Contiguous Positions Research Articles

TERRAIN CLASSIFICATION USING 3D CO-OCCURRENCE FEATURES AND NEURAL NETWORKS

Texture analysis has been efficiently utilized in the area of terrain classification. In this application, features have been obtained in the 2D image domain. In this paper we suggest 3D co-occurrence texture features by extending the concept of co-occurrence feature to the 3D world. The suggested 3D features are described as a 3D co-occurrence matrix by using a co-occurrence histogram of digital elevations at two contiguous positions. The practical construction of the co-occurrence matrix limits the number of levels of digital elevation. If the digital elevation is quantized into a few levels over the whole DEM (Digital Elevation Map), distinctive features cannot be obtained. To resolve this quantization problem, we employ the local quantization technique which can preserve the variation of elevations with a small number of quantization levels. SOM (Self-Organizing Maps), FCM (Fuzzy C-mean) and GBFCM (Gradient Based Fuzzy C-mean) clustering algorithms are employed to implement the terrain classifier, since these ANN clustering algorithms are known as robust against the high dimensionality problem in the classification process. Experimental results show that the classification accuracy with the addition of 3D co-occurrence features is significantly improved over the conventional classification method only with 2D features.

Synthesis of a malaria candidate glycosylphosphatidylinositol (GPI) structure: a strategy for fully inositol acylated and phosphorylated GPIs.

A congener of the glycosylphosphatidylinositol (GPI) membrane anchor present on the cell surface of the malaria pathogen Plasmodium falciparum has been synthesized. This GPI is an example of a small number of such membrane anchors that carry a fatty acyl group at O-2 of the inositol. Although the acyl group plays crucial roles in GPI biosynthesis, it rarely persits in mature molecules. Other notable examples are the mammalian GPIs CD52 and AchE. The presence of bulky functionalities at three contiguous positions of the inositol moiety creates a very crowded environment that poses difficulties for carrying out selective chemical manipulations. Thus installations of the axial long-chain acyl group and neighboring phosphoglyceryl complex were fraught with obstacles. The key solution to these obstacles in the successful synthesis of the malarial candidate and prototype structures involved stereoelectronically controlled opening of a cyclic ortho ester. The reaction proceeds in very good yields, the desired axial diastereomer being formed predominantly, even more so in the case of long-chain acyl derivatives. The myoinositol precursor was prepared from methyl alpha-d-glucopyranoside by the biomimetic procedure of Bender and Budhu. For the glycan array, advantage was taken of the fact that (a). n-pentenyl ortho ester donors are rapidly and chemospecifically activated upon treatment with ytterbium triflate and N-iodosuccinimide and (b). coupling to an acceptor affords alpha-coupled product exclusively. A strategy for obtaining the GPI's alpha-glucosaminide component from the corresponding alpha-mannoside employed Deshong's novel azide displacement procedure. Thus all units of the glycan array were obtained from a beta-d-manno-n-pentenyl ortho ester, this being readily prepared from d-mannose in three easy, high-yielding steps. The "crowded environment" at positions 1 and 2, noted above, could conceivably be relieved by migration of the acyl group to the neighboring cis-O-3-hydroxyl in the natural product. However, study of our synthetic intermediates and prototypes indicate that the O-2 acyl group is quite stable, and that such migration does not occur readily.

Experimental evidence for the existence of non-exo-anomeric conformations in branched oligosaccharides: NMR analysis of the structure and dynamics of aminoglycosides of the neomycin family.

It is commonly known that the exo-anomeric effect is a major factor governing the conformational behavior of naturally occurring oligosaccharides. Conformational flexibility in these molecules mainly concerns the aglycon psi angle since phi is restricted by this stereo-electronic effect. In fact, to the best of our knowledge no case of a natural glycoside adopting a non-exo-anomeric conformation in solution has yet been reported. With respect to the flexibility among naturally occurring carbohydrates, branched type oligosaccharides including sugar residues glycosidated at contiguous positions (such as blood type carbohydrate antigens Lewis X) have been considered as the paradigm of rigid saccharides--the rigidity being enhanced by van der Waals interactions. Herein, we demonstrate unambiguously that both common beliefs are not to be generalized. For example in neomycin B, a branched oligosaccharide antibiotic, a large number of non-exo-anomeric conformations was detected in solution for the first time in naturally occurring sugars. This unusual behavior is attributed to branching. Here, polar contacts between non-vicinal sugar units lead to an enhanced flexibility of the ribose glycosidic torsion phi. The influence of sugar flexibility on RNA recognition will also be discussed.

A single H:CDR3 residue in the anti-digoxin antibody 26-10 modulates specificity for C16-substituted digoxin analogs

We constructed Fab libraries of bacteriophage-displayed H:CDR3 mutants in the high-affinity anti-digoxin antibody 26-10 to determine structural constraints on affinity and specificity for digoxin. Libraries of mutant Fabs randomized at five or 10 contiguous positions were panned against digoxin and three C16-substituted analogs, gitoxin (16-OH), 16-formylgitoxin and 16-acetylgitoxin. The sequence data from 83 different mutant Fabs showed highly restricted consensus patterns at positions H:100, 100a and 100b for binding to digoxin; these residues contact digoxin in the 26-10:digoxin co-crystal structure. Several mutant Fabs obtained following panning on digoxin-BSA showed increased affinity for digoxin compared with 26-10 and retained the wild-type (wt) Trp at position 100. Those Fabs selected following panning on C16-substituted analogs showed enhanced binding to the analogs. Replacement of H:Trp100 by Arg resulted in mutants that bound better to the analogs than to digoxin. This specificity change was unexpected, as C16 lies on the opposite side of digoxin from H:CDR3. Substitution of wt Trp by Arg appears to alter specificity by allowing the hapten to shift toward H:CDR3, thereby providing room for C16 substituents in the region of H:CDR1.

Relationships among isoacceptor tRNAs seems to support the coevolution theory of the origin of the genetic code.

A new method for looking at relationships between nucleotide sequences has been used to analyze divergence both within and between the families of isoaccepting tRNA sets. A dendrogram of the relationships between 21 tRNA sets with different amino acid specificities is presented as the result of the analysis. Methionine initiator tRNAs are included as a separate set. The dendrogram has been interpreted with respect to the final stage of the evolutionary pathway with the development of highly specific tRNAs from ambiguous molecular adaptors. The location of the sets on the dendrogram was therefore analyzed in relation to hypotheses on the origin of the genetic code: the coevolution theory, the physicochemical hypothesis, and the hypothesis of ambiguity reduction of the genetic code. Pairs of 16 sets of isoacceptor tRNAs, whose amino acids are in biosynthetic relationships, occupied contiguous positions on the dendrogram, thus supporting the coevolution theory of the genetic code.

Description of the larval stages of Heterosternuta diversicornis (Sharp) (Coleoptera: Dytiscidae, Hydroporinae)

AbstractDescription of structures of all three larval instars of Heterosternuta diversicornis (Sharp) is presented. The chaetotaxy and porotaxy of the cephalic capsule, head appendages, legs, last abdominal segment, and urogomphi are discussed in detail. A close similarity between larvae of H. diversicornis, H. wickhami Zaitzev and H. cocheconis (Fall) is confirmed. All three species distinguish from the closely related species of the genus Neoporus Guignot by (i) a very short and constricted siphon, (ii) the primary setae FE8 and FE9 which are subequal in length to the maximum width of the metafemur (first instar), (iii) the absence of natatory setae on all tibiae and tarsi, and (iv) the contiguous position of the primary setae UR2 and UR3 on the urogomphomere 1.

Recurring Local Sequence Motifs in Proteins

We describe a completely automated approach to identifying local sequence motifs that transcend protein family boundaries. Cluster analysis is used to identify recurring patterns of variation at single positions and in short segments of contiguous positions in multiple sequence alignments for a non-redundant set of protein families. Parallel experiments on simulated data sets constructed with the overall residue frequencies of proteins but not the inter-residue correlations show that naturally occurring protein sequences are significantly more clustered than the corresponding random sequences for window lengths ranging from one to 13 contiguous positions. The patterns of variation at single positions are not in general surprising: chemically similar amino acids tend to be grouped together. More interesting patterns emerge as the window length increases. The patterns of variation for longer window lengths are in part recognizable patterns of hydrophobic and hydrophilic residues, and in part less obvious combinations. A particularly interesting class of patterns features highly conserved glycine residues. The patterns provide a means to abstract the information contained in multiple sequence alignments and may be useful for comparison of distantly related sequences or sequence families and for protein structure prediction.

DNA methylation and the origin of complement factor B polymorphism

BF is a polymorphic complement compnent encoded in the MHC. In each of two frequent alleles of BF, BF∗FA and BF∗FB, the difference in relation to the major allele BF∗S has been shown to consist in the nonsynonymous substitution of only one base of the coding sequence. Both substitutions occur within the same codon and affect contiguous positions, corresponding to the dinucleotide CpG in BF∗S. We propose here that BF∗FA and BF∗FB arose independently from BF∗S by the frequently described transition mutations associated with cytosine methylation at CpG sites. By probing sperm DNA with methylation-sensitive restriction enzymes, we obtained experimental evidence of germ line methylation of the CpG site considered. The dinucleotide of the BF gene probably constitutes a site for recurrent mutation, and this is of relevance for the use of BF as a genetic marker, and the origin of forms of the protein with altered functional properties

Looking in text windows: Their size and composition

A text window is a group of words appearing in contiguous positions in text. Intuitively, words in such close proximity should have something to do with each other. We can use the text window to exploit a variety of lexical, syntactic, and semantic relationships without having to analyze the text explicitly for their structure. This research supports the previously suggested idea that natural groupings of words are best treated as a unit of size 7 to 11 words, that is, plus or minus three to five words. Our text retrieval experiments varying the size of windows, both with full text and with stopwords removed, support these size ranges. The characteristics of windows that best match terms in queries are examined in detail, revealing interesting differences between those for queries with good results and those for queries with poorer results. Queries with good results tend to contain more content word phrases and fewer terms with high frequency of use in the database. Information retrieval systems may benefit from expanding thesaurus-style relationships or incorporating statistical dependencies for terms within these windows.

A universal nucleoside for use at ambiguous sites in DNA primers.

A non-discriminatory base analogue, or universal base, would be an invaluable component of oligonucleotide probes and primers for solving the design problems that arise as a result of the degeneracy of the genetic code, or when only fragmentary peptide sequence data are available. We have designed an alternative to previous universal nucleoside candidates, a new analogue, 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole (designated M; Fig. 1), which maximizes stacking while minimizing hydrogen-bonding interactions without sterically disrupting a DNA duplex. Oligonucleotides containing M at several sites were used as primers for sequencing and the polymerase chain reaction. The sequencing primer d(5'-CGT AAM CAM AAM ACM AT-3') is as effective as the exact match d(5'-CGT AAT CAG AAA ACA AT-3'). It is also possible to sequence using a primer containing M at several contiguous positions, for example d(5'-CGT AAT MMM MMM MMM AT-3'). Melting curves show that duplexes formed on hybridization of the sequences d(5'-CCT TTT TMT TTT TGG-3') and d(5'-CCA AAA AXA AAA AGG-3'), where X is A, C, G or T, melted at a lower temperature than the corresponding duplexes containing only d(A.T) and d(C.G) base pairs, but showing little variation among different X bases (Tm range 3 degrees C).

Updating Polygonizations*

AbstractIn this paper we consider polygonizations that are robust when faced with changes in the vertices that are present or in their position. We analyze the dynamic maintenance of different types of polygonizations (monotone, star‐shaped…) and we introduce monotone half‐convex polygonizations that are specially interesting because they provide minimum cost per insertion or deletion. If we had to delete not only one point but several external layers of the set, then the onion polygonizations would be suited, because they can be updated in constant time. We also consider the case of points that can be moved to contiguous positions and we show how to polygonize the set for updating in linear time. We deal too with security problems for a polygon: What is the maximum distance the vertices of a polygon could be moved away of their position in such a way that the topology on the boundary of the polygon (or its convexity) remains the same?.

N,N′-diacetate derivatives of some polyoxa-polyaza macrocyclic compounds: Protonation and complexation studies

The N,N'-diacetate derivatives of the 12-membered polyoxa-polyaza macrocycles 1-oxa-4,7,10-triazacyclododecane, 1,7-dioxa-4,10-diazacyclododecane and 1,4-dioxa-7,10- diazacyclododecane have been synthesized. Their protonation constants were determined by potentiometry and the sequences of protonation were studied by 1H NMR spectroscopy. These studies have shown that the first two steps of protonation in the three ligands occur on the nitrogen atoms, even when the molecule has the two nitrogen atoms of the ring in contiguous positions. The stability constants of the complexes formed by these ligands with the alkaline-earth, first-series transition metal ions Zn2+, Cd2+ and Pb2+ were determined by automated potentiometry at 25.0°C and 0.10 M ionic strength. In the case of 1,4-dioxa- 7,10-diazacyclododecane-7,10-diacetic acid, the constants for the Cu2+ and Pb2+ complexes had to be determined by a ligand-ligand competition potentiometric method. For the alkaline-earth metal ions the stability constants (log KML) are of the order 5–8 log units; for the other metals they vary from ca 11 to 18 log units. However, the results show that the replacement of one nitrogen by an oxygen atom in the ring leads to a considerable decrease in the stability of the complexes of the transition metal ions Zn2+ and Cd2+ (from 1.7 to 5.0 log units), and to an increase, albeit small, in the stability of the complexes of the alkaline-earth metal ions. The Irving-Williams' order of stability is not obeyed for the metal complexes of any of the ligands, probably due to the steric constraints of the rings. The comparison of the behaviour of the metal complexes formed with the ligands studied in the present work with those formed by 1-oxa-4,8,12-triazacyclotetradecane-4,12-diacetic acid, a 14-membered ligand with the same set of donor atoms in the ring, shows that all the complexes formed with the 12-membered ligands are generally more stable, but the 14- membered ligand has a far more marked selective behaviour towards the same series of metal ions. Hence, whereas the difference in stability of e.g. the copper and lead complexes of the 12-membered ligands varies from 0 to 3 log units, the difference for the complexes of 14-membered ligands formed with the same metals is of the order 10 log units.

Orogeny and large‐scale strike‐slip faulting on Venus: Tectonic evolution of Maxwell Montes

The Ishtar Terra highland region of Venus contains mountain belts morphologically similar to terrestrial orogenic belts. Akna Montes and Freyja Montes are long, linear mountain belts with about 4 km of relief above the 3‐ to 4‐km‐high Lakshmi Planum. The Maxwell Montes mountain belt, however, is more rectangular in plan view and has relief of approximately 8 km. We have investigated the nature of this latter range using complementary radar images obtained by the Arecibo Observatory and the Venera 15/16 spacecraft, as well as allimetry data obtained by the Venera 15/16 and Pioneer Venus spacecraft. Geological and structural maps have been compiled on the basis of these data, the individual features and their stratigraphic relationships interpreted, and a model for the origin and evolution of Maxwell Montes is proposed. The dominant features of this mountain range are long, parallel ridges and valleys that are intepreted to be anticlines and synclines and to have resulted from ENE‐WSW oriented compression. Two major shear zones bound Maxwell Montes on the north and south, converging toward the west. Nine narrow linear parallel features several hundreds of kilometers long (identified as cross‐strike discontinuities, CSDs) cut obliquely across the strike of the ridges and valleys in a NW‐SE direction and disrupt the structural fabric of the mountain range, dividing Maxwell Montes into 10 crustal domains. Among several possible origins, we find that the data are most consistent with their interpretation as right‐lateral strike‐slip faults with offsets of up to 125 km. Retrodeformation and reconstruction of Maxwell Montes using the offsets determined for individual domains produces a long linear mountain range similar to Akna Montes. Using geologic unit maps and topographic maps of the present configuration of Maxwell, similar reconstructions were made; these reconstructions restored several linear tectonic elements, topographic trends, and sinuous unit boundaries to more contiguous positions. On the basis of these data and observations we suggest that Akna Montes may represent the initial form of compressional orogenic belts on Venus, while Maxwell Montes attained its present morphology through a second stage of deformation involving large‐scale strike‐slip faulting. We examine several models for this second stage and favor the interpretation that it occurred as the Akna Montes‐like proto‐Maxwell Montes was transported to the west between two converging shear zones, accompanied by rotation of the entire mountain range. Thirty percent shortening of the mountain range is implied by the geometries of the present and reconstructed Maxwell Montes. On the basis of the deforamation in Maxwell Montes and the evidence for large‐scale transport we conclude that large‐scale horizontal a movement of crustal materials is a significant aspect of the tectonics of Venus.

Low-Cost Sanitation technology for the control of Intestinal Helminths

It can be seen from the above that the appropriate sample size for an experiment depends upon three quantities. (I) The size of the treatment difference which is regarded as of practical importance. (2) The rates of the various types of error which can be tolerated in the light of their costs. (3) The variability of the experimental material. Something needs to be said about variability. With a quantal response there is often not a great deal that can be done to reduce variability to any substantial extent, always provided that the normal standards of good experimentation (which include proper randomization) are adhered to. With a continuous response there are more possibilities. Arranging the experimental material in homogeneous pairs or larger blocks (such as those constituted by litter-mate animals, or by contiguous positions in the laboratory) can often lead to very substantial reductions in variability, enabling notable savings to be made in experimental material at negligible cost. It should be repeated that the statistical arguments given above only lead to a fairly rough assessment of the appropriate size for a proposed experiment. This does not detract from their usefulness. The drawbacks of undertaking an experiment which is unnecessarily large are fairly obvious. Those of embarking on one which is foreseeably too small to detect the required treatment effect are less obvious but may well be more serious, particularly if they are linked to the common fallacy of equating 'not significant' with 'nonexistent'.

Twin study methodology and variability in xenobiotic placental metabolism.

The present study assesses the contribution of genetic and environmental factors to variability in placental aryl hydrocarbon hydroxylase and glutathione transferase activities using twin study methodology. Twin placentas were collected at the time of delivery. The placenta, except for a single layer of maternal decidua, consists of fetal tissue exhibiting fetal genotype. Microsomal and cytosolic fractions were prepared under stringent protocols to prevent enzyme activity loss. There were two monozygotic-monochorionic pairs, five monozygotic-dichorionic pairs, and 21 dizygotic-dichorionic pairs that showed measurable aryl hydrocarbon hydroxylase activity using the direct fluorometric assay. Most of the mothers were smokers. Aryl hydrocarbon hydroxylase activity was measured with two different substrates, benzo(a)pyrene and 7-ethoxyresorufin. Glutathione transferase activity was measured using glutathione and 1-chloro-2,4-dinitrobenzene as substrates for a spectrophotometric assay that follows the conversion of the aromatic substrate. Twin pair similarity was calculated with intraclass correlation coefficients. There is a high correlation between the activities of the two aryl hydrocarbon hydroxylase substrates (r = .814), but no correlation between aryl hydrocarbon hydroxylase and glutathione transferase activity levels. There is little evidence of genetic variability underlying the variation in the enzyme activities because monozygotic-dichorionic twins are no more similar to each other for the three substrate activities than are the dizygotic twins. To delineate the prenatal environmental influences on placental enzyme variability, dichorionic placentation was subdivided further into contiguous and noncontiguous placental position. Lower intraclass correlation coefficients are obtained for the dizygotic twins whose placentas were noncontiguous compared with dizygotic twins with contiguous placentas. The results suggest that most of the variability seen in these placental enzyme systems is due to environmental differences within uteri, rather than genetic variability in the population. This does not negate the possibility that between-pair, or population, variability may have a genetic component, because even dizygotic twins share a large proportion of their genes. This study points out that a significantly variable environment exists within the human uterus.

Context and Contiguity in Survey Questionnaires

THE IMPORTANCE of context effects in survey questionnaires has been pointed up in several recent reports.' In the present paper we start from one of the most firmly established such effects and address a further important issue: to what degree are context effects due to placing questions in contiguous positions, with no intervening items, as against having them simply appear in the same questionnaire. Looked at from a practical standpoint, can investigators reduce context effects by interposing neutral items between questions that are known or thought likely to influence one another? We focus on a pair of items concerning Communist and American reporters where the context effect has been shown to be both strong and stable over time:

Dynamic storage allocation for a real-time system

The storage allocation algorithm considered brings programs and data into core as they are needed, directing the former to contiguous positions in lower core and the latter into contiguous positions in upper core.