Discrimination between Onchocerca volvulus and O. ochengi filarial larvae in Simulium damnosum (s.l.) and their distribution throughout central Ghana using a versatile high-resolution speciation assay

AbstractBackgroundGenetic surveillance of the human filarial parasite, Onchocerca volvulus, from onchocerciasis endemic regions will ideally focus on genotyping individual infective larval stages collected from their intermediate host, Simuliid blackflies. However, blackflies also transmit other Onchocerca species, including the cattle parasite O. ochengi, which are difficult to distinguish from the human parasite based on morphological characteristics alone. This study describes a versatile approach to discriminate between O. volvulus and O. ochengi that is demonstrated using parasite infective larvae dissected from blackflies.ResultsA speciation assay was designed based on genetic differentiation between O. volvulus and O. ochengi mitochondrial genome sequences that can be performed in highthroughput high-resolution melt (HRM)- or lower throughput conventional restriction fragment length polymorphism (RFLP) analyses. This assay was validated on 185 Onchocerca larvae dissected from blackflies captured from 14 communities in Ghana throughout 2011-13. The frequency of O. ochengi was approximately 67 % of all larvae analysed, which is significantly higher than previously reported in this region. Furthermore, the species distribution was not uniform throughout the study region, with 25 %, 47 % and 93 % of O. volvulus being found in the western-most (Black Volta, Tain and Tombe), the central (Pru) and eastern-most (Daka) river basins, respectively.ConclusionsThis tool provides a simple and cost-effective approach to determine the identity and distribution of two Onchocerca species, and will be valuable for future genetic studies that focus on parasites collected from blackflies. The results presented highlight the need to discriminate Onchocerca species in transmission studies, as the frequency of each species varied significantly between the communities studied.

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High-resolution root zone soil moisture-based indices for drought monitoring in the Ebro basin

10.5194/egusphere-egu21-5849 ◽

2021 ◽

Author(s):

Vivien-Georgiana Stefan ◽

Maria-José Escorihuela ◽

Pere Quintana-Seguí

Keyword(s):

Remote Sensing ◽

Soil Moisture ◽

High Resolution ◽

Root Zone ◽

Cost Effective ◽

Strong Relationship ◽

Drought Indices ◽

Ebro Basin ◽

Small Areas ◽

Cost Effective Approach

<h3>Agriculture is an important factor on water resources, given the constant population growth and the strong relationship between water availability and food production. In this context, root zone soil moisture (RZSM) measurements are used by modern irrigators in order to detect the onset of crop water stress and to trigger irrigations. Unfortunately, in situ RZSM measurements are costly; combined with the fact they are available only over small areas and that they might not be representative at the field scale, remote sensing is a cost-effective approach for mapping and monitoring extended areas. A recursive formulation of an exponential filter was used in order to derive 1 km resolution RZSM estimates from SMAP (Soil Moisture Active Passive) surface soil moisture (SSM) over the Ebro basin. The SMAP SSM was disaggregated to a 1 km resolution by using the DISPATCH (DISaggregation based on a Physical And Theoretical scale CHange) algorithm. The pseudodiffusivity parameter of the exponential filter was calibrated per land cover type, by using ISBA-DIF (Interaction Soil Biosphere Atmosphere) surface and root zone soil moisture data as an intermediary step. The daily 1 km RZSM estimates were then used to derive 1 km drought indices such as soil moisture anomalies and soil moisture deficit indices (SMDI), on a weekly time-scale, covering the entire 2020 year. Results show that both drought indices are able to capture rainfall and drying events, with the weekly anomaly being more responsive to sudden events such as heavy rainfalls, while the SMDI is slower to react do the inherent inertia it has. Moreover, a quantitative comparison with drought indices derived from a model-based RZSM estimates has also been performed, with results showing a strong correspondence between the different indices. For comparison purposes, the weekly soil moisture anomalies and SMDI derived using 1 km SMAP-derived SSM were also estimated. The analysis shows that the anomalies and SMDI based on the RZSM are more representative of the hydric stress level of the plants, given that the RZSM is better suited than the SSM to describe the moisture conditions at the deeper layers, which are the ones used by plants during growth and development.</h3><h3>The study provides an insight into obtaining robust, high-resolution remote-sensing derived drought indices based on remote-sensing derived RZSM estimates. The 1 km resolution proves an improvement from other currently available drought indices, such as the European Drought Observatory&#8217;s 5 km resolution drought index, which is not able to capture as well the spatial variability present within heterogeneous areas. Moreover, the SSM-derived drought indices are currently used in a drought observatory project, covering a region in the Tarragona province of Catalonia, Spain. The project aims at offering irrigation recommendations to water agencies, and the introduction of RZSM-derived drought indices will further improve such advice.</h3>

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Implementation of a Cost-Effective Unlabeled Probe High-Resolution Melt Assay for Genotyping of Factor V Leiden

Genetic Testing and Molecular Biomarkers ◽

10.1089/gtmb.2010.0137 ◽

2011 ◽

Vol 15 (4) ◽

pp. 207-213 ◽

Cited By ~ 5

Author(s):

Annika M. Svensson ◽

Lan-Szu Chou ◽

Cindy Meadows ◽

Christine E. Miller ◽

Robert Palais ◽

...

Keyword(s):

High Resolution ◽

Factor V Leiden ◽

Cost Effective ◽

Factor V ◽

High Resolution Melt ◽

Unlabeled Probe

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Endoscopy of Nasopharyngeal Cancer

Diagnostic and Therapeutic Endoscopy ◽

10.1155/dte.1.63 ◽

1994 ◽

Vol 1 (2) ◽

pp. 63-68 ◽

Cited By ~ 3

Author(s):

Brian B. Burkey ◽

Robert H. Ossoff

Keyword(s):

Quality Of Life ◽

High Risk ◽

High Resolution ◽

Local Anesthesia ◽

Nasopharyngeal Cancer ◽

Cost Effective ◽

Cost Effective Approach ◽

The World

Nasopharyngeal cancer (NPC) is a unique disease with increasing interest for many physicians due to its unusual etiology, histology, and epidemiology. The recent era of fiberoptic endoscopy now provides the clinician with better tools for the screening, diagnosis, staging, and follow-up of NPC. The use of high resolution flexible and rigid nasopharyngoscopy gives the physician an opportunity for a more sensitive examination in a higher proportion of patients. Ultimately, this will allow for earlier diagnosis of NPC, and improved prognosis and better quality of life for the patients with this disease. Also, by allowing the clinician to perform directed biopsies of the nasopharynx under local anesthesia, fiberoptic nasopharyngoscopy allows a less morbid and more cost-effective approach towards this disease, including screening protocols in certain high risk regions of the world.

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UAV SURVEY FOR THE ARCHAEOLOGICAL MAP OF LILYBAEUM (MARSALA, ITALY)

ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences ◽

10.5194/isprs-archives-xlii-2-w11-495-2019 ◽

2019 ◽

Vol XLII-2/W11 ◽

pp. 495-502 ◽

Cited By ~ 4

Author(s):

D. Ebolese ◽

M. Lo Brutto ◽

G. Dardanelli

Keyword(s):

High Resolution ◽

Spatial Data ◽

Cost Effective ◽

3D Models ◽

Archaeological Sites ◽

Archaeological Excavation ◽

Cost Effective Approach ◽

Ancient City ◽

Field Campaigns ◽

Archaeological Areas

Abstract. Collecting information and mapping are fundamental aspects of systematic archaeological excavation, documentation and interpretation. The process of recording physical evidence is the first step in the archaeological study with the goal to derive spatial and semantic information from the gathered and available data. Archaeological reports always include 2D maps, sections, data distribution and other spatial data. Indeed, the representation is inseparable from the archaeological practice, but this is undoubtedly a time-consuming activity. Nowadays, archaeologists can take advantages of various recording techniques to produce highly accurate 3D models and ortho-images of archaeological sites. Far from replacing the more traditional techniques, the development of new geomatics techniques tries to answer, in a more efficient way, to the needs of archaeological research. The use of Unmanned Aerial Vehicles (UAVs) has become more popular in archaeological excavations. In particular, UAV systems become a useful, versatile and cost-effective approach to record large archaeological areas in order to measure and completely document them. They are the fastest way to produce high-resolution 3D models of entire sites and allow archaeologists to collect accurate spatial data that can be used for spatial analyses using GIS platform. The paper presents the results of several UAV surveys of the archaeological remains of Lilybaeum, the ancient city of Marsala (Southern Italy), performed in the Archaeological Park of “Lilibeo”. The UAV acquisitions were planned and carried out to complete the previous traditional documentation of the site. Very detailed 3D models and high-resolution ortho-images, together with some new field campaigns, have been used for new analysis and documentation of the site and for the realization of the archaeological map of Lilybaeum.

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A simple and cost-effective approach for technical validation of next generation methylation sequencing data

10.21203/rs.2.14216/v1 ◽

2019 ◽

Author(s):

Ali Javadmanesh ◽

Afsaneh Mojtabanezhad Shariatpanahi ◽

Ehsan Shams Davodly ◽

Marjan Azghandi ◽

Maryam Yassi ◽

...

Keyword(s):

Dna Methylation ◽

High Resolution ◽

High Resolution Melting ◽

Cost Effective ◽

Next Generation ◽

Sequencing Data ◽

Cost Effective Approach ◽

Technical Validation ◽

R Programming ◽

And Control

Abstract Background DNA methylation is a fundamental epigenetic process that, in most cases, modulates genetic expression levels. Changes in DNA methylation, either hypo- or hypermethylation, have a key role in many biological processes and several human diseases such as cancer. In the current study, we offered an approach to validate the next generation methylation sequencing data.Methods Genomic DNA was extracted from target and control samples (6 in each group), followed by bisulfite conversion. Next generation methylation sequencing and methylation sensitive high-resolution melting assay were carried out. The primers for methylation sequencing validation were designed by R programming language.Results In the current study, two groups, case and control, were discriminated based on methylation sequencing results and the real time PCR-based results were in accordance with the next generation methylation sequencing.Discussion Methylation sensitive high-resolution melting validation assay is a simple and cost-effective method, which confirmed next generation methylation sequencing results.

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Investigating the effects of COVID-19 to crime rates through a geospatial approach: the case of New York, USA

10.5194/egusphere-egu21-15125 ◽

2021 ◽

Author(s):

Ioanna Tselka ◽

Isidora Isis Demertzi ◽

George P. Petropoulos

Keyword(s):

New York ◽

Scientific Evidence ◽

Cost Effective ◽

Crime Rates ◽

Added Value ◽

Web Gis ◽

Study Region ◽

Cost Effective Approach ◽

Before And After ◽

The Impact

Covid-19 pandemic has led to severe consequences to humanity worldwide. Yet, to our knowledge, little scientific evidence is available exploring the impact of the pandemic on criminality. Thus, it is imperative to examine their relationships spatially to obtain a better understanding of societal characteristics during the pandemic.This study aims at demonstrating the use of geoinformation in analyzing the spatial patterns between crime properties and Covid-19 spread using as a case study New York City, USA, one of the largest metropolitan cities of the world. To address our objectives, geostatistical analysis and data visualization methods have been implemented in real-world crime data acquired from a web-GIS platform. Our analysis concerns two equal time periods before and after the lockdown implementation.Results revealed some very interesting patterns spatially between the examined parameters and societal characteristics existing in the study region. The methodological framework presented underlined the added value of geoinformation as a robust and cost-effective approach in examining the impact of the pandemic to the society.&#160;Keywords: Covid-19, pandemic, crime rates, geoinformation, New York

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Efficacy of 16S rRNA variable regions high-resolution melt analysis for bacterial pathogens identification in periprosthetic joint infections

BMC Microbiology ◽

10.1186/s12866-021-02164-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Samaneh Bourbour ◽

Mohammad Emaneini ◽

Mahmoud Jabalameli ◽

Seyed Mohammad Javad Mortazavi ◽

Mohamad Naghi Tahmasebi ◽

...

Keyword(s):

High Resolution ◽

Cost Effective ◽

Culture Method ◽

Rapid Identification ◽

Molecular Techniques ◽

High Resolution Melt ◽

Variable Regions ◽

High Resolution Melt Analysis ◽

Joint Infections ◽

Sensitivity Specificity

Abstract Background Accurate and rapid identification of microorganisms causing periprosthetic joint infections (PJIs) are necessary for choosing an appropriate antibiotic therapy. Therefore, molecular techniques are suggested for diagnosis in suspected PJIs. The Broad-range PCR and High-Resolution Melt Analysis (HRMA) were evaluated for the identification of causative organisms of PJIs in this study. Results For 47 of 63 specimens, both the culture and broad-range PCR were positive. The culture was found to be able of organism’s detection in 74.6% (47/63) of patients. Of 47 positive cultures, 11 (23.4%) were polymicrobial and 36 (76.59%) were monomicrobial cultures, in which 34 (91.89%) cases were detected by HRM assay. The sensitivity, specificity of HRMA vs monomicrobial culture were 91.89, 93.75%, respectively. The sensitivity, specificity of total HRMA (mono + poly) vs culture were 82.92, 93.75%. Conclusions HRM assay coupled with broad-range PCR are effective screening, rapid, and relatively cost-effective methods for discrimination of PJIs especially in aiding culture method. Using computer programs such as the Matlab-2018b program for HRM data analysis is also valuable and helpful in diagnosis.

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