SEARCH · PubMed Health

Results for “spatial sequencing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61Linked to original sources

PubMed2004

Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences.

We sequenced mitochondrial (cytochrome b, 12S rRNA) and nuclear (IRBP, RAG1) genes for 17 species of the Old World murine genus Mus, drawn primarily from the Eurasian subgenus Mus. Phylogenetic analysis of the newly and previously available sequences support recognition of four subgenera within Mus (Mus, Coelomys, Nannomys, and Pyromys), with an unresolved basal polytomy. Our data further indicate that the subgenus Mus contains three distinct 'species groups': (1) a Mus booduga Species Group, also including Mus terricolor and Mus fragilicauda (probably also Mus famulus); (2) a Mus cervicolor Species Group, also including Mus caroli and Mus cookii; and (3) a Mus musculus Species Group, also including Mus macedonicus, Mus spicilegus, and Mus spretus. Species diversity in Eurasian Mus is probably explicable in terms of several phases of range expansion and vicariance, and by a propensity within the group to undergo biotope transitions. IRBP and RAG1 molecular clocks for Mus date the origin of subgenera to around 5-6 mya and the origin of Species Groups within subgenus Mus to around 2-3 mya. The temporal pattern of evolution among Eurasian Mus is more complex than that within the Eurasian temperate genus Apodemus.

Animals↗

PubMed1990

Knowledge-based prediction of protein structures.

We propose a knowledge-based approach to the prediction of protein structures in cases where there is no sequence-homology to proteins with known spatial structure. Using methods from Artificial Intelligence we attempt to take into account long-range interactions within the prediction process. This allows not only the assignment of secondary but also of supersecondary structure elements. In particular, the patterns used as conditions of prediction rules are generated by learning methods from information contained in the Protein Data Base. Patterns on higher levels of the protein structure hierarchy are used as constraints to reduce the combinatorial search space. These patterns may also be used to search for specified structure motifs by interactive retrieval.

Artificial Intelligence↗

PubMed2000

Linking remote sensing, land cover and disease.

Land cover is a critical variable in epidemiology and can be characterized remotely. A framework is used to describe both the links between land cover and radiation recorded in a remotely sensed image, and the links between land cover and the disease carried by vectors. The framework is then used to explore the issues involved when moving from remotely sensed imagery to land cover and then to vector density/disease risk. This exploration highlights the role of land cover; the need to develop a sound knowledge of each link in the predictive sequence; the problematic mismatch between the spatial units of the remotely sensed and epidemiological data and the challenges and opportunities posed by adding a temporal mismatch between the remotely sensed and epidemiological data. The paper concludes with a call for both greater understanding of the physical components of the proposed framework and the utilization of optimized statistical tools as prerequisites to progress in this field.

Animals↗

PubMed1997

An investigation of cued recall of multiattribute stimuli.

Memory performance for sequences of letters positioned in particular spatial locations in a 3 x 3 grid was examined by requiring participants to recall attributes of the target stimuli given 1 or 2 features of the stimuli as cues. Cuing asymmetry was observed between the serial-position curves of object and sequential-order information, and location and sequential-order information, when the stimuli were presented in both the same and different locations. After correcting for response bias, this asymmetry was attenuated for the stimuli presented in different locations and was eliminated for the stimuli presented in the same location. Contrary to the predictions of the fragmentation hypothesis (G. V. Jones, 1976), asymmetry was also observed between object and location information. The roles of spatial location and response bias are offered as explanations for previous contradictory claims for cuing symmetry between item and order information.

Adult↗

PubMed2003

Current applications and future direction of MR mammography.

Compared with triple assessment for symptomatic and occult breast disease, magnetic resonance mammography (MRM) offers higher sensitivity for the detection of multifocal cancer, which is important in selecting patients appropriately for breast-conserving surgery. It is an ideal tool for the screening of patients with a high risk of breast cancer or where there is axillary disease or nipple discharge and conventional imaging has not revealed the primary focus. Techniques are now available to biopsy lesions only apparent on MRM. MRM can differentiate scar tissue from tumour; therefore, it is useful in patients in which there is possible recurrent disease. Clinical and X-ray mammographic assessment of response to neoadjuvant chemotherapy may be unreliable because of replacement of the tumour with scar tissue. MRM can identify responders and nonresponders with more accuracy. It is the modality of choice for the assessment of breast implants for rupture with accuracy higher than X-ray mammography and ultrasound. Advances in both spatial and temporal resolutions, the imaging sequences employed, pharmacokinetic modelling of contrast uptake, the use of dedicated and now phased-array breast coils, and gadolinium-based contrast agents have all played their part in the advancement of this imaging technique. Despite the limitations of patient compliance, scan-time and cost, this review describes how MRM has become a valuable tool in breast disease, especially in cases of diagnostic uncertainty. However, MRM must make the transition from research institutions into routine clinical practice.

Breast Diseases↗

PubMed1996

Chicken Pax-1 gene: structure and expression during embryonic somite development.

Recent mouse genetic studies have implicated Pax-1, a paired-box-containing gene, in sclerotomal differentiation and vertebral body formation. To investigate Pax-1 function in somitic sclerotomal differentiation in the chick embryo, we have cloned the chicken Pax-1 gene, and its full length cDNA, and characterized its temporal and spatial expression pattern during somite development. Sequence analysis shows that chicken Pax-1 is highly homologous to murine and human Pax-1 genes with respect to the putative DNA-binding paired-box domain and the octapeptide domain. Northern analysis using probes derived from the paired-box domain and a unique non-paired box sequence of chicken Pax-1 detected 2-kb mRNA transcript. The expression profiles of Pax-1 were examined by in situ hybridization and Northern analysis. The first detectable expression of Pax-1 is seen in the most caudal epithelial somite. As the somite matures, Pax-1 expression takes on a medial distribution, thus corresponding to but preceding the emergence of the sclerotome. In the more mature, rostral somites (stage V and older), Pax-1 expression is found to be progressively localized first to the ventral-medial regions, and then to the caudal-ventral-medial quadrant of the mature somite. This pattern strongly supports the notion that Pax-1 expression is involved in somitogenesis and sclerotomal differentiation, and that it is subsequently a characteristic of the caudal half of the sclerotome, the presumptive precursor of vertebral cartilage. Northern analysis substantiated this expression profile and further revealed that the level of somitic Pax-1 expression increases as a function of embryonic development. Finally, we subjected chicken embryos to controlled heat shock treatment to perturb somite formation and segmentation. The pattern of Pax-1 expression in the anomalous somitic structures generated by controlled heat shock further supports a functional role for Pax-1 in somite development.

Amino Acid Sequence↗

PubMed1997

Liquid-crystalline structure of nucleic acids: effect of antracycline drugs and copper ions.

The formation of liquid-crystalline dispersions (L.C.D.) from double-stranded DNA and polynucleotide (NA) molecules complexed with a number of anthracycline derivatives was investigated. These drugs form two types of complexes (complex I and complex II) with NA, which differ in the mode of drug orientation in respect to the NA helical axis. When complex II forms, addition of copper ions causes bridging of neighboring NA molecules through polymeric copper-anthracycline links (Figure 1). This results in an extra-increase in the amplitude of the intense CD band, characteristic for complex II, in the drug absorption region. Comparison of data obtained for different analogs and derivatives of daunomycin, has shown that the presence of 4 coordinating oxygen atoms at positions 5,6 and 11,12 (or 1,12) of the anthracycline ring system represents the basic prerequisite for the formation of a long polymeric chelate bridge after addition of copper ions. A second requirement relates to the chemical and stereochemical properties of sugar residues at position 7. These are important for proper positioning of the neighboring anthracycline aglycones in the polymeric chelate bridges and for spatial fixation of Cu2+ ions. Base sequence of double-stranded polynucleotides plays, if any, a minor role in polymeric chelate bridge formation. The question concerning the sterical orientation of two neighbouring antracyclines in the linking bridges, formed between NA molecules fixed in the liquid-crystalline structure, remains open.

Anthracyclines↗

PubMed2006

Co-registration of cardiac MRI and rest gated SPECT in the assessment of myocardial perfusion, function and viability.

PURPOSE: Myocardial perfusion is routinely measured by SPECT--this technique has a rather low spatial resolution but covers the whole myocardium and is equipped with efficient image analysis software. Cardiac MRI has higher spatial resolution than SPECT and excellent sequences for myocardial function and viability detection but the lack of easy-to-use methods of acquisition and post-processing of perfusion images prevents this method from being used for perfusion evaluation in clinical practice. The aim of the study was to explore whether the 3-D co-registration of "cine" MRI (cine MRI), delayed enhancement MRI (DE MRI) and gated SPECT (GSPECT) images might be used for differentiating all reversible and irreversible effects of ischemia in anatomically matched myocardial regions. METHODS: We analyzed 685 segments of the heart (6 segments in each short axis slice)-obtained as a result of MRI and GSPECT studies performed in 18 patients. In each segment, myocardial function, perfusion and viability were analyzed. Myocardial wall function was evaluated using the matched images of diastolic and systolic phases of cine MRI. Perfusion as MIBI uptake per volume (MIV) (counts/mm3) in each myocardial segment was evaluated by co-registration of diastolic phases of cine MRI and GSPECT. Transmural extent of infarction was determined by co-registration of DE MRI and diastolic phase of cine MRI. RESULTS: We have found a close correlation between regional perfusion and function at rest in matched MRI and SPECT images: dysfunctional segments had significantly less MIV (MIV = 4.63 SD 1.58) than normal segments (MIV = 8.86 SD 2.77) (p < .05). There was no significant difference in MIV between viable and non-viable dysfunctional segments defined by DE MR due to a small number of nonviable segments in our study (18/685). CONCLUSION: Matching rest perfusion and function in anatomically co-registered myocardial segments in our study confirms that 3-D image co-registration of cine MRI, DE MRI and gated SPECT could be a precise method of integrated visualization of perfusion, function and viability helping in differentiating all forms of reversible and irreversible effects of myocardial ischemia.

Aged↗

PubMed1994

Functional cooperativity of human cortical motor areas during self-paced simple finger movements. A high-resolution MRI study.

Magnetic resonance imaging of changes in cerebral blood oxygenation (CBO) delineated areas of neural activation during self-paced unilateral middle finger tapping in five normal volunteers. Four contiguous imaging sections parallel to the bicommissural plane covered the hand area of the primary sensori-motor cortex bilaterally. All measurements were performed at 2.0 T using rapid gradient-echo sequences (TR/TE = 63/30 ms) with high spatial resolution (0.8 x 1.6 x 4 mm) and both strong (40 degrees flip angle) and weak (10 degrees) radiofrequency excitation pulses. This allows differentiation of flow and CBO contributions to the observed signal alterations. Functional cooperativity was analysed by a pixel-by-pixel correlation of signal intensity time courses with the stimulus protocol. Areas of activation included the contralateral primary motor cortex, the homologue part of the primary sensory cortex, the supplementary motor area (SMA) and the lateral premotor areas in all volunteers. Task-related activation of ipsilateral primary motor cortex above a threshold correlation coefficient of 0.5 was seen in two out of five volunteers (at 40 degrees) and one out of five (at 10 degrees) when performing the right-hand task. The present MRI findings readily demonstrate in single subjects that the SMA is involved in self-paced finger tapping. Only sparse activation in the ipsilateral primary motor cortex is consistent with the motor paradigm used.

Adult↗

PubMed2002

Bone morphogenetic protein-4-induced activation of Xretpos is mediated by Smads and Olf-1/EBF associated zinc finger (OAZ).

We have previously isolated Xretpos, a novel family of long terminal repeat (LTR)-retrotransposons in Xenopus laevis, whose transcript is restricted to ventro-posterior-specific regions and induced by bone morphogenetic protein-4 (BMP-4) signaling. To explore the molecular mechanism of the transcriptional regulation, we identified and characterized Xretpos promoter regions consisting of LTRs and a 5'-untranslated region. We demonstrated that this promoter region contains all the necessary regulatory elements for the spatial and temporal expression of XRETPOS: Sequence analysis of the Xretpos promoter revealed multiple Smad-binding elements and Olf-1/EBF-associated zinc finger (OAZ) binding sites similar to BMP-4 response element, which were identified and proved to be required for BMP-4 induction in the Xvent2 promoter. We further demonstrated that Smads and OAZ proteins bind to their response elements in the promoter and these bindings are essential for the BMP-4-induced activation of the Xretpos promoter. Furthermore, we showed that the endogenous expression of Xretpos protein indeed occurred and was temporally regulated and BMP-4-inducible during the early Xenopus development. Finally, overexpression and partial loss-of-function study revealed that Xretpos has a posterio-ventralizing activity. Together, our results place Xretpos downstream of BMP-4 and provide evidence for the conserved mechanism of transcriptional regulation of the BMP-4 target genes.

5' Flanking Region↗

PubMed2006

Cloning and expression of new microRNAs from zebrafish.

MicroRNAs (miRNAs) play an important role in development and regulate the expression of many animal genes by post-transcriptional gene silencing. Here we describe the cloning and expression of new miRNAs from zebrafish. By high-throughput sequencing of small-RNA cDNA libraries from 5-day-old zebrafish larvae and adult zebrafish brain we found 139 known miRNAs and 66 new miRNAs. For 65 known miRNAs and for 11 new miRNAs we also cloned the miRNA star sequence. We analyzed the temporal and spatial expression patterns for 35 new miRNAs and for 32 known miRNAs in the zebrafish by whole mount in situ hybridization and northern blotting. Overall, 23 of the 35 new miRNAs and 30 of the 32 known miRNAs could be detected. We found that most miRNAs were expressed during later stages of development. Some were expressed ubiquitously, but many of the miRNAs were expressed in a tissue-specific manner. Most newly discovered miRNAs have low expression levels and are less conserved in other vertebrate species. Our cloning and expression analysis indicates that most abundant and conserved miRNAs in zebrafish are now known.

Animals↗

PubMed2001

Quantification of blood flow in the carotid arteries: comparison of Doppler ultrasound and three different phase-contrast magnetic resonance imaging sequences.

RATIONALE AND OBJECTIVES: To compare blood flow velocities in the carotid arteries measured with three different magnetic resonance (MR) phase-contrast imaging techniques and with percutaneous Doppler ultrasound. METHODS: Fourteen healthy male volunteers with a mean age of 33 +/- 3.8 years were studied. Ultrasound and MR phase velocity mapping of both common carotid arteries (n = 28) was performed within 5 hours. A two-dimensional fast low-angle shot sequence with retrospective cardiac gating, a sequence with prospective cardiac triggering, and a breath-hold sequence with prospective cardiac triggering were used. Resistance indexes and pulsatility indexes were calculated for all modalities. RESULTS: The comparison of flow velocities obtained with ultrasound and the different MR techniques led to a moderate correlation of the retrospective gated and prospective triggered MR techniques (eg, r = 0.73 for maximum systolic velocity). The worst correlation was found between the breath-hold technique and retrospective cardiac gating (eg, r = 0.004 for pulsatility index). There was a weak correlation of all three MR sequences compared with ultrasound (r = 0.19-0.60) CONCLUSIONS: A moderate correlation was found between velocities and indexes measured with the prospective cardiac-triggered phase-contrast MR technique and the retrospective cardiac-gated phase-contrast MR technique. A weak correlation was found between the three different MR techniques and ultrasound, as well as between the breath-hold prospective cardiac-triggered MR sequence and both of the other MR sequences. The influence of temporal and spatial resolution on MR phase-contrast velocity mapping was confirmed.

Adult↗

PubMed1993

New methods for discriminating neural and optical losses of vision.

Visual acuity, the premier test of visual function, is analyzed as a three-stage, hierarchical sequence beginning with the detection of spatial contrast, followed by the resolution of that contrast into spatially separate elements, and ending with the identification of a particular arrangement of elements as one of several possible test objects, e.g., a letter in the Snellen alphabet. Each stage in this process has its own inherent limitations which are associated with different stages of the visual pathway. New methods are described for testing each stage of the hierarchy individually for the purpose of identifying the weak link in the chain, thus paving the way for differential diagnosis of optical and neural losses of vision.

Contrast Sensitivity↗

PubMed2003

Evolutionary foundations of number: spontaneous representation of numerical magnitudes by cotton-top tamarins.

Although animals of many species have been shown to discriminate between visual-spatial arrays or auditory-temporal sequences based on numerosity, most of the evidence for numerosity discrimination derives from experiments involving extensive laboratory training. Under these conditions, animals' discrimination of two numerosities depends on their ratio and is independent of their absolute value. It is an open question whether any untrained non-human animal spontaneously represents number in this way, as do human children and adults. We present the results of familiarization-discrimination experiments on cotton-top tamarin monkeys (Saguinus oedipus) that provide evidence for numerosity discrimination in the absence of training. Presented with auditory stimuli (speech syllables) controlled for the continuous variables of sequence duration, item duration, inter-stimulus interval and overall energy, tamarins readily discriminated sequences of 4 versus 8, 4 versus 6, and 8 versus 12 syllables. By contrast, tamarins failed to discriminate sequences of 4 versus 5 and 8 versus 10 syllables, providing evidence that their numerosity discrimination is approximate and shows the ratio signature of numerosity discrimination in humans and trained non-human animals. These results provide strong support for the hypothesis that representations of large, approximate numerosity are evolutionarily ancient and spontaneously available to non-human animals.

Acoustic Stimulation↗

PubMed2001

Copolymer-assisted generation of three-dimensional patterns by replicating two-dimensional substrate motifs.

We use a three-dimensional self-consistent field model to study copolymer adsorption from polymer melts onto chemically heterogeneous substrates. We show that in situations where the copolymer sequence distribution is commensurate with the spatial distribution of the substrate chemical impurities, the two-dimensional substrate pattern gets transcribed into three dimensions and propagates into the polymer mixture. This transference scheme can assist in designing nanostructures that find use in various areas of science and technology.

Journal Article↗

PubMed1995

A technique for measurement of the extent of spatial organization of atrial activation during atrial fibrillation in the intact human heart.

Atrial fibrillation (AF) is a common clinical problem, associated with considerable morbidity and mortality, for which effective management strategies have yet to be devised. The absence of objective measures to guide selection of antiarrhythmic drug therapy for maintenance of sinus rhythm leaves only clinical endpoints (either beneficial or detrimental) for assessment of drug action, with occasional catastrophic consequences. As part of an attempt to provide an objective framework for the assessment of antiarrhythmic drug action on the electrophysiologic determinants of atrial fibrillation, we have developed a measure of the spatial organization of atrial activation processes during atrial fibrillation. By recording activation sequences at multiple equally spaced locations on the endocardial surface of the atria during atrial fibrillation in humans and determining the degree of correlation between these activation sequences as a function of distance, we have been able to construct spatial correlation functions for atrial activation. We have found that atrial activation remains well-correlated, independent of distance during normal sinus rhythm and atrial flutter. During atrial fibrillation, correlation decays monotonically with distance and the space-constant for this decay may be used to describe the relative spatial organization of atrial fibrillation. We provide examples of the impact of antiarrhythmic agents on the space-constant and suggest that assessment of the relative spatial organization of atrial activation using this methodology may potentially provide an objective framework to guide therapy in patients with AF.

Adenosine↗

PubMed2006

Degradation of the Poliovirus 1 genome by chlorine dioxide.

AIMS: This study was undertaken to gain an understanding of the factors that influence viral RNA degradation in the presence of chlorine dioxide (ClO(2)), which will be very useful in helping to define the significance of the presence of the viral genome in disinfected water. METHODS AND RESULTS: We focused our investigation on the influence of ClO(2) on extracted RNA on the one hand, and on the infectious virus on the other. Our first results show that RNA degradation, like viral inactivation, is dose dependent. The influence of the spatial organization of the targeted genomic sequence, as well as that of its size and location (and/or sequence) on degradation of the Poliovirus 1 genome by ClO(2), was studied using real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The results show that the preferential sites of action of ClO(2) appear to be located in the untranslated regions, 5'- and 3'-UTR, a phenomenon influenced by both the presence of secondary structures and the genomic sequence in these regions. Our results also reveal a rapid decrease of infectious particles quantified by the cell culture for the applied dose. Comparison between cell culture and real-time PCR for viral detection reveals disagreement following disinfection treatment, even for the largest targeted fragment (a 6,989-base fragment representing the quasi-whole viral genome). CONCLUSIONS: The detection of genome fragments is insufficient to confirm the presence of the infectious virus, as each targeted fragment shows a different sensitivity. Hence, the smallest targeted fragment (76 bp) persisted throughout the analysis period, while the longest targeted fragment (6,989 bp) disappeared very rapidly. Highly sensitive regions (i.e. 5'- and 3'-UTR) should be targeted to avoid an overestimation of the risk of viral infection using molecular biology methods in water following disinfection. Further studies in this area are needed. SIGNIFICANCE AND IMPACT OF THE STUDY: To date, it has not been possible to routinely apply virological controls to drinking water because of the time-consuming nature of the gold standard technique (cell culture) and its inability to detect all serotypes (e.g. Norovirus). Molecular techniques (e.g. real-time RT-PCR) constitute a solution to the rapid and specific detection of all the serotypes. However, ignorance of the mechanisms of viral degradation prevents the validation of PCR for the measurement of the risk of infection to humans following disinfection treatment.

Chlorine Compounds↗

PubMed2001

High resolution gel-dosimetry by optical-CT and MR scanning.

The increased intricacy of Intensity-Modulated-Radiation-Therapy (IMRT) delivery has created the need for a high-resolution 3D-dosimetry (three-dimensional) system capable of measuring and verifying the complex delivery. Present clinical methods are inadequate being restricted to single points (e.g., ion-chambers) or to 2D planes (e.g., film), and are labor intensive. In this paper we show that gel-dosimetry in conjunction with optical-CT scanning can yield maps of dose that are of sufficient accuracy, resolution and precision to allow verification of complex radiosurgery deliveries, and by extension IMRT deliveries. The radiosurgery dose-distribution represents the most challenging case encountered in external beam therapy by virtue of the steep dose-gradients and high resolution of delivery. We characterize the stringent radiosurgery requirements by the RTAP (Resolution-Time-Accuracy-Precision) criteria defined as < or = 1 mm3 spatial resolution, < or = 1 hour imaging time, accurate to within 3%, and within -1% precision. The RTAP criteria is applied to an in-house laser-based optical-CT scanning system presented here, and evaluated using gel-flasks containing BANG3 gel. The same gel flasks were subsequently imaged using the MR imaging protocol recommended by the gel manufacturer, but modified to match as closely as possible the RTAP. The resulting dose-maps demonstrate the high precision (< 1.3% noise at high dose) achievable with optical CT scanning while preserving high spatial resolution (<1 mm3). Using the sequence above, the MR gel-dose maps were found to have poorer precision by a factor of 5, under the strict conditions of the RTAP. The optical CT gel-dosimetry system was further evaluated for the verification of a complex 3-isocenter radiosurgery delivery. In conclusion, this work demonstrates that gel-dosimetry and optical-CT scanning approach an important long-term goal of radiation dosimetry, as specified by the RTAP criteria, and have potential to impact the clinic by improving and facilitating clinical dose verification for the most complex external beam radiation treatments.

Calibration↗