Measuring the Temporal Structure in Serially-Sampled Phylogenies.

Nucleotide sequences sampled at different times (serially-sampled sequences) allow researchers to study the rate of evolutionary change and the demographic history of populations. Some phylogenies inferred from serially-sampled sequences are described as having strong 'temporal clustering', such that sequences from the same sampling time tend to to cluster together and to be the direct ancestors of sequences from the following sampling time. The degree to which phylogenies exhibit these properties is thought to reflect interesting biological processes, such as positive selection or deviation from the molecular clock hypothesis.Here we introduce the Temporal Clustering (TC) statistic, which is the first quantitative measure of the degree of topological 'temporal clustering' in a serially-sampled phylogeny. The TC statistic represents the expected deviation of an observed phylogeny from the null hypothesis of no temporal clustering, as a proportion of the range of possible values, and can therefore be compared among phylogeny of different sizes.We apply the TC statistic to a range of serially-sampled sequence datasets, which represent both rapidly-evolving viruses and ancient mitochondrial DNA. In addition, the TC statistic was calculated for phylogenies simulated under a neutral coalescent process.Our results indicate significant temporal clustering in many empirical datasets. However, we also find that such clustering is exhibited by trees simulated under a neutral coalescent process; hence the observation of significant 'temporal clustering' cannot unambiguously indicate that presence of strong positive selection in a population.Quantifying topological structure in this manner will provide new insights into the evolution of measurably evolving populations.

Evolutionary characterization of the West Nile Virus complete genome.

The spatial dynamics of the West Nile Virus epidemic in North America are largely unknown. Previous studies that investigated the evolutionary history of the virus used sequence data from the structural genes (prM and E); however, these regions may lack phylogenetic information and obscure true evolutionary relationships. This study systematically evaluated the evolutionary patterns in the eleven genes of the WNV genome in order to determine which region(s) were most phylogenetically informative. We found that while the E region lacks resolution and can potentially result in misleading conclusions, the full NS3 or NS5 regions have strong phylogenetic signal. Furthermore, we show that geographic structure of WNV infection within the US is more pronounced than previously reported in studies that used the structural genes. We conclude that future evolutionary studies should focus on NS3 and NS5 in order to maximize the available sequences while retaining maximal interpretative power to infer temporal and geographic trends among WNV strains.

Genetic variation at the mitochondrial DNA 9-bp repeat locus in the Sakha of Siberia.

Genetic variation at the mitochondrial DNA 9-bp repeat locus was assayed in 779 Sakha from Siberia. Fourteen deletion (1.8%), nine triplication (1.2%), and two 4-repeat alleles (0.26%) were identified. Several of these alleles were also detected as heteroplasmies. Among the four heteroplasmic individuals identified (0.51%), three different combinations of repeat alleles were present: 1/2, 2/3, and 2/3/4 copies. Hypervariable region I (HVRI) sequencing revealed that three different sets of haplogroups were associated with the three most frequent 9-bp polymorphisms: (1) haplo-groups B, T, and W for deletions; (2) haplogroups C, D, and K for triplications; and (3) haplogroups C, D, and T for heteroplasmies. Both of the two 4-repeat alleles were associated with haplogroup D. We detected more types of 9-bp polymorphisms and more genetic variation within classes of polymorphism than previously reported for any single population. We also present the largest and most geographically diverse sampling of the Sakha population to date. No neighboring populations have been reported to carry a non-haplogroup B deletion, triplication, or heteroplasmy, suggesting that shared ancestry or admixture or both are unlikely explanations for the presence of these polymorphisms in the Sakha. The identification of high levels of variation may be a function of the large sample size and the in-depth analysis of all derived polymorphisms. Further study of the Sakha is warranted to determine whether the level of variation is unexpectedly high, especially in light of the presence of different heteroplasmies, which suggests multiple recent events.

Molecular evolution of the tprC, D, I, K, G, and J genes in the pathogenic genus Treponema.

We investigated the evolution of 6 genes from the Treponema pallidum repeat (tpr) gene family, which encode potential virulence factors and are assumed to have evolved through gene duplication and gene conversion events. The 6 loci (tprC, D, G, J, I, and K) were sequenced and analyzed in several members of the genus Treponema, including the 3 subspecies of human T. pallidum (T. pallidum subsp. pallidum, pertenue, and endemicum), Treponema paraluiscuniculi (rabbit syphilis), and the unclassified Fribourg-Blanc (simian) isolate. Phylogenetic methods, recombination analysis, and measures of nucleotide diversity were used to investigate the evolutionary history of the tpr genes. Numerous instances of gene conversion were detected by all 3 methods including both homogenizing gene conversion that involved the entire length of the sequence as well as site-specific conversions that affected smaller regions. We determined the relative age and directionality of the gene conversion events whenever possible. Our data are also relevant to a discussion of the evolution of the treponemes themselves. Higher levels of variation exist between the human subspecies than within them, supporting the classification of the human treponemes into 3 subspecies. In contrast to published theories, the divergence and diversity of T. pallidum subsp. pertenue relative to the other subspecies does not support a much older origin of yaws at the emergence of modern human, nor is the level of divergence seen in T. pallidum subsp. pallidum consistent with a very recent (< 500 years) origin of this subspecies. In general, our results demonstrate that intragenomic recombination has played a significant role in the evolution of the studied tpr genes and emphasize that efforts to infer evolutionary history of the treponemes can be complicated if past recombination events are not recognized.

Analysis of early failure of tunneled hemodialysis catheters.

OBJECTIVE: Tunneled hemodialysis catheters are often placed by the interventional radiology service using sonographic guidance and fluoroscopy for safe and optimal placement. The aim of this study was to determine the causes of early failure (

Radiologic placement of central venous catheters: rates of success and immediate complications in 3412 cases.

OBJECTIVE: To determine the success and immediate complication rates associated with 3412 central venous catheter placements performed in an interventional radiology suite. METHODS: Success and immediate complication rates were prospectively recorded for 3412 consecutive patients who had central venous catheters radiologically placed at a tertiary care centre between July 1993 and October 2000. The indication for placement and the insertion site were also recorded. RESULTS: The most common indication for both short- and long-term venous access was hemodialysis, and the right internal jugular vein was the most common site for catheter insertion. Placement was successful for 98.8% of tunnelled lines and 99.3% of temporary catheters. The rate for immediate complications (including pneumothorax, air emboli, bleeding and arterial puncture) for tunnelled catheter placements was 3.8% and for temporary catheter placements was 1.6%; no major complications were documented. CONCLUSION: Our results lend further evidence to the claim that the success and immediate complication rates of radiologically placed central venous catheters compare favourably with blind placement and surgical placement of central venous catheters.

Image-guided central venous catheter placement for apheresis in allogeneic stem cell donors.

Peripheral blood stem cell harvest by apheresis is an increasingly important procedure utilized in the treatment of many malignancies. Whether autologous or allogeneic, it is frequently performed via peripheral access because of concern over major complications associated with central venous catheter placement. This study was to determine the safety and success, complications and premature failure rates for radiolocally placed ultrasound-guided non-tunneled central venous catheters placed for apheresis in a donor (allogeneic) population. One hundred central venous catheters were placed in ninety-one individuals for allogeneic stem cell harvest. Procedural success and complications relating to placement were noted in all. In 97 cases the number of needle passes required for venous cannulation and whether this was achieved with a single wall puncture was noted. Duration of catheterization and reason for removal were recorded in all cases. All catheters were placed by a right transjugular route. Venous cannulation and functioning line placement was achieved in every case; 92/97 (95%) required only a single needle pass and 84/97 (87%) only a single wall puncture. There were no placement related complications; 94 catheters were removed the same day with the remainder removed within 48 hr. All completed apheresis. Our study demonstrates the safe use of central venous catheters for apheresis in normal donors if ultrasound guidance is used for the puncture and the duration of catheterization is short.

Extraprostatic biopsy improves the staging of localized prostate cancer.

OBJECTIVE: To evaluate the role and safety of biopsy of the seminal vesicles and neurovascular bundles in determining the pathologic stage of prostatic carcinoma. METHODS: Eighty-one consecutive patients were enrolled in a comprehensive cryosurgical biopsy protocol that included sextant intraprostatic plus extraprostatic biopsy. The pathologic stage, determined after biopsy, was compared with the clinical stage, determined by digital rectal examination (DRE) and transrectal ultrasonographic (TRUS) evaluation. As well, complication rates for these patients were compared with rates for a separate group that underwent sextant intraprostatic biopsy alone. RESULTS: Of the 81 patients, 61 (75%) were confirmed to have cancer by biopsy. None of these patients was considered to have extraprostatic extension by clinical evaluation (DRE and TRUS), but 16 of 61 (26%) were identified to have extraprostatic cancer in the seminal vesicles (8 of 61, 13%) or in the neurovascular bundles (8 of 61, 13%) by extraprostatic biopsy. There was no significant difference in the complication rates between sextant intraprostatic biopsy and sextant intraprostatic plus extraprostatic biopsy (p>0.97). CONCLUSIONS: Extraprostatic biopsy identifies extension of carcinoma in a large proportion of patients in whom clinical evaluation by DRE and TRUS indicates organ-confined disease. Extraprostatic biopsy is therefore warranted as routine evaluation before surgery in order to correctly stage prostatic carcinoma and select appropriate therapy.

Value of frontal caval measurement in the placement of inferior vena cava filters.

OBJECTIVE: Inferior vena cavae (IVC) can be of unusual geometry, often having odd shapes and being oriented (in long axes) away from the horizontal plane. However, after insertion of a filter, most IVC adopt a circular cross-section. The objective of this study was to determine if the IVC diameter estimated by frontal measurement (cavogram equivalent) reflects the true circular diameter of the infrarenal vena cava. Diameter estimation is clinically important in the correct selection of a filter, because mega cavae (diameter 28 mm or greater) require a particular filter. METHODS: The infrarenal IVC was measured on computed tomographic (CT) scans in 136 patients. The frontal diameter was recorded as that which would be obtained by a cavogram. Corrected circular diameter was obtained by mapping the circumference of each cross-section on CT to a straight line and calculating diameter from circumference. RESULTS: The average frontal caval diameter was 20.5 (standard deviation 3.7) mm, whereas the average corrected circular diameter was 23.0 (standard deviation 3.4) mm. By frontal measurements, 6 IVC diameters were 28.0 mm or greater. Similarly, by corrected circular diameter, 6 IVC diameters were 28.0 mm or greater. However, of the 6 mega cavae extrapolated to cavograms, only 3 corresponded to mega cavae when corrected for true circular diameter. Yet, of the 6 mega cavae identified by corrected circular diameter measurement, 3 were not identified by frontal diameter assessment. Of the 6 patients with true mega cavae, 2 were being evaluated for right lower quadrant pain, 2 for lymphoma, 1 for a pelvic mass, and 1 for staging of a head and neck cancer. CONCLUSIONS: Cavograms can over- or underestimate the true diameter of an IVC, and may thus lead to incorrect filter choice. It is recommended that a sonogram or CT scan be obtained to visualize the IVC in cases of suspected mega cava, and that true circular diameters be used for selection and placement of IVC filters.

Should anticoagulant therapy be stopped or reversed before venous intervention?

PURPOSE: To determine the safety of venous intervention and the incidence of complications in patients undergoing venous interventional radiological procedures while receiving anticoagulant therapy. METHOD: Data were collected prospectively for a 1-year period. One hundred patients receiving anticoagulant therapy underwent interventional radiological procedures requiring venous cannulation. Of these, 87 had documented prolonged bleeding times. There were 50 inferior vena cavograms obtained and filters placed (29 transfemoral, 21 transjugular), and 50 transfemoral pulmonary angiogram obtained, all in patients with thrombo-embolic disease who were receiving anticoagulant therapy. In most cases venous access was achieved with real-time sonographic guidance. RESULTS: Venous access was gained in all patients in all groups. There were 41/50 filter placements and 46/50 pulmonary angiograms performed in the patients with prolonged clotting times in or above the therapeutic range. There were no cases of arterial puncture and no cases of venous bleeding either during or after the procedures. No other complications were recorded. CONCLUSION: Venous intervention in patients receiving therapeutic anticoagulation is safe, with no complications reported in our series. There is no need to discontinue anticoagulant therapy in patients with life-threatening thrombo-embolic disease. Real-time sonographic guidance greatly facilitates venous cannulation and avoids inadvertent arterial puncture.

A simplified method of gastropexy for transgastric enterostomy.

Radiological placement of gastrostomy tubes was first described in 1983. Percutaneous gastropexy to facilitate gastrostomy placement was reported in 1986. Debate has continued to this day regarding the necessity of gastric fixation. We describe our technique of a simplified gastropexy to facilitate transgastric enterostomy and advocate its more widespread use.

Radiologic placement of tunneled central catheters: rates of success and of immediate complications in a large series.

OBJECTIVE: The objective was to examine the success and immediate complication rates in a large series of radiologically placed tunneled central venous catheters. SUBJECTS AND METHODS: We prospectively recorded the success and immediate complication rates in 880 consecutive radiologically placed tunneled central venous catheters. We also recorded the indication for placement, the success of placement, the number of passes required, and whether a double- or single-wall puncture occurred. RESULTS: Hemodialysis was the most common indication for long-term venous access. Venous access was successful in all patients, and catheter placement was successful in 99.4% of patients, with only five failed placements. All patients in whom placement was initially unsuccessful underwent successful placement the same day. All catheters were placed using real-time sonographic guidance. Most were placed in an internal jugular vein, with 87.4% requiring only a single needle pass. The immediate complication rate was only 4.0%, and no major complications occurred. CONCLUSION: To our knowledge, this series is the largest for which the immediate complication and success rates for radiologically placed central venous catheters have been reported. Our results suggest that radiologic placement of tunneled central venous catheters is a safe and effective alternative to surgery.

Transrectal ultrasound-guided biopsy of the prostate: relation between ASA use and bleeding complications.

OBJECTIVE: To determine the relation between ASA ingestion and the incidence of bleeding complications after transrectal ultrasound (TRUS)-guided biopsy of the prostate. METHODS: Overall, 1810 patients with suspected prostate disease were followed after biopsy. ASA use was determined before the procedure. A TRUS-guided sextant biopsy was performed and patients were contacted immediately and by follow-up telephone call to determine whether there were any immediate or delayed bleeding complications. RESULTS: Overall, 46 subjects (2.5%) had bleeding complications. Of the 54 subjects reporting current use of ASA, 2 (3.7%) had such complications. This difference was not significant. CONCLUSION: There was no evidence of an association between the use of ASA and postbiopsy bleeding complications.

Apheresis: another indication for radiologically placed central venous catheters.

OBJECTIVE: Apheresis is an important technique, used increasingly for a variety of conditions. It is sometimes performed via peripheral access because of concern over major complications associated with central venous catheter (CVC) placement. This study was to determine the safety and success of radiologic placement of CVCs for apheresis. METHODS: Data were collected prospectively for 278 CVCs placed under real-time sonographic or fluoroscopic guidance in the radiology department. Complications were noted in all cases; the number of passes required for venipuncture and whether this was achieved with a single wall puncture were noted in 265 cases; duration of catheterization and reason for removal of the catheter were recorded in all cases. The study group included 83 donors providing peripheral blood stem cells for allogeneic transplant. RESULTS: CVCs were successfully placed in all patients, 269 in the internal jugular and 9 in the femoral vein. In 87% of cases, only a single pass was required, and in 80% of cases venipuncture was achieved with a single anterior wall puncture. There was inadvertent but clinically insignificant arterial puncture in 6 cases (2%). In no case did this prevent CVC placement. Most catheters (211/274, 77%) were removed the same day. Only 3 catheters were removed prematurely (1%), 1 because of infection and 2 because of clotting. There was 1 case of venous bleeding. CONCLUSION: CVCs are safe for apheresis if real-time sonographic guidance is used for the puncture, guide wire and catheter placement are confirmed fluoroscopically, and the duration of catheterization is short.

Predicting infection in localized intraabdominal fluid collections: value of pH and pO2 measurements.

PURPOSE: To evaluate the use of pH, pO2, and the subjective opinion of the radiologist compared with bacterial culture in accurate diagnoses of bacterial infection in intraabdominal fluid collections. MATERIALS AND METHODS: Prospectively, 79 patients who were suspected of having an intraabdominal fluid collection underwent diagnostic fluid aspiration. The aspirate was cultured and measured for pH and pO2. A pH < or = 7.1 and a PO2 < or = 49 mm Hg were threshold values used to separate infected from sterile fluid collections. RESULTS: pH alone had a 92% sensitivity and 79% specificity, whereas PO2 alone had a 51% sensitivity and 79% specificity. pH or pO2 combined yielded a 92% sensitivity and 60% specificity. The radiologist's opinion produced a 83% sensitivity and 92% specificity. pH and the radiologist's opinion combined produced a 78% sensitivity and 96% specificity. pH or the radiologist's opinion combined had a 95% sensitivity and a 63% specificity. CONCLUSION: pH is the most sensitive indicator of infection and the radiologist's opinion is the most specific. We recommend proceeding to drainage if the radiologist believes the collection to be infected and performing pH analysis if not. If the pH < or = 7.04, proceed to drainage. If neither of the above criteria are met, drainage could be delayed, pending the results of culture.

Image-guided central venous catheters for apheresis.

Apheresis is an increasingly important procedure in the treatment of a variety of conditions, sometimes performed via peripheral access because of concern over major complications associated with central venous catheter (CVC) placement. This study sought to determine the safety and success for ultrasound and fluoroscopically guided, non-tunneled dual lumen CVCs placed for apheresis. Prospective data collection was made of 200 attempted CVC placements in the radiology department utilizing real time sonographic guidance. The complications relating to placement were noted in all and the number of passes required for venepuncture and whether a single wall puncture was achieved was recorded in 185 cases. Duration of catheterization and reason for line removal were recorded in all. Our study group included 71 donors providing peripheral blood stem cells for allogeneic transplant. CVCs were successfully placed in all patients, 191 lines in the internal jugular and seven in the femoral vein. 86.5% required only a single pass and 80.5% with only anterior wall puncture. Inadvertent but clinically insignificant arterial puncture occurred in six (3%) cases. In no case did this prevent line placement. There were no other procedure-related complications. 173 (87.4%) catheters were removed the same day. No catheters were removed prematurely. There was one case of prolonged venous bleeding. Our study demonstrates the safety of central venous catheters for apheresis provided that duration of catheterization is short and real-time sonographic guidance is used for the puncture, and guide wire and catheter placement are confirmed fluoroscopically.