Interstitial hyperthermia in combination with brachytherapy

Flexible coaxial cables were modified to serve as microwave antennas operating at a frequency of 915 MHz. These antennas were inserted into nylon afterloading tubes that had been implanted in tumors using conventional interstitial implantation techniques for iridium-192 seed brachytherapy. The tumor volume was heated to 42-45 degrees C within 15 minutes and heating was continued for a total of 1 hour per treatment. Immediately following a conventional brachytherapy dose and removal of the iridium seeds the tumors were heated again in a second treatment. This interstitial technique for delivering local hyperthermia should be compatible with most brachytherapy methods. The technique has proved so far to be practical and without complications. Temperature distributions obtained in tissue phantoms and a patient are described.     

The Effect of Hemorrhage on Plasma Iron Turnover

The plasma iron turnover rate in rats following a single hemorrhage reachesa maximum in about 48 hours and returns to normal between the seventh andtenth day. There is considerable variation in individual rats in both the maximum rate attained and the time required for recovery. No significant difference in response was observed due to the severity of hemorrhage uponremoval of 2.7 to 18 per cent of total red cells.

Submitted on June 20, 1960 Accepted on November 20, 1960     

Improved surface coil imaging in MR: decoupling of the excitation and receiver coils

We obtained magnetic resonance images with good sensitivity and radio frequency (RF) uniformity using separate transmitter and receiver coils. The excitation, namely, the rotation of the magnetization vector into a plane perpendicular to the magnetic field, was done by applying a homogeneous RF magnetic field produced by a large saddle-shaped coil. Surface coils were used for detection only. Because two coils that operated on the same resonance frequency were used, a coupling problem developed. This problem, which involved inhomogeneity of the RF magnetic field caused by the large current induced in the surface coil during excitation, could only be solved by minimizing the mutual inductance or maximizing the impedance of the surface coil resonance circuit during excitation. We were able to solve this problem using an electronic detuning method.     

Pathway analysis for design of promiscuous drugs and selective drug mixtures

The decrease in the drug approval rate by the FDA and the recent failure of some blockbuster drugs has prompted a re-examination of the focus of the pharmaceutical industry on increasing drug selectivity. As a result, it has been proposed that the most efficient cure is in developing promiscuous drugs and selective drug mixtures. Rational design of drug mixtures has been nearly impossible due to the lack of information about in vivo cell regulation, mechanisms of pathway activation, and interactions between different pathways in vivo. We review the current state of the art for rational design of combination therapy and argue that the current industry-wide development of the infrastructure for pathway analysis provides unprecedented opportunity for the rational design of multicomponent and multifunctional drugs. We propose several ways how to use pathway analysis to rationally combine known drugs for either synergizing their efficacy or suppressing individual side effects.     

TLR9 bone marrow chimeric mice define a role for cerebral TNF in neuroprotection induced by CpG preconditioning

Systemic preconditioning with the TLR9 ligand CpG induces neuroprotection against brain ischemic injury through a tumor necrosis factor (TNF)-dependent mechanism. It is unclear how systemic administration of CpG engages the brain to induce the protective phenotype. To address this, we created TLR9-deficient reciprocal bone marrow chimeric mice lacking TLR9 on either hematopoietic cells or radiation-resistant cells of nonhematopoietic origin. We report that wild-type mice reconstituted with TLR9-deficient hematopoietic cells failed to show neuroprotection after systemic CpG preconditioning. Further, while hematopoietic expression of TLR9 is required for CpG-induced neuroprotection it is not sufficient to restore protection to TLR9-deficient mice that are reconstituted with hematopoietic cells bearing TLR9. To determine whether the absence of protection was associated with TNF, we examined TNF levels in the systemic circulation and the brain. We found that although TNF is required for CpG preconditioning, systemic TNF levels did not correlate with the protective phenotype. However, induction of cerebral TNF mRNA required expression of TLR9 on both hematopoietic and nonhematopoietic cells and correlated with neuroprotection. In accordance with these results, we show the therapeutic potential of intranasal CpG preconditioning, which induces brain TNF mRNA and robust neuroprotection with no concomitant increase in systemic levels of TNF.     

Morphological and Morphometrical Description of Trichostrongylus Species Isolated from Domestic Ruminants in Khuzestan Province,Southwest Iran

Backgrounds

Genus Trichostrongylus (Nematoda: Trichostrongylidae) is one of the most important zoonotic nematodes with wide geographic distribution in the world. The purpose of the present study was to describe morphological and morphometrical characteristics of male Trichostrongylus species, currently prevalent in domestic ruminants of Khuzestan Province, southwest Iran.

Methods

Gastro-intestinal organs of 1600 sheep, goats, cattle, and buffalos, slaughtered in Khuzestan Province, southwest Iran, were examined for infectivity with Trichostrongylus species. For examination and measurements of helminthes, Azo-carmine staining was performed, followed by camera lucida drawings of morphological characters and measurements of morphometrical criteria with a calibrated microscope. Using valid nematodes systematic keys, almost all the parasites were identified at the level of species.

Results

Overall, 114 animals were found infected with at least one species of Trichostrongylus. Considering morphological characteristics of male Trichostrongylus, six species were identified including T. colubriformis, T. vitrinus, T. probolorus, T. capricola, T. longispicularis and Trichostrongylus sp.

Conclusion

Although, compared to the previous decades, currently Trichostrongylus is much less prevalent in the domestic ruminants of the study area, but still different species occur in these animals.     

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.In recent years, there has been a rapid expansion in the number of next-generation sequencing platforms, including Illumina (Bentley et al. 2008), the Applied Biosystems SOLiD System (McKernan et al. 2009), 454 Life Sciences (Roche) (Margulies et al. 2005), Helicos HeliScope (Shendure and Ji 2008), and most recently Complete Genomics (Drmanac et al. 2010). Many tools have been created to work with next-generation sequencer data, from read based aligners like MAQ (Li et al. 2008a), BWA (Li and Durbin 2009), and SOAP (Li et al. 2008b), to single nucleotide polymorphism and structural variation detection tools like BreakDancer (Chen et al. 2009), VarScan (Koboldt et al. 2009), and MAQ. Although these tools are highly effective in their problem domains, there still exists a large development gap between sequencing output and analysis results, in part because tailoring these analysis tools to answer specific scientific questions can be laborious and difficult. General frameworks are available for processing next-generation sequencing data but tend to focus on specific classes of analysis problems—like quality assessment of sequencing data, as in PIQA (Martinez-Alcantara et al. 2009)—or require specialized knowledge of an existing framework, as in BioConductor in the ShortRead toolset (Morgan et al. 2009). The lack of sophisticated and flexible programming frameworks that enable downstream analysts to access and manipulate the massive sequencing data sets in a programmatic way has been a hindrance to the rapid development of new tools and methods.With the emergence of the SAM file specification (Li et al. 2009) as the standard format for storage of platform-independent next-generation sequencing data, we saw the opportunity to implement an analysis programming framework which takes advantage of this common input format to simplify the up-front coding costs for end users. Here, we present the Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce (Dean and Ghemawat 2008). By separating specific analysis calculations from common data management infrastructure, tools are easy to write while benefiting from ongoing improvements to the core GATK. The GATK engine is constantly being refined and optimized for correctness, stability, and CPU and memory efficiency; this well-structured software core allows the GATK to support advanced features such as distributed and automatic shared-memory parallelization. Here, we highlight the capabilities of the GATK, which has been used to implement a range of analysis methods for projects like The Cancer Genome Atlas (http://cancergenome.nih.gov) and the 1000 Genomes Project (http://www.1000genomes.org), by describing the implementation of depth of coverage analysis tools and a Bayesian single nucleotide polymorphism (SNP) genotyper, and show the application of these tools to the 1000 Genomes Project pilot data.