We determined and annotated the complete 2.2-megabase genome sequence of Pyrobaculum aerophilum, a facultatively aerobic nitratereducing hyperthermophilic (T opt ‫؍‬ 100°C) crenarchaeon. Clues were found suggesting explanations of the organism's surprising intolerance to sulfur, which may aid in the development of methods for genetic studies of the organism. Many interesting features worthy of further genetic studies were revealed. Whole genome computational analysis confirmed experiments showing that P. aerophilum (and perhaps all crenarchaea) lack 5 untranslated regions in their mRNAs and thus appear not to use a ribosome-binding site (Shine-Dalgarno)-based mechanism for translation initiation at the 5 end of transcripts. Inspection of the lengths and distribution of mononucleotide repeattracts revealed some interesting features. For instance, it was seen that mononucleotide repeat-tracts of Gs (or Cs) are highly unstable, a pattern expected for an organism deficient in mismatch repair. This result, together with an independent study on mutation rates, suggests a ''mutator'' phenotype. P yrobaculum aerophilum is a hyperthermophilic (T max ϭ 104°C, T opt ϭ 100°C) and metabolically versatile member of the crenarchaea ( Fig. 1), which are predominantly anaerobic respirers. Unlike most hyperthermophiles, P. aerophilum can withstand the presence of oxygen, growing efficiently in microaerobic conditions, thus making it relatively easy to work with in the laboratory. Unlike most of its phylogenetic neighbors, the growth of P. aerophilum is inhibited by the presence of elemental sulfur, but it grows well anaerobically using nitrate reduction (1). Here we have determined the complete genome sequence of P. aerophilum IM2, which was isolated from a boiling marine water hole at Maronti Beach, Italy (1). We obtained the sequence by a low coverage random shotgun sequencing strategy, with gap closure and resolution of ambiguities aided by the creation of a genomic fosmid map (2). We present an overview of the features and content of the genome, including a possible explanation of the organism's intolerance to sulfur and evidence of a possible lack of mismatch repair activity. Studies of the genus Pyrobaculum provide important opportunities for understanding the boundaries of life in extreme habitats. In a recent molecular sampling of a deep subsurface geothermal water pool, the only organisms detected were hyperthermophilic archaeal members closely related to Pyrobaculum (3).The P. aerophilum IM2 genome has 2,222,430 base pairs, 51% G ϩ C. Two thousand five hundred and eight-seven proteincoding regions were designated, with an average length of 759 amino acids, covering 88% of the genome (Table 1). Circular and linear maps of genome features, including many features discussed below, are published as supporting information (Figs. 4 and 5) on the PNAS web site, www.pnas.org. MethodsFosmid and pUC18 libraries were constructed as described (2). Approximately 26,000 sequences were obtained from Ϸ14,000 pUC18 clones by using both ...

In breast cancer preoperative determination of the tumor size is important for planning breast-conserving operations. In 100 patients with breast cancer, the preoperative tumor size was measured using clinical, mammographic and sonographic examinations and correlated with the results of a subsequent histological examination. Using a high-resolution real-time system, 98 tumors were visible. It was possible to detect not only early tumors under 1 cm in diameter, but also intraductal tumor components. This contributed greatly to the accuracy of the diagnosis. The sonographic measurement of tumor size demonstrated a correlation coefficient of 0.91 and was thus superior to mammography (0.79) and palpation (0.77). Measurement of the total tumor spread, including 39 multicentric lesions, showed an overestimation of 5% for the mammographic measurements and an overestimation of 4% for the sonographic measurements. Tumor extension was underestimated in 33% of the mammograms but in only 3% using ultrasound examination. The results, along with those of other studies, highlight the role of sonography in the diagnosis of breast cancer.

Background: Recent case reports have shown that ultrasonography can be used to diagnose ocular pathology in an emergency setting. Ultrasound may be especially useful when periorbital edema and pain interfere with the examination of the post-traumatic eye.Objective: This study evaluated the ability of emergency physicians to detect a ruptured globe in an ex-vivo porcine model. Methods:Following a brief training lecture, 15 emergency medicine residents and 4 emergency medicine attending physicians used ultrasonography to evaluate 18 porcine eyes, randomized as normal, ruptured, or completely devoid of vitreous humor. The consequences of ultrasound applanation with this method were evaluated by measuring intraocular pressure changes with and without a 1mm clear plastic shield.Results: Our study participants were able to identify abnormal eyes with a sensitivity of 79% (95% CI 73% to 84%) and a specificity of 51% (95% CI 41% to 61%). Intraocular pressure increased 5% with ultrasound applanation, though with a 1mm thick plastic shield there was no measurable change.