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Neural dynamics of motion integration and segmentation within and across apertures.

A neural model is developed of how motion integration and segmentation processes, both within and across apertures, compute global motion percepts. Figure-ground properties, such as occlusion, influence which motion signals determine the percept. For visible apertures, a line's terminators do not specify true line motion. For invisible apertures, a line's intrinsic terminators create veridical feature-tracking signals. Sparse feature-tracking signals can be amplified before they propagate across position and are integrated with ambiguous motion signals within line interiors. This integration process determines the global percept. It is the result of several processing stages: directional transient cells respond to image transients and input to a directional short-range filter that selectively boosts feature-tracking signals with the help of competitive signals. Then, a long-range filter inputs to directional cells that pool signals over multiple orientations, opposite contrast polarities, and depths. This all happens no later than cortical area MT. The directional cells activate a directional grouping network, proposed to occur within cortical area MST, within which directions compete to determine a local winner. Enhanced feature-tracking signals typically win over ambiguous motion signals. Model MST cells that encode the winning direction feed back to model MT cells, where they boost directionally consistent cell activities and suppress inconsistent activities over the spatial region to which they project. This feedback accomplishes directional and depthful motion capture within that region. Model simulations include the barberpole illusion, motion capture, the spotted barberpole, the triple barberpole, the occluded translating square illusion, motion transparency and the chopsticks illusion. Qualitative explanations of illusory contours from translating terminators and plaid adaptation are also given.

Computer Simulation↗

Objective clustering of proteins based on subcellular location patterns.

The goal of proteomics is the complete characterization of all proteins. Efforts to characterize subcellular location have been limited to assigning proteins to general categories of organelles. We have previously designed numerical features to describe location patterns in microscope images and developed automated classifiers that distinguish major subcellular patterns with high accuracy (including patterns not distinguishable by visual examination). The results suggest the feasibility of automatically determining which proteins share a single location pattern in a given cell type. We describe an automated method that selects the best feature set to describe images for a given collection of proteins and constructs an effective partitioning of the proteins by location. An example for a limited protein set is presented. As additional data become available, this approach can produce for the first time an objective systematics for protein location and provide an important starting point for discovering sequence motifs that determine localization.

Journal Article↗

Tricyclic compounds as selective antimuscarinics. 2. Structure-activity relationships of M1-selective antimuscarinics related to pirenzepine.

In order to gain some insight into those structural features that control M1 selectivity, a selected set of pirenzepine analogues has been studied in which both the tricyclic ring system and the basic side chain have been varied. Binding studies were conducted in rat tissue homogenates from cerebral cortex (M1) and gastric fundus (M2). The ratio of IC50 values of the test compounds in the two different tissues was taken as a measure of M1 receptor selectivity. Several derivatives, especially those with flexible side chains, i.e. high degree of freedom of rotation around single bonds, proved to be nonselective. Among semirigid compounds only those containing 6-membered ring systems (11, 13, 14, and 15) showed significant M1 selectivity. Principles of structure-activity and structure-selectivity are discussed.

Animals↗

Biomarker identification through spatial proteomics for the characterization of indeterminate thyroid nodules.

PURPOSE: The identification of novel molecular biomarkers may assist in the characterization of indeterminate thyroid nodules, which pose significant diagnostic challenges. Here, we aimed to explore the potential of proteomic analyses to support biomarker discovery in challenging thyroid lesions. METHODS: Linear Discriminant Analysis (LDA) was applied to Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) data from 44 thyroid neoplasms to select the most impactful molecular features for the classification of different tumor histologies, as well as for the distinction between NRAS-mutant (mNRAS) and NRAS-wild-type (wtNRAS) tumors. Relevant peaks were subsequently identified through nanoscale liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS). RESULTS: The LDA selected nine relevant molecular markers distinguishing noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTPs) from other tumor histologies (balanced accuracy = 73%), as well as 19 relevant markers able to identify mNRAS cases (balanced accuracy = 84%). Nine differentially expressed proteins were putatively identified: among them, ATP-dependent RNA helicase DDX42 showed a similar distribution between NIFTPs and papillary thyroid carcinomas (PTCs) / follicular variant PTCs (FVPTCs), while the distribution of the Histone H4 signal was similar between NIFTPs and follicular adenomas (FAs). In addition, Protein disulfide-isomerase A1 and Complement C4-B were overexpressed in wtNRAS compared to mNRAS cases, regardless of histology. CONCLUSION: The LDA-selected features enable to distinguish NIFTPs from morphologically similar lesions and to discriminate between mNRAS and wtNRAS cases. The identified markers might complement genetic analyses and provide insights into the distinct pathogenic drivers behind the development of mNRAS compared to wtNRAS lesions.

Humans↗

Mass surveys and selective case-finding; two tools for tuberculosis control.

The productivity and effectiveness of the traditional mass x-ray survey method of tuberculosis case-finding were compared with those of a selective use of mobile miniature x-ray equipment. In Tulare County, California, two mobile miniature x-ray units were operated independently of each other. One unit conducted community-wide, pre-planned surveys, while the other unit operated a regular weekly schedule of mobile screening clinics in four cities in the county. THE MAIN FEATURES OF THE SELECTIVE SCREENING PROGRAM WERE: (1) Extensive use of the physician referral method; (2) utilization of the unit for contact contact investigation; (3) interpretation of the minifilm and mailing of film and report to the family physician one day after the screening clinic. RESULTS: Mass survey found one case of tuberculosis per 2,200 minifilms taken; cost per case found, $475. Selective screening program found one case per 292 minifilms taken; cost per case found, $111. Of all cases of tuberculosis reported in 1953, 8 per cent were found by mass survey and 18 per cent by selective screening.

California↗

Evolution of antigen-specific T cell receptors in vivo: preimmune and antigen-driven selection of preferred complementarity-determining region 3 (CDR3) motifs.

Antigen (Ag)-driven selection of helper T cells (Th) in normal animals has been difficult to study and remains poorly understood. Using the major histocompatibility complex class II- restricted murine response to pigeon cytochrome c (PCC), we provide evidence for both preimmune and Ag-driven selection in the evolution of Ag-specific immunity in vivo. Before antigenic challenge, most Valpha11(+)Vbeta3(+) Th (70%) express a critical complementarity-determining region 3 (CDR3) residue (glutamic acid at TCR-alpha93) associated with PCC peptide contact. Over the first 5 d of the primary response, PCC-responsive Valpha11(+)Vbeta3(+) Th expressing eight preferred CDR3 features are rapidly selected in vivo. Clonal dominance is further propagated through selective expansion of the PCC-specific cells with T cell receptor (TCR) of the "best fit." Ag-driven selection is complete before significant emergence of the germinal center reaction. These data argue that thymic selection shapes TCR-alpha V region bias in the preimmune repertoire; however, Ag itself and the nongerminal center microenvironment drive the selective expansion of clones with preferred TCR that dominate the response to Ag in vivo.

Animals↗

Highly specific and accurate selection of siRNAs for high-throughput functional assays.

MOTIVATION: Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes. The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of a software capable of the high-throughput design of highly specific siRNA. The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity. Since all the available procedures require, to some extent, manual processing of the results to guarantee specific results, specificity constitutes to date, the major obstacle to the complete automation of all the steps necessary for the selection of optimal candidate siRNAs. RESULT: Here, we present a program that for the first time completely automates the search for siRNAs. In SiDE, the most complete set of rules for the selection of siRNA candidates (including G+C content, nucleotides at determined positions, thermodynamic properties, propensity to form internal hairpins, etc.) is implemented and moreover, specificity is achieved by a conceptually new method. After selecting possible siRNA candidates with the optimal functional properties, putative unspecific matches, which can cause cross-hybridization, are checked in databases containing a unique entry for each gene. These truly non-redundant databases are constructed from the genome annotations (Ensembl). Also intron/exon boundaries, presence of polymorphisms (single nucleotide polymorphisms) specificity for either gene or transcript, and other features can be selected to be considered in the design of siRNAs. AVAILABILITY: The program is available as a web server at http://side.bioinfo.cnio.es. The program was written under the GPL license. CONTACT: jdopazo@cnio.es.

Algorithms↗

The peptaibol antiamoebin as a model ion channel: similarities to bacterial potassium channels.

Antiamoebin (AAM) is a polypeptide antibiotic that is capable of forming ion channels in phospholipid membranes: planar bilayer studies have suggested the channels are octamers. The crystal structure of a monomeric form of AAM has provided the basis for molecular modelling of an octameric helical bundle channel. The channel model is funnel-shaped due to a substantial bend in the middle of the polypeptide chain caused by the presence of several imino acids. Inter-monomer hydrogen bonds orientate a ring of glutamine side chains to form a constriction in the pore lumen. The channel lumen is lined both by side chains of Gln11 and by polypeptide backbone carbonyl groups. Electrostatic calculations on the model are compatible with a channel that transports cations across membranes. The AAM channel model is compared with the crystal structures of two bacterial (KcsA andMthK) potassium channels. AAM and the potassium channels exhibit common functional features, such as cation-selectivity and similar single channel conductances. Common structural features include being multimers, each formed from a bundle of eight transmembrane helices, with lengths roughly comparable to the thickness of lipid bilayers. In addition, they all have aromatic amino acids that lie at the bilayer interfaces and which may aid in the stabilization of the transmembrane helices, as well as narrower constrictions that define the ion binding sites or selectivity filters in the pore lumen. The commonality of structural and functional features in these channels thus suggests that antiamoebin is a good, simple model for more complex bacterial and eukaryotic ion channels, capable of providing insight into details of the mechanisms of ion transport and multimeric channel stability.

Bacterial Proteins↗

Cardiovascular characterization of pyrrolo[2,1-d][1,5]benzothiazepine derivatives binding selectively to the peripheral-type benzodiazepine receptor (PBR): from dual PBR affinity and calcium antagonist activity to novel and selective calcium entry blockers.

The synthesis and cardiovascular characterization of a series of novel pyrrolo[2,1-d][1,5]-benzothiazepine derivatives (54-68) are described. Selective peripheral-type benzodiazepine receptor (PBR) ligands, such as PK 11195 and Ro 5-4864, have recently been found to possess low but significant inhibitory activity of L-type calcium channels, and this property is implicated in the cardiovascular effects observed with these compounds. In functional studies both PK 11195 (1-(2-chlorophenyl)-N-methyl-N-(1-methylpropyl)-3-isoquinolinecarboxa mide) and Ro 5-4864 (4'-chlorodiazepam) did not display selectivity between cardiac and vascular tissue. Therefore, several 7-(acyloxy)-6-arylpyrrolo[2,1-d][1,5]benzothiazepines, potent and selective peripheral-type benzodiazepine receptor ligands recently developed by us (3, 7-20), were subjected to calcium channel receptor binding assay. Some of these compounds showed an unexpected potency in displacing the binding of [3H]nitrendipine from L-type calcium channels, much higher than that reported for PK 11195 and Ro 5-4864 and equal to or higher than that of reference calcium antagonists such as verapamil and (+)-cis-diltiazem. Specifically, in rat cortex homogenate, our prototypic PBR ligand 7-acetoxy-6-(p-methoxyphenyl)pyrrolo[2,1-d][1,5]benzothiazepine (3) showed an IC50 equal to 0.13 nM for inhibition of [3H]nitrendipine binding. Furthermore, in functional studies this compound displayed a clear-cut selectivity for cardiac over vascular tissue. Comparison of calcium antagonist activity on guinea pig aorta strips with the negative inotropic activity, determined by using isolated guinea pig left atria, revealed that 3 displayed higher selectivity than the reference (+)-cis-diltiazem. Thus, the pyrrolobenzothiazepine 3 might represent a new tool for characterizing the relationship between the PBR and cardiac function. Furthermore, we have also investigated the structural dependence of binding to PBR and L-type calcium channels, and this study allowed us to identify a new class of potent calcium channel blockers selective for cardiac over vascular tissue, with no affinity for PBR. A number of structure-activity relationship trends have been identified, and a possible explanation is advanced in order to account for the observed differences in selectivity. Three structural features, namely, (i) the saturation of the C(6)-C(7) double bond, with a consequent higher molecular flexibility, (ii) the presence of a substituent in the benzofused ring, and (iii) a basic side chain at C-10 of the pyrrolobenzothiazepine ring system, were found to be responsible for potent L-type calcium channel antagonism and clear-cut selectivity for cardiac over vascular tissue. Among the synthesized compounds the pyrrolobenzothiazepine 62 was found to be the most promising selective calcium channel blocker. Additionally, the molecular structure determination of the key intermediate 48 by X-ray diffraction, molecular modeling, and NMR analysis is reported.

Animals↗

Selection of linkers for a catalytic single-chain antibody using phage display technology.

Phage display has been evaluated as a means of rapidly selecting tailored linkers for single-chain antibodies (scFvs) from protein linker libraries. Preliminary experiments with a conventional linker failed to yield a functional single-chain version of a catalytic antibody with chorismate mutase activity. A random linker library was therefore constructed in which the genes for the heavy and light chain variable domains were linked by a segment encoding an 18-amino acid polypeptide of variable composition. The scFv repertoire ( approximately 5 x 10(6) different members) was displayed on filamentous phage and subjected to affinity selection with hapten. The population of selected variants exhibited significant increases in binding activity but retained considerable sequence diversity. Screening 1054 individual variants subsequently yielded a catalytically active scFv that was produced efficiently in soluble form. Sequence analysis revealed a conserved proline in the linker two residues after the VH C terminus and an abundance of arginines and prolines at other positions as the only common features of the selected tethers. There are apparently many viable solutions to the problem of linking individual VH and VL domains, but subtle differences in sequence dramatically influence the production, stability, and recognition properties of the scFv. The success of these experiments suggests that phage display will be generally useful for identifying peptide sequences for covalently linking any two protein domains.

Amino Acid Sequence↗

Passive smoking in utero: its effects on neonatal appearance.

Smoking causes changes in the appearance of adults and has profound effects on the fetus, but little is known about its effects on the appearance of newborn infants. Two colour photographs (face and whole body) of 15 newborn infants (seven born to mothers who had smoked during pregnancy and eight born to mothers who had not) were shown to 100 medical and nursing staff, who in a double blind trial were asked to identify which babies had been born to smokers. The mean number correctly identified was 9.1, which was significant compared with the number expected by random selection (7.5). No specific features were identified that distinguished the two groups of infants; selection was intuitive. Nevertheless, the fact that differences can be detected in some way may be useful for antismoking health education.

Double-Blind Method↗

Conformational features of erythrocyte-bound chloroquine from double-selective 1H NMR relaxation.

The interaction between the antimalarial drug chloroquine and red blood cells was investigated by measuring 1H NMR spin-lattice relaxation rates upon double-selective excitation of dipolarly connected spin pairs within the ligand molecule. Geometric and dynamic features were inferred, for the free as well as for the bound ligand, by the cross-relaxation terms between protons at fixed and time-dependent distances, respectively. A change in orientation of the side chain in respect of the aromatic moiety was shown to result from the binding interaction.

Chloroquine↗

Clinicopathological features of eight Korean cases of primary hepatic lymphoma.

Primary hepatic lymphoma is very rare, accounting for less than 0.4% of extranodal lymphomas. Furthermore, hepatic lymphoma, either primary or metastatic, is infrequently confirmed histopathologically in needle biopsy specimens. The aim of the current study is to assess the clinicopathological characteristics of primary hepatic lymphomas in Korea, which is an endemic area of chronic B viral hepatitis. In total, 17 cases with liver needle biopsy specimens with involvement of malignant lymphoma, from whom eight cases met the criteria for primary hepatic lymphoma, were selected. The clinicopathological features were reviewed. Five of eight (62.5%) cases were T cell lymphoma, including three cases (37.5%) of hepatosplenic T cell lymphoma. Three cases (37.5%) were diffuse large B cell lymphomas. Seven patients had follow-up data from 25 days to 50 months that was available for evaluation. The partial remission was present in two of seven patients (28.6%) and five patients (71%) died of disease 25 days to 7 months after the diagnosis. The data indicate that the relatively high incidence of T-cell type in Korean cases of primary hepatic lymphoma may be related to its aggressive behavior and poor prognosis despite combination chemotherapy.

Adult↗

Clinical and immunological evaluation of patients with selective IgA deficiency.

The clinical and immunological features of 14 patients including 12 with selective and two with partial IgA deficiency are presented. One patient was asymptomatic, six patients had allergic diseases, three patients had hematologic disorders and the remaining patients had chronic-recurrent infections. The IgG and IgM serum concentrations were high in four and two patients, respectively. Delayed hypersensitivity skin tests were applied to seven patients, and were found positive in all. E-rosette forming cells were within the normal range. In vitro lymphoblastic transformation with PHA was normal in all the patients, except for one. Two patients had no sIgA+ B cells. The percentage of CD+4 T cells was decreased in one patient and the percentage of CD+8 T cells was increased in another, both of whom had a low CD4/CD8 ratio. The heterogeneity of clinical and immunological features in these patients suggests that various mechanisms may be responsible for the immunopathogenesis of IgA deficiency.

Adult↗

Epilepsy: a review of selected clinical syndromes and advances in basic science.

Epilepsy is a common neurologic disorder that manifests in diverse ways. There are numerous seizure types and numerous mechanisms by which the brain generates seizures. The two hallmarks of seizure generation are hyperexcitability of neurons and hypersynchrony of neural circuits. A large variety of mechanisms alters the balance between excitation and inhibition to predispose a local or widespread region of the brain to hyperexcitability and hypersynchrony. This review discusses five clinical syndromes that have seizures as a prominent manifestation. These five syndromes differ markedly in their etiologies and clinical features, and were selected for discussion because the seizures are generated at a different 'level' of neural dysfunction in each case: (1) mutation of a specific family of ion (potassium) channels in benign familial neonatal convulsions; (2) deficiency of the protein that transports glucose into the CNS in Glut-1 deficiency; (3) aberrantly formed local neural circuits in focal cortical dysplasia; (4) synaptic reorganization of limbic circuitry in temporal lobe epilepsy; and (5) abnormal thalamocortical circuit function in childhood absence epilepsy. Despite this diversity of clinical phenotype and mechanism, these syndromes are informative as to how pathophysiological processes converge to produce brain hyperexcitability and seizures.

Animals↗

Highly selective recognition of adenine nucleobases by synthetic hosts with a linked five-six-five-membered triheteroaromatic structure and the application to potentiometric sensing of the adenine nucleotide.

A new structure for an adenine-selective host molecule, featuring the pertinent link of five-six-five-membered heteroaromatic rings and two carbamoyl NH sites, was developed. This structure provides a correctly oriented array of complementary hydrogen bonding sites for the adenine nucleobase, which exploits both Watson-Crick and Hoogsteen-type interactions. The complexation with adenine nucleobases by multiple hydrogen bonding was supported by (1)H NMR spectroscopy. This type of host displayed high selectivity in complexation, with an accompanying fluorescent response to lipophilized adenosine in CHCl(3). Furthermore, a remarkably selective potentiometric response was attained for adenosine 5'-monophosphate over 5'-GMP, 5'-CMP, and 5'-UMP by using an ion-selective electrode with a PVC-supported solvent polymeric membrane. This indicates recognition of water-soluble nucleotide guests through the membrane-water interface. These findings are expected to form a reliable basis for the development of artificial sensing systems for mononucleotides in biological systems.

Adenine↗

Abdominal CT features and survival in acquired immunodeficiency.

PURPOSE: HIV-infected patients show a high incidence of abdominal disease. This investigation was made to determine whether abdominal CT provided prognostically relevant information in these patients. MATERIAL AND METHODS: Images from 533 abdominal CT examinations in 339 HIV-infected patients were retrospectively reviewed for signs of abdominal disease, and correlated with clinical data and survival rates. The Kaplan-Meier analysis and rank testing of survival, and proportional hazards regression were used to define prognostic clinical and imaging findings. RESULTS: Of the 339 patients, 278 (82%) showed abnormal abdominal findings on CT. Median survival was 29 months. Of the imaging findings, hepatic masses (n = 11), pathologically enlarged lymph nodes (n = 48), and ascites (n = 7) were associated with poor survival, giving a median survival of respectively 13 months, 15 months, and less than 1 month. These three features showed no association with CD4(+)-T-lymphocyte count or CDC category. Main determinants of survival were a low CD4(+)-T-lymphocyte count, and certain abnormal CT findings. Splenomegaly (n = 147), hepatomegaly (n = 144), and lymphadenopathy (n = 111) were the most common abdominal findings on CT but lacked prognostic relevance. CONCLUSION: Abdominal CT offered prognostic implications in HIV-infected patients and might serve in risk stratification in selected patients. CT features such as hepatic masses, grossly enlarged lymph nodes, or ascites indicate advanced immunosuppression.

Acquired Immunodeficiency Syndrome↗

Automatic identification of human helminth eggs on microscopic fecal specimens using digital image processing and an artificial neural network.

In order to automate routine fecal examination for parasitic diseases, we propose in this study a computer processing algorithm using digital image processing techniques and an artificial neural network (ANN) classifier. The morphometric characteristics of eggs of human parasites in fecal specimens were extracted from microscopic images through digital image processing. An ANN then identified the parasite species based on those characteristics. We selected four morphometric features based on three morphological characteristics representing shape, shell smoothness, and size. A total of 82 microscopic images containing seven common human helminth eggs were used. The first stage (ANN-1) of the proposed ANN classification system isolated eggs from confusing artifacts. The second stage (ANN-2) classified eggs by species. The performance of ANN was evaluated by the tenfold cross-validation method to obviate the dependency on the selection of training samples. Cross-validation results showed 86.1% average correct classification ratio for ANN-1 and 90.3% for ANN-2 with small variances of 46.0 and 39.0, respectively. The algorithm developed will be an essential part of a completely automated fecal examination system.

Algorithms↗