, and also because existing gene delivery technologies may be sufficient to achieve effective and safe therapeutic benefits for some of these indications (transient gene expression in some but not all affected cells is required to achieve a therapeutic effect at relatively low [safe] dose of vectors). For other diseases (including cancer) further developments in gene delivery vectors and gene expression systems will be required. It is important to note, that there will not be a "universal vector" and each clinical indication may require a specific set of technical hurdles to overcome. These will include modification of viral vectors (to reduce immunogenicity, change tropism and increase cloning capacity), engineering of non-viral vectors by mimicking the beneficial properties of viruses, cell-based gene delivery technologies, and development of innovative gene expression regulation systems. The technical advances together with the ever increasing knowledge and experience in the field will undoubtedly lead to the realization of the full potential of HGT in the future.

Animals↗
PubMed1993

Overview of paclitaxel (TAXOL).

The history of development of paclitaxel (TAXOL [Bristol-Myers Squibb Co., Princeton, NJ]) is a long story and serves as a model of perseverance for those involved in drug development. Notations of the use of products of the yew tree date back to the Celts, but it was in the 1950s to the 1960s that the National Cancer Institute (NCI) selected the product for trials and the current process began. The active agent was identified in the 1970s, and when its unique mechanism of action was isolated in 1979, interest reemerged. Paclitaxel is an antimicrotubule agent that, unlike other antimicrotubule agents, promotes microtubule assembly. This unique mechanism of action has generated considerable interest in oncology. The clinical trials in the 1980s documented the drug's safety, identified its side effects, and demonstrated its activity in patients with ovarian cancer who had received prior treatment. The many clinical trials currently under way will provide information on the drug's range of activity. Paclitaxel's development has been an arduous process. Its development and supply initially were complicated, but these hurdles have been overcome, and the drug's unique mechanism of action and initial clinical trial results hold promise in the 1990s.

Breast Neoplasms↗
PubMed1994

In utero hematopoietic stem cell transplants for inherited diseases.

PURPOSE: The treatment of choice for many inherited diseases is bone marrow transplantation (BMT). Limitations to using marrow transplants for inherited diseases include (a) the toxicity associated with high doses of chemotherapy necessary to obtain engraftment; (b) the complications associated with graft-versus-host disease (GVHD); (c) the fact that only 20-25% of children will have a human leukocyte antigen (HLA)-matched donor; and (d) the concern that, at least for some inherited diseases, significant organ damage, especially to the nervous system, has occurred by the time the child is diagnosed and evaluated for possible BMT. In utero transplantation of hematopoietic stem cells (HSCs) offers the possibility of overcoming many of these limitations. PATIENTS AND METHODS: One of the biggest hurdles to a successful transplant is the ability of the recipient to reject the donor marrow. Except in patients with severe combined immunodeficiency disease (SCID), overcoming this hurdle requires high doses of chemotherapy. Early in gestation, the fetus is significantly immunoincompetent. Before 14-15 weeks of gestation, the human fetus appears to be similar to a child with SCID in its inability to reject allogeneic cells. Potential sources for HSCs are HLA-matched sibling marrow, fetal liver, parental bone marrow, and cord blood. RESULTS: With fetal liver, only cells from fetuses < 10-12 weeks are acceptable because of the high risk of GVHD. With parental marrow, the cells must be T cell depleted in order to minimize the risk for GVHD. Problems in using fetal liver include the inability to obtain sufficient numbers of cells and inadequate supplies of donor tissue. The source and supply of parental bone marrow is almost unlimited, but, because of the need for T-cell depletion, bone marrow from a parent may have a lower engraftment rate in the child. CONCLUSIONS: Studies in fetal murine and Rhesus models using fetal liver or T cell-depleted bone marrow from adult animals suggest that engraftment can be successfully obtained, providing the transplant is performed sufficiently early in gestation. To date, at least a dozen in utero human transplants have been attempted worldwide in fetuses diagnosed with a variety of inherited diseases. Because of the small number of transplanted fetuses and the variety of diseases and differing transplant conditions, it is difficult to draw any firm conclusions regarding ultimate efficacy of the procedure and its risk. However, it does appear that the age of gestation of the recipient, the dose of cells infused, and possibly the route of administration of the HSCs will be critical factors in determining success rates for this approach. The successful application of in utero transplantation would allow treatment of a variety of inherited diseases early in gestation while eliminating many of the risks associated with conventional BMT.

Animals↗
PubMed2001

Development of new carboxylic acid-based MMP inhibitors derived from functionalized propargylglycines.

A series of carboxylic acids were prepared from a propargylglycine scaffold and tested for efficacy as matrix metalloproteinase (MMP) inhibitors. Detailed SAR for the series is reported for four enzymes within the MMP family. The inhibitors were typically potent against collagenase-3 (MMP-13) and gelatinase A (MMP-2), while they spared collagenase-1 (MMP-1) and only moderately inhibited stromelysin (MMP-3). Compound 40 represents a typical inhibition profile of a compound with reasonable potency. Introduction of polar groups was required in order to generate inhibitors with acceptable water solubility, and this often resulted in a loss of potency as in compound 63. High serum protein binding proved to be a difficult hurdle with many compounds such as 48 showing >99% binding. Some compounds such as 64 displayed approximately 90% binding, but no reliable method was discovered for designing molecules with low protein binding. Finally, selected data regarding the pharmacokinetic behavior of these compounds is presented.

Alkynes↗
PubMed2003

Post-transplant bronchiolitis obliterans.

Over the last decade, improvements in surgical techniques, lung preservation, immunosuppression, and management of ischaemia/reperfusion injury and infections have made intermediate-term survival after lung transplantation an achievable goal. However, chronic allograft dysfunction in the form of bronchiolitis obliterans remains a major hurdle that threatens both the quality of life and long-term survival of the recipients. It affects up to 50-60% of patients who survive 5 yrs after surgery, and it accounts for >30% of all deaths occurring after the third postoperative year. This article discusses the alloimmune-dependent and -independent risk factors for bronchiolitis obliterans, the current understanding of the pathogenesis of bronchiolitis obliterans based on results of animal and human studies, the clinical staging of the complication, strategies that may contribute to the prevention and/or early detection of bronchiolitis obliterans, and suggestions for future research.

Animals↗