scholarly journals The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020

2020 ◽  
Vol 66 (8) ◽  
pp. 1012-1029 ◽  
Author(s):  
Jim F Huggett ◽  
◽  
Alexandra S Whale ◽  
Ward De Spiegelaere ◽  
Wim Trypsteen ◽  
...  
Keyword(s):  
Digital Pcr ◽  
Experimental Information ◽  
Minimum Information ◽  
Software Applications ◽  
Technological Potential ◽  
Experimental Protocols ◽  
Experimental Process ◽  
Threshold Setting ◽  
The Impact ◽  
Process Adoption

Abstract Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology.

scholarly journals The Digital MIQE Guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments

2013 ◽  
Vol 59 (6) ◽  
pp. 892-902 ◽  
Author(s):  
Jim F Huggett ◽  
Carole A Foy ◽  
Vladimir Benes ◽  
Kerry Emslie ◽  
Jeremy A Garson ◽  
...  
Keyword(s):  
Rare Variants ◽  
Early Stage ◽  
New Technology ◽  
Digital Pcr ◽  
Substantial Impact ◽  
Minimum Information ◽  
Independent Evaluation ◽  
Precise Quantification ◽  
Diagnostic Applications ◽  
The Impact

Abstract There is growing interest in digital PCR (dPCR) because technological progress makes it a practical and increasingly affordable technology. dPCR allows the precise quantification of nucleic acids, facilitating the measurement of small percentage differences and quantification of rare variants. dPCR may also be more reproducible and less susceptible to inhibition than quantitative real-time PCR (qPCR). Consequently, dPCR has the potential to have a substantial impact on research as well as diagnostic applications. However, as with qPCR, the ability to perform robust meaningful experiments requires careful design and adequate controls. To assist independent evaluation of experimental data, comprehensive disclosure of all relevant experimental details is required. To facilitate this process we present the Minimum Information for Publication of Quantitative Digital PCR Experiments guidelines. This report addresses known requirements for dPCR that have already been identified during this early stage of its development and commercial implementation. Adoption of these guidelines by the scientific community will help to standardize experimental protocols, maximize efficient utilization of resources, and enhance the impact of this promising new technology.

Improvements for research data repositories: The case of text spam

2021 ◽  
pp. 016555152199863
Author(s):  
Ismael Vázquez ◽  
María Novo-Lourés ◽  
Reyes Pavón ◽  
Rosalía Laza ◽  
José Ramón Méndez ◽  
...  
Keyword(s):  
Web Application ◽  
Research Data ◽  
Data Sets ◽  
Data Repositories ◽  
Software Applications ◽  
Public Data ◽  
Protection Mechanisms ◽  
Experimental Protocols ◽  
Learning Research ◽  
Processing Steps

Current research has evolved in such a way scientists must not only adequately describe the algorithms they introduce and the results of their application, but also ensure the possibility of reproducing the results and comparing them with those obtained through other approximations. In this context, public data sets (sometimes shared through repositories) are one of the most important elements for the development of experimental protocols and test benches. This study has analysed a significant number of CS/ML ( Computer Science/ Machine Learning) research data repositories and data sets and detected some limitations that hamper their utility. Particularly, we identify and discuss the following demanding functionalities for repositories: (1) building customised data sets for specific research tasks, (2) facilitating the comparison of different techniques using dissimilar pre-processing methods, (3) ensuring the availability of software applications to reproduce the pre-processing steps without using the repository functionalities and (4) providing protection mechanisms for licencing issues and user rights. To show the introduced functionality, we created STRep (Spam Text Repository) web application which implements our recommendations adapted to the field of spam text repositories. In addition, we launched an instance of STRep in the URL https://rdata.4spam.group to facilitate understanding of this study.

scholarly journals Optimization of proppant parameters for CBM extraction using hydrofracturing by orthogonal experimental process

2020 ◽  
Vol 17 (3) ◽  
pp. 493-505 ◽  
Author(s):  
Haoze Li ◽  
Bingxiang Huang ◽  
Qingying Cheng ◽  
Xinglong Zhao
Keyword(s):  
Particle Size ◽  
Orthogonal Test ◽  
Coal Mass ◽  
Tensile Fracture ◽  
Experimental Conditions ◽  
Embedded Value ◽  
Fracture Area ◽  
Creep Time ◽  
Experimental Process ◽  
The Impact

Abstract Proppant placement concentration, particle size and creep time are important factors that affect the embedment of proppant into coal. Based on multistage creep, an orthogonal test is conducted, and an optimal proppant scheme for different closure stresses obtained. The results show that with increased proppant placement concentration, the number of coal fractures increases and the elastic modulus of the fracture area decreases. As the proppant particle size decreases, the plasticity of fracture-proppant assemblies increases gradually. The yield limit is highest when the particle size is 20/40 mesh. During the proppant embedding process, localization or uneven distribution of proppant results in tensile stress parallel to the fracture surface, which induces tensile fracture in the coal. In the fracture-proppant assembly areas, proppant fractures are severe and yield lines appear. As proppant concentration increases, more energy is accumulated during the proppant compaction stage, resulting in energy release producing craters and crevasses. The energy released also causes increased stress in the proppant-coal contact area and fracturing to the coal mass. The longer the creep time, the weaker the impact and the smaller is fluctuation. Moreover, we find that the orthogonal test can effectively analyze the importance of each parameter. Proppant placement concentration was found to have the highest influence on the process of proppant embedding into coal, followed by particle size and then time. Under experimental conditions, the lowest proppant-embedded value in coal samples was observed with proppant placement concentration of 2 kg m−2 and particle size of 20/40 mesh.

scholarly journals The use of mice in diabetes research: the impact of experimental protocols

2021 ◽  
Author(s):  
M.R. Kennard ◽  
L.F. Daniels Gatward ◽  
A. Roberts ◽  
E. White ◽  
M. Nandi ◽  
...  
Keyword(s):  
Diabetes Research ◽  
Experimental Protocols ◽  
The Impact

scholarly journals Treatment Tone Spacing and Acute Effects of Acoustic Coordinated Reset Stimulation in Tinnitus Patients

2021 ◽  
Vol 1 ◽  
Author(s):  
Tina Munjal ◽  
Alexander N. Silchenko ◽  
Kristina J. Pfeifer ◽  
Summer S. Han ◽  
Jessica K. Yankulova ◽  
...  
Keyword(s):  
Animal Studies ◽  
Symptomatic Improvement ◽  
Center Frequency ◽  
Acute Effects ◽  
Stimulus Amplitude ◽  
Neuronal Populations ◽  
Experimental Protocols ◽  
Relationship Of ◽  
The Impact ◽  
Coordinated Reset

Acoustic coordinated reset (aCR) therapy for tinnitus aims to desynchronize neuronal populations in the auditory cortex that exhibit pathologically increased coincident firing. The original therapeutic paradigm involves fixed spacing of four low-intensity tones centered around the frequency of a tone matching the tinnitus pitch, fT, but it is unknown whether these tones are optimally spaced for induction of desynchronization. Computational and animal studies suggest that stimulus amplitude, and relatedly, spatial stimulation profiles, of coordinated reset pulses can have a major impact on the degree of desynchronization achievable. In this study, we transform the tone spacing of aCR into a scale that takes into account the frequency selectivity of the auditory system at each therapeutic tone’s center frequency via a measure called the gap index. Higher gap indices are indicative of more loosely spaced aCR tones. The gap index was found to be a significant predictor of symptomatic improvement, with larger gap indices, i.e., more loosely spaced aCR tones, resulting in reduction of tinnitus loudness and annoyance scores in the acute stimulation setting. A notable limitation of this study is the intimate relationship of hearing impairment with the gap index. Particularly, the shape of the audiogram in the vicinity of the tinnitus frequency can have a major impact on tone spacing. However, based on our findings we suggest hypotheses-based experimental protocols that may help to disentangle the impact of hearing loss and tone spacing on clinical outcome, to assess the electrophysiologic correlates of clinical improvement, and to elucidate the effects following chronic rather than acute stimulation.

Integral Potential Effectiveness of Organizational and Technological and Managerial Decisions of Building Object

2014 ◽  
Vol 584-586 ◽  
pp. 2230-2232 ◽  
Author(s):  
Lapidus Azariy
Keyword(s):  
Systems Engineering ◽  
Integral Approach ◽  
Engineering Construction ◽  
Managerial Decisions ◽  
Technological Potential ◽  
Significant Difference ◽  
Project Life Cycle ◽  
Project Life ◽  
The Impact ◽  
Functional Purpose

<p class="p0">Investment and construction project from the perspective of systems engineering and using existing terminology systems engineering construction, formed from the studied model of organizational and technological modules ( OTM ) - potentials , representing a collection of process groups , united by a common organizational approach, process sequence , functional purpose , as well as other organizational, technological and managerial factors . The impact of these factors on the final figure will be provided throughout the project life cycle. The assessment of this impact - a key link in the task of monitoring the desired end point of the object construction - its security and comfort of life of people. Call this integral component of organizational and technological potential of the object. Significant difference from the building techniques used in the evaluation of the final index integral approach to the factors shaping it. To study the model of integral organizational and technological capabilities are introduced the following notation : PI - integral (integral) capacity (potential), represents a generic parameter that characterizes the achievement of the required endpoints construction.</p>

Appropriation Infrastructure

2012 ◽  
pp. 254-278 ◽  
Author(s):  
Gunnar Stevens ◽  
Volkmar Pipek ◽  
Volker Wulf
Keyword(s):  
Social Construction ◽  
Design Process ◽  
End User ◽  
Communication Infrastructure ◽  
Software Application ◽  
Empirical Results ◽  
Software Applications ◽  
The Social ◽  
The Impact ◽  
Technological Flexibility

End User Development offers technological flexibility to encourage the appropriation of software applications within specific contexts of use. Appropriation needs to be understood as a phenomenon of many collaborative and creative activities. To support appropriation, we propose integrating communication infrastructure into software application that follows an“easy-to-collaborate”-principle. Such an appropriation infrastructure stimulates the experience sharing among a heterogeneous product community and supports the situated development of usages. Taking the case of the BSCWeasel groupware, we demonstrate how an appropriation infrastructure can be realized. Empirical results from the BSCWeasel project demonstrate the impact of such an infrastructure on the appropriation and design process. Based on these results, we argue that the social construction of IT artifacts should be tightly integrated in the material construction of IT artifacts in bridging design and use discourses.

Lactate delivery (not oxygen) limits hepatic gluconeogenesis when blood flow is reduced

2006 ◽  
Vol 290 (1) ◽  
pp. E192-E198 ◽  
Author(s):  
Ken D. Sumida ◽  
Jerry H. Urdiales ◽  
Casey M. Donovan
Keyword(s):  
Blood Flow ◽  
Flow Rate ◽  
Oxygen Delivery ◽  
Liver Perfusion ◽  
Lactate Concentration ◽  
Oxygen Availability ◽  
Limiting Factor ◽  
Hepatic Gluconeogenesis ◽  
Experimental Protocols ◽  
The Impact

The purpose of this study was to determine, using the isolated liver perfusion technique, whether the limiting factor for hepatic gluconeogenesis (GNG) from lactate was precursor delivery or oxygen availability during reduced flow rates of 0.85 or 0.60 ml·min−1·g liver−1. After a 24-h fast, three different experimental protocols were employed. Protocol 1 examined the impact on GNG when reservoir lactate concentration was maintained but oxygen delivery was elevated via increases in hematocrit (Hct). Elevating the Hct from 22.5 ± 0.8% to 30.9 ± 0.4% at a blood flow of 0.89 ± 0.01 ml·min−1·g liver−1 increased the oxygen consumption (V̇o2) but did not augment GNG. Similarly, when the Hct was elevated from 22.5 ± 0.8% to 41.5 ± 0.7% at 0.59 ± 0.04 ml·min−1·g liver−1, V̇o2 was increased, but GNG was unaffected. Protocol 2 examined the impact on GNG when Hct was maintained but precursor delivery was elevated via increases in reservoir lactate concentration ([LA]). Specifically, elevating the [LA] from 2.31 ± 0.07 to 3.61 ± 0.33 mM at a flow rate of 0.82 ± 0.04 ml·min−1·g liver−1 significantly increased GNG. Similarly, elevating the [LA] from 2.31 ± 0.07 to 4.24 ± 0.37 mM at a flow rate of 0.58 ± 0.02 ml·min−1·g liver−1 increased GNG. Finally, we examined the impact of increasing both the oxygen and lactate delivery ( Protocol 3). Again, V̇o2 was elevated with increased oxygen delivery, but GNG was not augmented beyond that observed with elevations in lactate delivery alone, i.e., Protocol 2. The results indicate that, during decrements in blood flow, GNG is limited primarily by precursor delivery, not oxygen availability.

A discussion on deformation of solids by the impact of liquids, and its relation to rain damage in aircraft and missiles, to blade erosion in steam turbines, and to cavitation erosion - The collapse of cavitation bubbles and the pressures thereby produced against solid boundaries

1966 ◽  
Vol 260 (1110) ◽  
pp. 221-240 ◽  
Keyword(s):  
Cavitation Erosion ◽  
Experimental Information ◽  
Liquid Jets ◽  
Steam Turbines ◽  
Jet Formation ◽  
Cavitation Damage ◽  
Cavity Collapse ◽  
New Ideas ◽  
The Impact ◽  
Shape Changes

Our object is to present a broad review of this subject as a branch of hydrodynamics, referring both to the well known ‘implosion’ mechanism first analysed by Lord Rayleigh and, more particularly, to the recently perceived possibility that effects of equally great violence, such as to damage solid boundaries, may arise through the impact of liquid jets formed by collapsing cavities. In §2 a few practical facts about cavitation damage are recalled by way of background, and then in §3 the significance of available theoretical and experimental information about cavity collapse is discussed. The main exposition of new ideas is in §4, which is a review of the factors contributing to shape changes and eventual jet formation by collapsing cavities. Finally, in §5, some new experimental observations on the unsymmetrical collapse of vapour-filled cavities are presented.

scholarly journals Changes in Physiological and Pathological Behaviours Produced by Deep Microelectrode Implantation Surgery in Rats: A Temporal Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Gustavo A. Chiprés-Tinajero ◽  
Miguel A. Núñez-Ochoa ◽  
Laura Medina-Ceja
Keyword(s):  
Animal Models ◽  
Neurological Diseases ◽  
Behavioural Change ◽  
Temporal Analysis ◽  
Exploratory Activity ◽  
Male Wistar Rats ◽  
Experimental Protocols ◽  
Convulsive Seizures ◽  
The Impact ◽  
Mean Time

Physiological behaviours such as the sleep-wake cycle and exploratory behaviours are important parameters in intact and sham-operated animals and are usually thought to be unaffected by experimental protocols in which neurosurgery is performed. However, there is insufficient evidence in the literature on the behavioural and cognitive effects observed after deep microelectrode implantation surgery in animal models of neurological diseases. Similarly, in studies that utilize animal models of neurological diseases, the impact of surgery on the pathological phenomena being studied is often minimized. Based on these considerations, we performed a temporal analysis of the effects of deep microelectrode implantation surgery in the hippocampus of rats on quiet wakefulness, sleep, and exploratory activity and the pathological behaviours such as convulsive seizures according to the Racine scale. Male Wistar rats (210-300 g) were used and grouped in sham and epileptic animals. Single doses of pilocarpine hydrochloride (2.4 mg/2 μl; i.c.v.) were administered to the animals to generate spontaneous and recurrent seizures. Deep microelectrode implantation surgeries in both groups and analysis of Fast ripples were performed. Physiological and pathological behaviours were recorded through direct video monitoring of animals (24/7). Our principal findings showed that in epileptic animals, one of the main behaviours affected by surgery is sleep; as a consequence of this behavioural change, a decrease in exploratory activity was also found as well as the mean time spent daily in seizures of scale 4 and the number of seizure events of scales 4 and 5 was increased after surgery. No significant correlations between the occurrence of FR and seizure events of scale 4 (rho 0.63, p value 0.25) or 5 (rho -0.7, p value 0.18) were observed. In conclusion, microelectrode implantation surgeries modified some physiological and pathological behaviours; therefore, it is important to consider this fact when it is working with animal models.

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