scholarly journals DMAP – Graphical representation of physical and genetic map correlation

2016 ◽  
Author(s):  
David M.A. Martin ◽  
Glenn Bryan
Keyword(s):  
Genetic Map ◽  
Information Overload ◽  
Graphical Representation ◽  
Draft Genome ◽  
Cost Effective ◽  
Data Representation ◽  
Genetic Maps ◽  
Sequence Contigs ◽  
Effective Manner ◽  
Physical And Genetic Map

AbstractNext-generation sequencing approaches coupled with appropriate assembly software can provide draft genome sequences of complex organisms as a series of unordered contigs in a timely and cost effective manner. Likewise, high throughput mapping technologies such as DArT and SNP platforms can provide a high density of sequence-anchored markers with which high resolution genetic maps can be constructed. Visualising and interpreting these data requires a new generation of tools as the volume of data leads to considerable redundancy and information overload in graphical representation. DMAP provides a highly configurable visual representation of physical and genetic map correlation, reducing data representation to an aesthetically acceptable degree. It also calculates an optimal orientation for the ordered sequence contigs, highlighting markers that are anomalous and contigs which may be in erroneous positions. Output is as PDF, allowing subsequent refinement prior to print publication and vector based representation for online supplementary figures. The perl scripts have few dependencies and code is freely available under a creative commons license (CC-BY) from the author’s GitHub repository at http://github.com/davidmam/DMAP.git.

scholarly journals Autism Children’s App using PECS

2018 ◽  
Vol 2 (1) ◽  
pp. 7-16 ◽  
Author(s):  
Nareena Soomro ◽  
Safeeullah Soomro
Keyword(s):  
Learning Disabilities ◽  
Communication System ◽  
Mobile Application ◽  
Autistic Spectrum Disorder ◽  
Graphical Representation ◽  
Cost Effective ◽  
Picture Exchange Communication System ◽  
Autistic Children ◽  
Present Communication ◽  
Effective Manner

Since autistic children suffers from learning disabilities and communication barriers, this research aim to design, develop and evaluate an Android based mobile application (app) providing better learning environment with inclusion of graphical representation in a cost effective manner. This research evaluate various supporting technologies and finds Picture Exchange Communication System (PECS) to be better choice for integrating with the app. Evaluation results reveal that the inclusion of PECS helped the children suffering from Autistic Spectrum Disorder (ASD) to better communicate with others. The study included autistic children who do not speak, who are unintelligible and who are minimally effective communicators with their present communication system. The evolution results showed encouraging impacts of the Autism App in supporting autistic children to adapt to normal life and improve the standard of their life.

Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps

Genome ◽  
2008 ◽  
Vol 51 (4) ◽  
pp. 294-302 ◽  
Author(s):  
Randy C. Shoemaker ◽  
David Grant ◽  
Terry Olson ◽  
Wesley C. Warren ◽  
Rod Wing ◽  
...  
Keyword(s):  
Genetic Map ◽  
Physical Map ◽  
Genetic Maps ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Dinucleotide Repeats ◽  
Length Polymorphisms ◽  
Glycine Max L ◽  
Physical And Genetic Map ◽  
End Sequences

Whole-genome sequencing of the soybean ( Glycine max (L.) Merr. ‘Williams 82’) has made it important to integrate its physical and genetic maps. To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the ‘Williams 82’ physical map. SSRs were screened against 3 mapping populations. We found the AAT and ACT motifs produced the greatest frequency of length polymorphisms, ranging from 17.2% to 32.3% and from 11.8% to 33.3%, respectively. Other useful motifs include the dinucleotide repeats AG, AT, and AG, with frequency of length polymorphisms ranging from 11.2% to 18.4% (AT), 12.4% to 20.6% (AG), and 11.3% to 16.4% (GT). Repeat lengths less than 16 bp were generally less useful than repeat lengths of 40–60 bp. Two hundred and sixty-five SSRs were genetically mapped in at least one population. Of the 265 mapped SSRs, 60 came from BAC singletons not yet placed into contigs of the physical map. One hundred and ten originated in BACs located in contigs for which no genetic map location was previously known. Ninety-five SSRs came from BACs within contigs for which one or more other BACs had already been mapped. For these fingerprinted contigs (FPC) a high percentage of the mapped markers showed inconsistent map locations. A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4× assembly of the whole genome sequence of soybean.

Strategic planning in grassland farming: Principles andapplications

1997 ◽  
pp. 191-197
Author(s):  
W.J. Parker ◽  
N.M. Shadbolt ◽  
D.I. Gray
Keyword(s):  
Strategic Planning ◽  
Performance Indicators ◽  
Cost Effective ◽  
Key Performance Indicators ◽  
Strategic Plans ◽  
Effective Manner ◽  
Farm Business ◽  
Pastoral Farming ◽  
Financial Environment

Three levels of planning can be distinguished in grassland farming: strategic, tactical and operational. The purpose of strategic planning is to achieve a sustainable long-term fit of the farm business with its physical, social and financial environment. In pastoral farming, this essentially means developing plans that maximise and best match pasture growth with animal demand, while generating sufficient income to maintain or enhance farm resources and improvements, and attain personal and financial goals. Strategic plans relate to the whole farm business and are focused on the means to achieve future needs. They should be routinely (at least annually) reviewed and monitored for effectiveness through key performance indicators (e.g., Economic Farm Surplus) that enable progress toward goals to be measured in a timely and cost-effective manner. Failure to link strategy with control is likely to result in unfulfilled plans. Keywords: management, performance

scholarly journals Novel Regeneration Approach for Creating Reusable FO-SPR Probes with NTA Surface Chemistry

Nanomaterials ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 186
Author(s):  
Jia-Huan Qu ◽  
Karen Leirs ◽  
Remei Escudero ◽  
Žiga Strmšek ◽  
Roman Jerala ◽  
...  
Keyword(s):  
Surface Chemistry ◽  
Fluorescent Protein ◽  
Cost Effective ◽  
Nitrilotriacetic Acid ◽  
Antibody Fragments ◽  
Rapid Screening ◽  
Red Fluorescent Protein ◽  
Effective Manner ◽  
Surface Regeneration ◽  
Sensitivity Specificity

To date, surface plasmon resonance (SPR) biosensors have been exploited in numerous different contexts while continuously pushing boundaries in terms of improved sensitivity, specificity, portability and reusability. The latter has attracted attention as a viable alternative to disposable biosensors, also offering prospects for rapid screening of biomolecules or biomolecular interactions. In this context here, we developed an approach to successfully regenerate a fiber-optic (FO)-SPR surface when utilizing cobalt (II)-nitrilotriacetic acid (NTA) surface chemistry. To achieve this, we tested multiple regeneration conditions that can disrupt the NTA chelate on a surface fully saturated with His6-tagged antibody fragments (scFv-33H1F7) over ten regeneration cycles. The best surface regeneration was obtained when combining 100 mM EDTA, 500 mM imidazole and 0.5% SDS at pH 8.0 for 1 min with shaking at 150 rpm followed by washing with 0.5 M NaOH for 3 min. The true versatility of the established approach was proven by regenerating the NTA surface for ten cycles with three other model system bioreceptors, different in their size and structure: His6-tagged SARS-CoV-2 spike fragment (receptor binding domain, RBD), a red fluorescent protein (RFP) and protein origami carrying 4 RFPs (Tet12SN-RRRR). Enabling the removal of His6-tagged bioreceptors from NTA surfaces in a fast and cost-effective manner can have broad applications, spanning from the development of biosensors and various biopharmaceutical analyses to the synthesis of novel biomaterials.

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

scholarly journals Postnatal management of children with antenatal hydronephrosis

2020 ◽  
Vol 26 (1) ◽  
Author(s):  
Mohammed S. ElSheemy
Keyword(s):  
Renal Function ◽  
Urinary Tract Obstruction ◽  
Cost Effective ◽  
Voiding Cystourethrography ◽  
Main Body ◽  
Antenatal Hydronephrosis ◽  
Postnatal Management ◽  
Effective Manner ◽  
Lower Urinary Tract Obstruction

Abstract Background Postnatal management of infants with antenatal hydronephrosis (ANH) is still one of the most controversial issues. The majority of infants with ANH are asymptomatic with only few children who develop renal insufficiency. Thus, the biggest challenge for pediatric urologists is to distinguish children who will require further investigations and possible intervention prior to the development of symptoms, complications or renal damage in a cost effective manner without exposing them to the hazards of unnecessary investigations. Main body In this review article, literature on ANH were reviewed to present the current suggestions, recommendations, guidelines and their rational for postnatal management of ANH. It is agreed that a large portion of infants with ANH will improve; thus, the protocol of management is based mainly on observation and follow-up by ultrasound to detect either resolution, stabilization or worsening of hydronephrosis. The first 2 years of life are critical for this follow-up as the final picture is mostly reached during that period. Advanced imaging using voiding cystourethrography or renal scintigraphy are required for children at risk. Then, surgical intervention is selected only for a subgroup of these infants who showed worsening of hydronephrosis or renal function. Conclusions The protocol of management is based mainly on observation and follow-up by US to detect either resolution, stabilization or worsening of hydronephrosis. Postnatal evaluation should be performed for any neonate with a history ANH at any stage during pregnancy even if it was resolved during third trimester. Exclusion of UTI should be performed by urinalysis for all cases followed by urine culture if indicated. Serum creatinine should be performed especially in patients with bilateral ANH. US is the initial standard diagnostic imaging technique. Other imaging modalities like VCUG and nuclear renal scans may be required according to the results of the US evaluation. The most important items in decision making are the presence of bilateral or unilateral hydronephrosis, presence or absence of hydroureter, presence of lower urinary tract obstruction and degree of hydronephrosis on the initial postnatal US. Then an intervention is selected only for a subgroup of these patients who showed deterioration in renal function or degree of hydronephrosis or were complicated by UTIs. All these recommendations are based on the available literature. However, management of ANH is still a controversial issue due to lack of high evidence-based recommendations. Randomised controlled studies are still needed to provide a high level evidence for different aspects of management.

scholarly journals An Artificial-Intelligence-Discovered Functional Ingredient, NRT_N0G5IJ, Derived from Pisum sativum, Decreases HbA1c in a Prediabetic Population

Nutrients ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1635
Author(s):  
Sweeny Chauhan ◽  
Alish Kerr ◽  
Brian Keogh ◽  
Stephanie Nolan ◽  
Rory Casey ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Pisum Sativum ◽  
Cost Effective ◽  
Glycated Haemoglobin ◽  
Glucose Regulation ◽  
Functional Ingredient ◽  
Effective Manner ◽  
Human Skeletal Muscle Cells ◽  
Increased Risk

The prevalence of prediabetes is rapidly increasing, and this can lead to an increased risk for individuals to develop type 2 diabetes and associated diseases. Therefore, it is necessary to develop nutritional strategies to maintain healthy glucose levels and prevent glucose metabolism dysregulation in the general population. Functional ingredients offer great potential for the prevention of various health conditions, including blood glucose regulation, in a cost-effective manner. Using an artificial intelligence (AI) approach, a functional ingredient, NRT_N0G5IJ, was predicted and produced from Pisum sativum (pea) protein by hydrolysis and then validated. Treatment of human skeletal muscle cells with NRT_N0G5IJ significantly increased glucose uptake, indicating efficacy of this ingredient in vitro. When db/db diabetic mice were treated with NRT_N0G5IJ, we observed a significant reduction in glycated haemoglobin (HbA1c) levels and a concomitant benefit on fasting glucose. A pilot double-blinded, placebo controlled human trial in a population of healthy individuals with elevated HbA1c (5.6% to 6.4%) showed that HbA1c percentage was significantly reduced when NRT_N0G5IJ was supplemented in the diet over a 12-week period. Here, we provide evidence of an AI approach to discovery and demonstrate that a functional ingredient identified using this technology could be used as a supplement to maintain healthy glucose regulation.

scholarly journals Spectroscopic detection of forest diseases: a review (1970–2020)

2021 ◽  
Author(s):  
Lorenzo Cotrozzi
Keyword(s):  
Early Detection ◽  
Optical Sensors ◽  
Near Infrared ◽  
Sustainable Forest Management ◽  
Visible Spectrum ◽  
Cost Effective ◽  
Infrared Region ◽  
Forest Disturbances ◽  
Effective Manner ◽  
Forest Diseases

AbstractSustainable forest management is essential to confront the detrimental impacts of diseases on forest ecosystems. This review highlights the potential of vegetation spectroscopy in improving the feasibility of assessing forest disturbances induced by diseases in a timely and cost-effective manner. The basic concepts of vegetation spectroscopy and its application in phytopathology are first outlined then the literature on the topic is discussed. Using several optical sensors from leaf to landscape-level, a number of forest diseases characterized by variable pathogenic processes have been detected, identified and quantified in many country sites worldwide. Overall, these reviewed studies have pointed out the green and red regions of the visible spectrum, the red-edge and the early near-infrared as the spectral regions most sensitive to the disease development as they are mostly related to chlorophyll changes and symptom development. Late disease conditions particularly affect the shortwave-infrared region, mostly related to water content. This review also highlights some major issues to be addressed such as the need to explore other major forest diseases and geographic areas, to further develop hyperspectral sensors for early detection and discrimination of forest disturbances, to improve devices for remote sensing, to implement long-term monitoring, and to advance algorithms for exploitation of spectral data. Achieving of these goals will enhance the capability of vegetation spectroscopy in early detection of forest stress and in managing forest diseases.

scholarly journals To Trade or Not To Trade? Criteria for Applying Cap and Trade

2001 ◽  
Vol 1 ◽  
pp. 953-957 ◽  
Author(s):  
Stephanie Benkovic ◽  
Joseph Kruger
Keyword(s):  
Emissions Trading ◽  
Environmental Problem ◽  
Cost Effective ◽  
Cap And Trade ◽  
Policy Tool ◽  
Effective Manner ◽  
Effective Policy ◽  
Foreign Governments ◽  
Trading Program ◽  
The U.S

The use of emissions trading (cap and trade) is gaining worldwide recognition as an extremely effective policy tool. The U.S. Sulfur Dioxide (SO2) Emissions Trading Program has achieved an unprecedented level of environmental protection in a cost-effective manner. The successful results of the program have led domestic and foreign governments to consider the application of cap and trade to address other air quality issues. Certain analyses are particularly important in determining whether or not cap and trade is an appropriate policy tool. This paper offers a set of questions that can be used as criteria for determining whether or not cap and trade is the preferred policy approach to an environmental problem.

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