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Sequence analysis of the Puumala hantavirus Sotkamo strain L segment.

Sequence of the Puumala virus (PUU) Sotkamo strain L segment is provided, completing the total genome of this prototype PUU virus strain. The L segment is 6530 nucleotides long and it can encode 2156 amino-acids-long L protein, RNA-dependent RNA polymerase. The strain Sotkamo, originally isolated in Finland, showed for the L genome segment nucleotide (84.6%) and amino acid (97.3%) homology to a previously sequenced PUU Russian isolate, strain Bashkiria/CG1820 (B1820) and the L genome segment appeared to be at least as conserved as the S segment. Phylogenetic analysis based on the S, M and L segment sequences proposes that the three viral genes have a similar evolutionary history with no evidence for genome segment reassortment. Precise sequencing of the L segment termini demonstrated that the Puumala strains differ from the conserved sequences of the other hantaviruses at two positions.

Amino Acid Sequence↗

Sagittal plane segmental motion of the cervical spine. A new precision measurement protocol and normal motion data of healthy adults.

OBJECTIVE: (1) Precise documentation of sagittal plane segmental rotational and posteroanterior translational motion of segments C0/C1-C6/C7 of the human cervical spine from lateral radiographic views. (2) Compilation of a database describing normal motion. (3) Comparison of individual motion patterns with the normal database. DESIGN: Descriptive study based on computer-aided measurements from lateral radiographic views taken in flexion and extension. BACKGROUND: Previous studies concentrated on segmental rotational motion of the cervical spine. Normal data for translational motion were not available. Description of cervical spine motion patterns thus remained incomplete. METHODS: Based on computer-aided measurements from lateral radiographic views taken in flexion and extension, a new protocol determines rotational and translational motion for all segments (C0/C1-C6/C7) imaged on the radiographic views. Measured results are corrected for radiographic magnification and variation in stature; they are virtually uninfluenced by radiographic distortion and patient alignment errors. A database describing normal motion was compiled from 137 sets of lateral views of healthy adults taken in active flexion and extension. A specimen study as well as inter- and intra-observer studies quantify measurement errors. RESULTS: The error study demonstrated the error (SD) of a rotational motion measurement to amount to slightly less than 2 degrees. The error (SD) of a translational motion measurement amounts to less than 5% of vertebral depth; for a vertebra of 15 mm depth this corresponds to 0.7 mm. A normal database for rotational and translational motion was compiled. There was a linear relation between rotational and translational motion. This finding agrees qualitatively with results from previous studies; quantitative comparisons are not possible due to divergent definitions for translational motion. The relation between rotation and translation can be employed in individual cases to predict translational motion, in dependence on the rotation actually performed. A comparison of the rotational motion with the normal database and the difference between predicted and actual translational motion allow segmental hypo-, normal or hypermobility to be quantified. CONCLUSIONS: The new protocol measures segmental motion with high precision and corrects for radiographic distortion, variation in stature and alignment errors of patients. Thus, archive studies using existing radiographs are feasible. RELEVANCE: Flexion-extension radiographs of the cervical spine are performed to explore potential damage to the bony or ligamentous structure resulting in abnormal, segmental motion patterns. Determining rotational motion gives only an incomplete picture. The new protocol allows for precise quantification of translational motion and classification of segments as hypo- or hypermobile by comparison with normal motion data.

Adolescent↗

Segmenting brain white matter, gray matter and cerebro-spinal fluid using diffusion tensor-MRI derived indices.

Based on its ability to provide quantitative information about tissue microstructure, diffusion tensor magnetic resonance imaging (DT-MRI) might be a valuable approach to improve the reliability of segmentation of the various brain tissues. In this study, a fully automated and easy-to-implement technique based on 2D histogram analysis of DT-MRI derived images was used to segment white and gray matter of the brain from 10 healthy subjects (aged = 27-56 years). The results obtained with this novel segmentation strategy were compared to those achieved by two experienced observers using an operator-dependent segmentation on the dual-echo scans. Visual inspection of the segmented tissues from a third senior observer disclosed that the automated technique worked properly on all images from all subjects and was more accurate than the human raters in defining thalamus white and gray matter portions as well as in tissue classification at the external brain edge. In addition, this segmentation technique resulted in an average gray/white matter ratio similar to that reported by post-mortem assessment. The application of the operator-dependent segmentation strategy was extremely time-consuming and the two observers achieved poorly reproducible results. Segmenting brain white and gray matter using information from DT-MRI proved to be an accurate approach with the potential for improving the understanding of the pathophysiology of many neurologic conditions.

Anisotropy↗

Microalbuminuria modifies the mortality risk associated with electrocardiographic ST-T segment changes.

OBJECTIVES: We sought to investigate whether microalbuminuria, a proposed marker of generalized vascular damage, enhances the prognostic value of ST-T segment changes for all-cause and cardiovascular mortality in the general population. BACKGROUND: ST-T segment changes on the rest electrocardiogram (ECG) predict mortality in the general population. However, the excess risk seems to be low, particularly in nonhospitalized populations with a low cardiovascular risk profile. METHODS: In a population of 7,330 male and female subjects, a total of 89 deaths (1.2%) occurred during a median three-year follow-up. In 69 of these, the cause of death was obtained from the Central Bureau of Statistics: 25 subjects died of cardiovascular causes (36%). Using computerized Minnesota coding, ST-T segment changes were coded as 4.1-4 and 5.1-4. Microalbuminuria was defined as a urinary albumin excretion of 30 to 300 mg per 24 h. RESULTS: The combination of ST-T segment changes and microalbuminuria showed a higher hazard ratio (HR) for all-cause mortality (HR 8.6 [95% confidence interval [CI] 4.8 to 15.2, p < 0.0001), as compared with ST-T segment changes in the absence of microalbuminuria (HR 1.3 [95% CI 0.7 to 2.5]), which was independent of other cardiovascular risk factors (HR 3.3 [95% CI 1.5 to 7.1], p = 0.002). The combination showed a higher HR when only cardiovascular deaths were taken into account, as compared with all-cause mortality (HR 24.5 [95% CI 7.9 to 76.0], p < 0.0001), which also counted for ST-T segment changes alone (HR 4.4 [95% CI 1.4 to 14.5], p = 0.02). After controlling for other risk factors, the HRs were 10.4 (95% CI 2.5 to 43.6, p = 0.001) for the combination and 2.7 (95% CI 0.6 to 12.3) for ST-T segment changes alone. CONCLUSIONS: This study suggests that, in subjects with ST-T segment changes on their rest ECG, microalbuminuria could identify those at increased risk of all-cause and cardiovascular mortality.

Adult↗

Regional left ventricular systolic function in patients with segmental early relaxation and normal coronary arteries.

The purpose of the study was to determine whether regional differences of left ventricular systolic function exist in patients with normal coronary arteries who manifest segmental early relaxation. The presence or absence of segmental early relaxation was determined angiographically in 16 patients with normal coronary arteries who underwent diagnostic cardiac catheterization because of chest pain. Seven patients had early relaxation localized to the left ventricular anterior wall and nine patients had no evidence of segmental early relaxation. Regional function was assessed from ventriculograms obtained in the right anterior oblique projection using the area method to calculate the regional fractional area of shortening. The fractional area of shortening of the anterolateral region was greater in patients with than in those without segmental early relaxation (69 +/- 4 versus 55 +/- 11%; p less than 0.01). In addition, in patients with segmental early relaxation, this variable exceeded the fractional area of shortening of the diaphragmatic region (69 +/- 4 versus 53 +/- 9%; p less than 0.01). There was no difference in the fractional area of shortening between these two regions in patients who did not manifest segmental early relaxation. These results suggest that regional differences in systolic function are present in patients with but not in those without segmental early relaxation. Augmented regional systolic function was observed in patients with segmental early relaxation and was limited to regions that manifested early relaxation.

Adult↗

Automatic segmentation of the colon for virtual colonoscopy.

Virtual colonoscopy is a minimally invasive technique that enables early detection of colorectal polyps and cancer. Normally, a patient's bowel is prepared with colonic lavage and gas insufflation prior to computed tomography scanning. An important step for 3D analysis of the image volume is segmentation of the colon. The high-contrast gas/tissue interface that exists in the colon lumen makes segmentation of the majority of the colon relatively easy; however, two factors inhibit automatic segmentation of the entire colon. First, the colon is not the only gas-filled organ in the data volume: lungs, small bowel, and stomach also meet this criterion. User-defined seed points placed in the colon lumen have previously been required to spatially isolate the colon. Second, portions of the colon lumen may be obstructed by peristalsis, large masses, and/or residual feces. These complicating factors require increased user interaction during the segmentation process to isolate additional colonic segments. To automate the segmentation of the colon, we have developed a method to locate seed points and segment the gas-filled lumen sections without user supervision. We have also developed an automated approach to improve lumen segmentation by digitally removing residual contrast-enhanced fluid. Experimental results with 20 patient volumes show that our method is accurate and reliable.

Algorithms↗

Characterization of collagen fibril segments from chicken embryo cornea, dermis and tendon.

The cornea, dermis and tendon have extracellular matrix architectures with differences in fibril diameter, packing and organization. An early step in fibril assembly is the formation of a striated fibril of discrete length (segment). Fibril segments were isolated from developing chicken cornea, dermis and tendon by physical disruption and the structure characterized. In all three tissues, intact but relatively short fibril lengths were isolated. These segments were asymmetric, having long (alpha) and short (beta) tapered ends. They were also centrosymmetric with respect to molecular packing. Segments isolated from 12- to 16-day corneas, dermis and tendons had identical structures, but their lengths and diameters were distinct. We propose that the increase in length is, at least in part, the result of lateral associations of adjacent segments. In the developing tendon, there is a rapid increase in length and diameter between day 16 and 17, while in the dermis the increase is more linear with respect to time. In the cornea, the fibril segments grow longer, but their diameters remain constant. Disruption of corneas in phosphate-buffered saline yielded larger diameter segments than seen in situ, while tendon or dermis maintained tissue-specific diameters. When corneas were disrupted in buffers that stabilized the water layer associated with the collagen molecules or containing the corneal proteoglycans, then tissue-specific diameters were maintained. These data suggest differences in the stabilization of segments during growth in tissues where diameter increases versus those where diameter remains constant, and this may be related to collagen-proteoglycan interactions.

Animals↗

Blood supply of small fibula segments: an experimental study on human cadavers.

When vascularized fibula grafts are used in mandibular reconstruction, it is often necessary to divide the graft into segments so as to follow the mandibular curvature. The periosteal blood supply to the segments is usually sufficient. It is unclear, however, how short the segments can be without compromising the blood supply. The present study sought to clarify this issue by injecting Indian ink into the afferent vessels in human cadavers. The evaluation of 300 specimens showed the ink perfusion to be significantly higher in segments longer than 1 cm than in shorter segments. Furthermore, the perfusion in the cortical outer third of the shaft was markedly higher than in the cortical inner two-thirds. The staining was significantly more intense in the younger (32-55 years) than in the older (56-73 years) age group. With correct dissection and successful anastomosis, however, fibula segments 1 cm or longer are probably sufficiently perfused, independent of the patient's age. The perfusion in shorter segments is uncertain. Clinically this means that segments shorter than 1 cm ought to be used only in a surgically non-compromised recipient site, where they could also take as non-vascularized grafts.

Adult↗

Computer-assisted bone segment navigation.

Computer-assisted bone segment navigation is defined as the precise 3-D positioning of geometrically mapped and mathematically described skeletal segments. These bone segments are osteotomized, fractured or prefabricated according to a surgical plan. The high-precision positioning should have an accuracy of 1 mm or better. Segment navigation should be prepared with plain computed tomography (CT) without the implantation of registration markers before CT in order to reduce the number of CTs and operations. The Surgical Segment Navigator (SSN) was developed at the University of Regensburg with the support of Carl Zeiss. This is the first system to meet these criteria. The SSN is based on an infrared positioning device which is connected to a Hewlett Packard LD Pro Workstation. Infrared transmitters are connected to individual templates which are fixed to the bone segment by osteosynthesis screws. Intraoperative correlation between surgical planning and surgical site is achieved by use of a surface-pattern of the bone segment which fits equally well to the laboratory model and the conditions encountered in the patient. The concept of the SSN was submitted by Carl Zeiss as German Patent DE 19747427 A1 in 1997. The SSN system presented here has already been applied clinically and its precision has been evaluated by bone segment navigation in human cadavers.

Bone and Bones↗

Perioperative ST-segment depression is rare and may not indicate myocardial ischemia in moderate-risk patients undergoing noncardiac surgery.

OBJECTIVE: To identify a group of older asymptomatic patients in whom ST-segment changes are common and determine their correlation with occult coronary artery disease. DESIGN: Prospective, cohort study. SETTING: University hospital, single-center. PARTICIPANTS: Patients older than 45 years with at least one risk factor for coronary artery disease but without documented disease undergoing noncardiac, nonvascular surgery. INTERVENTIONS: Intraoperative and early postoperative continuous electrocardiographic monitoring, exercise treadmill testing, 24-month telephone follow-up. MEASUREMENTS AND MAIN RESULTS: A total of 190 patients were studied with a continuous ST-segment monitor, seven of whom demonstrated significant ST-segment changes during the intraoperative or early postoperative period. Three of the seven patients were evaluated by exercise treadmill testing, all of whom had a negative test. Follow-up was complete in 84% of the cohort without ST-segment changes and in all patients with ST-segment changes. One patient with perioperative ST-segment changes died of prostate cancer. None of the other patients showed any symptoms of coronary artery disease on follow-up. CONCLUSIONS: ST-segment changes are rare during the intraoperative and immediate postoperative period in asymptomatic patients at moderate risk for coronary artery disease. The low incidence of a positive stress test and lack of cardiovascular symptoms on follow-up in patients with perioperative ST-segment changes suggest that caution should be exercised before diagnosing myocardial ischemia and coronary artery disease.

Aged↗

Detection of postoperative myocardial ischemia by bedside ST-segment analysis in coronary artery bypass graft patients.

OBJECTIVE: To determine if the ST-segment monitoring software of a bedside electrocardiograph (ECG) monitor would detect postoperative myocardial ischemia (POMI) as reliably as the clinical gold standard 12-lead ECG, and to compare the characteristics of ischemia thus detected with prior studies performed using Holter monitoring. DESIGN: Prospective study. SETTING: University hospital. PARTICIPANTS: One hundred patients who had undergone coronary artery bypass grafting (CABG). INTERVENTIONS: Continuous ST-segment trends in leads II and V5 were recorded using Hewlett-Packard Merlin monitors postbypass until discharge from the postsurgical unit, and printouts were analyzed for episodes of ischemia. Simultaneous 12-lead ECGs and monitor strips were recorded during ischemic episodes in 24 patients and were independently analyzed by two blinded cardiologists quantitatively for ST-segment values and qualitatively for an overall ischemia rating. MEASUREMENTS AND MAIN RESULTS: The ST-segment values directly measured by the cardiologists on the simultaneous 12-lead ECGs and those recorded by the monitor during ischemic episodes were found to be clinically comparable (bias, 0.1 mm for both leads; precision, 0.5 mm lead II, 0.9 mm lead V5). The sensitivity of the monitor compared with 12-lead ECGs for the detection of POMI was 73%. Ninety-eight episodes of significant ST deviation were identified in 39 patients. The characteristics of the ischemia detected in this study were similar to those reported in other studies performed using continuous Holter-type monitoring. CONCLUSION: Bedside monitoring of the ST segment in leads II and V5 using Hewlett-Packard Merlin monitors after CABG surgery is as accurate for the measurement of ST deviation in those leads as the clinical gold standard of a 12-lead ECG read by an experienced cardiologist. However, the 12-lead ECG will detect POMI more reliably than an automated two-lead bedside ST-segment analyzer because it allows evaluation of more leads and of ST-segment and T-wave morphology. Bedside ST-segment monitoring in this study confirmed the high incidence of ischemia after CABG surgery shown previously using Holter monitoring.

Adult↗

Automatic brain tumor segmentation by subject specific modification of atlas priors.

RATIONALE AND OBJECTIVES: Manual segmentation of brain tumors from magnetic resonance images is a challenging and time-consuming task. An automated system has been developed for brain tumor segmentation that will provide objective, reproducible segmentations that are close to the manual results. Additionally, the method segments white matter, grey matter, cerebrospinal fluid, and edema. The segmentation of pathology and healthy structures is crucial for surgical planning and intervention. MATERIALS AND METHODS: The method performs the segmentation of a registered set of magnetic resonance images using an expectation-maximization scheme. The segmentation is guided by a spatial probabilistic atlas that contains expert prior knowledge about brain structures. This atlas is modified with the subject-specific brain tumor prior that is computed based on contrast enhancement. RESULTS: Five cases with different types of tumors are selected for evaluation. The results obtained from the automatic segmentation program are compared with results from manual and semi-automated methods. The automated method yields results that have surface distances at roughly 1-4 mm compared with the manual results. CONCLUSION: The automated method can be applied to different types of tumors. Although its performance is below that of the semi-automated method, it has the advantage of requiring no user supervision.

Automation↗

Short-segment Barrett's esophagus: A prevalent complication of gastroesophageal reflux disease with malignant potential.

The significance of finding specialized intestinal epithelium localized to the region of the gastroesophageal junction is unclear. We tested the hypothesis that short segments of specialized intestinal epithelium are a consequence of gastroesophageal reflux disease and are premalignant. Two hundred forty-one patients with reflux symptoms underwent gastroscopy with rigorous biopsy. Barrett's esophagus was diagnosed when specialized intestinal epithelium was present on biopsy. Patients with Barrett's esophagus were subdivided according to the length of Barrett's mucosa: short-segment Barrett's (<3 cm) and extended Barrett's (> or =3 cm). Esophageal function was evaluated by manometry and 24-hour pH monitoring. In another 16 patients with small noncircumferential adenocarcinomas, the endoscopic length of Barrett's mucosa was recorded. Thirty-three patients (14%) had short-segment Barrett's and 37 (15%) had extended Barrett's esophagus. Patients with short-segment Barrett's esophagus had significantly more acid exposure than patients without specialized intestinal epithelium. Eighty-one percent of patients with short-segment Barrett's esophagus had increased esophageal acid exposure as did 100% of those with extended Barrett's esophagus. All lengths of Barrett's mucosa were associated with poor esophageal sphincter function and reduced contraction amplitudes in the distal esophagus. Twelve percent of patients with short-segment Barrett's esophagus had dysplasia. The length of Barrett's mucosa was > or =3 cm in 25% (4 of 16) of patients with early Barrett's adenocarcinoma. Short-segment Barrett's esophagus is commonly associated with gastroesophageal reflux disease. Further, short segments of specialized intestinal epithelium are premalignant in nature.

Adenocarcinoma↗

[Experimental study of the influence of the segmental transverse colic reversion on the intestinal transit time].

OBJECTIVE: to study the feasibility of the transverse segment colic reversion and to evaluate its impact on the intestinal transit time in the rat Wistar. METHOD: On a test group of the rats Wistar males anaesthetized, we isolated a segment from the transverse colon vascularized by a feeder pedicle. This segment colic was reversed and anastomosed into antiperistaltic out of termino-terminal on its site with polyglactine 6/0. Into post-operative, we studied, the weight, the volume of the ingestats, the intestinal transit time, the survival and the histological lesions of the reversed segment colic. On the group controls, we carried out the anastomosis of a segment of the transverse colon isolated and anastomosed into isoperisaltic. RESULTS: Thirty rats males of 231.5 +/- 8.3g had been operated, 15 for the test group and 15 for the control group. The average weight of the ingestats of the rats of the test group was of 21.87 +/- 3g and of 21.75 +/- 4.8g in the control group without significant difference. The intestinal transit occured at 3 +/- 1 post-operatives days in the test group and at 2 postoperative days in the control group. A mechanical obstruction of the bowels before the 15th post-operative day involved a mortality of 87% in the test group. Thirteen percent of the rats of the test group survived, with a regular catch of weight. The histological analysis showed inflammatory lesions on the proximal portion of the reversed segment and a normal wall without ischaemic injury on its distal portion. No death was observed in the group controls. CONCLUSION: The antiperistaltic anastomosis of a transverse segment colic within the colic in the rat Wistar, causes a stop of the intestinal transit time by mechanical occlusion without ischaemic lesion of the segment colic reversed.

Anastomosis, Surgical↗

Segmentation of the skull in MRI volumes using deformable model and taking the partial volume effect into account.

Segmentation of the skull in medical imagery is an important stage in applications that require the construction of realistic models of the head. Such models are used, for example, to simulate the behavior of electro-magnetic fields in the head and to model the electrical activity of the cortex in EEG and MEG data. In this paper, we present a new approach for segmenting regions of bone in MRI volumes using deformable models. Our method takes into account the partial volume effects that occur with MRI data, thus permitting a precise segmentation of these bone regions. At each iteration of the propagation of the model, partial volume is estimated in a narrow band around the deformable model. Our segmentation method begins with a pre-segmentation stage, in which a preliminary segmentation of the skull is constructed using a region-growing method. The surface that bounds the pre-segmented skull region offers an automatic 3D initialization of the deformable model. This surface is then propagated (in 3D) in the direction of its normal. This propagation is achieved using level set method, thus permitting changes to occur in the topology of the surface as it evolves, an essential capability for our problem. The speed at which the surface evolves is a function of the estimated partial volume. This provides a sub-voxel accuracy in the resulting segmentation.

Computer Simulation↗

The distribution of gene segments in T-cell receptor gamma gene rearrangements demonstrates the need for multiple primer sets.

Limited data exist regarding the distribution of gene segments used in T-cell receptor gamma gene rearrangements (TCR gamma GR) in T-cell lymphoproliferative disorders. The reported efficacy of TCR gamma GR protocols ranges from 60% to greater than 90%. Laboratories reporting a lower detection rate tend to use a limited set of primers. The goal of our study was to provide TCR gamma GR data to demonstrate the molecular biological basis for needing multiple primer sets targeting all gene segments. Sixty cases with a confirmed histological diagnosis of a T-cell lymphoproliferative disorder and TCR gamma GR were identified in our lymphoma registry from 1995 to 2001. DNA was obtained from fresh/frozen tissue, cell lysates, or paraffin-embedded tissue. Variable (V gamma) region gene segments were identified using denaturing gradient gel electrophoresis, which was used to select the cases in the study. Capillary electrophoresis using fluorescent-labeled joining (J gamma) region primers was performed to identify J gamma segments. Sixty cases contained a total of 98 TCR gamma GR, as some cases have more than one rearrangement. The most frequent gene segment combination involved the V gamma 1-8 and J gamma 1/2 segments. If a single primer set directed at these two segments were used for clinical diagnosis, that pair of primers would only diagnose 67% of cases as positive for TCR gamma GR. Our gene segment distribution data emphasize the importance of using a comprehensive set of V gamma and J gamma primers for an optimal detection rate of TCR gamma GR. Protocols with limited numbers of primers should be reconsidered.

DNA↗

QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines.

Chromosome segment substitution (CSS) lines have the potential for use in QTL fine mapping and map-based cloning. The standard t-test used in the idealized case that each CSS line has a single segment from the donor parent is not suitable for non-idealized CSS lines carrying several substituted segments from the donor parent. In this study, we present a likelihood ratio test based on stepwise regression (RSTEP-LRT) that can be used for QTL mapping in a population consisting of non-idealized CSS lines. Stepwise regression is used to select the most important segments for the trait of interest, and the likelihood ratio test is used to calculate the LOD score of each chromosome segment. This method is statistically equivalent to the standard t-test with idealized CSS lines. To further improve the power of QTL mapping, a method is proposed to decrease multicollinearity among markers (or chromosome segments). QTL mapping with an example CSS population in rice consisting of 65 non-idealized CSS lines and 82 chromosome segments indicated that a total of 18 segments on eight of the 12 rice chromosomes harboured QTLs affecting grain length under the LOD threshold of 2.5. Three major stable QTLs were detected in all eight environments. Some minor QTLs were not detected in all environments, but they could increase or decrease the grain length constantly. These minor genes are also useful in marker-assisted gene pyramiding.

Chromosome Mapping↗

Orientation of structural segments in globular proteins.

Twelve globular proteins have been examined to test whether structural segments are oriented at random. Structural segments are defined as the primary sequence of linear chain neighbors bounded by consecutive peptide chain turns. It is shown that, with this definition, a structural segment can be well approximated by a straight-line segment. Each protein in the test set was exhaustively partitioned into its constituent structural segments, and a method is presented for comparing pairwise intersegment orientations. Within a protein, it is found that three-dimensionally close-segments exhibit a pronounced tendency toward parallel orientation while distant segments are randomly oriented. Finally, some conclusions are presented relating to the general problem of segment packing in globular proteins.

Globulins↗