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PubMed2005

A space-efficient construction of the Burrows-Wheeler transform for genomic data.

Algorithms for exact string matching have substantial application in computational biology. Time-efficient data structures which support a variety of exact string matching queries, such as the suffix tree and the suffix array, have been applied to such problems. As sequence databases grow, more space-efficient approaches to exact matching are becoming more important. One such data structure, the compressed suffix array (CSA), based on the Burrows-Wheeler transform, has been shown to require memory which is nearly equal to the memory requirements of the original database, while supporting common sorts of query problems time efficiently. However, building a CSA from a sequence in efficient space and time is challenging. In 2002, the first space-efficient CSA construction algorithm was presented. That implementation used (1+2 log2 |summation|)(1+epsilon) bits per character (where epsilon is a small fraction). The construction algorithm ran in as much as twice that space, in O(| summation|n log(n)) time. We have created an implementation which can also achieve these asymptotic bounds, but for small alphabets, and only uses 1/2 (1+|summation|)(1+epsilon) bits per character, a factor of 2 less space for nucleotide alphabets. We present time and space results for the CSA construction and querying of our implementation on publicly available genome data which demonstrate the practicality of this approach.

Animals↗

PubMed2004

Good spaced seeds for homology search.

MOTIVATION: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. RESULTS: Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.

Algorithms↗

PubMed1997

Merging of oculomotor and somatomotor space coding in the human right precentral gyrus.

Using PET and H215O, we investigated the cortical areas that merge two different ways of coding space in the cerebral cortex, those concerned with the oculomotor and the somatomotor space. Normal subjects performed a visuomotor task that required the spatial coding of visual stimuli in oculomotor space and of motor responses in somatomotor space. We manipulated the mapping of oculomotor and somatomotor space by instructing subjects to respond in half of the PET scans with uncrossed hands, i.e. each hand was in the homonymous hemispace (standard oculomotor-somatomotor mapping), and in the other half with crossed hands, i.e. with the left hand in the right hemispace and the right hand in the left hemispace (nonstandard oculomotor-somatomotor mapping). Reaction times were slower for crossed hands than uncrossed hands. Crossed hands produced increases in blood flow in the precentral and postcentral gyri of the right hemisphere. Increases in blood flow in the precentral gyrus were correlated with increases in reaction time comparing the crossed-hand task with the uncrossed one, whereas the increases in blood flow in the postcentral gyrus were not. These findings suggest that the right precentral gyrus merges oculomotor and somatomotor space coding in the human brain.

Adult↗

PubMed1996

Evaluation of K-space segmented cine sequences for fast functional cardiac imaging.

RATIONALE AND OBJECTIVES: In functional cardiac magnetic resonance imaging, reduction of measuring time is very important for many patients who are not able to rest motionless for long-lasting examinations. In this study, the image quality of sequences with k-space segmented data recording was compared with conventional gradient-echo sequences for cine imaging with flow compensation in applications on patients with normal and reduced ejection fractions. METHODS: Thirty-one subjects (4 volunteers and 27 patients with cardiac diseases) were examined using different techniques for cine imaging of the left and right ventricles. The ejection fraction in the patients was calculated based on images of a conventional two-dimensional gradient-echo technique using a biplane ellipsoid model. The results from k-space segmented methods (3 to 9 Fourier lines per cardiac cycle for each phase image) were compared with the conventional images of the same short-axis view separately for groups of subjects with normal and reduced ejection fraction. The contrast between blood and myocardium at several sites of the heart and the homogeneity of the blood signal in the ventricle were evaluated for several phases of the heart cycle. RESULTS: The segmentation in the acquisition of raw data allows reduction of measuring time to approximately 20% to 40% of the time required for conventional sequences in cine imaging of the heart. In patients with normal or only slightly reduced heart function (ejection fraction > or = 60%) the image quality of k-space segmented sequences was not significantly different from the conventionally recorded images. In contrast, patients with markedly lowered ejection fraction (< 60%) showed degraded results of the k-space segmented sequences compared with the conventional sequence (P < 0.001). The anterolateral border and the right ventricle especially were not sufficiently delineated by the k-space segmented sequences in these patients. CONCLUSION: The k-space segmentation for the reduction of examination time is suitable for measuring heart volumes and functional parameters of patients expected to have a nearly normal ejection fraction, whereas for patients with markedly reduced cardiac function further technical improvements of segmented techniques are necessary.

Adult↗

PubMed2002

Comparison of posterior approaches to the posterior incisural space: microsurgical anatomy and proposal of a new method, the occipital bi-transtentorial/falcine approach.

OBJECTIVE: Direct surgical approaches to the posterior incisural space, including the pineal region, remain as challenges for neurosurgeons. The purposes of this study were 1) to compare the surgical views in the various posterior approaches to the posterior incisural space and 2) to propose a new approach, which is a modification of the occipital transtentorial approach. METHODS: Ten adult cadaveric specimens (20 sides) were studied, using x3 to x40 magnification, after perfusion of the arteries and veins with colored silicone. Intraoperative views in the posterior approaches to lesions were examined in stepwise dissections. In addition, the efficacy of the occipital bi-transtentorial/falcine approach was studied. RESULTS: The posterior incisural space has a roof, a floor, and anterior and lateral walls and extends backward to the level of the tentorial apex. The operative views defined by each approach differ in the extent to which they allow observation of the anatomic structures in the posterior incisural space. The occipital bi-transtentorial/falcine approach permits better observation of the contralateral half of the quadrigeminal cistern. CONCLUSION: Precise surgical anatomic knowledge of each approach is required for the treatment of lesions in the posterior incisural space, because the operative fields obtained with different approaches differ significantly. The occipital bi-transtentorial/falcine approach provides greater contralateral exposure of the posterior incisural space than does the occipital transtentorial approach.

Adult↗

PubMed2001

The vascular anatomy anterior to the L5-S1 disk space.

STUDY DESIGN: Dissection of 37 human cadavers was performed to assess the variability in the vascular anatomy anterior to the L5-S1 disc space. OBJECTIVES: To determine the variability of the anterior vascular anatomy at the L5-S1 disc space, and to assess its reliability as an anatomic landmark for the placement of anterior interbody fusion devices. SUMMARY OF BACKGROUND DATA: Although multiple studies have defined both the lumbar spinal anatomy and the anatomy of the great vessels, the relation of the great vessels to the anterior L5-S1 disc space has not been quantified directly. METHODS: This study investigated 35 human cadavers (17 males and 18 females). The anterior L5-S1 disc space and great vessel bifurcation were exposed through a transabdominal approach. Two independent observers each obtained 10 measurements in each specimen. RESULTS: The middle sacral artery was present in 100% of the specimens, averaging 2.5 mm in width. Its location in relation to the midline was quite variable, with a range greater than 2 cm in both the top and bottom of the disc. The distance from the bifurcation to the top of the L5-S1 disc averaged 18 mm (range, 7-36 mm). The total width between the left common iliac vein and the right common iliac artery averaged 33.5 mm (range, 12-50 mm). CONCLUSIONS: The middle sacral artery, present in 100% of the specimens, is a poor anatomic landmark for locating the midline at L5-S1. Because the average space available between the left common iliac vein and the right common iliac artery is 33.5 mm, and because the left common iliac vein averages only 12 mm from midline, the surgeon must be prepared to mobilize the local vasculature in most cases to expose the L5-S1 disc space adequately.

Aged↗

PubMed2002

Endoscopic resection of benign breast tumors: retromammary space approach.

Endoscopic surgery is characterized by the creation of a working space. At our department, we have obtained good results with a retromammary space approach in which the tumor is resected after creation of a working space in the retromammary space. The special instruments used for this purpose comprise an endoscopic vein harvesting system to dissect the retromammary space, a dissecting balloon to compress the space to achieve hemostasis, and laparosonic coagulating shears to incise the tumor. This surgical technique provides a superior cosmetic result, and the level of patient satisfaction has been high.

Biopsy↗

PubMed2005

Morphological changes of the posterior airway space after tongue base suspension.

OBJECTIVES/HYPOTHESIS: The objectives were 1) to demonstrate the efficacy of tongue base suspension with the Repose System in modifying the posterior airway space on the basis of morphological changes in the retrolingual space and 2) to determine the implications of this procedure for the treatment of obstructive sleep apnea syndrome on polysomnographic and psychometric data. STUDY DESIGN: A prospective, nonrandomized study. METHODS: Polysomnography was performed before as well as 3 and 12 months after surgery in patients undergoing tongue base suspension using the Repose System. To identify morphological changes in the posterior airway space, lateral cephalometric radiography and videoendoscopy of the pharynx were performed preoperatively and postoperatively. Twenty-eight male patients with obstructive sleep apnea syndrome were included in the study. A suspension suture anchored intraorally at the mandible was passed submucosally in the body of the tongue, with suture tightness adjusted individually. RESULTS: The posterior airway space was widened by at least 2 mm in 60% of cases. Daytime sleepiness improved subjectively in 67% of patients, and the respiratory disturbance index improved postoperatively in 55%. The correlation between posterior airway space widening and the improvements in daytime sleepiness and respiratory disturbance index was not significant. CONCLUSION: Surgical intervention in obstructive sleep apnea syndrome with the Repose System does not result in permanent anatomical change in the posterior airway space.

Bone Screws↗

PubMed2005

Advances in our understanding of the Reinke space.

PURPOSE OF REVIEW: Normal vocal fold vibration depends critically upon the composition of the Reinke space or the lamina propria extracellular matrix. Alterations in the normal composition of the extracellular matrix result in a loss of normal vibratory function. In this article, the present literature on the Reinke space in normal and disease states is reviewed including publications in the multidisciplinary fields of biomechanics, histology, molecular biology, and tissue engineering. RECENT FINDINGS: With recent technology advances, the etiology for benign lesions has been investigated with computer models and bioreactors. Particular extracellular matrix constituents in various benign vocal fold lesions--fibronectin, fibromodulin and hyaluronan--appear to be involved in altering the viscoelastic properties of the Reinke space. Significant basic science approaches to the investigation of the characterization of the Reinke space in vocal fold scarring has produced several potential future treatment avenues. Tissue-engineering approaches for regeneration of the Reinke space are the most recent addition to the literature showing promising research directions. SUMMARY: Voice disorders represent a significant clinical problem. Research attempting to discover the underlying molecular and genetic regulation and homeostasis of the extracellular matrix of the Reinke space are essential. Effective future clinical interventions must be based upon the knowledge of how genetic and biologic features are disturbed in vocal diseases and how they relate to vocal symptoms.

Biomechanical Phenomena↗

PubMed2000

High-order level-spacing distributions for mixed systems

We apply some of the methods that have been successfully used to describe the nearest-neighbor-spacing distributions of levels of systems with mixed regular-chaotic dynamics to the calculation of high-order spacing distributions. The distributions for chaotic spectra are described in terms of a previously suggested generalization of Wigner's surmise, which assumes that the high-order level repulsion function is given by a product of the zero-order ones and that all of the spacing distributions are nearly Gaussian functions at large spacings. We compare the expressions obtained by the different methods for the next-nearest-neighbor spacing distribution with the outcome of a recently published numerical experiment on systems in transition between order and chaos. We show that the evolution of the shape of that distribution during the transition of the system from a chaotic to a regular regime is slower than the corresponding transition for the nearest-neighbor spacing distribution.

Journal Article↗

PubMed1983

Maintenance of air in intercellular spaces of plants.

Although air-filled intercellular spaces are necessary and ubiquitous in higher plants, little attention has been paid to the possible mechanisms by which these spaces are kept from being flooded. The most likely mechanism is that the living plant cell may maintain a hydrophobic monolayer on the surfaces of adjacent intercellular spaces. The existence of ;apparent free space' in cell walls and the fact that detergent solutions do not enter the intercellular spaces argue against this hypothesis. It is concluded that the mechanism by which these important air spaces are maintained is still unknown.

Journal Article↗

PubMed2003

Apocrustacyanin C(1) crystals grown in space and on earth using vapour-diffusion geometry: protein structure refinements and electron-density map comparisons.

Models of apocrustacyanin C(1) were refined against X-ray data recorded on Bending Magnet 14 at the ESRF to resolutions of 1.85 and 2 A from a space-grown and an earth-grown crystal, respectively, both using vapour-diffusion crystal-growth geometry. The space crystals were grown in the APCF on the NASA Space Shuttle. The microgravity crystal growth showed a cyclic nature attributed to Marangoni convection, thus reducing the benefits of the microgravity environment, as reported previously [Chayen et al. (1996), Q. Rev. Biophys. 29, 227-278]. A subsequent mosaicity evaluation, also reported previously, showed only a partial improvement in the space-grown crystals over the earth-grown crystals [Snell et al. (1997), Acta Cryst. D53, 231-239], contrary to the case for lysozyme crystals grown in space with liquid-liquid diffusion, i.e. without any major motion during growth [Snell et al. (1995), Acta Cryst. D52, 1099-1102]. In this paper, apocrustacyanin C(1) electron-density maps from the two refined models are now compared. It is concluded that the electron-density maps of the protein and the bound waters are found to be better overall for the structures of apocrustacyanin C(1) studied from the space-grown crystal compared with those from the earth-grown crystal, even though both crystals were grown using vapour-diffusion crystal-growth geometry. The improved residues are on the surface of the protein, with two involved in or nearby crystal lattice-forming interactions, thus linking an improved crystal-growth mechanism to the molecular level. The structural comparison procedures developed should themselves be valuable for evaluating crystal-growth procedures in the future.

Carrier Proteins↗

PubMed2004

Collection of reciprocal space maps using imaging plates at the Australian National Beamline Facility at the Photon Factory.

Weissenberg screens and a translating cassette have been employed to allow an imaging plate to collect 30 scans per readout. In this configuration the imaging plate functions as a curved one-dimensional position-sensitive detector and, by changing the sample angle for each of the scans, two-dimensional images were produced in reciprocal space. This method of data collection leads to a reduction in scan time compared with methods based on a scintillation detector, particularly for asymmetric reflections. The data-collection method was tested using InGaN/GaN/AlN multilayers on sapphire substrates, since these exhibit broad features in reciprocal space. The geometry of the scans in reciprocal space required the data to be interpolated onto a Cartesian grid. Several interpolation schemes were investigated, with the results compared with the reciprocal space maps collected using a triple-axis scheme with a point detector. The quality of the interpolated reciprocal space maps depends upon the size and shape of the feature in reciprocal space, the interpolation method used, and the step size of the sample rotation. The method can be extended to three dimensions without an increase in data-collection time.

Journal Article↗

PubMed2000

Caricature effects, distinctiveness, and identification: testing the face-space framework.

According to the multidimensional space framework, faces are represented as locations in a psychological face-space. Our aim was to test whether the locations of veridical, caricatured, and anticaricatured face stimuli in face-space, derived from multidimensional scaling analyses, could account for identification accuracy and distinctiveness ratings for these stimuli. Caricatures were identified more accurately and rated as more distinctive than veridical images, whereas anticaricatures were identified less accurately but were not significantly less distinctive than veridical images. In the face-space derived from multidimensional scaling, caricatures were further from the origin and less densely clustered than veridical images, whereas anticaricatures were closer to the origin and located in denser regions of the space. A quantitative model successfully predicted identification performance from the spatial locations of the stimuli. In general, the physically transformed faces were systematically mapped in the psychological space.

Adult↗

PubMed2002

Behavioral adaptations increase the value of enemy-free space for Heliothis subflexa, a specialist herbivore.

We investigated the importance of specialized behaviors in the use of enemy-free space by comparing the host-use behavior of two closely related moths, Heliothis subflexa Guenee and H. virescens Fabricius. Heliothis subflexa is a specialist on plants in the genus Physalis, whereas H. virescens is an extreme generalist, feeding on plants in at least 14 families. Heliothis subflexa uses the inflated calyx surrounding Physalis fruits as enemy-free space, and field rates of parasitism for H. subflexa on Physalis are much lower than for H. virescens on tobacco and cotton, common hosts found in the same habitat as Physalis. If Physalis, architecture were solely responsible for H. subflexa's low rates of parasitism on Physalis, we predicted that H. virescens larvae experimentally induced to feed on Physalis would experience parasitism rates similar to those of H. subflexa. We found, however, that specialized host-use and host-acceptance behaviors are integral to the use of enemy-free space on Physalis and strongly augment the effects of the structural refuge. In laboratory assays, we found considerable differences between the larval behavior of the specialist. H. subflexa, and the generalist, H. virescens, and these contributed to H. subflexa's superior use of enemy-free space on Physalis. We tested the importance of these behavioral differences in the field by comparing parasitism of H. virescens on Physalis, H. virescens on tobacco, and H. subflexa on Physalis by Cardiochiles nigriceps Vierick, a specialist braconid parasitoid. For H. virescens, a threefold decrease in parasitism occurred when feeding on Physalis (mean parasitism +/- SEM = 13 +/- 4%) rather than tobacco (43 +/- 4%), a difference we attribute to the structural refuge provided by Physalis. However, parasitism of H. virescens on Physalis was more than ten times as great as that of H. subflexa on Pliv.salis (1 +/- 4%), supporting the hypothesis that specialized behaviors have a substantial impact on use of Physalis as enemy-free space. Behavioral adaptations may be central to the use of enemy-free space by phytophagous insects and may act as an important selective force in the evolution of dietary specialization.

Animals↗

PubMed2004

Clinical response to a vacant post space.

AIM: To report a case demonstrating a radiolucency of developing adjacent to an unfilled post space. SUMMARY: A mandibular left first molar was root filled before post-space preparation. The tooth was restored coronally but the post space was left empty, and 14 months later, pain and furcal radiolucency developed. Cleaning, shaping, medicating and filling the post space resulted in the resolution of symptoms and healing of the radiolucency. KEY LEARNING POINTS: Post space should be prepared under conditions of asepsis. A post space must not be allowed to remain empty when a tooth is restored.

Adult↗

PubMed1998

The vascular space-like structure in melanocytic nevus is not an injection artifact: report of a case and an experimental study.

Melanocytic nevi may microscopically associate with clefts or slits of the nests resembling lymphatic or vascular spaces. This unique histologic feature has been known as an artifact of injection or tissue-processing. We present a case of melanocytic nevus with a prominent vascular space-like structure. We also studied whether intralesional injection of local anesthetic could reproduce similar histologic findings. A 45-year-old Japanese female visited us with a solitary, brownish papule on the chest. Histology revealed numerous nests composed of round to oval-shaped nevus cells throughout the entire dermis. In the mid-dermis, nevus cells were lined up in a layer anastomosing and forming a vascular space-like structure. These nevus cells were uniformly stained with vimentin and S100 protein but not with factor VIII-related antigen. They were also positively immunoreactive with anti-type IV collagen and anti-fibronectin. There were no significant differences in staining intensity in the nevus cells between the solid portion and the vascular space-like structure. In the experimental study, eight melanocytic nevi were removed under local anesthesia. The local anesthetic solution was then injected into the excised nevus. Intralesional injection of a considerable volume of local anesthetic was capable of causing slits or clefts of the nests and dermal edema; however, it failed to reproduce a vascular space-like structure similar to that in the present case. These findings suggest that a vascular space-like structure in melanocytic nevus is not caused by the injection alone. Some other factor(s) may play a major role in the development of such structures in melanocytic nevus.

Adolescent↗

PubMed1998

Radiology of the parapharyngeal space.

The parapharyngeal space (PPS) is a central space in the deep neck. Intrinsic lesions within this space are limited. Other spaces in the neck are closely related to the PPS and the direction of displacement of this space often suggests the origin of a lesion. The morphology of a lesion, together with the site of origin, helps in narrowing the diagnostic possibilities. The behaviour of the PPS often helps to determine whether a lesion is an intrinsic abnormality or whether it arises from a neighbouring space. Such information is crucial in the planning of surgical approach and the placement of drains.

Humans↗