Medical Ultrasound Video Coding with H.265/HEVC Based on ROI Extraction

High-efficiency video compression technology is of primary importance to the storage and transmission of digital medical video in modern medical communication systems. To further improve the compression performance of medical ultrasound video, two innovative technologies based on diagnostic region-of-interest (ROI) extraction using the high efficiency video coding (H.265/HEVC) standard are presented in this paper. First, an effective ROI extraction algorithm based on image textural features is proposed to strengthen the applicability of ROI detection results in the H.265/HEVC quad-tree coding structure. Second, a hierarchical coding method based on transform coefficient adjustment and a quantization parameter (QP) selection process is designed to implement the otherness encoding for ROIs and non-ROIs. Experimental results demonstrate that the proposed optimization strategy significantly improves the coding performance by achieving a BD-BR reduction of 13.52% and a BD-PSNR gain of 1.16 dB on average compared to H.265/HEVC (HM15.0). The proposed medical video coding algorithm is expected to satisfy low bit-rate compression requirements for modern medical communication systems.     

Landscape scale assessment of stream channel and riparian habitat restoration needs

Human modifications of streams and rivers have caused extensive stream channel and riparian degradation. Cost-effective, rapid assessment tools can be used to better manage such areas by identifying the status of habitats for restoration planning and protection. We used a spatially explicit, reach-scale geographic information system modeling strategy to examine stream channel and riparian condition and prioritize restoration actions. The stream channel condition index uses information on land use, road and railroad density, and sinuosity. The riparian condition index uses calculations of percent forest, patch density, and convexity based on land cover in the floodplain. Reaches were classified into restoration categories based on stream channel and riparian condition model results, land ownership, slope, position in the subwatershed, and adjacency to high-quality habitat. We compared modeled restoration priority rankings with those in the management plan for the East Credit subwatershed in Ontario, Canada. Predicted stream channel restoration priority rankings matched field-based classifications for 86% of the reaches in the East Credit subwatershed. Predicted riparian restoration priority rankings matched field-based classifications for 81% of the reaches. Our methods replicate with fairly good accuracy the results obtained using intensive field surveys and stakeholder input. Managers can use these cost-effective strategy development tools to identify candidate reaches for further study and prioritize stream channel and riparian restoration actions over large regions.     

Barbieri’s Organic Codes Enable Error Correction of Genomes

Barbieri introduced and developed the concept of organic codes. The most basic of them is the genetic code, a set of correspondence rules between otherwise unrelated sequences: strings of nucleotides on the one hand, polypeptidic chains on the other hand. Barbieri noticed that it implies ‘coding by convention’ as arbitrary as the semantic relations a language establishes between words and outer objects. Moreover, the major transitions in life evolution originated in new organic codes similarly involving conventional rules. Independently, dealing with heredity as communication over time and relying on information theory, we asserted that the conservation of genomes over the ages demands that error-correcting codes make them resilient to casual errors. Moreover, the better conservation of very old parts of the genome demands that they result from combining successively established nested codes such that the older an information, the more numerous component codes protect it. Barbieri’s concept of organic code and that of genomic error-correcting code may seem unrelated. We show however that organic codes actually entail error-correcting properties. Error-correcting, in general, results from constraints being imposed on a set of sequences. Mathematical equalities are conveniently used in communication engineering for expressing constraints but error correction only needs that constraints exist. Biological sequences are similarly endowed with error-correcting ability by physical-chemical or linguistic constraints, thus defining ‘soft codes’. These constraints are moreover presumably efficient for correcting errors. Insofar as biological sequences are subjected to constraints, organic codes necessarily involve soft codes, and their successive onset results in the nested structure we hypothesized. Organic codes are generated and maintained by means of molecular ‘semantic feedback loops’. Each of these loops involves genes which code for proteins, the enzymatic action of which controls a function needed for the protein assembly. Taken together, thus, they control the assembly of their own structure as instructed by the genome and, once closed, these loops ensure their own conservation. However, the semantic feedback loops do not prevent the genome lengthening. It increases both the redundancy of the genome (as an error-correcting code) and the information quantity it bears, thus improving the genome reliability and the specificity of the enzymes, which enables further evolution.     

Controlled release experiments to determine the effects of shade and plants on nutrient retention in a lowland stream

Understanding nutrient uptake and retention in streams remains an important challenge for lotic scientists. In this study a series of pulse and continuous releases of dissolved nutrients were made to shaded and unshaded (reference) reaches of a small lowland stream to determine whether suppression of macrophyte growth by riparian shade impaired nutrient retention. The nutrients were dissolved reactive phosphorus (DRP), total ammoniacal nitrogen (NH₄–N) and nitrate nitrogen (NO₃–N). Nutrient reductions ranged from 100% of DRP when stream water was anoxic, to 5–10% for NH₄–N and NO₃–N in the reference reach. Nutrient removals were affected by travel times in each reach. Percentage removals of NH₄–N (46 ± 10) and NO₃–N (52 ± 14) were higher in the shaded reach than in the swifter moving reference reach (15 ± 8 and 16 ± 10, respectively). DRP (%) removals were 75± 7 and 57 ± 12 for the shaded and reference reaches, respectively. The presence of emergent marginal macrophytes (Persicaria hydropiper) increased stream velocity in the reference reach by reducing the effective channel cross-section area. Shading reduced plant biomass, increased the channel cross-section and lowered velocity in the experimental reach, effecting dramatic reductions in nutrient concentrations over short distances. The opposite effect is more typical for larger, swifter streams having dense stands of submerged macrophytes, where lowering channel plant biomass will cause increased velocities and lower relative nutrient losses. Riparian shade does not necessarily impair nutrient uptake from small streams. Where invasive marginal species such as P. hydropiper dominate headwater streams shade may be beneficial to the protection of downstream waters from eutrophication. Where reduction of nutrient fluxes from small streams is a key objective for protection of downstream waters, active management of streams should seek to increase travel times, allowing greater potential for nutrient uptake. This will need to be weighed against the need for effective drainage in pastoral areas where reduced travel times are usually sought.     

Group graph of the genetic code

The genetic code doublets can be divided into two octets of completely degenerate and ambiguous coding dinucleotides. These two octets have the algebraic property of lying on continuously connected planes on the group graph (a tesseract) of the Cartesian product of two Klein 4-groups of nucleotide exchange operators. The K X K group can also be broken into four cosets, one of which has completely degenerate coding elements, and another that has completely ambiguous coding elements. The two octets of coding doublets have the further algebraic property that the product of their internal exchange operators naturally divide into two exactly equivalent sets. These properties of the genetic code are relevant to unraveling error-detecting and error-correcting (proof-reading) aspects of the genetic code and may be helpful in understanding the context-sensitive grammar of genetic language.     

ECG compression using the context modeling arithmetic coding with dynamic learning vector–scalar quantization

Electrocardiogram (ECG) compression can significantly reduce the storage and transmission burden for the long-term recording system and telemedicine applications. In this paper, an improved wavelet-based compression method is proposed. A discrete wavelet transform (DWT) is firstly applied to the mean removed ECG signal. DWT coefficients in a hierarchical tree order are taken as the component of a vector named tree vector (TV). Then, the TV is quantized with a vector–scalar quantizer (VSQ), which is composed of a dynamic learning vector quantizer and a uniform scalar dead-zone quantizer. The context modeling arithmetic coding is finally employed to encode those quantized coefficients from the VSQ. All tested records are selected from the Massachusetts Institute of Technology-Beth Israel Hospital arrhythmia database. Statistical results show that the compression performance of the proposed method outperforms several published compression algorithms.     

Spatial sampling bias and model complexity in stream‐based species distribution models: A case study of Paddlefish (Polyodon spathula) in the Arkansas River basin,USA

Leveraging existing presence records and geospatial datasets, species distribution modeling has been widely applied to informing species conservation and restoration efforts. Maxent is one of the most popular modeling algorithms, yet recent research has demonstrated Maxent models are vulnerable to prediction errors related to spatial sampling bias and model complexity. Despite elevated rates of biodiversity imperilment in stream ecosystems, the application of Maxent models to stream networks has lagged, as has the availability of tools to address potential sources of error and calculate model evaluation metrics when modeling in nonraster environments (such as stream networks). Herein, we use Maxent and customized R code to estimate the potential distribution of paddlefish (Polyodon spathula) at a stream‐segment level within the Arkansas River basin, USA, while accounting for potential spatial sampling bias and model complexity. Filtering the presence data appeared to adequately remove an eastward, large‐river sampling bias that was evident within the unfiltered presence dataset. In particular, our novel riverscape filter provided a repeatable means of obtaining a relatively even coverage of presence data among watersheds and streams of varying sizes. The greatest differences in estimated distributions were observed among models constructed with default versus AIC_C‐selected parameterization. Although all models had similarly high performance and evaluation metrics, the AIC_C‐selected models were more inclusive of westward‐situated and smaller, headwater streams. Overall, our results solidified the importance of accounting for model complexity and spatial sampling bias in SDMs constructed within stream networks and provided a roadmap for future paddlefish restoration efforts in the study area.     

ECG Data Compression Using Modified Run Length Encoding of Wavelet Coefficients for Holter Monitoring

ObjectiveIn cardiac patient-care, compression of long-term ECG data is essential to minimize the data storage requirement and transmission cost. Hence, this paper presents a novel electrocardiogram data compression technique which utilizes modified run-length encoding of wavelet coefficients.MethodFirst, wavelet transform is applied to the ECG data which decomposes it and packs maximum energy to less number of transform coefficients. The wavelet transform coefficients are quantized using dead-zone quantization. It discards small valued coefficients lying in the dead-zone interval while other coefficients are kept at the formulated quantized output interval. Among all the quantized coefficients, an average value is assigned to those coefficients for which energy packing efficiency is less than 99.99%. The obtained coefficients are encoded using modified run-length coding. It offers higher compression ratio than conventional run-length coding without any loss of information.ResultsCompression performance of the proposed technique is evaluated using different ECG records taken from the MIT-BIH arrhythmia database. The average compression performance in terms of compression ratio, percent root mean square difference, normalized percent mean square difference, and signal to noise ratio are 17.18, 3.92, 6.36, and 28.27 dB respectively for 48 ECG records.ConclusionThe compression results obtained by the proposed technique is better than techniques recently introduced by others. The proposed technique can be utilized for compression of ECG records of Holter monitoring.     

Responses to Riparian Restoration in the Spring Creek Watershed, Central Pennsylvania

Riparian treatments, consisting of 3‐ to 4‐m buffer strips, stream bank stabilization, and rock‐lined stream crossings, were installed in two streams with livestock grazing to reduce sediment loading and stream bank erosion. Cedar Run and Slab Cabin Run, the treatment streams, and Spring Creek, an adjacent reference stream without riparian grazing, were monitored prior to (1991–1992) and 3–5 years after (2001–2003) riparian buffer installation to assess channel morphology, stream substrate composition, suspended sediments, and macroinvertebrate communities. Few changes were found in channel widths and depths, but channel‐structuring flow events were rare in the drought period after restoration. Stream bank vegetation increased from 50% or less to 100% in nearly all formerly grazed riparian buffers. The proportion of fine sediments in stream substrates decreased in Cedar Run but not in Slab Cabin Run. After riparian treatments, suspended sediments during base flow and storm flow decreased 47–87% in both streams. Macroinvertebrate diversity did not improve after restoration in either treated stream. Relative to Spring Creek, macroinvertebrate densities increased in both treated streams by the end of the posttreatment sampling period. Despite drought conditions that may have altered physical and biological effects of riparian treatments, goals of the riparian restoration to minimize erosion and sedimentation were met. A relatively narrow grass buffer along 2.4 km of each stream was effective in improving water quality, stream substrates, and some biological metrics.     

Two-Level Scheduling for Video Transmission over Downlink OFDMA Networks

This paper presents a two-level scheduling scheme for video transmission over downlink orthogonal frequency-division multiple access (OFDMA) networks. It aims to maximize the aggregate quality of the video users subject to the playback delay and resource constraints, by exploiting the multiuser diversity and the video characteristics. The upper level schedules the transmission of video packets among multiple users based on an overall target bit-error-rate (BER), the importance level of packet and resource consumption efficiency factor. Instead, the lower level renders unequal error protection (UEP) in terms of target BER among the scheduled packets by solving a weighted sum distortion minimization problem, where each user weight reflects the total importance level of the packets that has been scheduled for that user. Frequency-selective power is then water-filled over all the assigned subcarriers in order to leverage the potential channel coding gain. Realistic simulation results demonstrate that the proposed scheme significantly outperforms the state-of-the-art scheduling scheme by up to 6.8 dB in terms of peak-signal-to-noise-ratio (PSNR). Further test evaluates the suitability of equal power allocation which is the common assumption in the literature.     

The RCE: a Riparian, Channel, and Environmental Inventory for small streams in the agricultural landscape

1. The Riparian, Channel and Environmental (RCE) Inventory has been developed to assess the physical and biological condition of small streams in the lowland, agricultural landscape. It consists of sixteen characteristics which define the structure of the riparian zone, stream channel morphology, and the biological condition in both habitats. 2. The inventory is based on the view that in landscapes where non-point source pollution and agriculture dominate, the environmental condition of small streams can be assessed by an appraisal of the physical condition of the riparian zone and stream channel. It is assumed that disturbance of this physical structure is a major cause for reduction of stream biological structure and function. This assumption is supported by a case study using fifteen Italian stream locations in which the RCE was found to be positively correlated to the benthic macroinvertebrate community as measured by the Extended Biotic Index (r = 0.80, P < 0.001) and the Shannon Diversity Index (r = 0.73; P < 0.001). 3. The inventory is designed for quick use to cover a large number of streams in a short period of time. When used it generates a numerical score which can be used to compare the physical and biological condition between different streams within a region. The numerical score is divided into five, colour-coded classes to facilitate use in streammonitoring programmes and to allow comparison with biological indices.     

A new species of tusked weta from the Raukumara Range,North Island,New Zealand (Orthoptera: Anostostomatidae: Motuweta)

Abstract

A new species of weta from mainland New Zealand is described and assigned to the previously monotypic genus Motuweta Johns and the genus redefined. Mandibles of adult males bear prominent horns. Motuweta riparia n. sp. is a moderate‐sized species (36 mm) found on the margins of first or second order streams in the eastern mid North Island ranges. Its escape reaction is to leap into the stream and remain underwater until danger has passed, a strategy which has probably enabled it to survive in predator‐infested areas.     

Comparing the Fish and Benthic Macroinvertebrate Diversity of Restored Urban Streams to Reference Streams

Urbanization is associated with substantial losses to stream biological diversity throughout the United States' mid‐Atlantic. Stream restoration has been used to improve stream conditions and, in part, to ameliorate these losses. However, the relationship between restoration and recovery of biological diversity is unclear. Our objective was to critically examine the efficacy of urban stream restorations with regard to biological diversity. We compared restored urban streams to urban nonrestored, nonurban, and reference (minimally degraded) streams using five measures each of fish and benthic macroinvertebrate diversity. Both multivariate and univariate statistical analyses show biological diversity of restored urban streams to be similar to nonrestored urban streams and lower than nonurban and reference streams. Restored urban sites showed no apparent increase in biological diversity through time, while diversity decreased at two of the reference streams coincident with increased urban development within their catchments. Our results indicate that restoration approaches commonly used regionally as in these urban streams are not leading to recovery of native stream biodiversity. Evidence from several sources indicates a need for dramatic changes in restoration approach, and we argue for a watershed‐scale focus including protection of the least impacted streams and adopting other land‐based actions within the watershed where possible.     

Amazon deforestation alters small stream structure, nitrogen biogeochemistry and connectivity to larger rivers

Human activities that modify land cover can alter the structure and biogeochemistry of small streams but these effects are poorly known over large regions of the humid tropics where rates of forest clearing are high. We examined how conversion of Amazon lowland tropical forest to cattle pasture influenced the physical and chemical structure, organic matter stocks and N cycling of small streams. We combined a regional ground survey of small streams with an intensive study of nutrient cycling using ¹⁵N additions in three representative streams: a second-order forest stream, a second-order pasture stream and a third-order pasture stream. These three streams were within several km of each other and on similar soils. Replacement of forest with pasture decreased stream habitat complexity by changing streams from run and pool channels with forest leaf detritus (50% cover) to grass-filled (63% cover) channel with runs of slow-moving water. In the survey, pasture streams consistently had lower concentrations of dissolved oxygen and nitrate (NO₃ ^?) compared with similar-sized forest streams. Stable isotope additions revealed that second-order pasture stream had a shorter NH₄ ⁺ uptake length, higher uptake rates into organic matter components and a shorter ¹⁵NH₄ ⁺ residence time than the second-order forest stream or the third-order pasture stream. Nitrification was significant in the forest stream (19% of the added ¹⁵NH₄ ⁺) but not in the second-order pasture (0%) or third-order (6%) pasture stream. The forest stream retained 7% of added ¹⁵N in organic matter compartments and exported 53% (¹⁵NH₄ ⁺?=?34%; ¹⁵NO₃ ^??=?19%). In contrast, the second-order pasture stream retained 75% of added ¹⁵N, predominantly in grasses (69%) and exported only 4% as ¹⁵NH₄ ⁺. The fate of tracer ¹⁵N in the third-order pasture stream more closely resembled that in the forest stream, with 5% of added N retained and 26% exported (¹⁵NH₄ ⁺?=?9%; ¹⁵NO₃ ^??=?6%). These findings indicate that the widespread infilling by grass in small streams in areas deforested for pasture greatly increases the retention of inorganic N in the first- and second-order streams, which make up roughly three-fourths of total stream channel length in Amazon basin watersheds. The importance of this phenomenon and its effect on N transport to larger rivers across the larger areas of the Amazon Basin will depend on better evaluation of both the extent and the scale at which stream infilling by grass occurs, but our analysis suggests the phenomenon is widespread.     

Use of benthic macroinvertebrates to assess the biological status of Pampean streams in Argentina

Macro-invertebrate communities and environmental variables were assessed seasonally for two years in seven streams in North-Eastern of Buenos Aires province (Argentina) in order to analyse changes in their structure and composition in relation with the quality of the water. The study includes pristine streams and others affected by urban and industrial effluents with high conductivity, nitrates, nitrites, phosphates and low oxygen content. Organisms with well-known pollution tolerance were identified to assess biological water quality, using a new Biotic Index (IBPAMP: Biotic Index for PAMPean rivers and streams) in comparison with other existing biotic indices. The usefulness of principal component analysis (PCA) and correlation matrices were examined to evaluate the efficiency of the method to assess disturbances. In general IBPAMP did well correlate with several classical measures of biological water quality (taxon richness, diversity and several biotic indices). The El Gato stream was the most disturbed ecosystem among all studied sites. It was characterised by low dissolved oxygen levels, high turbidity in the middle course, high BOD5 (>30 mg l^–1) and COD (>40 mg l^–1) values. The Buñirigo stream has a bad quality in the industrial area, but varying according to the dry and wet periods. In general, in the mountainous areas the water quality of streams was good with the exception of the stations located downstream of cities like Ayacucho on the Tandileofú stream.     

Ecological values of Hamilton urban streams (North Island, New Zealand): constraints and opportunities for restoration

Urban streams globally are characterised by degraded habitat conditions and low aquatic biodiversity, but are increasingly becoming the focus of restoration activities. We investigated habitat quality, ecological function, and fish and macroinvertebrate community composition of gully streams in Hamilton City, New Zealand, and compared these with a selection of periurban sites surrounded by rural land. A similar complement of fish species was found at urban and periurban sites, including two threatened species, with only one introduced fish widespread (Gambusia affinis). Stream macroinvertebrate community metrics indicated low ecological condition at most urban and periurban sites, but highlighted the presence of one high value urban site with a fauna dominated by sensitive taxa. Light-trapping around seepages in city gullies revealed the presence of several caddisfly species normally associated with native forest, suggesting that seepage habitats can provide important refugia for some aquatic insects in urban environments. Qualitative measures of stream habitat were not significantly different between urban and periurban sites, but urban streams had significantly lower hydraulic function and higher biogeochemical function than periurban streams. These functional differences are thought to reflect, respectively, (1) the combined effects of channel modification and stormwater hydrology, and (2) the influence of riparian vegetation providing shade and enhancing habitat in streams. Significant relationships between some macroinvertebrate community metrics and riparian vegetation buffering and bank protection suggest that riparian enhancement may have beneficial ecological outcomes in some urban streams. Other actions that may contribute to urban stream restoration goals include an integrated catchment approach to resolving fish passage issues, active reintroduction of wood to streams to enhance cover and habitat heterogeneity, and seeding of depauperate streams with native migratory fish to help initiate natural recolonisation.     

Effects of Road Crossings on Stream and Streamside Salamanders

Abstract: Salamanders are important members of faunal communities in Appalachian Mountain (USA) streams, and the use of salamanders as bioindicators is increasing. Roads are a part of the modern landscape, but effects of roads on stream and streamside salamander diversity and abundance is not clear. We sampled streams in central West Virginia, USA, using quadrats placed along transects in the flowing channel, dry channel, and stream bank to assess salamander diversity, richness, and abundance during 2004. We used Akaike's Information Criterion for model selection at reach (i.e., above and below culverts) and stream scales. Salamander diversity and richness was affected by elevation, stream gradient, canopy cover, and the presence of roads. Overall, stream and riparian habitat quality was the most important factor affecting salamander richness. The presence of roads, stream gradient, and elevation received the most empirical support for predicting species' abundances. Roads benefited disturbance-tolerant species but negatively affected other species. Impacts of roads and culverts on habitat should be considered by federal and state transportation agencies and natural resources agencies during the planning process and addressed through mitigation efforts. Managers should install culverts that are as wide as the stream channel, at grade with the streambed, and dominated by rubble substrate to provide maximum benefit for salamanders. (JOURNAL OF WILDLIFE MANAGEMENT 72(3):760–771; 2008)     

Biogeography,ecoregions, and geomorphology affect fish species composition in streams of eastern Oklahoma,USA

Stream fish assemblages are structured by biogeographical, physical and biological factors acting on different spatial scales. We determined how physical factors, geomorphology and stream habitat, influenced fish species composition (presence–absence) in eastern Oklahoma, USA relative to the ecoregion and biogeographic effects previously reported. We sampled fish assemblages and surveyed geomorphology and habitat at 107 stream sites in the Boston Mountains, Ouachita Mountains, and Ozark Highlands ecoregions in eastern Oklahoma. Partial canonical correspondence analyses (pCCAs) and variance partitioning showed that patterns of endemism related to drainage basins and ecoregions explained important variation in fish species composition in all streams, but stream size and local channel morphology explained more variation overall. Stream size effects were most important in explaining variability in fish species composition in both northeastern and southeastern Oklahoma streams. Local channel morphology and substrate characteristics were secondarily important. Variables typically considered important as fish habitat (aquatic vegetation, etc.) had little effect on fish species composition.     

A comparison of streams in logged and unlogged areas of Great Smoky Mountains National Park

Second order streams draining areas of virgin forest in Great Smoky Mountains National Park, Tennessee and North Carolina, U.S.A., are compared to those which drain forests logged before the establishment of the park in the 1930's. Water quality of two main study streams (one unlogged and one formerly logged) was compared and the unlogged stream had generally higher levels of dissolved solids and lower levels of suspended particulates than the logged stream. Stream channel characteristics were compared on four logged and four unlogged streams. The unlogged streams had over four times more (by volume) of woody debris and 10 times more material in debris dams than the logged streams. Only minor differences in substrate composition were observed. Macroinvertebrate samples from the four logged and four unlogged streams showed that the logged streams contained greater numbers of organisms and more taxa. More detailed sampling on the two main study streams showed similar patterns of more individuals and more taxa in the logged stream, as well as differences in the composition of five functional groups. These differences in invertebrate fauna may be due to differences in quantity and quality of leaf litter inputs, although other explanations are also possible.