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PURPOSE: Water removal is one of the computational bottlenecks in the processing of high-resolution MRSI data. The purpose of this work is to propose an approach to reduce the computing time required for water removal in large MRS data. METHODS: In this work, we describe a singular value decomposition-based approach that uses the partial position-time separability and the time-domain linear predictability of MRSI data to reduce the computational time required for water removal. Our approach arranges MRS signals in a Casorati matrix form, applies low-rank approximations utilizing singular value decomposition, removes residual water from the most prominent left-singular vectors, and finally reconstructs the water-free matrix using the processed left-singular vectors. RESULTS: We have demonstrated the effectiveness of our proposed algorithm for water removal using both simulated and in vivo data. The proposed algorithm encompasses a pip-installable tool ( https://pypi.org/project/CSVD/), available on GitHub ( https://github.com/amirshamaei/CSVD), empowering researchers to use it in future studies. Additionally, to further promote transparency and reproducibility, we provide comprehensive code for result replication. CONCLUSIONS: The findings of this study suggest that the proposed method is a promising alternative to existing water removal methods due to its low processing time and good performance in removing water signals.
Mutations of the K-ras gene are found in a subset of non-small- cell lung carcinomas (NSCLC). The aim of our study was to determine the K-ras codon 12 mutation in the first, singular bronchoscopy specimen in parallel with the cytological examination for the diagnosis of lung cancer. Samples were obtained by diagnostic bronchoscopy in 140 patients with suspected lung tumors. The analysis of K-ras mutations was carried out by a sensitive two-step mutation- enriched polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. This method has been confirmed earlier to be positive for mutated tumor cells and negative for normal lung parenchyma and bronchus. Of the 140 patients with suspected cancer, 93 were diagnosed as NSCLC by cytology or histology in either the same specimen used for the detection of K-ras mutation or in later biopsies. However, only four K-ras codon 12 mutations were detected in the first bronchoscopic material: one in adenocarcinoma, two in squamous cell tumors, and one mutation was found in a patient with dysplasia which was diagnosed later as a squamous cell carcinoma. Our findings indicate that although the K-ras (codon 12) mutation is a gene lesion infrequently detectable in a singular specimen taken at the first bronchoscopy examination in cases of clinically suspected lung cancer, the detection of this mutation can help to confirm the cytological diagnosis of NSCLC or may be even diagnostic in cytologically negative cases.
- MeSH
- bronchoskopie MeSH
- dospělí MeSH
- financování organizované MeSH
- geny ras genetika MeSH
- kodon MeSH
- lidé středního věku MeSH
- lidé MeSH
- mutace MeSH
- nádory plic diagnóza genetika MeSH
- nemalobuněčný karcinom plic diagnóza genetika MeSH
- polymerázová řetězová reakce MeSH
- polymorfismus délky restrikčních fragmentů MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
This paper describes a comparative systems level analysis of the developmental proteome and transcriptome in the model antibiotic-producing eubacterium Streptomyces coelicolor, cultured on different media. The analysis formulates expression as the superposition of effects of regulatory networks and biological processes which can be identified using singular value decomposition (SVD) of a data matrix formed by time series measurements of expression of individual genes throughout the cell cycle of the bacterium. SVD produces linearly orthogonal factors, each of which can represent an independent system behavior defined by a linear combination of the genes/proteins highly correlated with the corresponding factor. By using SVD of the developmental time series of gene expression, as measured by both protein and RNA levels, we show that on the highest level of control (representing the basic kinetic behavior of the population), the results are identical, regardless of the type of experiment or cultivation method. The results show that this approach is capable of identifying basic regulatory processes independent of the environment in which the organism lives. It also shows that these processes are manifested equally on protein and RNA levels. Biological interpretation of the correlation of the genes and proteins with significant eigenprofiles (representing the highest level kinetic behavior of protein and/or RNA synthesis) revealed their association with metabolic processes, stress responses, starvation, and secondary metabolite production.
- MeSH
- bakteriální proteiny genetika metabolismus MeSH
- bakteriální RNA genetika metabolismus MeSH
- citrátový cyklus MeSH
- financování organizované MeSH
- interpretace statistických dat MeSH
- messenger RNA genetika metabolismus MeSH
- proteiny teplotního šoku genetika metabolismus MeSH
- proteomika metody statistika a číselné údaje MeSH
- stanovení celkové genové exprese metody statistika a číselné údaje MeSH
- Streptomyces genetika metabolismus růst a vývoj MeSH
- systémová biologie MeSH
- Publikační typ
- srovnávací studie MeSH
... Laurento vy řady a izolované singularity 152 -- 28. ... ... Odstranitelné singularity 167 -- 34. Póly 168 -- 35. Podstatné singularity 171 -- VI. ...
Matematika pro vysoké školy technické ; seš. 13
Vyd. 1. 227 s. : il. ; 24 cm
- MeSH
- analýza dat MeSH
- matematika MeSH
- Konspekt
- Matematika
- Učební osnovy. Vyučovací předměty. Učebnice
- NLK Obory
- přírodní vědy
- NLK Publikační typ
- učebnice vysokých škol
The adaptive immune receptors repertoire is highly plastic, with its ability to produce antigen-binding molecules and select those with high affinity for their antigen. Species have developed diverse genetic and structural strategies to create their respective repertoires required for their survival in the different environments. Camelids, until now, considered as a case of evolutionary innovation because of their only heavy-chain antibodies, represent a new mammalian model particularly useful for understanding the role of diversity in the immune system function. Here, we review the structural and functional characteristics and the current status of the genomic organization of camel immunoglobulins (IG) or antibodies, α/ß and γ/δ T cell receptors (TR), and major histocompatibility complex (MHC). In camelid humoral response, in addition to the conventional antibodies, there are IG with "only-heavy-chain" (no light chain, and two identical heavy gamma chains lacking CH1 and with a VH domain designated as VHH). The unique features of these VHH offer advantages in biotechnology and for clinical applications. The TRG and TRD rearranged variable domains of Camelus dromedarius (Arabian camel) display somatic hypermutation (SHM), increasing the intrinsic structural stability in the γ/δ heterodimer and influencing the affinity maturation to a given antigen similar to immunoglobulin genes. The SHM increases the dromedary γ/δ repertoire diversity. In Camelus genus, the general structural organization of the TRB locus is similar to that of the other artiodactyl species, with a pool of TRBV genes positioned at the 5' end of three in tandem D-J-C clusters, followed by a single TRBV gene with an inverted transcriptional orientation located at the 3' end. At the difference of TRG and TRD, the diversity of the TRB variable domains is not shaped by SHM and depends from the classical combinatorial and junctional diversity. The MHC locus is located on chromosome 20 in Camelus dromedarius. Cytogenetic and comparative whole genome analyses revealed the order of the three major regions "Centromere-ClassII-ClassIII-ClassI". Unexpectedly low extent of polymorphisms and haplotypes was observed in all Old World camels despite different geographic origins.
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
AIM: To present the technical principles of the hydrogen peroxide head preparation method, and to demonstrate the high quality of anatomical studies performed using these specimens, particularly for arachnoid exploration. MATERIAL AND METHODS: Five cadaveric heads were set with a 10% formalin solution and then injected with coloured latex. Thereafter, the heads were bleached with hydrogen peroxide solution 20%. Anatomical dissection of all specimens was performed. The skull base was drilled, dura mater gradually resected and outer arachnoid membranes examined and opened. The topographical anatomy was studied. RESULTS: All soft tissues, the brain, cranial nerves, the vasculature, the dura mater and even the arachnoid, were macroscopically intact, which enabled high-quality skull base specimens. In addition, the bone was softened, facilitating the drilling process. The topographical anatomy of anterior clinoid process was selected as an example and depicted in photos. CONCLUSION: High-quality anatomical specimens were obtained using the hydrogen peroxide head preparation. The topographic anatomy was studied from a unique downside-up angle, as well as by following the passage of the key neurovascular structures during its course. We propose the use of this method in neurosurgical training, especially to practice extradural approaches. Moreover this method seems promising as a complementary method for arachnoid studies.
- MeSH
- baze lební anatomie a histologie diagnostické zobrazování chirurgie MeSH
- dura mater MeSH
- klínová kost MeSH
- lidé MeSH
- mrtvola MeSH
- neurochirurgické výkony * MeSH
- peroxid vodíku * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH