scholarly journals Machine-Learning-Based Proteomic Predictive Modeling with Thermally-Challenged Caribbean Reef Corals

Diversity ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 33
Author(s):  
Anderson B. Mayfield
Keyword(s):  
Machine Learning ◽  
Elevated Temperatures ◽  
Host Coral ◽  
Reef Corals ◽  
Proteomic Data ◽  
Coral Colony ◽  
Orbicella Faveolata ◽  
Quality Control Criteria ◽  
Coral Health ◽  
Control Criteria

Coral health is currently diagnosed retroactively; colonies are deemed “stressed” upon succumbing to bleaching or disease. Ideally, health inferences would instead be made on a pre-death timescale that would enable, for instance, environmental mitigation that could promote coral resilience. To this end, diverse Caribbean coral (Orbicella faveolata) genotypes of varying resilience to high temperatures along the Florida Reef Tract were exposed herein to elevated temperatures in the laboratory, and a proteomic analysis was taken with a subset of 20 samples via iTRAQ labeling followed by nano-liquid chromatography + mass spectrometry; 46 host coral and 40 Symbiodiniaceae dinoflagellate proteins passed all stringent quality control criteria, and the partial proteomes of biopsies of (1) healthy controls, (2) sub-lethally stressed samples, and (3) actively bleaching corals differed significantly from one another. The proteomic data were then used to train predictive models of coral colony bleaching susceptibility, and both generalized regression and machine-learning-based neural networks were capable of accurately forecasting the bleaching susceptibility of coral samples based on their protein signatures. Successful future testing of the predictive power of these models in situ could establish the capacity to proactively monitor coral health.

Advances in standardizing and validating research techniques for pathogen monitoring in water

2004 ◽  
Vol 4 (2) ◽  
pp. 23-30
Author(s):  
K. Connell ◽  
M. Pope ◽  
K. Miller ◽  
J. Scheller ◽  
J. Pulz
Keyword(s):  
Validation Studies ◽  
Development Process ◽  
Monitoring Methods ◽  
Microbiological Method ◽  
Validation Process ◽  
Method Performance ◽  
Target Analytes ◽  
Interlaboratory Validation ◽  
Quality Control Criteria ◽  
Control Criteria

Designing and conducting standardized microbiological method interlaboratory validation studies is challenging because most methods are manual, rather than instrument-based, and results from the methods are typically subjective. Determinations of method recovery, in particular, are problematic, due to difficulties in assessing the true spike amount. The standardization and validation process used for the seven most recent USEPA 1600-series pathogen monitoring methods has begun to address these challenges. A staged development process was used to ensure that methods were adequately tested and standardized before resources were dedicated to interlaboratory validation. The interlaboratory validation studies for USEPA Method 1622, for Cryptosporidium, USEPA Method 1601 for coliphage, and USEPA Method 1605 for Aeromonas assessed method performance using different approaches, due the differences in the nature of the target analytes and the data quality needs of each study. However, the use of enumerated spikes in all of the studies allowed method recovery and precision to be assessed, and also provided the data needed to establish quantitative quality control criteria for the methods.

scholarly journals Physiological and ecological consequences of the water optical properties degradation on reef corals

Coral Reefs ◽  
2021 ◽  
Author(s):  
Tomás López-Londoño ◽  
Claudia T. Galindo-Martínez ◽  
Kelly Gómez-Campo ◽  
Luis A. González-Guerrero ◽  
Sofia Roitman ◽  
...  
Keyword(s):  
Optical Properties ◽  
Population Decline ◽  
Light Availability ◽  
Potential Effect ◽  
Optical Quality ◽  
Light Penetration ◽  
Reef Corals ◽  
Orbicella Faveolata ◽  
Light Quantity ◽  
Reduced Light

AbstractDegradation of water optical properties due to anthropogenic disturbances is a common phenomenon in coastal waters globally. Although this condition is associated with multiple drivers that affect corals health in multiple ways, its effect on light availability and photosynthetic energy acquisition has been largely neglected. Here, we describe how declining the water optical quality in a coastal reef exposed to a turbid plume of water originating from a man-made channel compromises the functionality of the keystone coral species Orbicella faveolata. We found highly variable water optical conditions with significant effects on the light quantity and quality available for corals. Low-light phenotypes close to theoretical limits of photoacclimation were found at shallow depths as a result of reduced light penetration. The estimated photosynthetically fixed energy depletion with increasing depth was associated with patterns of colony mortality and vertical habitat compression. A numerical model illustrates the potential effect of the progressive water quality degradation on coral mortality and population decline along the depth gradient. Collectively, our findings suggest that preserving the water properties seeking to maximize light penetration through the water column is essential for maintaining the coral reef structure and associated ecosystem services.

scholarly journals Assessment of SARS-CoV-2 genome sequencing: quality criteria and low frequency variants

2021 ◽  
Author(s):  
Damien Jacot ◽  
Trestan Pillonel ◽  
Gilbert Greub ◽  
Claire Bertelli
Keyword(s):  
Sample Selection ◽  
Low Frequency ◽  
Pcr Amplification ◽  
Quality Criterion ◽  
Quality Criteria ◽  
Sequencing Errors ◽  
Sequencing Quality ◽  
Quality Control Criteria ◽  
Control Criteria ◽  
Sequence Quality

Although many laboratories worldwide have developed their sequencing capacities in response to the need for SARS-CoV-2 genome-based surveillance of variants, only few reported some quality criteria to ensure sequence quality before lineage assignment and submission to public databases. Hence, we aimed here to provide simple quality control criteria for SARS-CoV-2 sequencing to prevent erroneous interpretation of low quality or contaminated data. We retrospectively investigated 647 SARS-CoV-2 genomes obtained over ten tiled amplicons sequencing runs. We extracted 26 potentially relevant metrics covering the entire workflow from sample selection to bioinformatics analysis. Based on data distribution, critical values were established for eleven selected metrics to prompt further quality investigations for problematic samples, in particular those with a low viral RNA quantity. Low frequency variants (<70% of supporting reads) can result from PCR amplification errors, sample cross contaminations or presence of distinct SARS-CoV2 genomes in the sample sequenced. The number and the prevalence of low frequency variants can be used as a robust quality criterion to identify possible sequencing errors or contaminations. Overall, we propose eleven metrics with fixed cutoff values as a simple tool to evaluate the quality of SARS-CoV-2 genomes, among which cycle thresholds, mean depth, proportion of genome covered at least 10x and the number of low frequency variants combined with mutation prevalence data.

scholarly journals FireProtDB: database of manually curated protein stability data

2020 ◽  
Vol 49 (D1) ◽  
pp. D319-D324
Author(s):  
Jan Stourac ◽  
Juraj Dubrava ◽  
Milos Musil ◽  
Jana Horackova ◽  
Jiri Damborsky ◽  
...  
Keyword(s):  
Machine Learning ◽  
Elevated Temperatures ◽  
Recent Literature ◽  
Single Point ◽  
Biotechnological Applications ◽  
Computational Tools ◽  
Mild Conditions ◽  
Naturally Occurring ◽  
Stability Data ◽  
Living Organisms

Abstract The majority of naturally occurring proteins have evolved to function under mild conditions inside the living organisms. One of the critical obstacles for the use of proteins in biotechnological applications is their insufficient stability at elevated temperatures or in the presence of salts. Since experimental screening for stabilizing mutations is typically laborious and expensive, in silico predictors are often used for narrowing down the mutational landscape. The recent advances in machine learning and artificial intelligence further facilitate the development of such computational tools. However, the accuracy of these predictors strongly depends on the quality and amount of data used for training and testing, which have often been reported as the current bottleneck of the approach. To address this problem, we present a novel database of experimental thermostability data for single-point mutants FireProtDB. The database combines the published datasets, data extracted manually from the recent literature, and the data collected in our laboratory. Its user interface is designed to facilitate both types of the expected use: (i) the interactive explorations of individual entries on the level of a protein or mutation and (ii) the construction of highly customized and machine learning-friendly datasets using advanced searching and filtering. The database is freely available at https://loschmidt.chemi.muni.cz/fireprotdb.

scholarly journals Problems and practical considerations in assessing accuracy with NIST SRM 909a: report of defective vials

1996 ◽  
Vol 42 (11) ◽  
pp. 1832-1837 ◽  
Author(s):  
B K De ◽  
B A Karr ◽  
S Ghosn ◽  
B E Copeland
Keyword(s):  
Monitoring Program ◽  
Experimental Period ◽  
Medical Monitoring ◽  
Electron Microscopic ◽  
Value Analysis ◽  
Assigned Value ◽  
Technology Standard ◽  
Quality Control Criteria ◽  
Glucose Recovery ◽  
Control Criteria

Abstract During an experimental period of 12 months in 1992-1993, while we were comparing the effectiveness of monthly vs quarterly use of the National Institute for Standards and Technology Standard Reference Material (NIST SRM) 909a as an accuracy material for the projected 30-year Fernald Medical Monitoring Program, we encountered three random defective vials with a glucose recovery of less than 30% of the NIST-assigned value. Analysis with five different multichannel instruments confirmed the original finding. Concomitant glucose recovery from adjacent vials was 97%-104%, as determined by using the same instruments, reagents, calibrators, and quality-control criteria on the same days. Recoveries of uric acid and cholesterol were also low (53-75% and 75-80%, respectively) in the three defective vials. Other analytes were unaffected. Studies to identify the cause of the defective vials were carried out with microbiological, electron microscopic, and biochemical techniques. When used for accuracy studies, each vial of NIST SRM 909a should have a concomitant check for glucose recovery to detect whether the vial is defective.

scholarly journals Tool wear estimation in turning of Inconel 718 based on wavelet sensor signal analysis and machine learning paradigms

2020 ◽  
Vol 14 (5-6) ◽  
pp. 693-705
Author(s):  
Tiziana Segreto ◽  
Doriana D’Addona ◽  
Roberto Teti
Keyword(s):  
Machine Learning ◽  
Tool Wear ◽  
Inconel 718 ◽  
Signal Analysis ◽  
Elevated Temperatures ◽  
Wavelet Packet ◽  
Research Work ◽  
High Strength ◽  
Signal Features ◽  
Tool Wear Estimation

AbstractIn the last years, hard-to-machine nickel-based alloys have been widely employed in the aerospace industry for their properties of high strength, excellent resistance to corrosion and oxidation, and long creep life at elevated temperatures. As the machinability of these materials is quite low due to high cutting forces, high temperature development and strong work hardening, during machining the cutting tool conditions tend to rapidly deteriorate. Thus, tool health monitoring systems are highly desired to improve tool life and increase productivity. This research work focuses on tool wear estimation during turning of Inconel 718 using wavelet packet transform (WPT) signal analysis and machine learning paradigms. A multiple sensor monitoring system, based on the detection of cutting force, acoustic emission and vibration acceleration signals, was employed during experimental turning trials. The detected sensor signals were subjected to WPT decomposition to extract diverse signal features. The most relevant features were then selected, using correlation measurements, in order to be utilized in artificial neural network based machine learning paradigms for tool wear estimation.

scholarly journals Oscillometric and Spirometric Bronchodilator Response in Preschool Children with and without Asthma

2012 ◽  
Vol 19 (4) ◽  
pp. 273-277 ◽  
Author(s):  
Youn Ho Shin ◽  
Sun Jung Jang ◽  
Jung Won Yoon ◽  
Hye Mi Jee ◽  
Sun Hee Choi ◽  
...  
Keyword(s):  
Preschool Children ◽  
Forced Vital Capacity ◽  
Vital Capacity ◽  
Forced Expiratory Volume ◽  
Bronchodilator Response ◽  
Asthmatic Children ◽  
Before And After ◽  
Forced Expiratory Flow ◽  
Quality Control Criteria ◽  
Control Criteria

BACKGROUND: Bronchodilator responses (BDR) are routinely used in the diagnosis and management of asthma; however, their acceptability and repeatability have not been evaluated using quality control criteria for preschool children.OBJECTIVES: To compare conventional spirometry with an impulse oscillometry system (IOS) in healthy and asthmatic preschool children.METHODS: Data from 30 asthmatic children and 29 controls (two to six years of age) who underwent IOS and spirometry before and after salbutamol administration were analyzed.RESULTS: Stable asthmatic subjects significantly differed versus controls in their spirometry-assessed BDR (forced expiratory volume in 1 s [FEV1], forced vital capacity and forced expiratory flow at 25% to 75% of forced vital capacity) as well as their IOS-assessed BDR (respiratory resistance at 5 Hz [Rrs5], respiratory reactance at 5 Hz and area under the reactance curve). However, comparisons based on the area under the ROC curve for ΔFEV1% initial versus ΔRrs5% initial were 0.82 (95% CI 0.71 to 0.93) and 0.75 (95% CI 0.62 to 0.87), respectively. Moreover, the sensitivity and specificity for ΔFEV1≥9% were 0.53 and 0.93, respectively. Importantly, sensitivity increased to 0.63 when either ΔFEV1≥9% or ΔRrs5≥29% was considered as an additional criterion for the diagnosis of asthma.CONCLUSION: The accuracy of asthma diagnosis in preschool children may be increased by combining spirometry with IOS when measuring BDR.

scholarly journals Proteomic Signatures of Corals from Thermodynamic Reefs

2020 ◽  
Vol 8 (8) ◽  
pp. 1171
Author(s):  
Anderson B. Mayfield
Keyword(s):  
Molecular Mechanisms ◽  
Elevated Temperatures ◽  
Variable Temperature ◽  
Deep South ◽  
Lipid Trafficking ◽  
Reef Corals ◽  
Temperature Conditions ◽  
Temperature Regimes ◽  
Unique Nature ◽  
Seriatopora Hystrix

Unlike most parts of the world, coral reefs of Taiwan’s deep south have generally been spared from climate change-induced degradation. This has been linked to the oceanographically unique nature of Nanwan Bay, where intense upwelling occurs. Specifically, large-amplitude internal waves cause shifts in temperature of 6–9 °C over the course of several hours, and the resident corals not only thrive under such conditions, but they have also been shown to withstand multi-month laboratory incubations at experimentally elevated temperatures. To gain insight into the sub-cellular basis of acclimation to upwelling, proteins isolated from reef corals (Seriatopora hystrix) featured in laboratory-based reciprocal transplant studies in which corals from upwelling and non-upwelling control reefs (<20 km away) were exposed to stable or variable temperature regimes were analyzed via label-based proteomics (iTRAQ). Corals exposed to their “native” temperature conditions for seven days (1) demonstrated highest growth rates and (2) were most distinct from one another with respect to their protein signatures. The latter observation was driven by the fact that two Symbiodiniaceae lipid trafficking proteins, sec1a and sec34, were marginally up-regulated in corals exposed to their native temperature conditions. Alongside the marked degree of proteomic “site fidelity” documented, this dataset sheds light on the molecular mechanisms underlying acclimatization to thermodynamically extreme conditions in situ.

scholarly journals Size-specific recolonization success by coral-dwelling damselfishes moderates resilience to habitat loss

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Morgan S. Pratchett ◽  
Vanessa Messmer ◽  
Shaun K. Wilson
Keyword(s):  
Coral Reef ◽  
Habitat Loss ◽  
Reef Fishes ◽  
Host Coral ◽  
Proximate Cause ◽  
Coral Colony ◽  
Colonization Success ◽  
Coral Reef Ecosystems ◽  
Pomacentrus Moluccensis ◽  
Dascyllus Aruanus

Abstract Increasing degradation of coral reef ecosystems and specifically, loss of corals is causing significant and widespread declines in the abundance of coral reef fishes, but the proximate cause(s) of these declines are largely unknown. Here, we examine specific responses to host coral mortality for three species of coral-dwelling damselfishes (Dascyllus aruanus, D. reticulatus, and Pomacentrus moluccensis), explicitly testing whether these fishes can successfully move and recolonize nearby coral hosts. Responses of fishes to localized coral loss was studied during population irruptions of coral feeding crown-of-thorns starfish, where starfish consumed 29 (34%) out of 85 coral colonies, of which 25 (86%) were occupied by coral-dwelling damselfishes. Damselfishes were not tagged or individually recognizable, but changes in the colonization of different coral hosts was assessed by carefully assessing the number and size of fishes on every available coral colony. Most damselfishes (> 90%) vacated dead coral hosts within 5 days, and either disappeared entirely (presumed dead) or relocated to nearby coral hosts. Displaced fishes only ever colonized corals already occupied by other coral-dwelling damselfishes (mostly conspecifics) and colonization success was strongly size-dependent. Despite movement of damselfishes to surviving corals, the local abundance of coral-dependent damselfishes declined in approximate accordance with the proportional loss of coral habitat. These results suggest that even if alternative coral hosts are locally abundant, there are significant biological constraints on movement of coral-dwelling damselfishes and recolonization of alternative coral habitats, such that localized persistence of habitat patches during moderate or patchy disturbances do not necessarily provide resilience against overall habitat loss.

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