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PubMed1992

Gonadotropin-releasing hormone neurons and pathways in the brain of the female mink (Mustela vison).

The distribution of gonadotropin-releasing hormone-immunoreactive neurons and processes was mapped in the female mink brain using coronal, horizontal and sagittal sections. Perikarya were found along a ventral continuum including the olfactory tubercle, the diagonal band of Broca, the lateral septum, the preoptic and anterior hypothalamic area and the mediobasal hypothalamus; 80% of the perikarya were counted in the mediobasal hypothalamus. Fibres were mainly observed in the organum vasculosum of the lamina terminalis and the median eminence. A few processes terminated in the ependymal cells lining the third and lateral ventricles. The total number of immunoreactive perikarya was the highest in the brains of females sacrificed in July; it then significantly decreased until December. This variation is discussed in relation to the annual breeding cycle.

Animals↗
PubMed1991

Cerebellar development: afferent organization and Purkinje cell heterogeneity.

Olivo- and spinocerebellar maps in the adult cerebellum of small rodents are discontinuous, with sharp boundaries. Cortical Purkinje cells constitute a heterogeneous population, organized into parasagittal, mutually exclusive compartments. The boundaries of the intrinsic cortical compartments and those of the projectional maps are congruent. During development; (i) The incoming olivary fibres, once they penetrate in the cerebellar parenchyma, are attracted toward their ultimate terminal fields, without passing through a stage of random dispersion. (ii) Migrating Purkinje cells and inferior olivary neurons begin, asynchronously, to express cellular markers in an independent manner, giving rise to a transient compartmentation of the cerebellar cortex and the inferior olivary complex respectively. In both instances, the biochemical heterogeneity disappears during the first postnatal week, simultaneously with the acquisition of adult-like cerebellar maps. (iii) The formation of the maps is an early event, prior to the establishment of the synaptology of the cerebellar cortical circuitry. Moreover, the organization of the spinocerebellar projection in adult mutant mice does not depend on the presence of granule cells (staggerer) but on the presence of normal Purkinje cells (weaver), indicating that synaptogenesis with their target neurons is not involved in the process of map formation. The matching of region specific chemical labels between incoming afferent fibres and heterogeneous sets of Purkinje cells is the most appealing mechanism for the formation of cerebellar maps.

Afferent Pathways↗
PubMedDate not supplied

Representing information in patient reports using natural language processing and the extensible markup language.

OBJECTIVE: To design a document model that provides reliable and efficient access to clinical information in patient reports for a broad range of clinical applications, and to implement an automated method using natural language processing that maps textual reports to a form consistent with the model. METHODS: A document model that encodes structured clinical information in patient reports while retaining the original contents was designed using the extensible markup language (XML), and a document type definition (DTD) was created. An existing natural language processor (NLP) was modified to generate output consistent with the model. Two hundred reports were processed using the modified NLP system, and the XML output that was generated was validated using an XML validating parser. RESULTS: The modified NLP system successfully processed all 200 reports. The output of one report was invalid, and 199 reports were valid XML forms consistent with the DTD. CONCLUSIONS: Natural language processing can be used to automatically create an enriched document that contains a structured component whose elements are linked to portions of the original textual report. This integrated document model provides a representation where documents containing specific information can be accurately and efficiently retrieved by querying the structured components. If manual review of the documents is desired, the salient information in the original reports can also be identified and highlighted. Using an XML model of tagging provides an additional benefit in that software tools that manipulate XML documents are readily available.

Humans↗
PubMedDate not supplied

Acute stroke evaluated by time-to-peak mapping during initial and early follow-up perfusion CT studies.

BACKGROUND AND PURPOSE: Early diagnosis of perfusion deficits in patients with acute stroke could guide treatment decisions and improve prognosis. We investigated the sensitivity of perfusion CT studies using parametric time-to-peak maps to assess ischemic brain tissue with respect to early infarct signs on native CT scans. METHODS: First-pass, single-section perfusion CT was performed in 20 patients who presented with symptoms of acute stroke within 6 hours of onset. Initial CT perfusion studies were compared with follow-up studies within 30 hours in 10 patients. A manual, region of interest (ROI)-based, local evaluation procedure was performed to determine delayed time-to-peak values and diminished peak amplitudes. In addition, time-to-peak parameter maps were processed off-line from the dynamic CT data sets to identify areas of perfusion deficits, which were expressed as hemispheric lesion areas (HLAs). Evolution of the ischemic regions was assessed by comparing the HLA on the initial and follow-up studies as well as on the native CT scan of the follow-up studies. RESULTS: Diagnostic time-to-peak maps were generated in 19 of 20 initial and in nine of 10 follow-up perfusion CT studies. The initial time-to-peak map showed perfusion deficits in 14 of 20 patients. Hemispheric territorial infarcts were diagnosed with a sensitivity of 93%. Perfusion deficits in two patients with brain stem infarctions and three patients with lacunar strokes were missed. Follow-up time-to-peak maps showed the extent of reperfusion after various therapeutic strategies. CONCLUSION: Perfusion CT is potentially useful for detecting cerebral perfusion deficits in acute ischemic stroke before morphologic changes are observable on native CT scans. Compared with a locally restricted ROI-based evaluation, time-to-peak maps provide sensitive, global indications of malperfused brain areas, facilitate lesion localization, and allow assessment of the evolution of the infarction during follow-up.

Acute Disease↗
PubMed1990

In vitro regulation of human hepatitis B virus core gene transcription.

In the present study we used a HeLa whole cell extract transcription system to map the transcription start sites and the minimal promoter of the hepatitis B virus core gene. Two initiation sites located at residues 1792 +/- 5 and 1817 +/- 5 were identified. The minimal upstream region essential and sufficient for transcription was defined to a 105-base pair DNA fragment. These results are identical to the in vivo mapping of the transcription start sites and the minimal core gene promoter. When in vitro transcription elongation was carried out in the presence of the anionic detergent Sarkosyl, known to enhance premature transcription termination (attenuation), two short transcripts (as well as two run-offs) were synthesized. Kinetic studies indicated that the short transcripts resulted from a block to transcription elongation and not from RNA processing. RNA mapping showed that the short attenuated transcripts indeed initiated at the two core gene initiation sites and both prematurely terminated at nucleotide 1966 +/- 5, defined as the attenuation site. This site is located in the attenuator RNA within a uridine-rich sequence preceded by a stable hairpin structure. Attenuation at the same site occurred when transcription of the core gene was directed by the Ad2 major late promoter (MLP) and when the poly(A) signal, which precedes the attenuation site, was mutated from TATAAA to TAGAAA. We suggest that the elongation block at nt 1966 +/- 5 in vivo exerts a dual function: first, it regulates the level of RNA by attenuation during the first cycle of transcription and, second, it acts as a termination site at the end of the primary RNA transcript.

Base Sequence↗
PubMed1984

Cotranscription and processing of 23S, 4.5S and 5S rRNA in chloroplasts from Zea mays.

The termini of rRNA processing intermediates and of mature rRNA species encoded by the 3' terminal region of 23S rDNA, by 4.5S rDNA, by the 5' terminal region of 5S rDNA and by the 23S/4.5S/5S intergenic regions from Zea mays chloroplast DNA were determined by using total RNA isolated from maize chloroplasts and 32P-labelled rDNA restriction fragments of these regions for nuclease S1 and primer extension mapping. Several processing sites detectable by both 3' and 5' terminally labelled probes could be identified and correlated to the secondary structure for the 23S/4.5S intergenic region. The complete 4.5S/5S intergenic region can be reverse transcribed and a common processing site for maturation of 4.5S and 5S rRNA close to the 3' end of 4.5S rRNA was detected. It is therefore concluded that 23S, 4.5S and 5S rRNA are cotranscribed.

Base Sequence↗
PubMed2025

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.

SUMMARY: Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into "virtual colors." These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct "colors" from the perspective of the pseudoalignment algorithm. We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac. We compare alevin-fry-atac to both Chromap and Cell Ranger ATAC. Alevin-fry-atac is highly scalable and, when using 32 threads, is 2.8 times faster than Chromap (the second fastest approach) while using only 33% of the memory required by Chromap. The resulting peaks and clusters generated from alevin-fry-atac show high concordance with those obtained from both Chromap and the Cell Ranger ATAC pipeline, demonstrating that virtual color-enhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing. The development of alevin-fry-atac brings single-cell ATAC-seq processing into a unified ecosystem with single-cell RNA-seq processing (via alevin-fry) to work toward providing a truly open alternative to many of the varied capabilities of CellRanger. AVAILABILITY AND IMPLEMENTATION: Alevin-fry-atac is written in Rust and C++17, and is freely-available under a BSD 3-clause license. It is integrated into piscem (https://github.com/COMBINE-lab/piscem) and alevin-fry (https://github.com/COMBINE-lab/alevin-fry), and is also supported directly as part of simpleaf (https://github.com/COMBINE-lab/simpleaf).

Single-Cell Analysis↗
PubMed1991

Functional reorganization of adult cat somatosensory cortex is dependent on NMDA receptors.

We studied effects of selective blockade of N-methyl-D-aspartate (NMDA) receptors in the primary somatosensory cortex (SI) of the adult cat on reorganization of cortical maps after selective deafferentation. About two weeks after hindlimb deafferentation, cortical loci representing the 'trunk' seemingly expanded and 'migrated' into areas originally devoted to the 'hindlimb'. Selective blockade of NMDA receptors of the SI cells by continuous infusion of 2-amino-5-phosphonovalerate (APV) into the cortex disrupted such change. The APV treatment also depressed responses of SI cells to natural sensory stimulation, but left no long-lasting side effects. The results suggest that the processes of map reorganization take place within the SI and involve mechanisms dependent on NMDA-receptor-mediated activity.

2-Amino-5-phosphonovalerate↗
PubMedDate not supplied

Patching. Restitching business portfolios in dynamic markets.

In turbulent markets, businesses and opportunities are constantly falling out of alignment. New technologies and emerging markets create fresh opportunities. Converging markets produce more. And of course, some markets fade. In this landscape of continuous flux, it's more important to build corporate-level strategic processes that enable dynamic repositioning than it is to build any particular defensible position. That's why smart corporate strategists use patching, a process of mapping and remapping business units to create a shifting mix of highly focused, tightly aligned businesses that can respond to changing market opportunities. Patching is not just another name for reorganizing; patchers have a distinctive mindset. Traditional managers see structure as stable; patching managers believe structure is inherently temporary. Traditional managers set corporate strategy first, but patching managers keep the organization focused on the right set of business opportunities and let strategy emerge from individual businesses. Although the focus of patching is flexibility, the process itself follows a pattern. Patching changes are usually small in scale and made frequently. Patching should be done quickly; the emphasis is on getting the patch about right and fixing problems later. Patches should have a test drive before they're formalized but then be tightly scripted after they've been announced. And patching won't work without the right infrastructure: modular business units, fine-grained and complete unit-level metrics, and companywide compensation parity. The authors illustrate how patching works and point out some common stumbling blocks.

Commerce↗
PubMed1993

ODS: ordering DNA sequences--a physical mapping algorithm based on simulated annealing.

In the program ODS we provide a methodology for quickly ordering random clones into a physical map. The process of ordering individual clones with respect to their position along a chromosome is based on the similarity of binary signatures assigned to each clone. This binary signature is obtained by hybridizing each clone to a panel of oligonucleotide probes. By using the fact that the amount of overlap between any two clones is reflected in the similarity of their binary signatures, it is possible to reconstruct a chromosome by minimizing the sum of linking distances between an ordered sequence of clones. Unlike other programs for physical mapping, ODS is very general in the types of data that can be utilized for chromosome reconstruction. Any trait that can be scored in a presence--absence manner, such as hybridized synthetic oligonucleotides, restriction endonuclease recognition sites or single copy landmarks, can be used for analysis. Furthermore, the computational requirements for the construction of large physical maps can be measured in a matter of hours on work-stations such as the VAX2000.

Algorithms↗
PubMed2001

Human glycosaminoglycan glucuronyltransferase I gene and a related processed pseudogene: genomic structure, chromosomal mapping and characterization.

Here we describe the characterization of the human glycosaminoglycan glucuronyltransferase I gene (GlcAT-I) and a related pseudogene. The GlcAT-I gene was localized to human chromosome 11q12-q13 by in situ hybridization of metaphase chromosomes. GlcAT-I spanned 7 kb of human genomic DNA and was divided into five exons. Northern blot analysis showed that GlcAT-I exhibited ubiquitous but markedly different expressions in the human tissues examined. The GlcAT-I promoter was approx. 3-fold more active in a melanoma cell line than in a hepatoma cell line, providing evidence for the differential regulation of the gene's expression. Stepwise 5' deletions of the promoter identified a strong enhancer element between -303 and -153 bp that included binding motifs for Ets, CREB (cAMP-response-element-binding protein) and STAT (signal transducers and activators of transcription). Screening of a human genomic library identified one additional distinct genomic clone containing an approx. 1.4 kb sequence region that shared an overall 95.3% nucleotide identity with exons 1-5 of GlcAT-I. However, a lack of intron sequences, as well as the presence of several nucleotide mutations, insertions and deletions that disrupted the potential GlcAT-I reading frame, suggested that the clone contained a processed pseudogene. The pseudogene was localized to chromosome 3. The human genome therefore contains two related GlcAT-I genes that are located on separate chromosomes.

Base Sequence↗
PubMed1990

Problems and pitfalls in the performance and interpretation of color Doppler flow imaging: observations based on the influences of technical and physiological factors on the color Doppler examination of mitral regurgitation.

Color Doppler flow imaging has become an integral part of the echocardiographic examination. By providing real-time, two-dimensional spatial maps of normal and abnormal cardiac blood flows, this technique provides important information that may be used to guide patient management. The acquisition and display of color Doppler flow information may be influenced by technical factors, by the physiological condition of the patient, by abnormalities of cardiac morphology, and, on occasion, by artifact. In this article, the results of a study performed to evaluate the influence of technical factors on the color Doppler assessment of mitral regurgitation are reported. Mitral regurgitation jet area size changed significantly with variation in the control settings for color gain, color process, color map, color image resolution, and sector width. A review of those factors that influence the performance and interpretation of the color Doppler flow examination is provided and their significance discussed.

Echocardiography, Doppler↗
PubMed1985

DNA-mediated transfer of human melanoma cell surface glycoprotein gp130: identification of transfectants by erythrocyte rosetting.

DNA sequences encoding a human melanoma membrane-bound sialoglycoprotein of 130,000 molecular weight (gp130) were introduced into a clonal derivative of mouse B-16 melanoma cells with the selectable neomycin resistance gene (aminoglycoside phosphotransferase). Mouse transfectants were identified by a rapid and precise screening method with mouse monoclonal antibodies and erythrocyte rosetting. The frequency of gp130 transfectants was approximately 1 in 2,000 to 5,000 colonies with neo+ cells. Analysis of secondary mouse transfectants has revealed that the transfected gp130 has a molecular weight, isoelectric point, intracellular processing, peptide map, and spatial orientation of surface-exposed epitopes indistinguishable from those seen with gp130 from human melanoma cells. In contrast to primary transfectants, secondary transfectants expressing gp130 lack demonstrable human repetitive sequences.

Animals↗
PubMed2002

False memories of the future: a critique of the applications of probabilistic reasoning to the study of cognitive processes.

The authors argue that the ways in which people-scientists and laymen-use probabilistic reasoning is predicated on a set of often questionable assumptions that are implicit and frequently go untested. They relate to the correspondence between the terms of a theory and the observations used to validate the theory and to the implicit understandings of intention and prior knowledge that arise between the conveyer and the receiver of information. The authors show several ways in which the use of probabilistic reasoning rests on a priori commitments to a partitioning of an outcome space and demonstrate that there are many more assumptions underlying the use of probabilistic reasoning than are usually acknowledged. They unfold these assumptions to show how several different interpretations of the same results in behavioral decision theory and cognitive psychology are equally well supported by "the facts." They then propose a more comprehensive approach to mapping cognitive processes than those currently used, one that is based on the analysis of all of the relevant alternative interpretations presented in the article.

Cognition↗
PubMedDate not supplied

Comparison of MultiMap and TSP/CONCORDE for constructing radiation hybrid maps.

Radiation hybrid (RH) map construction allows investigators to locate both type I and type II markers on a given genome map. The process is composed of two steps. The first consists of determining the pattern distribution of a set of markers within the different cell lines of an RH panel. This is mainly done by polymerase chain reaction (PCR) amplification and gel electrophoresis, and results in a series of numbers indicating the presence or the absence of each marker in each cell line. The second step consists of a comparison of these numbers, using various algorithms, to group and then order markers. Because different algorithms may provide (slightly) different orders, we have compared the merits of the MultiMap and TSP/CONCORDE packages using a data set of information currently under analysis for construction of the canine genome RH map.

Animals↗
PubMed2006

Nested deletion analysis of Wheat streak mosaic virus HC-Pro: Mapping of domains affecting polyprotein processing and eriophyid mite transmission.

A series of in-frame and nested deletion mutations which progressively removed 5'-proximal sequences of the Wheat streak mosaic virus (WSMV) HC-Pro coding region (1152 nucleotides) was constructed and evaluated for pathogenicity to wheat. WSMV HC-Pro mutants with 5'-proximal deletions of 12 to 720 nucleotides systemically infected wheat. Boundary sequences flanking the deletions were stable and unaltered by passage through plants for all deletion mutants except HCD12 (lacking HC-Pro codons 3-6) that exhibited strong bias for G to A substitution at nucleotide 1190 in HC-Pro codon 2 (aspartic acid to asparagine). HC-Pro mutants with 5'-proximal deletions of up to 720 nucleotides retained autoproteolytic activity in vitro. In contrast, 5'-proximal deletion of 852 nucleotides of the HC-Pro coding region (HCD852) abolished both infectivity and in vitro proteolytic activity, confirming that the proteolytic domain of WSMV HC-Pro resides within the carboxy-terminal third of the protein and includes the cysteine proteinase motif (GYCY) conserved among four genera of the family Potyviridae. Inoculation of wheat with HC-Pro deletion mutants also bearing the GUS reporter gene revealed that HCD852 was unable to establish primary infection foci in inoculated leaves, indicating that processing of the P3 amino-terminus was essential. Deletion of as few as 24 nucleotides of HC-Pro (codons 3-10) eliminated transmission by the eriophyid mite vector Aceria tosichella Keifer. Collectively, these results demonstrated similar organization of proteinase and vector transmission functional domains among divergent HC-Pro homologues encoded by potyviruses and tritimoviruses.

Amino Acid Sequence↗
PubMed2006

Altered brain activity processing in high-anxiety rodents revealed by challenge paradigms and functional mapping.

Pathological anxiety involves aberrant processing of emotional information that is hypothesized to reflect perturbations in fear/anxiety pathways. The affected neurobiological substrates in patients with different anxiety disorders are just beginning to be revealed. Important leads for this research can be derived from findings obtained in psychopathologically relevant rodent models of enhanced anxiety, by revealing where in the brain neuronal processing in response to diverse challenges is different to that in animals with lower anxiety levels. Different functional mapping methods in various rodent models, including psychogenetically selected lines or genetically modified animals, have been used for this purpose. These studies show that the divergent anxiety-related behavioral response of high-anxiety- vs. normal and/or low-anxiety rodents to emotional challenges is associated with differential neuronal activation in restricted parts of proposed fear/anxiety circuitries including brain areas thought to be important in stress, emotion and memory. The identification of neuronal populations showing differential activation depends in part on the applied emotional challenge, indicating that specific facets of elicited fear or anxiety preferentially engage particular parts of the fear/anxiety circuitry. Hence, only the use of an array of different challenges will reveal most affected brain areas. A number of the neuronal substrates identified are suggested as candidate mediators of dysfunctional brain activation in pathological anxiety. Indeed, key findings revealed in these rodent models show parallels to observations in human symptom provocation studies comparing anxiety disorder patients with healthy volunteers. Work to investigate exactly which of the changed neuronal activation patterns in high-anxiety rodents has to be modulated by therapeutic drugs to achieve effective anxiolysis and via which neurochemical pathways this can be accomplished is at its early stages but has identified a small number of promising candidates. Extending these approaches should help to provide further insight into these mechanisms, revealing new leads for therapeutic targets and strategies.

Animals↗
PubMed2002

How to make mapping images of biological specimens--data collection and image processing.

To make high-quality elemental mapping images of biological specimens, the conditions of data collection were optimized, and image-processing methods were examined. The most important step was to obtain a sufficient number of electrons to make the images. The exposure time was limited by the characteristics of the CCD camera. Obtaining a long exposure time exceeded the limitations of the camera, so exposures of the same area were performed many times and recorded in many images. The divided images were merged after observation. To merge images, a new software, 'Rotate & Merge' (R&M), was developed. Because of the characteristics of biological specimens, R&M must have several functions. Picture-zoom and image rotation are necessary because of shrinkage of the specimens due to irradiation during exposure, since even cryo techniques, including low-dose techniques, do not prevent shrinkage of specimens. Merged phosphorus-mapping images of ultra-thin slices of yeast cells were made. In these images, ribosome particles and DNA in the nucleus were observed clearly. The merging was very useful for improving the quality of mapping images.

Cyanobacteria↗