Property Suffix Array with Applications in Indexing Weighted Sequences

Summary Aim: Minimally invasive resection of hyperfunctional parathyroid glands is an alternative to open surgery. However, it requires a precise preoperative localization. This study evaluated the diagnostic use of magnetic resonance (MR) imaging, parathyroid scintigraphy, and consecutive image fusion. Patients, methods: 17 patients (9 women, 8 men; age: 29-72 years; mean: 51.2 years) with primary hyperparathyroidism were included. Examination by MRI used unenhanced T1- and T2-weighted sequences as well as contrast-enhanced T1-weighted sequences. 99mTc-MIBI scintigraphy consisted of planar and SPECT (single photon emission tomography) imaging techniques. In order to improve the anatomical localization of a scintigraphic focus, SPECT-data were fused with the corresponding MR-data using a modified version of the Express 5.0 software (Advanced Visual Systems, Waltham, MA). Results of image fusion were then compared to histopathology. Results: In 14/17 patients, a single parathyroid adenoma was found. There were 3 cases with hyperplastic glands. MRI detected 10 (71%), scintigraphy 12 (86%) adenomas. Both modalities detected 1/3 patients with hyperplasia. Image fusion improved the anatomical assignment of the 13 scintigraphic foci in five patients and was helpful in the interpretation of inconclusive MR-findings in two patients. Conclusions: Both MRI and 99mTc-MIBI scintigraphy sensitively detect parathyroid adenomas but are less reliable in case of hyperplastic glands. In case of a scintigraphic focus, image fusion considerably improves its topographic assignment. Furthermore, it facilitates the evaluation of inconclusive MRI findings.

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An Efficient Tool for Searching Maximal and Super Maximal Repeats in Large DNA/Protein Sequences via Induced-Enhanced Suffix Array

Recent Patents on Computer Science ◽

10.2174/2213275911666181107095645 ◽

2019 ◽

Vol 12 (2) ◽

pp. 128-134

Author(s):

Sanjeev Kumar ◽

Suneeta Agarwal ◽

Ranvijay

Keyword(s):

Protein Sequences ◽

Input Sequence ◽

Suffix Array ◽

Secondary Memory ◽

Time And Space ◽

Efficient Tool ◽

Frequency Distributions ◽

Alignment Algorithms ◽

Common Prefix ◽

Art Works

Background: DNA and Protein sequences of an organism contain a variety of repeated structures of various types. These repeated structures play an important role in Molecular biology as they are related to genetic backgrounds of inherited diseases. They also serve as a marker for DNA mapping and DNA fingerprinting. Efficient searching of maximal and super maximal repeats in DNA/Protein sequences can lead to many other applications in the area of genomics. Moreover, these repeats can also be used for identification of critical diseases by finding the similarity between frequency distributions of repeats in viruses and genomes (without using alignment algorithms). Objective: The study aims to develop an efficient tool for searching maximal and super maximal repeats in large DNA/Protein sequences. Methods: The proposed tool uses a newly introduced data structure Induced Enhanced Suffix Array (IESA). IESA is an extension of enhanced suffix array. It uses induced suffix array instead of classical suffix array. IESA consists of Induced Suffix Array (ISA) and an additional array-Longest Common Prefix (LCP) array. ISA is an array of all sorted suffixes of the input sequence while LCP array stores the lengths of the longest common prefixes between all pairs of consecutive suffixes in an induced suffix array. IESA is known to be efficient w.r.t. both time and space. It facilitates the use of secondary memory for constructing the large suffix-array. Results: An open source standalone tool named MSR-IESA for searching maximal and super maximal repeats in DNA/Protein sequences is provided at https://github.com/sanjeevalg/MSRIESA. Experimental results show that the proposed algorithm outperforms other state of the art works w.r.t. to both time and space. Conclusion: The proposed tool MSR-IESA is remarkably efficient for the analysis of DNA/Protein sequences, having maximal and super maximal repeats of any length. It can be used for identification of well-known diseases.

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Pituitary MRI characteristics in 297 acromegaly patients based on T2-weighted sequences

Endocrine Related Cancer ◽

10.1530/erc-14-0305 ◽

2015 ◽

Vol 22 (2) ◽

pp. 169-177 ◽

Cited By ~ 46

Author(s):

Iulia Potorac ◽

Patrick Petrossians ◽

Adrian F Daly ◽

Franck Schillo ◽

Claude Ben Slama ◽

...

Keyword(s):

Large Population ◽

Optic Chiasm ◽

Research Priority ◽

Maximal Diameter ◽

Magnetic Resonance Imaging Mri ◽

Multimodal Management ◽

Mri Characteristics ◽

Weighted Sequences ◽

The Relationship

Responses of GH-secreting adenomas to multimodal management of acromegaly vary widely between patients. Understanding the behavioral patterns of GH-secreting adenomas by identifying factors predictive of their evolution is a research priority. The aim of this study was to clarify the relationship between the T2-weighted adenoma signal on diagnostic magnetic resonance imaging (MRI) in acromegaly and clinical and biological features at diagnosis. An international, multicenter, retrospective analysis was performed using a large population of 297 acromegalic patients recently diagnosed with available diagnostic MRI evaluations. The study was conducted at ten endocrine tertiary referral centers. Clinical and biochemical characteristics, and MRI signal findings were evaluated. T2-hypointense adenomas represented 52.9% of the series, were smaller than their T2-hyperintense and isointense counterparts (P<0.0001), were associated with higher IGF1 levels (P=0.0001), invaded the cavernous sinus less frequently (P=0.0002), and rarely caused optic chiasm compression (P<0.0001). Acromegalic men tended to be younger at diagnosis than women (P=0.067) and presented higher IGF1 values (P=0.01). Although in total, adenomas had a predominantly inferior extension in 45.8% of cases, in men this was more frequent (P<0.0001), whereas in women optic chiasm compression of macroadenomas occurred more often (P=0.0067). Most adenomas (45.1%) measured between 11 and 20 mm in maximal diameter and bigger adenomas were diagnosed at younger ages (P=0.0001). The T2-weighted signal differentiates GH-secreting adenomas into subgroups with particular behaviors. This raises the question of whether the T2-weighted signal could represent a factor in the classification of acromegalic patients in future studies.

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Letter to the Editor: Craniopharyngiomas in the elderly: the crucial influence of tumor topography on surgical risk assessment

Neuroendocrinology ◽

10.1159/000516172 ◽

2021 ◽

Author(s):

José M. Pascual ◽

Ruth Prieto

Keyword(s):

Risk Assessment ◽

Elderly Patients ◽

Tumor Tissue ◽

Significant Proportion ◽

Wide Band ◽

The Elderly ◽

Surgical Risk ◽

Definition Of ◽

Weighted Sequences ◽

Tumor Topography

Classifying CPs within the overly vague, uninformative category “suprasellar” prevents gaining any true insight regarding the risks associated with the surgical procedure employed. Routine MRI obtained with conventional T1- and T2-weighted sequences along the midsagittal and coronal trans-infundibular planes allow an accurate and reliable preoperative definition of CP topography. CPs developing primarily within the infundibulum and/or tuberal region of the hypothalamus, as well as those wholly located within the 3V, should be distinguished preoperatively from those lesions originally expanding beneath the 3V floor (3VF), the true suprasellar tumors. Among adult patients, about 40% of CPs correspond to infundibulo-tuberal tumors expanding primarily within the 3VF, above an intact pituitary gland and stalk. This subgroup of CPs shows strong adherences to the surrounding hypothalamus, as they are embedded within a wide band of reactive gliotic tissue, usually infiltrated by microscopic finger-like solid cords of tumor tissue. In elderly patients, a significant proportion of CPs correspond to papillary tumors developing above an intact 3VF, usually showing small pedicle-like or sessile-like attachments to the infundibulum. With the current diagnostic MRI workup routinely employed for CPs, it is possible, for the majority of lesions, to preoperatively differentiate these topographical variants and predict the type of CP-hypothalamus relationship that will be found during surgery.

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Delayed post-hypoxic leukoencephalopathy: Case report

European Psychiatry ◽

10.1016/j.eurpsy.2017.01.1654 ◽

2017 ◽

Vol 41 (S1) ◽

pp. s839-s839 ◽

Cited By ~ 1

Author(s):

M. Solerdelcoll Arimany ◽

M. Garriga ◽

E. Parellada

Keyword(s):

Neuropsychiatric Symptoms ◽

Brain Mri ◽

Clinical History ◽

Good Prognosis ◽

Mri Findings ◽

The Mean ◽

Competing Interest ◽

Weighted Sequences ◽

Direct Toxicity ◽

Progressive Cognitive Impairment

IntroductionDelayed post-hypoxic leukoencephalopathy (DPHL) is an underrecognized syndrome of delayed demyelination, where patients manifest neuropsychiatric symptoms after a period of 2–40 days of apparent recovery from a cerebral hypo-oxygenation episode.ObjectivesWe report a case of a patient who successfully recovered from an overdose of heroin, but then suffered a delayed abrupt neurological deterioration.AimsTo improve assessment and recognition of DPHL.MethodsAn adequate retrospective collection of clinical data and nonsystematic review of the literature was performed.ResultsA 43-year-old male with schizoaffective disorder who attempted suicide with an overdose of heroin, was successfully revived and return to his previously mental status, but 3 weeks after, he abruptly developed progressive cognitive impairment with akinetic mutism and ataxia. He was admitted to our acute psychiatric unit after brain CT and chemistry analyses were unremarkable. Brain MRI showed diffusely symmetric hyperintensity in the white matter (WM), pronominally the periventricular WM, on FLAIR and T2 weighted sequences. At 16 weeks postoverdose, he presented improvement both cognitive and motor symptoms, lasting deficits in frontal-executive functions.DiscussionDPHL is characterized by similar clinical and neuroimaging features regardless of the initial insult. The mean lucid interval coincides with the replacement half-life for myelin related lipids and proteins. Prolonged mild-to-moderate hypo-oxygenation of WM is thought to disrupt myelin turnover. It appears probable that these were responsible for DPHL in our patient rather than a direct toxicity.ConclusionDPHL can be diagnosed when clinical history, laboratory assessments and MRI findings are concordant. DPHL requires extensive support care and carries a relatively good prognosis.Disclosure of interestThe authors have not supplied their declaration of competing interest.

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MR Imaging–Pathologic Correlation of Uveal Melanomas Undergoing Secondary Enucleation after Proton Beam Radiotherapy

Applied Sciences ◽

10.3390/app11094310 ◽

2021 ◽

Vol 11 (9) ◽

pp. 4310

Author(s):

Pietro Valerio Foti ◽

Corrado Inì ◽

Mario Travali ◽

Renato Farina ◽

Stefano Palmucci ◽

...

Keyword(s):

Mr Imaging ◽

Proton Beam ◽

Uveal Melanoma ◽

Vitreous Hemorrhage ◽

Nerve Degeneration ◽

Proton Beam Radiotherapy ◽

Iris Neovascularization ◽

Weighted Sequences ◽

Histopathologic Findings ◽

Optic Nerve Degeneration

Background: Currently, radiotherapy represents the most widely employed therapeutic option in patients with uveal melanoma. Although the effects of proton beam radiotherapy on uveal melanoma end ocular tissues have been histologically documented, their appearance at MR imaging is still poorly understood. The purpose of our study was to elucidate the magnetic resonance (MR) semiotics of radiotherapy-induced changes to neoplastic tissues and ocular structures in patients with uveal melanoma undergoing secondary enucleation after proton beam radiotherapy. Methods: Nine patients with uveal melanoma who had undergone proton beam radiotherapy, MR imaging, and subsequent secondary enucleation were retrospectively selected. The histopathologic findings evaluated for irradiated tumors were necrosis, fibrosis, and viable tumor, while the histopathologic findings evaluated for extratumoral ocular/periocular tissues were radiation-related intraocular inflammation, vitreous hemorrhage, optic nerve degeneration, iris neovascularization, and periocular fibrotic adhesions. On MR images, the appearance of the abovementioned histologic features was assessed on conventional and diffusion-weighted sequences. Results: T2-weighted sequences performed better in detecting radiation-induced necrosis, fibrosis, optic nerve degeneration, and periocular fibrotic adhesions. T1-weighted sequences were preferable for identifying cataracts, vitreous hemorrhage, and inflammatory complications. Contrast-enhanced T1-weighted sequences were irreplaceable in assessing iris neovascularization, and in confirming inflammatory complications. Conclusions: In the light of their increasing role in the multidisciplinary management of patients with uveal melanoma, radiologists should be aware of the MR appearance of the effects of radiotherapy on neoplastic and ocular tissue, in order to improve the accuracy of follow-up MR examinations.

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Suffix array for multi-pattern matching with variable length wildcards

Intelligent Data Analysis ◽

10.3233/ida-205087 ◽

2021 ◽

Vol 25 (2) ◽

pp. 283-303

Author(s):

Na Liu ◽

Fei Xie ◽

Xindong Wu

Keyword(s):

Dynamic Programming ◽

Data Structure ◽

Pattern Matching ◽

Edit Distance ◽

State Of The Art ◽

Suffix Array ◽

Variable Length ◽

Distance Method ◽

Efficient Data ◽

Comparison Algorithms

Approximate multi-pattern matching is an important issue that is widely and frequently utilized, when the pattern contains variable-length wildcards. In this paper, two suffix array-based algorithms have been proposed to solve this problem. Suffix array is an efficient data structure for exact string matching in existing studies, as well as for approximate pattern matching and multi-pattern matching. An algorithm called MMSA-S is for the short exact characters in a pattern by dynamic programming, while another algorithm called MMSA-L deals with the long exact characters by the edit distance method. Experimental results of Pizza & Chili corpus demonstrate that these two newly proposed algorithms, in most cases, are more time-efficient than the state-of-the-art comparison algorithms.

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