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Intrathecal baclofen for the treatment of tetanus.

Tetanus remains a serious problem in public health, particularly in developing countries, despite efficient prevention programs. A retrospective study was conducted at an infectious diseases intensive care unit during 1998-2003 involving patients admitted with grade III tetanus. The aim of the study was to evaluate the efficacy and safety of intrathecal baclofen for the treatment of tetanus. Lumbar puncture was performed, and a subarachnoid catheter was inserted for drug administration. An intrathecal bolus of baclofen was followed by a continuous infusion of 20 microg/h, until a maximum daily dose of 2 mg was provided. Twenty-two patients were treated overall. Control of the symptoms was achieved in all patients but one. Seven patients had colonization of the catheter, and 1 patient developed meningitis. All patients except one recovered. In our study, this means of treatment was efficacious and well tolerated.

Adult↗

The TH1 and TH2 cytokine network in healthy subjects: suggestions for experimental studies to create prognostic and diagnostic indices for biotherapeutic treatments.

In vivo and in vitro studies have demonstrated the selective regulatory effect that TH1 and TH2 cytokines reciprocally exert in the regulation of the polarization of precursor cells into TH1 or TH2 types. The study of the network relationships between TH1 and TH2 (TH1/TH2) cytokines in healthy subjects could lead to a better understanding of how the physiological network of cytokines regulates the immune response. Such study could lead to gain suggestions for follow-up experiments to create prognostic and diagnostic indices for biotherapeutic treatments of patients. Hence we determined serum levels (environment network) and PBMC production (cellular network) of IL2, IFN gamma, IL4, IL6 and IL10 in the peripheral blood of healthy subjects; these cytokines made up our networks under basic conditions. Both men and women were studied as hormones can influence the polarization of TH1 and TH2 cells. Cytokines within the physiological network function simultaneously so multivariate statistical methods were used to study TH1/TH2 relationships. The use of mathematical modelling is the only effective way of studying the immune system as a whole. The physiological TH1/TH2 network under activation conditions was evaluated by incorporating: sIL2R and sIL6R into the basic environment network model and the production levels of cytokines by PBMC after PHA stimulus, into the basic cellular network model. The influence of APC was evaluated by adding: serum levels of TNF alpha and IL1 beta to the environment network model, and production levels of IFN gamma, IL10 and IL6, after stimulus with LPS, to the cellular network model. Our results led us to hypothesize that the physiological network of TH1/TH2 cytokines regulates TH polarization by means of specific relationships between TH1 and TH2 cytokines, which may be different in men and women. These relationships could be studied experimentally to create prognostic and diagnostic indices for more efficient prevention programs and biotherapeutic treatments of patients.

Adult↗

Protein isoelectric point as a predictor for increased crystallization screening efficiency.

MOTIVATION: Increased efficiency in initial crystallization screening reduces cost and material requirements in structural genomics. Because pH is one of the few consistently reported parameters in the Protein Data Bank (PDB), the isoelectric point (pI) of a protein has been explored as a useful indirect predictor for the optimal choice of range and distribution of the pH sampling in crystallization trials. RESULTS: We have analyzed 9596 unique protein crystal forms from the August 2003 PDB and have found a significant relationship between the calculated pI of successfully crystallized proteins and the difference between pI and reported pH at which they were crystallized. These preferences provide strong prior information for the design of crystallization screening experiments with significantly increased efficiency and corresponding reduction in material requirements, leading to potential cost savings of millions of US$ for structural genomics projects involving high-throughput crystallographic structure determination. AVAILABILITY: A prototype example of a screen design and efficiency estimator program, CrysPred, is available at http://www-structure.llnl.gov/cryspred/

Computer Simulation↗

Divide-and-conquer approach for the exemplar breakpoint distance.

MOTIVATION: A one-to-one correspondence between the sets of genes in the two genomes being compared is necessary for the notions of breakpoint and reversal distances. To compare genomes where there are paralogous genes, Sankoff formulated the exemplar distance problem as a general version of the genome rearrangement problem. Unfortunately, the problem is NP-hard even for the breakpoint distance. RESULTS: This paper proposes a divide-and-conquer approach for calculating the exemplar breakpoint distance between two genomes with multiple gene families. The combination of our approach and Sankoff's branch-and-bound technique leads to a practical program to answer this question. Tests with both simulated and real datasets show that our program is much more efficient than the existing program that is based only on the branch-and-bound technique. AVAILABILITY: Code for the program is available from the authors.

Algorithms↗

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.

MOTIVATION: Since the whole genome sequences of many species have been determined, computational prediction of RNA secondary structures and computational identification of those non-coding RNA regions by comparative genomics become important. Therefore, more advanced alignment methods are required. Recently, an approach of structural alignment for RNA sequences has been introduced to solve these problems. Pair hidden Markov models on tree structures (PHMMTSs) proposed by Sakakibara are efficient automata-theoretic models for structural alignment of RNA secondary structures, although PHMMTSs are incapable of handling pseudoknots. On the other hand, tree adjoining grammars (TAGs), a subclass of context-sensitive grammars, are suitable for modeling pseudoknots. Our goal is to extend PHMMTSs by incorporating TAGs to be able to handle pseudoknots. RESULTS: We propose pair stochastic TAGs (PSTAGs) for aligning and predicting RNA secondary structures including a simple type of pseudoknot which can represent most known pseudoknot structures. First, we extend PHMMTSs defined on alignment of 'trees' to PSTAGs defined on alignment of 'TAG trees' which represent derivation processes of TAGs and are functionally equivalent to derived trees of TAGs. Then, we develop an efficient dynamic programming algorithm of PSTAGs for obtaining an optimal structural alignment including pseudoknots. We implement the PSTAG algorithm and demonstrate the properties of the algorithm by using it to align and predict several small pseudoknot structures. We believe that our implemented program based on PSTAGs is the first grammar-based and practically executable software for comparative analyses of RNA pseudoknot structures, and, further, non-coding RNAs.

Algorithms↗

LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage.

UNLABELLED: The scale of genetic-variation datasets has increased enormously and the linkage equilibrium (LD) structure of these polymorphisms, particularly in whole-genome association studies, is of great interest. The significant computational complexity of calculating single- and multiple-marker correlations at a genome-wide scale remains challenging. We have developed a program that efficiently characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations. AVAILABILITY: LdCompare is licensed under the GNU General Public License (GPL). Source code, documentation, testing datasets and precompiled executables are available for download at: http://www.affymetrix.com/support/developer/tools/devnettools.affx

Algorithms↗

Cryopreservation of biopsied embryos at the blastocyst stage.

BACKGROUND: The availability of an efficient cryopreservation program is especially important in the case of embryos that have undergone blastomere biopsy for PGD. Unfortunately, the freezing/thawing of biopsied embryos has given disappointing results when performed at the cleavage stage. In this study, embryos diagnosed as normal after PGD were grown to the blastocyst stage, frozen and thawed for successive frozen embryo transfer. METHODS: A total of 34 patients performed a thawing cycle in which 47 blastocysts were thawed. The cryopreservation solutions were based on HEPES-buffered medium supplemented with human serum albumin (HSA), sucrose and 1,2-propanediol. The same protocol was applied to embryos from 88 IVF/ICSI patients, which underwent 92 thawing cycles with 150 thawed blastocysts. RESULTS: The survival rate was similar in the two groups (53% after PGD and 58% in IVF/ICSI cycles), as well as the cumulative pregnancy rate per patient (59% after PGD versus 47% in IVF/ICSI cycles), despite a higher maternal age and a lower proportion of embryos available for transfer or cryopreservation in the PGD group. CONCLUSIONS: Neither the survival rate nor the subsequent development and chances of implantation, differed between embryos frozen at the blastocyst stage following biopsy and those frozen intact.

Biopsy↗

The effects of nucleoside analogs on telomerase and telomeres in Tetrahymena.

The ribonucleoprotein enzyme telomerase is a specialized type of cellular reverse transcriptase which synthesizes one strand of telomeric DNA, using as the template a sequence in the RNA moiety of telomerase. We analyzed the effects of various nucleoside analogs, known to be chain-terminating inhibitors of retroviral reverse transcriptases, on Tetrahymena thermophila telomerase activity in vitro. We also analyzed the effects of such analogs on telomere length and maintenance in vivo, and on vegetative growth and mating of Tetrahymena cells. Arabinofuranyl-guanosine triphosphate (Ara-GTP) and ddGTP both efficiently inhibited telomerase activity in vitro, while azidothymidine triphosphate (AZT-TP), dideoxyinosine triphosphate (ddITP) or ddTTP were less efficient inhibitors. All of these nucleoside triphosphate analogs, however, produced analog-specific alterations of the normal banding patterns seen upon gel electrophoresis of the synthesis products of telomerase, suggesting that their chain terminating and/or competitive actions differ at different positions along the RNA template. The analogs AZT, 3'-deoxy-2',3'-didehydrothymidine (d4T) and Ara-G in nucleoside form caused consistent and rapid telomere shortening in vegetatively growing Tetrahymena. In contrast, ddG or ddI had no effect on telomere length or cell growth rates. AZT caused growth rates and viability to decrease in a fraction of cells, while Ara-G had no such effects even after several weeks in culture. Neither AZT, Ara-G, acycloguanosine (Acyclo-G), ddG nor ddI had any detectable effect on cell mating, as assayed by quantitation of the efficiency of formation of progeny from mated cells. However, AZT decreased the efficiency of programmed de novo telomere addition during macronuclear development in mating cells.

Animals↗

Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit.

The efficiency of programmed ribosomal frameshifting in decoding antizyme mRNA is the sensor for an autoregulatory circuit that controls cellular polyamine levels in organisms ranging from the yeast Schizosaccharomyces pombe to Drosophila to mammals. Comparison of the frameshift sites and flanking stimulatory signals in many organisms now permits a reconstruction of the likely evolutionary path of the remarkably conserved mRNA sequences involved in the frameshifting.

Animals↗

Robotic surgical training in an academic institution.

OBJECTIVE: To detail robotic procedure development and clinical applications for mitral valve, biliary, and gastric reflux operations, and to implement a multispecialty robotic surgery training curriculum for both surgeons and surgical teams. SUMMARY BACKGROUND DATA: Remote, accurate telemanipulation of intracavitary instruments by general and cardiac surgeons is now possible. Complex technologic advancements in surgical robotics require well-designed training programs. Moreover, efficient robotic surgical procedures must be developed methodically and safely implemented clinically. METHODS: Advanced training on robotic systems provides surgeon confidence when operating in tiny intracavitary spaces. Three-dimensional vision and articulated instrument control are essential. The authors' two da Vinci robotic systems have been dedicated to procedure development, clinical surgery, and training of surgical specialists. Their center has been the first United States site to train surgeons formally in clinical robotics. RESULTS: Established surgeons and residents have been trained using a defined robotic surgical educational curriculum. Also, 30 multispecialty teams have been trained in robotic mechanics and electronics. Initially, robotic procedures were developed experimentally and are described. In the past year the authors have performed 52 robotic-assisted clinical operations: 18 mitral valve repairs, 20 cholecystectomies, and 14 Nissen fundoplications. These respective operations required 108, 28, and 73 minutes of robotic telemanipulation to complete. Procedure times for the last half of the abdominal operations decreased significantly, as did the knot-tying time in mitral operations. There have been no deaths and few complications. One mitral patient had postoperative bleeding. CONCLUSION: Robotic surgery can be performed safely with excellent results. The authors have developed an effective curriculum for training teams in robotic surgery. After training, surgeons have applied these methods effectively and safely.

Academic Medical Centers↗

Evaluation of simultaneous teaching of extremities in gross anatomy program.

A gross anatomy program was designed to expose medical students to all areas of the body but shortened the dissection time on the extremities by having half the class dissect either the upper or lower extremity and then study the opposite extremity already dissected by other classmates. The program has been used for six years and was evaluated via an analysis of covariance by comparing the intramural examination performance on both the dissected and undissected extremities. There was no statistical difference in the students' performances regardless of the extremity dissected. The program was also evaluated externally by student performance on Part I of the examinations of the National Board of Medical Examiners. Students (n = 191) performed at the national average (69 percent) on all gross anatomy questions and on those questions pertaining to either extremity (66 percent). The program has efficiently utilized laboratory time with no measurable change in performance by six medical classes.

Anatomy↗

A strategy against pancreatic cancer.

Pancreatic cancer kills 99% of those it afflicts. Despite an increasing array of expensive diagnostic tests, the disease manifests itself and is identified too late for the possibility of complete resection in most patients. Palliation and extension of comfortable and useful life, therefore, become prime goals, cure being rare. This essay suggests an efficient, pragmatic program for the diagnosis and treatment of pancreatic cancer based upon the current experience of the Massachusetts General Hospital.

Humans↗

Effect of transplacentally acquired tetanus antibodies on the antibody responses to Haemophilus influenzae type b-tetanus toxoid conjugate and tetanus toxoid vaccines in Filipino infants.

BACKGROUND: Pregnant women in developing countries are vaccinated with tetanus toxoid (TT) to prevent neonatal tetanus. In populations in which the maternal TT-vaccination program is efficiently implemented, responses of the infant to TT and TT-conjugated vaccines such as Haemophilus influenzae type b (Hib) capsular polysaccaride (PS) TT-conjugate (Hib-TT) vaccine may be depressed. OBJECTIVES: To study the influence of transplacentally acquired anti-TT antibodies on responses to TT vaccination and to Hib-TT vaccine. METHODS: One hundred ninety-four healthy Filipino infants received three doses of a Hib conjugate (either Hib-TT, PRP-OMP or HbOC) with diphtheria-tetanus-pertussis vaccine (DTP) given simultaneously but in a separate syringe at the age of 6, 10 and 14 weeks (primary series). In addition 54 of the study children received a booster dose of Hib-TT at 9 months simultaneously with the measles vaccine. RESULTS: Transplacentally acquired anti-TT did not interfere with the anti-Hib PS antibody (anti-Hib PS) response to any of the conjugates. The transplacentally acquired anti-TT was not significantly associated with the concentration of anti-Hib PS either before or after the booster dose of Hib-TT. High concentrations (> or =1 IU/ml) of transplacentally acquired anti-TT inhibited the infants' anti-TT responses. CONCLUSIONS: High concentration of transplacentally acquired anti-TT did not depress anti-Hib PS responses to the Hib-TT vaccine. On the other hand the high anti-TT concentrations somewhat depressed the anti-TT responses of the infants. However, the anti-TT concentrations attained were in the protective range in all study children after either the primary series (DTP + Hib-TT) or the booster dose of Hib-TT.

Antibodies, Bacterial↗

A proposal for improved cadaver kidney allocation.

The allocation of cadaver kidneys for transplantation should have two objectives: a fair distribution of kidneys among the waiting recipients and a high success rate. Currently, organ exchange organizations are following mainly a policy of success oriented allocation in that the kidneys are distributed according to the best achievable HLA match. A consequence of this policy is that patients with rare HLA phenotypes experience prolonged waiting times and that there are large kidney exchange imbalances among transplant centers. Based on theoretical considerations, we described previously the selection routine COMB which was aimed at decreasing excessive waiting times. In this study we present an extension of this routine called XCOMB which builds on realistic conditions according to the current Euro-transplant waiting list. This new procedure decreases the average and maximum waiting time, adjusts for rare HLA phenotypes and HLA homozygosity, provides for a reasonably balanced kidney exchange rate among centers, and guarantees an HLA match distribution and overall transplant success rate near the theoretically possible optimum. The program was tested in an extensive simulation based on actual data derived from 35,000 cadaver kidney transplants. Although more complex than procedures currently in use, the program's efficient software allows the selection of a patient within one second from a waiting list of 10,000 potential recipients, using readily available computer hardware.

Algorithms↗

Developing an integrated public health information system for Missouri.

The Missouri Department of Health realized it had a problem with 67 different information systems that ran on different platforms and could not communicate with one another. A new, integrated information system, the Missouri Health Strategic Architectures and Information Cooperative (MOHSAIC) is being developed based on information engineering (IE). This article describes IE, the process of developing MOHSAIC, and some key lessons learned in developing the system. Some of the lessons learned include the importance of executive sponsorship, tension between efficiency and program accountability, importance of confidentiality, and difficulties of funding an integrated system. The article stresses how integrated information systems will be important for the viability of public health under health care reform.

Computer Communication Networks↗

New aspects on critical care medicine training.

Recently, three fundamental changes have been introduced in medical education, all of particular importance to critical care medicine: (1) clinical teaching and medical practice now emphasize evidence-based medicine, (2) patient safety aspects are increasingly stressed, and (3) use of simulation in medical training is spreading rapidly. In 1999, the disturbingly high frequency of life-threatening or even lethal medical complications was emphasized by the Institute of Medicine in the book To Err Is Human. The Institute of Medicine recommended establishing interdisciplinary team training programs incorporating efficient methods such as simulation. Although simulation has been used by the aviation industry and the military for several decades, only during the past decade has this become a teaching method in medicine. Currently, two full-scale computerized simulators are available: METI, provided by Medical Education Technologies, Sarasota, Florida, and SimMan, manufactured by Laerdal Medical, in Stavanger, Norway. The simulation center at the University of Pittsburgh Medical Center was established in 1994 and has grown quickly to its current large facility, where, in academic year 2003 to 2004, approximately 8000 healthcare professionals were trained on the SimMan. Courses taught include clinical procedures and decision making in perioperative medicine, acute medicine, pharmacology, anesthesiology, airway management, bronchoscopy, pediatric versus adult crisis management, critical events in obstetrics, and crisis team training. Advantages of simulation training over traditional medical education methods include (1) provision of a safe environment for both patient and student during training in risky procedures, (2) unlimited exposure to rare but complicated and important clinical events, (3) the ability to plan and shape training opportunities rather than waiting for a suitable situation to arise clinically, (4) the ability to provide immediate feedback, (5) the opportunity to repeat performance, (6) the opportunity for team training, and (7) lower costs, both direct and indirect. Within the next decade, use of computerized simulators for evidence-based education and training in medicine is expected to develop considerably and spread rapidly into a very important domain of medical schools throughout the entire world.

Computer Simulation↗

Activator mutagenesis of the pink scutellum1/viviparous7 locus of maize.

The transposable elements Activator/Dissociation (Ac/Ds) were first discovered in maize, yet they have not been used extensively in their native host for gene-tagging experiments. This can be attributed largely to the low forward mutation rate and the propensity for closely linked transpositions associated with Ac and its nonautonomous deletion derivative Ds. To overcome these limitations, we are developing a series of nearly isogenic maize lines, each with a single active Ac element positioned at a well-defined location. These Ac elements are distributed at 10- to 20-centimorgan intervals throughout the genome for use in regional mutagenesis. Here, we demonstrate the utility of this Ac-based gene-tagging approach through the targeted mutagenesis of the pink scutellum1/viviparous7 (ps1/vp7) locus. Using a novel PCR-based technique, the Ps1 gene was cloned and Ac elements positioned precisely in each of the seven alleles recovered. The Ps1 gene is predicted to encode lycopene beta-cyclase and is necessary for the accumulation of both abscisic acid and the carotenoid zeaxanthin in mature maize embryos. This study demonstrates the utility of an Ac mutagenesis program to efficiently generate allelic diversity at closely linked loci in maize.

Abscisic Acid↗

Robust contour matching via the order-preserving assignment problem.

A common approach to determining corresponding points on two shapes is to compute the cost of each possible pairing of points and solve the assignment problem (weighted bipartite matching) for the resulting cost matrix. We consider the problem of solving for point correspondences when the shapes of interest are each defined by a single, closed contour. A modification of the standard assignment problem is proposed whereby the correspondences are required to preserve the ordering of the points induced from the shapes' contours. Enforcement of this constraint leads to significantly improved correspondences. Robustness with respect to outliers and shape irregularity is obtained by required only a fraction of feature points to be matched. Furthermore, the minimum matching size may be specified in advance. We present efficient dynamic programming algorithms to solve the proposed optimization problem. Experiments on the Brown and MPEG-7 shape databases demonstrate the effectiveness of the proposed method relative to the standard assignment problem.

Algorithms↗