Frequency Distribution Of Distances Research Articles

Nest Site Fidelity of Northern Map Turtles, Graptemys geographica

Northern map turtles (Graptemys geographica) are a species of conservation concern with a limited distribution in Pennsylvania. We examined nest site fidelity of G. geographica along the Juniata River at Mount Union, the largest reported nesting area in the commonwealth. Nesting habitat included a mitigation area bordering a highway, partitioned by a turtle exclusion fence, and an adjacent pile of coal tailings. A linear grid along the turtle fence allowed us to determine distances between nests of individual females. Our results indicate that female G. geographica at Mount Union exhibit nest site fidelity, as the frequency distribution of distances between nests of individual females was positively skewed, and distances between nests (both within and among seasons) were smaller than distances between randomly selected pairs of nests from different individuals. Females placed different clutches of eggs as close together as 0.30 m. Within-season (first and second clutch) internest distances were significantly smaller than internest distances among years, which increased over time. We also attached radio transmitters to a sample of adult females following nesting to determine the extent of riverine migrations, as long-distance nesting migrations are associated with fidelity to particular nesting sites. Following nesting, 2 females remained in the river near the Mount Union nesting habitat and 3 females moved downstream 4.3–5.6 km, yet all of the turtles returned to their previous nesting areas the following summer. Nest site fidelity can benefit map turtles if the habitat remains stable, results in high nest survivorship, and produces high-quality hatchlings, yet the behavior may be detrimental if it exposes turtles to significant risks such as road mortality or environmental contaminants. Our results indicate that maintaining long-term nesting habitat and ensuring suitable river quality at Mount Union may be essential for the conservation of G. geographica in central Pennsylvania.

Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose: Glycoprotein glucosyltransferase

SummaryUDP-glucose:glycoprotein glucosyltransferase (UGGT) flags misfolded glycoproteins for ER retention. We report crystal structures of full-length Chaetomium thermophilum UGGT (CtUGGT), two CtUGGT double-cysteine mutants, and its TRXL2 domain truncation (CtUGGT-ΔTRXL2). CtUGGT molecular dynamics (MD) simulations capture extended conformations and reveal clamping, bending, and twisting inter-domain movements. We name “Parodi limit” the maximum distance on the same glycoprotein between a site of misfolding and an N-linked glycan that can be reglucosylated by monomeric UGGT in vitro, in response to recognition of misfold at that site. Based on the MD simulations, we estimate the Parodi limit as around 70–80 Å. Frequency distributions of distances between glycoprotein residues and their closest N-linked glycosylation sites in glycoprotein crystal structures suggests relevance of the Parodi limit to UGGT activity in vivo. Our data support a “one-size-fits-all adjustable spanner” UGGT substrate recognition model, with an essential role for the UGGT TRXL2 domain.

GIS-Based Spatial Analysis of Regional-Scale Structural Controls on Gold Mineralization Along the Bétaré-Oya Shear Zone, Eastern Cameroon

Betare-Oya is one of the gold mining districts in the eastern region of Cameroon. Structural controls on gold mineralization were examined along the Betare-Oya Shear Zone, providing further clues on favorable areas for mineral exploration. GIS-based methods combining point pattern (i.e., quadrat count, Fry analysis) and distance distribution analysis were employed here to delineate the spatial patterns of known gold deposits and to evaluate their spatial association with geological structures. Results show that the gold deposits in this area are spatially clustered. At the regional scale, the Fry plot indicates an alignment of deposits, suggesting that gold mineralization is controlled by structures oriented NNE–SSW and NE–SW. At the deposit scale, an alignment is also evident, indicating that the mineralization is also controlled by ENE–WSW-trending structures. The cumulative relative frequency distribution of distances from lineament features to gold occurrence points (DM) and to non-occurrence points (DN) ratio (DM/DN) was used to rank these two major structural trends and their relative importance as mineralization control. The yielded grades show that NE–SW-trending lineaments, akin to P-type structures, play a major role in controlling the gold mineralization in the area compared to other structures. Beyond the goal to foster mineral prospection in the Betare-Oya gold district, information yielded in the present study provides relevant criteria for further exploration in the eastern region of Cameroon.

Cluster pattern analysis of energy deposition sites for the brachytherapy sources 103Pd, 125I, 192Ir, 137Cs, and 60Co

Analysing the pattern of energy depositions may help elucidate differences in the severity of radiation-induced DNA strand breakage for different radiation qualities. It is often claimed that energy deposition (ED) sites from photon radiation form a uniform random pattern, but there is indication of differences in RBE values among different photon sources used in brachytherapy. The aim of this work is to analyse the spatial patterns of EDs from 103Pd, 125I, 192Ir, 137Cs sources commonly used in brachytherapy and a 60Co source as a reference radiation. The results suggest that there is both a non-uniform and a uniform random component to the frequency distribution of distances to the nearest neighbour ED. The closest neighbouring EDs show high spatial correlation for all investigated radiation qualities, whilst the uniform random component dominates for neighbours with longer distances for the three higher mean photon energy sources (192Ir, 137Cs, and 60Co). The two lower energy photon emitters (103Pd and 125I) present a very small uniform random component. The ratio of frequencies of clusters with respect to 60Co differs up to 15% for the lower energy sources and less than 2% for the higher energy sources when the maximum distance between each pair of EDs is 2 nm. At distances relevant to DNA damage, cluster patterns can be differentiated between the lower and higher energy sources. This may be part of the explanation to the reported difference in RBE values with initial DSB yields as an endpoint for these brachytherapy sources.

The extension of lightning flashes from thunderstorms near Cape Canaveral, Florida

AbstractThe horizontal distance that intracloud (IC) and cloud to ground (CG) lightning flashes extend from thunderstorms is presented for warm season nonsevere storms near Cape Canaveral, FL. The Warning Decision Support System–Integrated Information (WDSS‐II) software allowed us to ingest, display, and make distance calculations using radar reflectivity data from nearby National Weather Service Offices and lightning information from the National Lightning Detection Network and the local Lightning Detection and Ranging network. The flash distances were determined manually using a measuring tool within WDSS‐II. Six categories of flashes were investigated: (a) CG flashes measured from the edge of the convective core (30 dBZ) to the ground strike location that is beneath the attached anvil, (b) CG “bolt from the blue” flashes measured from cloud edge (0 dBZ) to the ground strike point that contains only 0 dBZ overhead, (c) CG bolt from the blue flashes as in Category B but measured from the edge of the precipitation (18 dBZ), (d) IC flashes that exit a portion of the cloud that is not an anvil, measured from cloud edge (0 dBZ), (e) IC flashes within anvils measured from the edge of convective precipitation (30 dBZ) to the termination point within the anvil, and (f) IC flashes exiting the edge (0 dBZ) of anvils. Results for each category are presented in the forms of frequency distributions of distances and their cumulative frequency distributions.

Constraint consensus concentration for identifying disjoint feasible regions in nonlinear programmes

It is usually not known in advance whether a nonlinear set of constraints has zero, one, or multiple feasible regions. Further, if one or more feasible regions exist, their locations are usually unknown. We propose a method for exploring the variable space quickly, using constraint consensus (CC) to identify promising areas that may contain a feasible region. Multiple CC solution points are clustered to identify regions of attraction. A new inter-point distance frequency distribution technique is used to determine the critical distance for the single-linkage clustering algorithm, which in turn determines the estimated number of disjoint feasible regions. The effectiveness of multistart global optimization is increased due to better exploration of the variable space, and efficiency is also increased because the expensive local solver is launched just once near each identified feasible region. The method is demonstrated on a variety of highly nonlinear models.

Genetic Diversity and Global Distribution of Citrus tristeza virus (CTV) Strains

Citrus tristeza virus (CTV), the most devastating viral pathogen in citrus, causes tremendous economic losses to citrus industry worldwide. The CTV isolates exhibit variable pathogenicities on their hosts indicating a mixed population of the CTV in nature. Several fragments within the CTV genome have been used for studying the genetic diversity of the CTV, however, the best region for rapid the CTV strain differentiation is still absent at present. In present study, a systemic analysis was carried out to evaluate the best region within the CTV genome for rapid CTV strain differentiation. Results of our study showed that the major coat protein (CP) coding region was the best region for this purpose. Using pair-wise distance frequency distribution plot, a reasonable genetic distance cut-off value was set for the CTV CP gene for the CTV strain differentiation. Using this criterion, eight CTV strains, including seven well characterized and a new strain, were successfully differentiated using 537 CTV isolates reported from 38 countries. The global strain distribution pattern was then determined and discussed. Our results also provided a new insight into the evolution and spreading of the virus, as well as the information for developing proper disease management strategy.

No Evidence of Coordination Between Different Subgroups in the Fission–Fusion Society of Spider Monkeys (Ateles geoffroyi)

Flexibility in spatial cohesion allows species with high fission–fusion dynamics to exploit variable habitats and decrease the costs of feeding competition. However, coordination among highly dispersed group members becomes problematic. In spider monkeys (Ateles spp.), individuals can spread over wide areas, forming several subgroups that appear to travel independently from each other. To explore their relative travel patterns, we compare the distance between different subgroups with the distance predicted by a null model of independent travel. Observations of distance between subgroups come from simultaneous follows of ≥2 subgroups in 2 different groups of spider monkeys in Punta Laguna, Mexico. We estimated space use using the kernel method, which produces areas with a given probability of presence of the subgroups, based on the frequency with which they were observed in each location. The null model consisted of the frequency distribution of distances between randomly chosen pairs of points within the home range, choosing each point independently with a probability proportional to the corresponding observed probability of presence. In all cases, the observed distances between subgroups were very close to those predicted by the null model, which suggests that subgroups do not coordinate their relative travel patterns. Also, the distance separating 2 individuals when in different subgroups was not affected by their sex or association index. These findings underscore the low cohesiveness between group members in species with high fission–fusion dynamics and challenge us to find the mechanisms by which groups maintain their social structure.

3-base periodicity in coding DNA is affected by intercodon dinucleotides.

All coding DNAs exhibit 3-base periodicity (TBP), which may be defined as the tendency of nucleotides and higher order n-tuples, e.g. trinucleotides (triplets), to be preferentially spaced by 3, 6, 9 etc, bases, and we have proposed an association between TBP and clustering of same-phase triplets. We here investigated if TBP was affected by intercodon dinucleotide tendencies and whether clustering of same-phase triplets was involved. Under constant protein sequence intercodon dinucleotide frequencies depend on the distribution of synonymous codons. So, possible effects were revealed by randomly exchanging synonymous codons without altering protein sequences to subsequently document changes in TBP via frequency distribution of distances (FDD) of DNA triplets. A tripartite positive correlation was found between intercodon dinucleotide frequencies, clustering of same-phase triplets and TBP. So, intercodon C|A (where "|" indicates the boundary between codons) was more frequent in native human DNA than in the codon-shuffled sequences; higher C|A frequency occurred along with more frequent clustering of C|AN triplets (where N jointly represents A, C, G and T) and with intense CAN TBP. The opposite was found for C|G, which was less frequent in native than in shuffled sequences; lower C|G frequency occurred together with reduced clustering of C|GN triplets and with less intense CGN TBP. We hence propose that intercodon dinucleotides affect TBP via same-phase triplet clustering. A possible biological relevance of our findings is briefly discussed.

Estimating time since infection in early homogeneous HIV-1 samples using a poisson model

BackgroundThe occurrence of a genetic bottleneck in HIV sexual or mother-to-infant transmission has been well documented. This results in a majority of new infections being homogeneous, i.e., initiated by a single genetic strain. Early after infection, prior to the onset of the host immune response, the viral population grows exponentially. In this simple setting, an approach for estimating evolutionary and demographic parameters based on comparison of diversity measures is a feasible alternative to the existing Bayesian methods (e.g., BEAST), which are instead based on the simulation of genealogies.ResultsWe have devised a web tool that analyzes genetic diversity in acutely infected HIV-1 patients by comparing it to a model of neutral growth. More specifically, we consider a homogeneous infection (i.e., initiated by a unique genetic strain) prior to the onset of host-induced selection, where we can assume a random accumulation of mutations. Previously, we have shown that such a model successfully describes about 80% of sexual HIV-1 transmissions provided the samples are drawn early enough in the infection. Violation of the model is an indicator of either heterogeneous infections or the initiation of selection.ConclusionsWhen the underlying assumptions of our model (homogeneous infection prior to selection and fast exponential growth) are met, we are under a very particular scenario for which we can use a forward approach (instead of backwards in time as provided by coalescent methods). This allows for more computationally efficient methods to derive the time since the most recent common ancestor. Furthermore, the tool performs statistical tests on the Hamming distance frequency distribution, and outputs summary statistics (mean of the best fitting Poisson distribution, goodness of fit p-value, etc). The tool runs within minutes and can readily accommodate the tens of thousands of sequences generated through new ultradeep pyrosequencing technologies. The tool is available on the LANL website.

Thresholds of erosion and sediment movement in bedrock channels

This study examines the erosive resistance of the discontinuous, loose joint blocks of various sizes that comprise the bed material of the Etobicoke Creek, an incised bedrock channel found in an urbanized setting within the city of Toronto, Ontario, Canada. In order to accomplish this, both field and laboratory experiments were conducted on the bed material found in this channel. The field work involved repeated detailed surveying of the channel bed and estimations of distances of movement of various clasts during many sediment transport events. We found that rates of erosion and/or deposition can be significant during the snowmelt spring events and that there was a greater loss of bed material over the study reach than was gained in several spots, with bed lowering > 0.10 m in some locations. The field work also showed that the distances moved by the rock clasts scaled directly with shear stresses observed during rain events and that average distances of transport tend to be short. The frequency distributions of distance of transport scaled with particle size is log-normally distributed. Flume experiments demonstrated that the clasts offered different levels of resistance to movement, depending on their orientation. The platy nature of the rock fragments, clast orientation, and their imbrication significantly affect the threshold of erosion. The results have significant implications for the understanding of bedrock rivers from a management perspective, especially in the case of those rivers experiencing the effects of urban development in their drainage basins.

Characterization of individual tree crowns using three-dimensional shape signatures derived from LiDAR data

Three-dimensional (3D) shape signatures based on the distance distribution of random point pairs are introduced and the effectiveness evaluated using computer simulations and samples of oak and Douglas fir crowns selected from Light Detection and Ranging (LiDAR) point clouds and Digital Surface Models (DSMs). The results suggest that comparison of 3D crown shapes can be effectively reduced to the comparison of frequency distributions of distances between random points, and that it is more computationally efficient when shape signatures are derived from raster surfaces. The results also suggest that the statistically based 3D shape signatures are relatively insensitive to noise and other small local variations, which is important for crown shape analysis in real-world environments.

On the Evolution of the Standard Genetic Code: Vestiges of Critical Scale Invariance from the RNA World in Current Prokaryote Genomes

Herein two genetic codes from which the primeval RNA code could have originated the standard genetic code (SGC) are derived. One of them, called extended RNA code type I, consists of all codons of the type RNY (purine-any base-pyrimidine) plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. In order to test if putative nucleotide sequences in the RNA World and in both extended RNA codes, share the same scaling and statistical properties to those encountered in current prokaryotes, we used the genomes of four Eubacteria and three Archaeas. For each prokaryote, we obtained their respective genomes obeying the RNA code or the extended RNA codes types I and II. In each case, we estimated the scaling properties of triplet sequences via a renormalization group approach, and we calculated the frequency distributions of distances for each codon. Remarkably, the scaling properties of the distance series of some codons from the RNA code and most codons from both extended RNA codes turned out to be identical or very close to the scaling properties of codons of the SGC. To test for the robustness of these results, we show, via computer simulation experiments, that random mutations of current genomes, at the rates of 10−10 per site per year during three billions of years, were not enough for destroying the observed patterns. Therefore, we conclude that most current prokaryotes may still contain relics of the primeval RNA World and that both extended RNA codes may well represent two plausible evolutionary paths between the RNA code and the current SGC.

A Shape-Based Classifier of Domain-Independent 3D Models

This paper proposes D2a, a new 3D model classifier that extends the D2 classifier from Osada et al. of Princeton University. The probability distribution of the ratio of areas of faces containing two random points from a 3D model is stored as the second dimension of a 2D array; while the first dimension contains the frequency distribution of distances of randomly generated point pairs (the D2 distribution). The resulting descriptor, D2a, is a two-dimensional histogram that incorporates these two shape features. The results of the classifier using four bins for the D2a descriptor are presented. The effectiveness is tested using the Princeton Shape Benchmark which shows an improvement over the original D2 classifier in several performance metrics.

Supragenotypic groups of the hepatitis B virus genome

Phylogenetic relationships among hepatitis B virus (HBV) genotypes were investigated using different regions across the genome. The phylogenetic analysis in conjunction with graphical examination of phylogenetic distance matrices and distance frequency distribution plotting suggest the clustering of HBV genotypes into three higher-order hierarchical groups: group I, comprising genotypes A-E and G; group II, comprising genotypes F and H; and a hypothetical group III. Present-day genotype G is postulated to be a recombinant with the non-polymerase region of group III virus and the polymerase gene of an ancestral virus belonging to group I.

Structural Relatedness Between the 18S rRNA Genes and the Formyl Peptide Receptor Genes: New Insights into the Phylogenesis of Immune Receptors

In this study the authors examined the sequences of the ribosomal 18S rRNA of Drosophila and man and 16 mRNA sequences coding for different members of the family of the mammalian formyl peptide receptors (FPRs). The positions in the sequences of all ≥7-base oligonucleotide identities occurring in at least one of the 18S rRNAs and one of the FPR mRNAs were recorded. On the basis of the positional data, the Drosophila 18S-FPR and human 18S-FPR distances (in nucleotides) were determined for each identity. Then the actual frequency distribution of the distances (grouped into 200-unit classes) was derived. The theoretical frequency distribution of distances was also calculated under the assumption of non-relatedness between the 18S and FPR sequences. Comparison between the theoretical and the actual distributions showed that at class –500 (range from − 400 to − 600) of the 18S-FPR values the actual frequency was significantly (p < 0.01) higher than the theoretical frequency, in both Drosophila and man, suggesting that the second section of the FPR genes (approximately from nucleotide 400 to the end of sequence) may be structurally related to the first section of the ribosomal 18S genes (approximately nucelotides 1–650). The authors advance the hypothesis that the two families of genes may have used common ancestral raw genetic materials in the building of the extant sequences.

Three-base periodicity patterns and self-similarity in whole bacterial chromosomes

It has been reported that in a collection of mRNAs the triplets GhN or RNY had a higher propensity to be separated by either three/six/nine, etc., bases than by two/four/five, etc., bases. This has been called three-base periodicity (TBP). In this work the frequency distribution of distances (FDDs) for all triplets in the Borrelia burgdorferi chromosome and selected triplets in other model sequences were determined. The FDDs produced oscillatory decaying patterns with TBP for most triplets and not only for those encompassed by the above formulas. Furthermore, we also found TBP for di- and mononucleotides. However, TBP was not observed for intergenic regions, sequences with a low content of coding regions or when the coding potential of sequences was disrupted by base shuffling. Excluding closely related species the FDDs between bacterial genomes were different and appeared characteristic of the analyzed genome. FDDs also showed self-similarity, since 1 Mb sequences rendered FDDs that were very similar to those for the entire sequence.

Canada: Clariant — plastics masterbatch

This study examines the erosive resistance of the discontinuous, loose joint blocks of various sizes that comprise the bed material of the Etobicoke Creek, an incised bedrock channel found in an urbanized setting within the city of Toronto, Ontario, Canada. In order to accomplish this, both field and laboratory experiments were conducted on the bed material found in this channel. The field work involved repeated detailed surveying of the channel bed and estimations of distances of movement of various clasts during many sediment transport events. We found that rates of erosion and/or deposition can be significant during the snowmelt spring events and that there was a greater loss of bed material over the study reach than was gained in several spots, with bed lowering > 0.10 m in some locations. The field work also showed that the distances moved by the rock clasts scaled directly with shear stresses observed during rain events and that average distances of transport tend to be short. The frequency distributions of distance of transport scaled with particle size is log-normally distributed. Flume experiments demonstrated that the clasts offered different levels of resistance to movement, depending on their orientation. The platy nature of the rock fragments, clast orientation, and their imbrication significantly affect the threshold of erosion. The results have significant implications for the understanding of bedrock rivers from a management perspective, especially in the case of those rivers experiencing the effects of urban development in their drainage basins.

On a higher-order neural network for distortion invariant pattern recognition

This paper proposed some methods upon a second-order neural network. These networks apply the normalized frequency distribution of distance between two points on an object. 0.766 of the recognition accuracy for 2D two-class mixture distributions and 0.960 for hand-written characters are achieved.

Dispersion of Seedlings of the Prairie Compass Plant, Silphium laciniatum (Asteraceae)

Although the dispersal of seeds around individual plants (the seed shadow) has frequently been characterized, the dispersion of seedlings around plants (the seedling shadow) has rarely been examined. We mapped 101 and 149 seedlings of the prairie compass plant (Silphium laciniatum) that appeared in our study area in 1987 and 1990 following mass flowering in 1986 and 1989. We also mapped the locations of flowering stems which appeared in 1986 and 1989 and recorded the number of flowerheads at each stem location. The frequency distributions of distance between a seedling and the nearest flowering stem were identical in the 2 years, with a median distance of 1.0 m. The large size and lack of wind-dispersal structures of compass plant seeds (achenes) are responsible for their limited dispersal. From estimates of the total seed production in the study area in 1986 and 1989, we calculated that about 1% of seeds became seedlings in each year. Flowering stem locations with a higher number of flowerheads had a significantly higher density of seedlings around them. This indicates that recruitment to compass plant populations is not a “lottery”; individual plants that produce more seeds produce, on average, more seedlings.