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Generalized principal component analysis (GPCA).

This paper presents an algebro-geometric solution to the problem of segmenting an unknown number of subspaces of unknown and varying dimensions from sample data points. We represent the subspaces with a set of homogeneous polynomials whose degree is the number of subspaces and whose derivatives at a data point give normal vectors to the subspace passing through the point. When the number of subspaces is known, we show that these polynomials can be estimated linearly from data; hence, subspace segmentation is reduced to classifying one point per subspace. We select these points optimally from the data set by minimizing certain distance function, thus dealing automatically with moderate noise in the data. A basis for the complement of each subspace is then recovered by applying standard PCA to the collection of derivatives (normal vectors). Extensions of GPCA that deal with data in a high-dimensional space and with an unknown number of subspaces are also presented. Our experiments on low-dimensional data show that GPCA outperforms existing algebraic algorithms based on polynomial factorization and provides a good initialization to iterative techniques such as K-subspaces and Expectation Maximization. We also present applications of GPCA to computer vision problems such as face clustering, temporal video segmentation, and 3D motion segmentation from point correspondences in multiple affine views.

Algorithms↗

Construction of peptides encompassing multideterminant clusters of human immunodeficiency virus envelope to induce in vitro T cell responses in mice and humans of multiple MHC types.

To make synthetic peptide vaccines effective in a broad population of outbred humans, one would have to incorporate enough antigenic determinants to elicit recognition by T cells of most HLA types. We have previously defined multideterminant regions of the human immunodeficiency virus (HIV) envelope that include overlapping determinants seen by proliferating T cells of three or four haplotypes of mice. We have now tested the hypothesis that synthetic peptides encompassing such multideterminant regions will be recognized by T cells of multiple murine MHC types as well as by human T cells representing multiple HLA types. Six such peptides of 20-33 residues in length were prepared, and tested for their ability to stimulate T cells from mice of four distinct MHC types immunized with recombinant envelope protein rgp 160, as well as from 42 HIV-infected humans of different HLA types. Results identify several such peptides that are broadly recognized by mice of four H-2 types and by 52-73% of infected humans who still retain IL-2 productive responses to control recall antigens such as influenza A virus or tetanus toxoid. 86% of such infected donors tested against at least three peptides respond to at least one of the six peptides, and 77% of an additional group of seropositives respond to a mixture of the peptides. Moreover, the peptides can be used to immunize mice to elicit T cells reactive with the intact HIV envelope protein. These peptides therefore may be useful for both vaccine development in the broad human population, and diagnostic or prognostic use.

Animals↗

Interactions between bilateral clusters of neuroendocrine cells in Aplysia.

1. Activity of bilateral clusters of electrotonically coupled neuroendocrine cells (the bag cells) was studied using multiple-site intracellular and extracellular recording techniques in isolated parietovisceral ganglia of three species of Aplysia. Bilateral afterdischarges typically began with spike initiation on one side near the neurite terminals along the pleurovisceral connective; propagation of action potentials then proceeded toward the somata with potentiation to full somatic invasion in the ipsilateral bag cell cluster. This activity potentiated across the parietovisceral ganglion until contralateral spikes were initiated at a point near the bag cell somata (designated site A) and compound bag cell activity was then propagated both inward toward the somata and outward toward the circumesophageal ring of head ganglia. This sequence of events, i.e., "in one side, out the other," could occur several times during an afterdischarge, although outward propagation of activity was rarely maintained for more than 20 spikes. Synchrony between clusters was best during these periods of activity. Usually after a few episodes of this sequence, the sites of spike initiation spontaneously shifted to near the neurite terminals of each side and activity was initiated distally and propagated inward. Asychrony between clusters commonly developed when the sites for spike initiation were near the neurite terminals of each side. 2. Waveforms and temporal sequence of recorded events indicate that at least two sites for spike initiation exist within the neuritic tree of each bag cell cluster. These are the distal terminations of the neurites and a proximal site near the somata. Action potentials could be generated at this proximal site spontaneously or when electrotonically driven by contralateral activity. Removal of the bag cell somata did not interfere with bilateral behavior of the bag cell system. The proximal site is, therefore, not somatic. Activity initiated there was always more synchronous and propagated with a higher conduction velocity than activity initiated at the distal ends of the neurites. 3. Experiments were performed with and without the circumesophageal ring of head ganglia intact. Removal of the head ganglia had no effect on bilaterality of or synchrony within the bag cell system. Systematic stimulations and cuts of head ring connectives suggested that the cerebral ganglion may participate in orthodromic activation of the bag cells. 4. Our findings indicate the bag cells of Aplysia are a homogeneous population of neuroendocrine cells with multiple sites for spike initiation. Either cluster can serve as a pacemaker for the other through potentiation and electrotonic activation of the contralateral cluster at proximal sites on the neurites.

Action Potentials↗

Single-Cell Proteomics Reveals Proteome Remodeling and Cellular Heterogeneity During NGF-Induced PC12 Neuronal Differentiation.

Single-cell proteomics enables direct measurement of cellular heterogeneity during dynamic biological processes, but its application to fragile and highly adherent neuronal models remains challenging. Here, we developed and applied an optimized single-cell proteomics workflow to characterize proteome remodeling during nerve growth factor (NGF)-induced differentiation of PC12 cells. To enable reliable single-cell analysis, we implemented gentle dissociation, antiaggregation strategies, and thermal inkjet-based cell dispensing, achieving high accuracy in single-cell isolation. Inclusion of n-dodecyl-β-d-maltoside (DDM) improved recovery of membrane-associated and low-solubility proteins. Coupled with LC-ion mobility-mass spectrometry, this workflow enabled quantification of 2,000-3,000 proteins per cell across the differentiation time course. Single-cell proteomic analysis revealed progressive and heterogeneous proteome remodeling during differentiation. While undifferentiated cells formed a relatively homogeneous population, later stages (Days 4-6) exhibited increased variability, including multimodal protein abundance distributions and separation into distinct subpopulations. Dimensionality reduction, clustering, and non-negative matrix factorization identified multiple coexisting proteomic states within the same time points, reflecting asynchronous differentiation trajectories. These subpopulations were characterized by coordinated differences in pathways related to intracellular trafficking, protein translation, cytoskeletal organization, and neuronal maturation. Comparison with bulk proteomics demonstrated that proteins associated with differentiated neuronal states, including those involved in neurite formation and structural remodeling, are underrepresented in population-averaged measurements but are enriched within specific single-cell subpopulations. Temporal and cluster-resolved analyses further revealed distinct protein expression trajectories, including early decreases in cell cycle and metabolic pathways and later increases in neuronal structural and regulatory proteins. Together, this study establishes an optimized workflow for single-cell proteomics of neuronal systems and demonstrates that NGF-induced PC12 differentiation proceeds through heterogeneous and divergent proteomic states that are not resolved by bulk analysis.

Animals↗

A neurological disease cluster at a manufacturing plant.

A case-control study was conducted an at automotive carburetor plant to investigate exposures associated with a cluster of cases exhibiting neurological symptoms that resembled multiple sclerosis. Eighteen cases were identified with symptom onset between 1970 and 1985. Four controls per case were selected randomly from the plant population, and they were matched by year of birth, gender, and ethnicity. From work histories and telephone interviews, cumulative exposures for 10 chemical or process categories were computed, based on rank estimates of exposure levels. Mantel-Haenszel procedures and logistic regression modeling produced statistically significant relative risks associated with die-casting and organophosphate exposures, using unweighted and latency-weighted cumulative exposures. The study was hampered by the inability to pursue further clinical neurological evaluation of the cases, by the small number of cases, and by uncertainties of exposure assessment. A delayed neuropathy arising from organophosphate exposure in hydraulic and machining fluids is proposed.

Adult↗

Empirical support for psychological profiles observed in multiple sclerosis.

Though increasing attention is being paid to psychological aspects of multiple sclerosis, much research continues to examine patients as differing in quantity rather than quality of psychological abnormality or response. Cluster analysis was used to identify distinctive psychological profiles in a large sample of patients with multiple sclerosis. It employed three measures, carefully chosen to capture the main responses historically observed in multiple sclerosis. These measures were (1) the patient's physical disability-impairment, assessed by a neurologist; (2) physical disability-impairment as perceived and reported by the patient; and (3) self-reported psychological well-being (or distress) independent of physical signs and symptoms. The optimal solution from the cluster analysis separated the 99 patients into 10 clusters, which were collapsed into four profiles, consistent with the labels "depression," "denial," "exaggerated somatic," and "severity-related." These data give strong empirical support to the existence of discrete and distinctive coping styles in multiple sclerosis.

Adult↗

Relationship of actin and tubulin distribution to bud growth in wild-type and morphogenetic-mutant Saccharomyces cerevisiae.

The distribution of actin in wild-type cells and in morphogenetic mutants of the budding yeast Saccharomyces cerevisiae was explored by staining cells with fluorochrome-labeled phallotoxins after fixing and permeabilizing the cells by several methods. The actin appeared to be localized in a set of cortical spots or patches, as well as in a network of cytoplasmic fibers. Bundles of filaments that may possibly correspond to the fibers visualized by fluorescence were observed with the electron microscope. The putative actin spots were concentrated in small and medium-sized buds and at what were apparently the sites of incipient bud formation on unbudded cells, whereas the putative actin fibers were generally oriented along the long axes of the mother-bud pairs. In several morphogenetic mutants that form multiple, abnormally elongated buds, the actin patches were conspicuously clustered at the tips of most buds, and actin fibers were clearly oriented along the long axes of the buds. There was a strong correlation between the occurrence of active growth at particular bud tips and clustering of actin spots at those same tips. Near the end of the cell cycle in wild-type cells, actin appeared to concentrate (as a cluster of spots or a band) in the neck region connecting the mother cell to its bud. Observations made using indirect immunofluorescence with a monoclonal anti-yeast-tubulin antibody on the morphogenetic mutant cdc4 (which forms multiple, abnormally elongated buds while the nuclear cycle is arrested) revealed the surprising occurrence of multiple bundles of cytoplasmic microtubules emanating from the one duplicated spindle-pole body per cell. It seems that most or all of the buds contain one or more of these bundles of microtubules, which often can be seen to extend to the very tips of the buds. These observations are consistent with the hypotheses that actin, tubulin, or both may be involved in the polarization of growth and localization of cell-wall deposition that occurs during the yeast cell cycle.

Actins↗

Malignant fibrous histiocytoma of the deep peri-articular tissue of the stifle in a dog.

A Belgian shepherd dog aged 4 years and 9 months was presented with acute onset of non-weight bearing lameness and stifle effusion of the left hind limb, caused by the deep form of a malignant fibrous histiocytoma originating in the deep musculature and fascia surrounding the stifle joint. The tumour progressed rapidly in the tissues along the femoral diaphysis with marked periosteal new bone formation. Cytology of a stifle joint aspirate revealed numerous large polygonal neoplastic cells with considerable anisocytosis and anisokaryosis. These cells were present in clusters, with cytoplasmic projections between the cells, but occasionally also occurred singly. Several cells contained multiple cytoplasmic vacuoles and occasional giant cells were also encountered. Adequate tumour-free margins were not possible with radical limb amputation and the dog was euthanased. Macroscopically the tumour appeared as an extensive pale tan, firm mass with scattered small haemorrhages and foci of yellow discolouration. Histologically the tumour consisted of dense neoplastic expanses or multiple nodules, composed of spindle-shaped fibroblastic cells, polygonal histiocytic cells or cell clusters and scattered giant cells with 2-3 nuclei. The polygonal neoplastic cells were frequently present around and invading lymphatics and blood vessels, causing neoplastic emboli. This is the 1st report of the clinical behaviour, radiography and cytology of the deep form of malignant fibrous histiocytoma in the dog.

Animals↗

The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned.

It is widely believed that most or all Y-chromosomal genes were once shared with the X chromosome. The DAZ gene is a candidate for the human Y-chromosomal Azoospermia Factor (AZF). We report multiple copies of DAZ (> 99% identical in DNA sequence) clustered in the AZF region and a functional DAZ homologue (DAZH) on human chromosome 3. The entire gene family appears to be expressed in germ cells. Sequence analysis indicates that the Y-chromosomal DAZ cluster arose during primate evolution by (i) transposing the autosomal gene to the Y, (ii) amplifying and pruning exons within the transposed gene and (iii) amplifying the modified gene. These results challenge prevailing views of sex chromosome evolution, suggesting that acquisition of autosomal fertility genes is an important process in Y chromosome evolution.

Amino Acid Sequence↗

Globin gene server: a prototype E-mail database server featuring extensive multiple alignments and data compilation for electronic genetic analysis.

The sequence of virtually the entire cluster of beta-like globin genes has been determined from several mammals, and many regulatory regions have been analyzed by mutagenesis, functional assays, and nuclear protein binding studies. This very large amount of sequence and functional data needs to be compiled in a readily accessible and usable manner to optimize data analysis, hypothesis testing, and model building. We report a Globin Gene Server that will provide this service in a constantly updated manner when fully implemented. The Server has two principal functions. The first (currently available) provides an annotated multiple alignment of the DNA sequences throughout the gene cluster from representatives of all species analyzed. The second compiles data on functional and protein binding assays throughout the gene cluster. A prototype of this compilation using the aligned 5' flanking region of beta-globin genes from five species shows examples of (1) well-conserved regions that have demonstrated functions, including cases in which the functional data are in apparent conflict, (2) proposed functional regions that are not well conserved, and (3) conserved regions with no currently assigned function. Such an electronic genetic analysis leads to many readily testable hypotheses that were not immediately apparent without the multiple alignment and compilation. The Server is accessible via E-mail on computer networks, and printed results can be obtained by request to the authors. This prototype will be a helpful guide for developing similar tools for many genomic loci.

Animals↗

Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation.

A large family of neural protocadherin (Pcdh) proteins is encoded by three closely linked mammalian gene clusters (alpha, beta, and gamma). Pcdh alpha and gamma clusters have a striking genomic organization. Specifically, each "variable" exon is spliced to a common set of downstream "constant" exons within each cluster. Recent studies demonstrated that the cell-specific expression of each Pcdh gene is determined bya combination of variable-exon promoter activation and cis-splicing of the corresponding variable exon to the first constant exon. To determine whether there are other similarly organized gene clusters in mammalian genomes, we performed a genome-wide search and identified a large number of mammalian genes containing multiple variable first exons. Here we describe several clusters that contain about a dozen variable exons arrayed in tandem, including UDP glucuronosyltransferase (UGT1), plectin, neuronal nitric oxide synthase (NOS1), and glucocorticoid receptor (GR) genes. In all these cases, multiple variable first exons are each spliced to a common set of downstream constant exons to generate diverse functional mRNAs. As an example, we analyzed the tissue-specific expression profile of the mouse UGT1 repertoire and found that multiple isoforms are expressed in a tissue-specific manner. Therefore, this variable and constant genomic organization provides a genetic mechanism for directing distinct cell- and tissue-specific patterns of gene expression.

Animals↗

Genetic diversity among Mycoplasma species bovine group 7: clonal isolates from an outbreak of polyarthritis, mastitis, and abortion in dairy cattle.

A comprehensive genetic analysis of 60 Mycoplasma sp. bovine group 7 isolates from different geographic origins and epidemiological settings is presented. Twenty-four isolates were recovered from the joints of calves during sporadic episodes of polyarthritis in geographically distinct regions of Queensland and New South Wales, Australia, including two clones of the type strain PG5O. A further three Australian isolates were also recovered from the tympanic bulla, retropharyngeal lymph node and the lung and another three isolates had unconfirmed histories. Six isolates originated from Germany, Portugal, Nigeria, and France. Twenty-four epidemiologically related isolates of Mycoplasma sp. bovine group 7 were recovered from multiple tissue sites and body fluids of infected calves with polyarthritis, mastitic milk, and from the stomach contents, lung and liver from aborted foetuses in three large, centrally managed dairy herds in New South Wales, Australia. Restriction endonuclease analysis (REA) of genomic DNA differentiated 29 Cfol profiles among these 60 isolates and grouped all 24 epidemiologically related isolates in a defined pattern showing a clonal origin. Three isolates of this clonal cluster were recovered from mastitic milk and the synovial exudate of clinically-affected calves and appeared sporadically for periods up to 18 months after the initial outbreak of polyarthritis indicating a persistent, close association of the organism with cattle in these herds. The Cfol profile representative of the clonal cluster was distinguishable from profiles of isolates recovered from multiple, unrelated cases of polyarthritis in Queensland and New South Wales and from other countries. All 24 isolates from the clonal cluster possessed a plasmid (pBG7AU) with a molecular size of 1022 bp. DNA sequence analysis of pBG7AU identified two open reading frames sharing 81 and 99% DNA sequence similarity with hypothetical replication control proteins A and B respectively, previously described in plasmid pADB201 isolated from M. mycoides subspecies mycoides. Other isolates of bovine group 7, epidemiologically unrelated to the clonal cluster, including two clones of the type strain PG5O, possessed a similar-sized plasmid. These data confirm that Mycoplasma sp. bovine group 7 is capable of migrating to, and multiplying within, different tissue sites within a single animal and among different animals within a herd.

Abortion, Veterinary↗

Clinical and subclinical neurological involvement in children of conjugal multiple sclerosis patients.

We report the occurrence of clinically definite multiple sclerosis in an offspring of a couple with conjugal multiple sclerosis. Extensive investigation of all members of this family, which includes two additional asymptomatic children, eliminated the possibility of alternative neurological diagnoses. All family members were studied with magnetic resonance imaging (MRI), evoked potentials, and human leukocyte antigen (HLA) typing. An asymptomatic child had subtle white matter abnormalities on MRI, suggesting subclinical neurological involvement. This study documents the third case of multiple sclerosis in the child of conjugal multiple sclerosis patients and provides the first report of MRI lesions in an asymptomatic offspring of the same parents. Neurodiagnostic and immunogenetic investigations of such rare family clusters may contribute to the elucidation of the pathogenesis of multiple sclerosis.

Adolescent↗

Clonal hematopoiesis in familial polycythemia vera suggests the involvement of multiple mutational events in the early pathogenesis of the disease.

Familial clustering of malignancies provides a unique opportunity to identify molecular causes of cancer. Polycythemia vera (PV) is a myeloproliferative disorder due to an unknown somatic stem cell defect that leads to clonal myeloid hyperproliferation. We studied 6 families with PV. The familial predisposition to PV appears to follow an autosomal dominant inheritance pattern with incomplete penetrance. All examined females informative for a transcriptional clonality assay had clonal hematopoiesis. We excluded linkage between PV and a number of previously proposed candidate disease loci (c-mpl, EPOR, 20q, 13q, 5q, 9p). Therefore, mutations at these loci are unlikely primary causes of familial PV. The finding of erythropoietin-independent erythroid progenitors in healthy family members indicated the presence of the PV stem cell clone in their hematopoiesis. This finding, together with clonal hematopoiesis in the affected individuals, supports the hypothesis of multiple genetic defects involved in the early pathogenesis of PV.

Adult↗

The Caulobacter crescentus flaFG region regulates synthesis and assembly of flagellin proteins encoded by two genetically unlinked gene clusters.

At a specific time in the Caulobacter crescentus cell cycle, a single flagellar filament and multiple receptor sites for the swarmer-specific phage phi Cbk are assembled at one pole of the predivisional cell. One cluster of genes required for this morphogenesis, the flaYG region, includes the flgJKL genes, which encode structural proteins of the flagellar filament. These flagellin genes are flanked by genes required for filament assembly, the flaYE genes at one end and the flaF-flbT-flbA-flaG genes at the other. In this study, we characterized mutants carrying large chromosomal deletions within this region. Several of these strains are phi CbK resistant and produce a novel 22-kDa flagellin that is not assembled into flagella. Merodiploid strains containing either the entire flaFG region or individual fla transcription units from this region were constructed. These strains were used to correlate the presence or absence of specific gene products to changes in flagellin synthesis, filament assembly, or phage sensitivity. As a result of these studies, we were able to conclude that (i) the production of the 22-kDa flagellin results from the absence of the flbA and flaG gene products, which appear to be components of a flagellin-processing pathway common to the 25-, 27-, and 29-kDa flagellins; (ii) flbT negatively modulates the synthesis of the 27- and 25-kDa flagellins from two genetically unlinked gene clusters; (iii) flgL is the only flagellin gene able to encode the 27-kDa flagellin, and this flagellin appears to be required for the efficient assembly of the 25-kDa flagellins; (iv) flaF is required for filament assembly; and (v) phi CbK resistance results from the deletion of at least two genes in the flaFG region.

Caulobacter crescentus↗

Spike detection II: automatic, perception-based detection and clustering.

OBJECTIVES: We developed perception-based spike detection and clustering algorithms. METHODS: The detection algorithm employs a novel, multiple monotonic neural network (MMNN). It is tested on two short-duration EEG databases containing 2400 spikes from 50 epilepsy patients and 10 control subjects. Previous studies are compared for database difficulty and reliability and algorithm accuracy. Automatic grouping of spikes via hierarchical clustering (using topology and morphology) is visually compared with hand marked grouping on a single record. RESULTS: The MMNN algorithm is found to operate close to the ability of a human expert while alleviating problems related to overtraining. The hierarchical and hand marked spike groupings are found to be strikingly similar. CONCLUSIONS: An automatic detection algorithm need not be as accurate as a human expert to be clinically useful. A user interface that allows the neurologist to quickly delete artifacts and determine whether there are multiple spike generators is sufficient.

Adolescent↗

Isolated growth hormone (GH) deficiency type 1A associated with a double deletion in the human GH gene cluster.

The gene deletions responsible for isolated GH deficiency type 1A were characterized by direct analysis of genomic DNA prepared from the leukocytes of two affected children. The probands had typical symptoms of severe isolated GH deficiency complicated by antibody development and growth arrest after human (h) GH treatment. DNA analysis using the restriction endonucleases Eco RI, Bam HI, and Hind III revealed that the restriction fragment containing the hGH-N gene was absent along with those bearing the human chorionic somatomammotropin (hCS)-A and -B and hGH-V sequences. A total of about 40 kilobases DNA were absent due to two separate deletions flanking the hCS-L gene. The two affected siblings are homozygous for this rearrangement of the hGH/hCS gene cluster, which could have been generated by homologous crossing over between two different chromosomes, one bearing one of the previously described deletions of the hGH-N gene, and one bearing a deletion of DNA containing the hCS-A, hCS-B, and hGH-V sequences. Alternatively, this abnormality could have been generated by a complex intrachromosomal rearrangement. The parents, who are consanguinous, have DNA restriction patterns consistent with heterozygosity for this double deletion. This type of deletional mutation is the first involving multiple deletion of the hGH and hCS gene cluster.

Adolescent↗