scholarly journals Mapping specificity, entropy, allosteric changes and substrates in blood proteases by a high-throughput protease screen

2020 ◽  
Author(s):  
Federico Uliana ◽  
Matej Vizovišek ◽  
Laura Acquasaliente ◽  
Rodolfo Ciuffa ◽  
Andrea Fossati ◽  
...  
Keyword(s):  
Blood Coagulation ◽  
High Throughput ◽  
Fluorescent Probes ◽  
Protease Activity ◽  
Vast Number ◽  
Biochemical Processes ◽  
Wide Range ◽  
Protease Substrate ◽  
Physiological Substrates

AbstractProteases are among the largest protein families in eukaryotic phylae with more than 500 genetically encoded proteases in humans. By cleaving a wide range of target proteins, proteases are critical regulators of a vast number of biochemical processes including apoptosis and blood coagulation. Over the last 20 years, knowledge of proteases has been drastically expanded by the development of proteomic approaches to identify and quantify proteases and their substrates. In spite of their merits, some of these methods are laborious, not scalable or incompatible with native environments. Consequentially, a large number of proteases remain poorly characterized. Here, we introduce a simple proteomic method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter and their analysis in a mass spectrometer. The method is significantly faster, cheaper, technically less demanding, easily multiplexed and produces accurate protease fingerprints in near-native conditions. By using the blood cascade proteases as a case study we obtained protease substrate profiles of unprecedented depth that can be reliably used to map specificity, entropy and allosteric changes of the protease and to design fluorescent probes and predict physiological substrates. The native protease characterization method is comparable in performance, but largely exceeds the throughput of current alternatives.

scholarly journals Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Federico Uliana ◽  
Matej Vizovišek ◽  
Laura Acquasaliente ◽  
Rodolfo Ciuffa ◽  
Andrea Fossati ◽  
...  
Keyword(s):  
Data Analysis ◽  
Analysis Pipeline ◽  
Simple Method ◽  
Biochemical Processes ◽  
Biochemical Assays ◽  
Protease Substrate ◽  
Data Analysis Pipeline ◽  
Selection Of ◽  
Physiological Substrates

AbstractProteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays.

Site specific agricultural soil management with the use of new technologies

2013 ◽  
Vol 16 (1) ◽  
pp. 59-67
Keyword(s):  
New Technologies ◽  
Digital Interface ◽  
Appropriate Treatment ◽  
Wide Range ◽  
Soil Variation ◽  
Soil Information ◽  
Remote Sensing Techniques ◽  
Agricultural Areas

<p>The Soil Science Institute of Thessaloniki produces new digitized Soil Maps that provide a useful electronic database for the spatial representation of the soil variation within a region, based on in situ soil sampling, laboratory analyses, GIS techniques and plant nutrition mathematical models, coupled with the local land cadastre. The novelty of these studies is that local agronomists have immediate access to a wide range of soil information by clicking on a field parcel shown in this digital interface and, therefore, can suggest an appropriate treatment (e.g. liming, manure incorporation, desalination, application of proper type and quantity of fertilizer) depending on the field conditions and cultivated crops. A specific case study is presented in the current work with regards to the construction of the digitized Soil Map of the regional unit of Kastoria. The potential of this map can easily be realized by the fact that the mapping of the physicochemical properties of the soils in this region provided delineation zones for differential fertilization management. An experiment was also conducted using remote sensing techniques for the enhancement of the fertilization advisory software database, which is a component of the digitized map, and the optimization of nitrogen management in agricultural areas.</p>

Oxford Studies in Ancient Philosophy, Volume 55

2018 ◽  
Keyword(s):  
Middle Ages ◽  
Ancient Philosophy ◽  
Recent Book ◽  
Loss Of Control ◽  
Ancient Greek ◽  
Original Essays ◽  
Constant Change ◽  
Wide Range ◽  
Metaphysical Principle

Oxford Studies in Ancient Philosophy provides, twice each year, a collection of the best current work in the field of ancient philosophy. Each volume features original essays that contribute to an understanding of a wide range of themes and problems in all periods of ancient Greek and Roman philosophy, from the beginnings to the threshold of the Middle Ages. From its first volume in 1983, OSAP has been a highly influential venue for work in the field, and has often featured essays of substantial length as well as critical essays on books of distinctive importance. Volume LV contains: a methodological examination on how the evidence for Presocratic thought is shaped through its reception by later thinkers, using discussions of a world soul as a case study; an article on Plato’s conception of flux and the way in which sensible particulars maintain a kind of continuity while undergoing constant change; a discussion of J. L. Austin’s unpublished lecture notes on Aristotle’s Nicomachean Ethics and his treatment of loss of control (akrasia); an article on the Stoics’ theory of time and in particular Chrysippus’ conception of the present and of events; and two articles on Plotinus, one that identifies a distinct argument to show that there is a single, ultimate metaphysical principle; and a review essay discussing E. K. Emilsson’s recent book, Plotinus.

scholarly journals Principled Decision-Making Workflow with Hierarchical Bayesian Models of High-Throughput Dose-Response Measurements

Entropy ◽  
2021 ◽  
Vol 23 (6) ◽  
pp. 727
Author(s):  
Eric J. Ma ◽  
Arkadij Kummer
Keyword(s):  
Decision Making ◽  
High Throughput ◽  
Noisy Data ◽  
Hierarchical Bayesian ◽  
Hierarchical Bayesian Models ◽  
Melting Temperatures ◽  
Hierarchical Bayesian Estimation ◽  
The Face ◽  
Point Data

We present a case study applying hierarchical Bayesian estimation on high-throughput protein melting-point data measured across the tree of life. We show that the model is able to impute reasonable melting temperatures even in the face of unreasonably noisy data. Additionally, we demonstrate how to use the variance in melting-temperature posterior-distribution estimates to enable principled decision-making in common high-throughput measurement tasks, and contrast the decision-making workflow against simple maximum-likelihood curve-fitting. We conclude with a discussion of the relative merits of each workflow.

scholarly journals Assessing the Relation between Mud Components and Rheology for Loss Circulation Prevention Using Polymeric Gels: A Machine Learning Approach

Energies ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1377
Author(s):  
Musaab I. Magzoub ◽  
Raj Kiran ◽  
Saeed Salehi ◽  
Ibnelwaleed A. Hussein ◽  
Mustafa S. Nasser
Keyword(s):  
Machine Learning ◽  
Rheological Properties ◽  
Nearest Neighbor ◽  
Drilling Fluid ◽  
Gradient Boosting ◽  
K Nearest Neighbor ◽  
Wide Range ◽  
Machine Learning Approach ◽  
Drilling Operations

The traditional way to mitigate loss circulation in drilling operations is to use preventative and curative materials. However, it is difficult to quantify the amount of materials from every possible combination to produce customized rheological properties. In this study, machine learning (ML) is used to develop a framework to identify material composition for loss circulation applications based on the desired rheological characteristics. The relation between the rheological properties and the mud components for polyacrylamide/polyethyleneimine (PAM/PEI)-based mud is assessed experimentally. Four different ML algorithms were implemented to model the rheological data for various mud components at different concentrations and testing conditions. These four algorithms include (a) k-Nearest Neighbor, (b) Random Forest, (c) Gradient Boosting, and (d) AdaBoosting. The Gradient Boosting model showed the highest accuracy (91 and 74% for plastic and apparent viscosity, respectively), which can be further used for hydraulic calculations. Overall, the experimental study presented in this paper, together with the proposed ML-based framework, adds valuable information to the design of PAM/PEI-based mud. The ML models allowed a wide range of rheology assessments for various drilling fluid formulations with a mean accuracy of up to 91%. The case study has shown that with the appropriate combination of materials, reasonable rheological properties could be achieved to prevent loss circulation by managing the equivalent circulating density (ECD).

scholarly journals Using citizen science data to monitor the Sustainable Development Goals: a bottom-up analysis

2021 ◽  
Author(s):  
Laura Ballerini ◽  
Sylvia I. Bergh
Keyword(s):  
Sustainable Development ◽  
Citizen Science ◽  
Sustainable Development Goals ◽  
Comparative Case Study ◽  
Science Data ◽  
The Sustainable Development ◽  
Case Study Analysis ◽  
Wide Range ◽  
Development Goals

AbstractOfficial data are not sufficient for monitoring the United Nations Sustainable Development Goals (SDGs): they do not reach remote locations or marginalized populations and can be manipulated by governments. Citizen science data (CSD), defined as data that citizens voluntarily gather by employing a wide range of technologies and methodologies, could help to tackle these problems and ultimately improve SDG monitoring. However, the link between CSD and the SDGs is still understudied. This article aims to develop an empirical understanding of the CSD-SDG link by focusing on the perspective of projects which employ CSD. Specifically, the article presents primary and secondary qualitative data collected on 30 of these projects and an explorative comparative case study analysis. It finds that projects which use CSD recognize that the SDGs can provide a valuable framework and legitimacy, as well as attract funding, visibility, and partnerships. But, at the same time, the article reveals that these projects also encounter several barriers with respect to the SDGs: a widespread lack of knowledge of the goals, combined with frustration and political resistance towards the UN, may deter these projects from contributing their data to the SDG monitoring apparatus.

scholarly journals Action plan for hit identification (APHID): KAT6A as a case study

2020 ◽  
Vol 12 (5) ◽  
pp. 423-437 ◽  
Author(s):  
Xiangyan Yi ◽  
Lian Xue ◽  
Tim Thomas ◽  
Jonathan B Baell
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Action Plan ◽  
Hit Identification

Here, we describe our action plan for hit identification (APHID) that guides the process of hit triage, with elimination of less tractable hits and retention of more tractable hits. We exemplify the process with reference to our high-throughput screening (HTS) campaign against the enzyme, KAT6A, that resulted in successful identification of a tractable hit. We hope that APHID could serve as a useful, concise and digestible guide for those involved in HTS and hit triage, especially those that are relatively new to this exciting and continually evolving technology.

scholarly journals Evaluating the efficacy of technical measures: a case study of selection device legislation in the UK Crangon crangon (brown shrimp) fishery

2008 ◽  
Vol 65 (2) ◽  
pp. 267-275 ◽  
Author(s):  
Tom L. Catchpole ◽  
Andrew S. Revill ◽  
James Innes ◽  
Sean Pascoe
Keyword(s):  
Brown Shrimp ◽  
Crangon Crangon ◽  
Shrimp Fishery ◽  
The North ◽  
Ex Post ◽  
Wide Range ◽  
The Uk ◽  
The Impact ◽  
Technical Measures

Abstract Catchpole, T. L., Revill, A. S., Innes, J., and Pascoe, S. 2008. Evaluating the efficacy of technical measures: a case study of selection device legislation in the UK Crangon crangon (brown shrimp) fishery. – ICES Journal of Marine Science, 65: 267–275. Bycatch reduction devices are being introduced into a wide range of fisheries, with shrimp and prawn fisheries particularly targeted owing to the heavy discarding common in these fisheries. Although studies are often undertaken to estimate the impact of a technical measure on the fishery before implementation, rarely have the impacts been assessed ex post. Here, the efficacy of the UK legislation pertaining to the use of sievenets in the North Sea Crangon crangon fishery is assessed. Three impacts were evaluated: on fisher behaviour (social), on the level of bycatch (biological), and on vessel profitability (economic). An apparent high level of compliance by skippers was identified despite a low level of enforcement. The estimated reduction in fleet productivity following the introduction of the legislation was 14%, equalling the mean loss of Crangon landings when using sievenets calculated from catch comparison trawls. Sievenets did reduce the unnecessary capture of unwanted marine organisms, but were least effective at reducing 0-group plaice, which make up the largest component of the bycatch. Clearly the legislation has had an effect in the desired direction, but it does not address sufficiently the bycatch issue in the Crangon fishery.

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