Designing a Cost-Effective Invertebrate Survey: A Test of Methods for Rapid Assessment of Biodiversity

Borehole television survey and acoustic televiewer logging provide rapid, cost-effective, and accurate methods of surveying fractures and their characteristics within boreholes varying in diameter from 7.6 to 15.3 cm. In the television survey, a camera probe is used to inspect the borehole walls. Measurements of location, orientation, infilling width, and aperture of fractures are made on the television screen and recorded on computer data record sheets. All observations are recorded on video cassette tapes. With the acoustic televiewer, oriented images of fractures in the borehole walls are recorded on a strip–chart log and also on video cassette tapes. The images are displayed as if the walls were split vertically along magnetic north and spread out horizontally. Measurements of fracture characteristics are made on the strip–chart log, using a digitizing table and a microcomputer, and the data recorded on floppy diskettes. In both surveys, an inclined fracture is displayed as a sinusoidal curve, from which the apparent orientation of the fracture can be measured. Once the borehole orientation is known, the true orientation of the fracture can be computed from its apparent orientation. Computer analysis of the fracture data, provides a rapid assessment of fracture occurrence, fracture aperture, and statistically significant concentrations of fracture orientations. Key words: borehole, television survey, acoustic televiewer logging, fractures, distribution, orientation, aperture.

Download Full-text

Vibrational Spectroscopy of Peritoneal Dialysis Effluent for Rapid Assessment of Patient Characteristics

Biomolecules ◽

10.3390/biom10060965 ◽

2020 ◽

Vol 10 (6) ◽

pp. 965

Author(s):

Tom Grunert ◽

Rebecca Herzog ◽

Florian M. Wiesenhofer ◽

Andreas Vychytil ◽

Monika Ehling-Schulz ◽

...

Keyword(s):

Peritoneal Dialysis ◽

Ftir Spectroscopy ◽

Controlled Trial ◽

Rapid Assessment ◽

Principal Component ◽

Cost Effective ◽

Patient Characteristics ◽

Biological Information ◽

Molecular Fingerprinting ◽

Transport Parameters

Peritoneal dialysis (PD) offers specific advantages over hemodialysis, enabling increased autonomy of patients with end-stage renal disease, but PD-related complications need to be detected in a timely manner. Fourier transform infrared (FTIR) spectroscopy could provide rapid and essential insights into the patients’ risk profiles via molecular fingerprinting of PD effluent, an abundant waste material that is rich in biological information. In this study, we measured FTIR spectroscopic profiles in PD effluent from patients taking part in a randomized controlled trial of alanyl-glutamine addition to the PD-fluid. Principal component analysis of FTIR spectra enabled us to differentiate between effluent samples from patients immediately after completion of instillation of the PD-fluid into the patients’ cavity and 4 h later as well as between patients receiving PD-fluid supplemented with 8 mM alanyl-glutamine compared with control. Moreover, feasibility of FTIR spectroscopy coupled to supervised classification algorithms to predict patient-, PD-, as well as immune-associated parameters were investigated. PD modality (manual continuous ambulatory PD (CAPD) vs. cycler-assisted automated PD (APD)), residual urine output, ultrafiltration, transport parameters, and cytokine concentrations showed high predictive potential. This study provides proof-of-principle that molecular signatures determined by FTIR spectroscopy of PD effluent, combined with machine learning, are suitable for cost-effective, high-throughput diagnostic purposes in PD.

Download Full-text

Potential methodologies and strategies for the rapid assessment of feed-grain quality

Australian Journal of Agricultural Research ◽

10.1071/ar98167 ◽

1999 ◽

Vol 50 (5) ◽

pp. 789 ◽

Cited By ~ 11

Author(s):

C. W. Wrigley

Keyword(s):

Grain Quality ◽

Near Infrared ◽

Animal Feed ◽

Rapid Assessment ◽

Cost Effective ◽

Beta Glucan ◽

Site Analysis ◽

Direct Indication ◽

Systematic Strategy

The efficient use of grains for animal feed requires the use of analytical methods that can provide rapid indications of the suitability of the grain for animal nutrition. Ideally, these methods need to be applied at the site of grain receival within the tight time and cost confines of grain delivery. In addition, methods are needed in plant breeding to efficiently screen for target aspects of feed-grain quality to facilitate the development of genotypes with improved nutritional quality. This review describes a range of techniques that can fulfil these analytical requirements. These include visual examination of grain samples for species identification and for recognition of defects and contaminants. This long-standing approach is rapid, but it is subjective and dependent on the expertise of the operator. The newer technology of image analysis offers the prospect of providing similar information automatically and quantitatively, without the risk of operator bias. Near-infrared (NIR) analysis is already in general use for grain analysis at many receival depots in wheat-growing countries, mainly for the determination of moisture and protein content. There are promising indications that NIR can be extended to the determination of many other aspects of grain composition, both the positive aspects that contribute to feed quality, as well as components such as beta-glucan content that have negative contributions for non-ruminants. Furthermore, NIR is being developed to provide a direct indication of metabolisable energy for a range of grain types. Whereas NIR is primarily suited to the determination of quantitatively major components of the grain, without the requirement of significant sample preparation, immunological analyses are appropriate for the determination of specific and minor components, such as mycotoxins, lectins, alkaloids, and pesticide residues. These and other methods, suited for on-site analysis, need to be combined with effective sampling to ensure that the results of testing are representative of the whole of the grain consignment, and also integrated into a systematic strategy to ensure cost-effective testing.

Download Full-text

Evaluation of using digital photography as a cost-effective tool for the rapid assessment of soil organic carbon at a regional scale

Soil Security ◽

10.1016/j.soisec.2021.100023 ◽

2021 ◽

pp. 100023

Author(s):

Jannis Heil ◽

Christoph Jörges ◽

Britta Stumpe

Keyword(s):

Organic Carbon ◽

Soil Organic Carbon ◽

Regional Scale ◽

Rapid Assessment ◽

Cost Effective ◽

Digital Photography

Download Full-text

A Review of Terrestrial Carbon Assessment Methods Using Geo-Spatial Technologies with Emphasis on Arid Lands

Remote Sensing ◽

10.3390/rs12122008 ◽

2020 ◽

Vol 12 (12) ◽

pp. 2008

Author(s):

Salem Issa ◽

Basam Dahy ◽

Taoufik Ksiksi ◽

Nazmi Saleous

Keyword(s):

Regional Scale ◽

Management Strategies ◽

Rapid Assessment ◽

Cost Effective ◽

Arid Lands ◽

Biomass Estimation ◽

Terrestrial Carbon ◽

Carbon Management ◽

Optical Radar ◽

Insight Into

Geo-spatial technologies (i.e., remote sensing (RS) and Geographic Information Systems (GIS)) offer the means to enable a rapid assessment of terrestrial carbon stock (CS) over large areas. The utilization of an integrated RS-GIS approach for above ground biomass (AGB) estimation and precision carbon management is a timely and cost-effective solution for implementing appropriate management strategies at a localized and regional scale. The current study reviews various RS-related techniques used in the CS assessment, with emphasis on arid lands, and provides insight into the associated challenges, opportunities and future trends. The study examines the traditional methods and highlights their limitations. It explores recent and developing techniques, and identifies the most significant RS variables in depicting biophysical predictors. It further demonstrates the usefulness of geo-spatial technologies for assessing terrestrial CS, especially in arid lands. RS of vegetation in these ecosystems is constrained by unique challenges specific to their environmental conditions, leading to high inaccuracies when applying biomass estimation techniques developed for other ecosystems. This study reviews and highlights advantages and limitations of the various techniques and sensors, including optical, RADAR and LiDAR, that have been extensively used to estimate AGB and assess CS with RS data. Other new methods are introduced and discussed as well. Finally, the study highpoints the need for further work to fill the gaps and overcome limitations in using these emerging techniques for precision carbon management. Geo-spatial technologies are shown to be a valuable tool for estimating carbon sequestered especially in difficult and remote areas such as arid land.

Download Full-text

Heterozygous KCNH2 variant phenotyping using Flp-In HEK293 and high-throughput automated patch clamp electrophysiology

Biology Methods and Protocols ◽

10.1093/biomethods/bpab003 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Chai-Ann Ng ◽

Jessica Farr ◽

Paul Young ◽

Monique J Windley ◽

Matthew D Perry ◽

...

Keyword(s):

Patch Clamp ◽

Cell Lines ◽

High Throughput ◽

Rapid Assessment ◽

Cost Effective ◽

Missense Variant ◽

Loss Of Function ◽

Channel Expression ◽

Automated Patch Clamp ◽

Patch Clamp Electrophysiology

Abstract KCNH2 is one of the 59 medically actionable genes recommended by the American College of Medical Genetics for reporting of incidental findings from clinical genomic sequencing. However, half of the reported KCNH2 variants in the ClinVar database are classified as variants of uncertain significance. In the absence of strong clinical phenotypes, there is a need for functional phenotyping to help decipher the significance of variants identified incidentally. Here, we report detailed methods for assessing the molecular phenotype of any KCNH2 missense variant. The key components of the assay include quick and cost-effective generation of a bi-cistronic vector to co-express Wild-type (WT) and any KCNH2 variant allele, generation of stable Flp-In HEK293 cell lines and high-throughput automated patch clamp electrophysiology analysis of channel function. Stable cell lines take 3–4 weeks to produce and can be generated in bulk, which will then allow up to 30 variants to be phenotyped per week after 48 h of channel expression. This high-throughput functional genomics assay will enable a much more rapid assessment of the extent of loss of function of any KCNH2 variant.

Download Full-text

Rapid Assessment of Binding Affinity of SARS-COV-2 Spike Protein to the Human Angiotensin-Converting Enzyme 2 Receptor and to Neutralizing Biomolecules Based on Computer Simulations

Frontiers in Immunology ◽

10.3389/fimmu.2021.730099 ◽

2021 ◽

Vol 12 ◽

Author(s):

Damiano Buratto ◽

Abhishek Saxena ◽

Qun Ji ◽

Guang Yang ◽

Sergio Pantano ◽

...

Keyword(s):

Angiotensin Converting Enzyme ◽

Binding Affinity ◽

Rapid Assessment ◽

Cost Effective ◽

Spike Protein ◽

Converting Enzyme ◽

Spike Glycoprotein ◽

Host Cell Membrane ◽

Angiotensin Converting Enzyme 2 ◽

Dynamics Simulations

SARS-CoV-2 infects humans and causes Coronavirus disease 2019 (COVID-19). The S1 domain of the spike glycoprotein of SARS-CoV-2 binds to human angiotensin-converting enzyme 2 (hACE2) via its receptor-binding domain, while the S2 domain facilitates fusion between the virus and the host cell membrane for entry. The spike glycoprotein of circulating SARS-CoV-2 genomes is a mutation hotspot. Some mutations may affect the binding affinity for hACE2, while others may modulate S-glycoprotein expression, or they could result in a virus that can escape from antibodies generated by infection with the original variant or by vaccination. Since a large number of variants are emerging, it is of vital importance to be able to rapidly assess their characteristics: while changes of binding affinity alone do not always cause direct advantages for the virus, they still can provide important insights on where the evolutionary pressure is directed. Here, we propose a simple and cost-effective computational protocol based on Molecular Dynamics simulations to rapidly screen the ability of mutated spike protein to bind to the hACE2 receptor and selected neutralizing biomolecules. Our results show that it is possible to achieve rapid and reliable predictions of binding affinities. A similar approach can be used to perform preliminary screenings of the potential effects of S-RBD mutations, helping to prioritize the more time-consuming and expensive experimental work.

Download Full-text

FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters

10.1101/610394 ◽

2019 ◽

Author(s):

Michael M. Weinstein ◽

Aishani Prem ◽

Mingda Jin ◽

Shuiquan Tang ◽

Jeffrey M. Bhasin

Keyword(s):

Rapid Assessment ◽

Cost Effective ◽

Bioinformatic Analysis ◽

18S Rrna Gene ◽

Rrna Gene ◽

Sequence Information ◽

Bioinformatic Tools ◽

Zymo Research ◽

High Throughput Dna Sequencing ◽

The Cost

ABSTRACTSummaryMicrobiome studies continue to provide tremendous insight into the importance of microorganism populations to the macroscopic world. High-throughput DNA sequencing technology (i.e., Next-generation Sequencing) has enabled the cost-effective, rapid assessment of microbial populations when combined with bioinformatic tools capable of identifying microbial taxa and calculating the diversity and composition of biological and environmental samples. Ribosomal RNA gene sequencing, where 16S and 18S rRNA gene sequences are used to identify prokaryotic and eukaryotic species, respectively, is one of the most widely-used techniques currently employed in microbiome analysis. Prior to bioinformatic analysis of these sequences, trimming parameters must be set so that post-trimming sequence information is maximized while expected errors in the sequences themselves are minimized. In this application note, we present FIGARO: a Python–based application designed to maximize read retention after trimming and filtering for quality. FIGARO was designed specifically to increase reproducibility and minimize trial-and-error in trimming parameter selection for a DADA2–based pipeline and will likely be useful for optimizing trimming parameters and minimizing sequence errors in other pipelines as well where paired-end overlap is required.Availability and implementationThe FIGARO application is freely available as source code at https://github.com/Zymo-Research/figaro.

Download Full-text

The cost-effectiveness of comprehensive school reform and rapid assessment.

Education Policy Analysis Archives ◽

10.14507/epaa.v16n13.2008 ◽

2008 ◽

Vol 16 ◽

pp. 13 ◽

Cited By ~ 5

Author(s):

Stuart S. Yeh

Keyword(s):

Cost Effectiveness ◽

School Reform ◽

Math Achievement ◽

Rapid Assessment ◽

Cost Effective ◽

Comprehensive School ◽

Comprehensive School Reform ◽

Reading And Math ◽

Order Of Magnitude ◽

The Cost

Analysis of the cost-effectiveness of 29 Comprehensive School Reform (CSR) models suggests that all 29 models are less cost-effective than an alternative approach for raising student achievement, involving rapid assessment systems that test students 2 to 5 times per week in math and reading and provide rapid feedback of the results to students and teachers. Results suggest that reading and math achievement could increase approximately one order of magnitude greater for every dollar invested in rapid assessment rather than CSR. The results also suggest that reading and math achievement could increase two orders of magnitude for every dollar invested in rapid assessment rather than class size reduction and three orders of magnitude for every dollar invested in rapid assessment rather than high quality preschool.

Download Full-text

Multidisciplinary Post-Earthquake Critique of Masonry Substation Retrofits

Earthquake Spectra ◽

10.1193/040717eqs065m ◽

2018 ◽

Vol 34 (3) ◽

pp. 1363-1382 ◽

Cited By ~ 1

Author(s):

Aina Noor Misnon ◽

Dmytro Dizhur ◽

John Mackenzie ◽

Shannon Abeling ◽

Jason Ingham

Keyword(s):

Rapid Assessment ◽

Cost Savings ◽

Cost Effective ◽

Brick Masonry ◽

Clay Brick ◽

Improvement Program ◽

Significant Damage ◽

Earthquake Performance ◽

Heritage Building ◽

Multidisciplinary Perspective

The earthquake performance of retrofitted clay brick masonry substation buildings was investigated from a multidisciplinary perspective that included structural, economic, and social considerations. One-hundred-fifteen single-story double-leaf clay-brick masonry substation buildings located within the wider Christchurch, New Zealand, region were investigated in detail. In the mid-1990s, these substation buildings were seismically retrofitted using a system of simple and cost-effective steel elements as part of a natural disaster improvement program, with an overall cost of N.Z. $6 million (approximately U.S. $4 million). Rapid assessment evaluation was conducted following the 2010/2011 Canterbury earthquakes with the determination that 82% of these clay-brick masonry substation buildings sustained minor damage, and 15% had moderate damage. Meanwhile, one substation building suffered significant damage, and two substation buildings experienced heavy damage. Investment in the seismic improvement program resulted in cost savings of approximately N.Z. $60 million (U.S. $44 million) and contributed to heritage building preservation.

Download Full-text