Minimum Number Of Sites Research Articles

Accurate prediction of pan-cancer types using machine learning with minimal number of DNA methylation sites.

DNA methylation analysis has been applied to determine the primary site of cancer; however, robust and accurate prediction of cancer types with a minimum number of sites is still a significant scientific challenge. To build an accurate and robust cancer type prediction tool with a minimum number of DNA methylation sites, we internally benchmarked different DNA methylation site selection and ranking procedures, as well as different classification models. We used The Cancer Genome Atlas dataset (26 cancer types with 8296 samples) to train and test models and used an independent dataset (17 cancer types with 2738 samples) for model validation. A deep neural network model using a combined feature selection procedure (named MethyDeep) can predict 26 cancer types using 30 methylation sites with superior performance compared with the known methods for both primary and metastatic cancers in independent validation datasets. In conclusion, MethyDeep is an accurate and robust cancer type predictor with the minimum number of DNA methylation sites; it could help the cost-effective clarification of cancer of unknown primary patients and the liquid biopsy-based early screening of cancers.

A decade of monitoring micropollutants in urban wet-weather flows: What did we learn?

Urban wet-weather discharges from combined sewer overflows (CSO) and stormwater outlets (SWO) are a potential pathway for micropollutants (trace contaminants) to surface waters, posing a threat to the environment and possible water reuse applications. Despite large efforts to monitor micropollutants in the last decade, the gained information is still limited and scattered. In a metastudy we performed a data-driven analysis of measurements collected at 77 sites (683 events, 297 detected micropollutants) over the last decade to investigate which micropollutants are most relevant in terms of 1) occurrence and 2) potential risk for the aquatic environment, 3) estimate the minimum number of data to be collected in monitoring studies to reliably obtain concentration estimates, and 4) provide recommendations for future monitoring campaigns. We highlight micropollutants to be prioritized due to their high occurrence and critical concentration levels compared to environmental quality standards. These top-listed micropollutants include contaminants from all chemical classes (pesticides, heavy metals, polycyclic aromatic hydrocarbons, personal care products, pharmaceuticals, and industrial and household chemicals). Analysis of over 30,000 event mean concentrations shows a large fraction of measurements (> 50%) were below the limit of quantification, stressing the need for reliable, standard monitoring procedures. High variability was observed among events and sites, with differences between micropollutant classes. The number of events required for a reliable estimate of site mean concentrations (error bandwidth of 1 around the “true" value) depends on the individual micropollutant. The median minimum number of events is 7 for CSO (2 to 31, 80%-interquantile) and 6 for SWO (1 to 25 events, 80%-interquantile). Our analysis indicates the minimum number of sites needed to assess global pollution levels and our data collection and analysis can be used to estimate the required number of sites for an urban catchment. Our data-driven analysis demonstrates how future wet-weather monitoring programs will be more effective if the consequences of high variability inherent in urban wet-weather discharges are considered.

Weight-of-evidence approach to identify regionally representative sites for air-quality monitoring network: Satellite data-based analysis

The methodology discussed in Lekinwala et al., 2020, hereinafter referred to as the ‘parent article’, is used to setup a nation-wide network for background PM2.5 measurement at strategic locations, optimally placing sites to obtain maximum regionally representative PM2.5 concentrations with minimum number of sites. Traditionally, in-situ PM2.5 measurements are obtained for several potential sites and compared to identify the most regionally representative sites [4], Wongphatarakul et al., 1998) at the location. The ‘parent article’ proposes the use of satellite-derived proxy for aerosol (Aerosol Optical Depth, AOD) data in the absence of in-situ PM2.5 measurements. This article focuses on the details about satellite-data processing which forms part of the methodology discussed in the ‘parent article’. Following are some relevant aspects:•High resolution AOD is retrieved from Moderate Resolution Imaging Spectroradiometer (MODIS) instruments aboard NASA's Aqua and Terra satellite using Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm. The data is stored as grids of size 1200 × 1200 and a total of seven such grids cover the Indian land mass. These grids were merged, regridded and multiplied by conversion factors from GEOS-Chem Chemical Transport Model to obtain PM2.5 values. Standard set of tools like CDO and NCL are used to manipulate the satellite-data (*.nc files).•The PM2.5 values are subjected to various statistical analysis using metrics like coefficient of divergence (CoD), Pearson correlation coefficient (PCC) and mutual information (MI).•Computations for CoD, MI are performed using Python codes developed in-house while a function in NumPy module of Python was used for PCC calculations.

A regional approach to Nordic crop wild relativein situconservation planning

AbstractCrop wild relatives (CWR) can provide one solution to future challenges on food security, sustainable agriculture and adaptation to climate change. Diversity found in CWR can be essential for adapting crops to these new demands. Since the need to improvein situconservation of CWR has been recognized by the Convention on Biological Diversity (CBD) (2010) and the Global Strategy for Plant Conservation (2011–2020), it is important to develop ways to safeguard these important genetic resources. The Nordic flora includes many species related to food, forage and other crop groups, but little has been done to systematically secure these important wild resources. A Nordic regional approach to CWR conservation planning provided opportunities to network, find synergies, share knowledge, plan the conservation and give policy inputs on a regional level. A comprehensive CWR checklist for the Nordic region was generated and then prioritized by socio-economic value and utilization potential. Nordic CWR checklist was formed of 2553 taxa related to crop plants. Out of these, 114 taxa including 83 species were prioritized representing vegetable, cereal, fruit, berry, nut and forage crop groups. Thein situconservation planning of the priority CWR included ecogeographic and complementarity analyses to identify a potential network of genetic reserve sites in the region. Altogether 971,633 occurrence records of the priority species were analysed. A minimum number of sites within and outside existing conservation areas were identified that had the potential to support a maximum number of target species of maximum intraspecific diversity.

Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites

BackgroundTargeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by targeting housekeeping genes that provide resolution down to the family, genera, and sometimes species level. Unfortunately, this level of resolution is not sufficient in many applications where strain-level identification of bacteria is required (biodefense, forensics, clinical diagnostics, and outbreak investigations). Adding more genomic targets will increase the resolution, but the challenge is identifying the appropriate targets. VaST was developed to address this challenge by finding the minimum number of targets that, in combination, achieve maximum strain-level resolution for any strain complex. The final combination of target regions identified by the algorithm produce a unique haplotype for each strain which can be used as a fingerprint for identifying unknown samples in a TAS assay. VaST ensures that the targets have conserved primer regions so that the targets can be amplified in all of the known strains and it also favors the inclusion of targets with basal variants which makes the set more robust when identifying previously unseen strains.ResultsWe analyzed VaST’s performance using a number of different pathogenic species that are relevant to human disease outbreaks and biodefense. The number of targets required to achieve full resolution ranged from 20 to 88% fewer sites than what would be required in the worst case and most of the resolution is achieved within the first 20 targets. We computationally and experimentally validated one of the VaST panels and found that the targets led to accurate phylogenetic placement of strains, even when the strains were not a part of the original panel design.ConclusionsVaST is an open source software that, when provided a set of variant sites, can find the minimum number of sites that will provide maximum resolution of a strain complex, and it has many different run-time options that can accommodate a wide range of applications. VaST can be an effective tool in the design of strain identification panels that, when combined with TAS technologies, offer an efficient and inexpensive strain typing protocol.

Optimal redistribution of an urban air quality monitoring network using atmospheric dispersion model and genetic algorithm

Air quality monitoring networks play a significant role in identifying the spatiotemporal patterns of air pollution, and they need to be deployed efficiently, with a minimum number of sites. The revision and optimal adjustment of existing monitoring networks is crucial for cities that have undergone rapid urban expansion and experience temporal variations in pollution patterns. The approach based on the Weather Research and Forecasting–California PUFF (WRF-CALPUFF) model and genetic algorithm (GA) was developed to design an optimal monitoring network. The maximization of coverage with minimum overlap and the ability to detect violations of standards were developed as the design objectives for redistributed networks. The non-dominated sorting genetic algorithm was applied to optimize the network size and site locations simultaneously for Shijiazhuang city, one of the most polluted cities in China. The assessment on the current network identified the insufficient spatial coverage of SO2 and NO2 monitoring for the expanding city. The optimization results showed that significant improvements were achieved in multiple objectives by redistributing the original network. Efficient coverage of the resulting designs improved to 60.99% and 76.06% of the urban area for SO2 and NO2, respectively. The redistributing design for multi-pollutant including 8 sites was also proposed, with the spatial representation covered 52.30% of the urban area and the overlapped areas decreased by 85.87% compared with the original network. The abilities to detect violations of standards were not improved as much as the other two objectives due to the conflicting nature between the multiple objectives. Additionally, the results demonstrated that the algorithm was slightly sensitive to the parameter settings, with the number of generations presented the most significant effect. Overall, our study presents an effective and feasible procedure for air quality network optimization at a city scale.

Improved Radio Network Dimensioning for Real-Time Polling Service on IEEE 802.16 Wireless Networks with QoS Consideration

Recently, applications of real-time polling service (rtPS) in IEEE 802.16 wireless networks have gained considerable popularity. These applications generate large amounts of real time traffic in the network and thus maintaining the quality of service (QoS) such as packet delay requirement in rtPS dominant networks is critical. Existing dimensioning methodology does not consider QoS parameters of rtPS in network dimensioning. Moreover, exhaustive and time-consuming simulations are required to evaluate the performance and QoS of rtPS. To overcome this problem, we propose an improved radio network dimensioning framework which considers QoS parameters of rtPS in network dimensioning. In this framework, an analytical model is developed to evaluate the capacity and performance of rtPS in IEEE 802.16 wireless networks. The proposed framework provides a fast and accurate means of finding the trade-off between system load and packet delay, thus providing network operators with an analytical tool that jointly considers coverage, capacity and QoS requirements for obtaining the minimum number of sites required. The accuracy of the proposed model is validated through simulations.

Location optimization of strategic alert sites for homeland defense

This research uses a location analysis approach for selecting aircraft alert sites for the defense of important national areas of interest identified by the US Department of Defense. Solutions are generated in a two step approach where the minimum number of sites is first identified using the location set covering problem and then the result is improved by finding the minimum aggregate network distance or p-median solution from the alternate optimal solutions to the LSCP. This approach also identifies the p-center solution to the problem ensuring equitable response to all areas of interest. Sensitivity analysis is performed to determine the impact of altering aircraft launch and flying times on the number of required alert sites and the amount of coverage provided by selecting fewer locations. Results indicate a significant increase in the number of alert locations needed in comparison to original military estimates. The research points out significant implications about future military base closure decisions and the trade-offs between cost and required response times of aircraft in a defense emergency.

Comparison of GA Based Heuristic and GRASP Based Heuristic for Total Covering Problem

This paper discusses the comparison of two different heuristics for total covering problem. The total covering problem is a facility location problem in which the objective is to identify the minimum number of sites among the potential sites to locate facilities to cover all the customers. This problem is a combinatorial problem. Hence, heuristic development to provide solution for such problem is inevitable. In this paper, two different heuristics, viz., GA based heuristic and GRASP based heuristic are compared and the best is suggested for implementation.

Efficiency and effectiveness in representative reserve design in Canada: The contribution of existing protected areas

To be effective, reserve networks should represent all target species in protected areas that are large enough to ensure species persistence. Given limited resources to set aside protected areas for biodiversity conservation, and competing land uses, a prime consideration for the design of reserve networks is efficiency (the maximum biodiversity represented in a minimum number of sites). However, to be effective, networks may sacrifice efficiency. We used reserve selection algorithms to determine whether collections of existing individual protected areas in Canada were efficient and/or effective in terms of representing the diversity of disturbance-sensitive mammals in Canada in comparison to (1) an optimal network of reserves, and (2) sites selected at random. Unlike previous studies, we restricted our analysis to individual protected areas that met a criterion for minimum reserve size, to address issues of representation and persistence simultaneously. We also tested for effectiveness and efficiency using historical and present-day data to see whether protected area efficiency and/or effectiveness varied over time. In general, existing protected areas did not effectively capture the full suite of mammalian species diversity, nor are most existing protected areas part of a near-optimal solution set. To be effective, Canada’s network of reserves will require at minimum 22 additional areas of >2700 km 2. This study shows that even when only those reserves large enough to be effective are considered, protected areas systems may not be representative, nor were they representative at the time of establishment.

Quantitative method for identifying networks of minimum priority sites for protection of rare and endangered plant species in Guangdong, China

The approaches to enlarge the protected areas are deeply embedded in the conservation planning. In practice, however, even in some sites of top conservation priority, there exist problems of inefficient conservation for lack of funding, to say nothing of assisting all species under threat from the viewpoint of conservationists. Identifying priority sites for conservation and establishing networks of minimum priority sites (NOMPS) are helpful for promoting the transition from number and size oriented, to quality and effectiveness oriented practices of biological conservation, and for realizing the target of biodiversity conservation with the most benefits for the least costs. Based on heuristic algorithm and integer linear programming (ILP), we propose a refined method of heuristic integer linear programming (HILP) for quantitative identification of the NOMPS to protect rare and endangered plant species (REPS) in Guangdong Province, China. The results indicate that there are 19 priority sites which are essential for protecting all of the 107 REPS distributed in 83 sites in Guangdong. These should be the paramount targets of financing and management. Compared with the ILP, which uses minimum number of sites as the only constraint, HILP takes into consideration of the effect of species richness, and is thus more suitable for conservation practices though with a little more number of priority sites selected. It is suggested that ILP and HILP are both effective quantitative methods for identifying NOMPS and can yield important information for decision making, especially when economic factors are constraints for biological conservation.

A history of the Geological Conservation Review

Abstract A particularly ambitious programme for overhauling site assessment and documentation for geoconservation in Great Britain was initiated in the mid-1970s by the Nature Conservancy Council (NCC) resulting in the formal launch of the ‘Geological Conservation Review’ (GCR) in 1977. The GCR was a world-first project of its type in the assessment of the whole geological heritage or ‘geodiversity’ of a country from first principles. Criteria and assessment methods were developed, with a view to selecting the very best sites to represent the diversity of British geology and geomorphology. A list of selection categories—GCR ‘Blocks’—encompassing British geology and geomorphology was devised. Widespread consultation with geologists and geomorphologists across Great Britain was co-ordinated; and the criteria refined and interpreted to suit the selection category at hand. Field investigation of proposed sites was a key component of site selection, although the selection process relied heavily on expert knowledge, literature-review and consensus-building. Almost 3000 sites had been selected for around 100 site selection categories for the GCR ‘register’ by 1990. Most GCR sites are now conserved under British law as Sites of Special Scientific Interest. In Great Britain, the GCR has formed the ‘benchmark’ for attainment of national importance (in a British context), rather than regional importance; a ‘minimum number of sites’ criterion is enshrined in the GCR ethos to assist in defining this benchmark. As part of the site-selection process, a considerable archive of information about sites was amassed. A major publication exercise detailing all of the GCR sites in what was to become the GCR series of books was devised early on in the GCR programme of work. An electronic GCR database was also created in the 1980s and has been the subject of ongoing revision. Although this paper has a historical outlook, the GCR project is not intended to be a finished record of Britain's best sites up to 1990. Instead, the GCR register will keep pace with new discoveries and developments in geological research. In the future, further re-evaluation and confirmation of the ‘conservation value’ of each site is envisaged; assessment of additional sites will also take place, so that the GCR designation can continue to be a hallmark for quality in geoconservation for years to come.

Erratum: Species richness and biodiversity conservation priorities in British Columbia, Canada

Patterns in the geographic distribution of seven species groups were used to identify important areas for conservation in British Columbia, Canada. Potential priority sites for conservation were determined using an integer programming algorithm that maximized the number of species represented in the minimum number of sites. Sweep analyses were used to determine how well the set of priority sites identified for each species group represented the other species groups. Although areas of highest species richness were different for each species group, they all included sites in the southern interior of British Columbia, where there is limited protection. Furthermore, less than 13% of the distribution ranges for 23 of 25 bird species of special conservation concern were located within existing protected areas. Species at risk of extinction were poorly represented (26%–42%) in priority sets of sites selected for amphibians, reptiles, birds, and mammals, since these sites were generally scattered throughout the p...

A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays

The high affinity of certain cellular polyanions for many proteins (polyanion-binding proteins (PABPs)) has been demonstrated previously. It has been hypothesized that such polyanions may be involved in protein structure stabilization, stimulation of folding through chaperone-like activity, and intra- and extracellular protein transport as well as intracellular organization. The purpose of the proteomics studies reported here was to seek evidence for the idea that the nonspecific but high affinity interactions of PABPs with polyanions have a functional role in intracellular processes. Utilizing yeast protein arrays and five biotinylated cellular polyanion probes (actin, tubulin, heparin, heparan sulfate, and DNA), we identified proteins that interact with these probes and analyzed their structural and amino acid sequence requirements as well as their predicted functions in the yeast proteome. We also provide evidence for the existence of a network-like system for PABPs and their potential roles as critical hubs in intracellular behavior. This investigation takes a first step toward achieving a better understanding of the nature of polyanion-protein interactions within cells and introduces an alternative way of thinking about intracellular organization.

LQGraph: A software package for optimizing connectivity in conservation planning

LQGraph implements methods for optimizing the connectivity of sites administered to protect biodiversity (a conservation area network). The methods are suitable for existing protected areas (for example, national parks) or a proposed network. We model the landscape using graphs. The user provides a quality score for each site in the landscape outside the conservation areas. Based on these scores, LQGraph finds contiguity areas of maximum quality to link the conservation areas. The contiguity areas can be filtered to prioritize those that connect the conservation areas with the minimum number of sites or area. Compared with existing methods for establishing connectivity in a conservation area network, LQGraph can analyze substantially larger networks. LQGraph also identifies sites that efficiently isolate conservation areas, which is useful for halting the spread of pathogens or invasive species. The software provides routines for constructing the required input files and for visualizing several properties of the landscape, including site quality and the shortest paths between conservation areas. LQGraph and the accompanying documentation can be freely downloaded from the worldwide web.

Species richness and biodiversity conservation priorities in British Columbia, Canada

Patterns in the geographic distribution of seven species groups were used to identify important areas for conservation in British Columbia, Canada. Potential priority sites for conservation were determined using an integer programming algorithm that maximized the number of species represented in the minimum number of sites. Sweep analyses were used to determine how well the set of priority sites identified for each species group represented the other species groups. Although areas of highest species richness were different for each species group, they all included sites in the southern interior of British Columbia, where there is limited protection. Furthermore, less than 13% of the distribution ranges for 23 of 25 bird species of special conservation concern were located within existing protected areas. Species at risk of extinction were poorly represented (26%–42%) in priority sets of sites selected for amphibians, reptiles, birds, and mammals, since these sites were generally scattered throughout the province. However, priority sites for species at risk represented 72%–91% of the species in other groups. Therefore, conservation activities in sites identified for such species have the potential to benefit many other species. These sites could be investigated in more detail to augment existing conservation and protection efforts in British Columbia.

A comparison of reserve selection algorithms using data on terrestrial vertebrates in Oregon

We compare the number of species represented and the spatial pattern of reserve networks derived using five types of reserve selection algorithms on a set of vertebrate distribution data for the State of Oregon (USA). The algorithms compared are: richness-based heuristic algorithms (four variations), weighted rarity-based heuristic algorithms (two variations), progressive rarity-based heuristic algorithms (11 variations), simulated annealing, and a linear programming-based branch-and-bound algorithm. The linear programming algorithm provided optimal solutions to the reserve selection problem, finding either the maximum number of species for a given number of sites or the minimum number of sites needed to represent all species. Where practical, we recommend the use of linear programming algorithms for reserve network selection. However, several simple heuristic algorithms provided near-optimal solutions for these data. The near-optimality, speed and simplicity of heuristic algorithms suggests that they are acceptable alternatives for many reserve selection problems, especially when dealing with large data sets or complicated analyses.

Ca2+ Modulation of sarcoplasmic reticulum Ca2+ release in rat skeletal muscle fibers

Ca2+ transients and the rate of Ca2+ release (dCaREL/dt) from the sarcoplasmic reticulum (SR) in voltage-clamped, fast-twitch skeletal muscle fibers from the rat were studied with the double Vaseline gap technique and using mag-fura-2 and fura-2 as Ca2+ indicators. Single pulse experiments with different returning potentials showed that Ca2+ removal from the myoplasm is voltage independent. Thus, the myoplasmic Ca2+ removal (dCaREM/dt) was studied by fitting the decaying phase of the Ca2+ transient (Melzer, Ríos & Schneider, 1986) and dCaREL/dt was calculated as the difference between dCa/dt and dCaREM/dt. The fast Ca2+ release decayed as a consequence of Ca2+ inactivation of Ca2+ release. Double pulse experiments showed inactivation of the fast Ca2+ release depending on the prepulse duration. At constant interpulse interval, long prepulses (200 msec) induced greater inactivation of the fast Ca2+ release than shorter depolarizations (20 msec). The correlation (r) between the myoplasmic [Ca2+]i and the inhibited amount of Ca2+ release was 0.98. The [Ca2+]i for 50% inactivation of dCaREL/dt was 0.25 microM, and the minimum number of sites occupied by Ca2+ to inactivate the Ca2+ release channel was 3.0. These data support Ca2+ binding and inactivation of SR Ca2+ release.

On the design of a query processing strategy in a distributed database environment

An algorithm is given to process a given query in a fragmented distributed data base environment. Unlike previous algorithms, it has the following desired features.(1) It makes use of redundant relations to reduce communication cost;(2) a copy of each relation referenced by the query is selected so that the set of relations are contained in the minimum number of sites;(3) an efficient algorithm to process fragments is provided;(4) all relations that need not be sent to the assembly site to produce the answer are identified. Thus, unnecessary sending of these relations across sites and processing on these relations, which are common in earlier algorithms, are avoided;(5) useless semi-joins are discarded and "worse" semi-joins are replaced by better ones;(6) a process to estimate the cost and the benefit of a semi-join, based on dynamic execution of semi-joins is introduced. It is expected that the new process is more accurate than earlier estimation process.The algorithm is easy to implement and is operational.

Genetic determination of kinetic parameters in beta-glucuronidase induction by androgen.

A regulatory locus, Gus-r, determines the rate and extent of androgen inducibility of beta-glucuronidase in mouse kidney epithelial cells. The kinetics of induction are strikingly similar when enzyme concentration, rates of enzyme synthesis, and beta-glucuronidase mRNA are measured. After an initial lag period the accumulation of mRNA activity obeys simple turnover kinetics defined by ka, a zero order rate constant for acquisition of mRNA activity, and kb, a first order rate constant for loss of activity. The induced state is approached with a half-life of 8-9 days in the presence of testosterone and decays rapidly in the absence of testosterone. The half-life of both beta-glucuronidase and its mRNA appear to be much shorter, approximately 1-2 days, in both the presence and absence of testosterone. We conclude that the material accumulating in response to androgen is probably a transcriptionally activated state of beta-glucuronidase chromatin. Comparison of the a and b alleles of Gus-r, and a newly described h allele, shows that Gus-r determines ka and the duration of the lag period, but not kb, which was genetically invariant. The changes in ka and the duration of the lag are inversely related, suggesting that they reflect a common step during induction. These results are most simply accounted for by assuming that beta-glucuronidase regions in chromatin react with many molecules of androgen receptor protein-testosterone complex and that the rate of transcription is a function of the number of molecules bound. The lag period, then, reflects a requirement that a minimum number of sites must be occupied before transcription begins to increase. We suggest that the Gus-r locus determines the accessibility or affinity of androgen receptor complexes to chromatin. Because of this Gus-r determine both ka and the duration of the lag and the two parameters are inversely related to each other.