scholarly journals PyInteraph2 and PyInKnife2 to analyze networks in protein structural ensembles

2020 ◽  
Author(s):  
Valentina Sora ◽  
Matteo Tiberti ◽  
Shahriyar Mahdi Robbani ◽  
Joshua Rubin ◽  
Elena Papaleo
Keyword(s):  
Network Models ◽  
Version Control ◽  
Complex Nature ◽  
Cellular Functions ◽  
Diverse Range ◽  
Link Type ◽  
Network Properties ◽  
Protein Ensembles ◽  
The Stability ◽  
Definition Of

AbstractMotivationProtein dynamic is essential for cellular functions. Due to the complex nature of non-covalent interactions and their long-range effects, the analysis of protein conformations using network theory can be enlightening. Protein Structure Networks (PSNs) rely on different philosophies, and the currently available tools suffer from limitations in terms of input formats, supported network models, and version control. Another issue is the precise definition of cutoffs for the network calculations and the assessment of the stability of the parameters, which ultimately affect the outcome of the analyses.ResultsWe provide two open-source software packages, i.e., PyInteraph2 and PyInKnife2, to implement and analyze PSNs in a harmonized, reproducible, and documented manner. PyInteraph2 interfaces with multiple formats for protein ensembles and calculates a diverse range of network models with the possibility to integrate them into a macro-network and perform further downstream graph analyses. PyInKnife2 is a standalone package that supports the network models implemented in PyInteraph2. It employs a jackknife resampling approach to estimate the convergence of network properties and streamline the selection of distance cutoffs. Several functionalities are based on MDAnalysis and NetworkX, including parallelization, and are available for Python 3.7. PyInteraph2 underwent a massive restructuring in terms of setup, installation, and test support compared to the original PyInteraph software.ConclusionsWe foresee that the modular structure of the code and the version control system of GitHub will promote the transition to a community-driven effort, boost reproducibility, and establish harmonized protocols in the PSN field. As developers, we will guarantee the introduction of new functionalities, assistance, training of new contributors, and maintenance of the package.AvailabilityThe packages are available at https://github.com/ELELAB/pyinteraph2 and https://github.com/ELELAB/PyInKnife2 with guides provided within the packages.

Postmodern More

Moreana ◽  
2003 ◽  
Vol 40 (Number 153- (1-2) ◽  
pp. 219-239
Author(s):  
Anne Lake Prescott
Keyword(s):  
Human Language ◽  
Thomas More ◽  
The Stability ◽  
Definition Of ◽  
Recent Critic

Thomas More is often called a “humanist,” and rightly so if the word has its usual meaning in scholarship on the Renaissance. “Humanist” has by now acquired so many different and contradictory meanings, however, that it needs to be applied carefully to the likes of More. Many postmodernists tend to use the word, pejoratively, to mean someone who believes in an autonomous self, the stability of words, reason, and the possibility of determinable meanings. Without quite arguing that More was a postmodernist avant la lettre, this essay suggests that he was not a “humanist” who stalks the pages of much recent postmodernist theory and that in fact even while remaining a devout Catholic and sensible lawyer he was quite as aware as any recent critic of the slipperiness of human selves and human language. It is time that literary critics tightened up their definition of “humanist,” especially when writing about the Renaissance.

Fiduciary Principles in Investment Advice

2019 ◽  
pp. 144-165
Author(s):  
Arthur B. Laby
Keyword(s):  
Fiduciary Duty ◽  
Duty Of Care ◽  
Complex Nature ◽  
State Law ◽  
Fiduciary Duties ◽  
Legal Obligations ◽  
Standards Of Conduct ◽  
Investment Advisers ◽  
Definition Of ◽  
Investment Advice

This chapter examines the fiduciary principles governing investment advice. Fiduciary principles in investment advice are both straightforward and complex. They are straightforward because most investment advisers are considered fiduciaries and subject to strict fiduciary duties under federal and state law. Their complex nature arises from the fact that many individuals and firms provide investment advice but are not deemed investment advisers and, therefore, are not subject to a fiduciary obligation. This chapter first explains whether and when an advisory relationship gives rise to fiduciary duties by focusing on both federal and state law, as well as the individuals and firms that typically provide investment advice. In particular, it looks at certain persons and entities excluded from the definition of investment adviser and thus not subject to the Investment Advisers Act of 1940, namely broker-dealers, banks, and family offices as well as accountants, lawyers, teachers, and engineers. The chapter also considers fiduciaries under ERISA, the Investment Company Act, and the Commodity Exchange Act before discussing the fiduciary duty of loyalty and how it is expressed and applied in investment advisory relationships; the fiduciary duty of care and how it differs from other standards of conduct, such as a duty of suitability; and other legal obligations imposed on investment advisers and how those obligations relate to an adviser’s fiduciary duty. Finally, the mandatory or default terms with regard to an investment adviser’s fiduciary duties are explored, along with remedies available for breach of fiduciary duty.

scholarly journals Influence of study model, baseline catalytic concentrations and analytical system on the stability of serum alanine aminotransferase

2020 ◽  
Vol 1 (2) ◽  
Author(s):  
Josep Miquel Bauça ◽  
Andrea Caballero ◽  
Carolina Gómez ◽  
Débora Martínez-Espartosa ◽  
Isabel García del Pino ◽  
...  
Keyword(s):  
Alanine Aminotransferase ◽  
Experimental Models ◽  
Individual Variability ◽  
Serum Samples ◽  
Multicentric Study ◽  
Different Temperatures ◽  
The Stability ◽  
Analytical System ◽  
Definition Of ◽  
Analytical Platforms

AbstractObjectivesThe stability of the analytes most commonly used in routine clinical practice has been the subject of intensive research, with varying and even conflicting results. Such is the case of alanine aminotransferase (ALT). The purpose of this study was to determine the stability of serum ALT according to different variables.MethodsA multicentric study was conducted in eight laboratories using serum samples with known initial catalytic concentrations of ALT within four different ranges, namely: <50 U/L (<0.83 μkat/L), 50–200 U/L (0.83–3.33 μkat/L), 200–400 U/L (3.33–6.67 μkat/L) and >400 U/L (>6.67 μkat/L). Samples were stored for seven days at two different temperatures using four experimental models and four laboratory analytical platforms. The respective stability equations were calculated by linear regression. A multivariate model was used to assess the influence of different variables.ResultsCatalytic concentrations of ALT decreased gradually over time. Temperature (−4%/day at room temperature vs. −1%/day under refrigeration) and the analytical platform had a significant impact, with Architect (Abbott) showing the greatest instability. Initial catalytic concentrations of ALT only had a slight impact on stability, whereas the experimental model had no impact at all.ConclusionsThe constant decrease in serum ALT is reduced when refrigerated. Scarcely studied variables were found to have a significant impact on ALT stability. This observation, added to a considerable inter-individual variability, makes larger studies necessary for the definition of stability equations.

scholarly journals Reliable Learning with PDE-Based CNNs and DenseNets for Detecting COVID-19, Pneumonia, and Tuberculosis from Chest X-Ray Images

Mathematics ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 434
Author(s):  
Anca Nicoleta Marginean ◽  
Delia Doris Muntean ◽  
George Adrian Muntean ◽  
Adelina Priscu ◽  
Adrian Groza ◽  
...  
Keyword(s):  
Transfer Learning ◽  
Negative Impact ◽  
X Ray ◽  
Domain Specific ◽  
Direct Training ◽  
Public Data ◽  
Normal Chest ◽  
Chest X Ray ◽  
The Stability ◽  
Definition Of

It has recently been shown that the interpretation by partial differential equations (PDEs) of a class of convolutional neural networks (CNNs) supports definition of architectures such as parabolic and hyperbolic networks. These networks have provable properties regarding the stability against the perturbations of the input features. Aiming for robustness, we tackle the problem of detecting changes in chest X-ray images that may be suggestive of COVID-19 with parabolic and hyperbolic CNNs and with domain-specific transfer learning. To this end, we compile public data on patients diagnosed with COVID-19, pneumonia, and tuberculosis, along with normal chest X-ray images. The negative impact of the small number of COVID-19 images is reduced by applying transfer learning in several ways. For the parabolic and hyperbolic networks, we pretrain the networks on normal and pneumonia images and further use the obtained weights as the initializers for the networks to discriminate between COVID-19, pneumonia, tuberculosis, and normal aspects. For DenseNets, we apply transfer learning twice. First, the ImageNet pretrained weights are used to train on the CheXpert dataset, which includes 14 common radiological observations (e.g., lung opacity, cardiomegaly, fracture, support devices). Then, the weights are used to initialize the network which detects COVID-19 and the three other classes. The resulting networks are compared in terms of how well they adapt to the small number of COVID-19 images. According to our quantitative and qualitative analysis, the resulting networks are more reliable compared to those obtained by direct training on the targeted dataset.

scholarly journals Mutualistic strategies minimize coextinction in plant–disperser networks

2017 ◽  
Vol 284 (1854) ◽  
pp. 20162302 ◽  
Author(s):  
Evan C. Fricke ◽  
Joshua J. Tewksbury ◽  
Elizabeth M. Wandrag ◽  
Haldre S. Rogers
Keyword(s):  
Network Structure ◽  
Field Experiments ◽  
Empirical Relationship ◽  
Network Models ◽  
Mutualistic Interactions ◽  
Simulated Network ◽  
Direct And Indirect Impacts ◽  
Indirect Impacts ◽  
The Stability ◽  
Seed Dispersal Mutualism

The global decline of mutualists such as pollinators and seed dispersers may cause negative direct and indirect impacts on biodiversity. Mutualistic network models used to understand the stability of mutualistic systems indicate that species with low partner diversity are most vulnerable to coextinction following mutualism disruption. However, existing models have not considered how species vary in their dependence on mutualistic interactions for reproduction or survival, overlooking the potential influence of this variation on species' coextinction vulnerability and on network stability. Using global databases and field experiments focused on the seed dispersal mutualism, we found that plants and animals that depend heavily on mutualistic interactions have higher partner diversity. Under simulated network disruption, this empirical relationship strongly reduced coextinction because the species most likely to lose mutualists depend least on their mutualists. The pattern also reduced the importance of network structure for stability; nested network structure had little effect on coextinction after simulations incorporated the empirically derived relationship between partner diversity and mutualistic dependence. Our results highlight a previously unknown source of stability in mutualistic networks and suggest that differences among species in their mutualistic strategy, rather than network structure, primarily accounts for stability in mutualistic communities.

Measurement of Angular Acceleration of a Rigid Body Using Linear Accelerometers

1975 ◽  
Vol 42 (3) ◽  
pp. 552-556 ◽  
Author(s):  
A. J. Padgaonkar ◽  
K. W. Krieger ◽  
A. I. King
Keyword(s):  
Experimental Data ◽  
Rigid Body ◽  
Simple Procedure ◽  
Three Dimensional ◽  
Angular Acceleration ◽  
Theory And Practice ◽  
Body Segments ◽  
Impact Biomechanics ◽  
The Stability ◽  
Definition Of

The computation of angular acceleration of a rigid body from measured linear accelerations is a simple procedure, based on well-known kinematic principles. It can be shown that, in theory, a minimum of six linear accelerometers are required for a complete definition of the kinematics of a rigid body. However, recent attempts in impact biomechanics to determine general three-dimensional motion of body segments were unsuccessful when only six accelerometers were used. This paper demonstrates the cause for this inconsistency between theory and practice and specifies the conditions under which the method fails. In addition, an alternate method based on a special nine-accelerometer configuration is proposed. The stability and superiority of this approach are shown by the use of hypothetical as well as experimental data.

scholarly journals ‘A transverse scar on the neck’ – psychosomatic approach in the differential diagnosis and surgical treatment of hyperthyroidism in post-war Finland

2021 ◽  
Vol 65 (2) ◽  
pp. 140-156
Author(s):  
Eve-Riina Hyrkäs
Keyword(s):  
Surgical Treatment ◽  
Psychiatric Patients ◽  
Differential Diagnostics ◽  
Historical Study ◽  
Complex Nature ◽  
Surgical Interventions ◽  
Somatic Illness ◽  
Post War ◽  
Definition Of ◽  
The Mind

AbstractIn the Finnish medical discussion during the middle decades of the twentieth century, the challenging differential diagnostics between hyperthyroidism and various neuroses was perceived to yield a risk of unnecessary surgical interventions of psychiatric patients. In 1963, the Finnish surgeon Erkki Saarenmaa claimed that ‘the most significant mark of a neurotic was a transverse scar on the neck’, a result of an unnecessary thyroid surgery. The utterance was connected to the complex nature of thyroid diseases, which seemed to be to ‘a great extent psychosomatic’. Setting forth from this statement, the article aims to decipher the connection between hyperthyroidism, unnecessary surgical treatment and the psychosomatic approach in Finnish medicine. Utilising a wide variety of published medical research and discussion in specialist journals, the article examines the theoretical debate around troublesome diagnostics of functional complaints. It focuses on the introduction of new medical ideas, namely the concepts of ‘psychosomatics’ and ‘stress’. In the process, the article aims to unveil a definition of psychosomatic illness that places it on a continuum between psychological and somatic illness. That psychosomatic approach creates a space with interpretative potential can be applied to the historiography of psychosomatic phenomena more generally. Further inquiry into the intersections of surgery and psychosomatics would enrich both historiographies. It is also argued that the historical study of psychosomatic syndromes may become skewed, if the term ‘psychosomatic’ is from the outset taken to signify something that is all in the mind.

scholarly journals Multi-model inference of network properties from incomplete data

2006 ◽  
Vol 3 (2) ◽  
pp. 123-136 ◽  
Author(s):  
Michael P. H. Stumpf ◽  
Thomas Thorne
Keyword(s):  
Network Models ◽  
Network Data ◽  
Global Networks ◽  
New Approach ◽  
Model Inference ◽  
Novel Approach ◽  
Eukaryotic Species ◽  
Network Properties ◽  
Experimental Approaches ◽  
Saccaromyces Cerevisiae

Summary It has previously been shown that subnets differ from global networks from which they are sampled for all but a very limited number of theoretical network models. These differences are of qualitative as well as quantitative nature, and the properties of subnets may be very different from the corresponding properties in the true, unobserved network. Here we propose a novel approach which allows us to infer aspects of the true network from incomplete network data in a multi-model inference framework. We develop the basic theoretical framework, including procedures for assessing confidence intervals of our estimates and evaluate the performance of this approach in simulation studies and against subnets drawn from the presently available PIN network data in Saccaromyces cerevisiae. We then illustrate the potential power of this new approach by estimating the number of interactions that will be detectable with present experimental approaches in sfour eukaryotic species, inlcuding humans. Encouragingly, where independent datasets are available we obtain consistent estimates from different partial protein interaction networks. We conclude with a discussion of the scope of this approaches and areas for further research

Stability Considerations in Downward Miscible Displacements

1964 ◽  
Vol 4 (04) ◽  
pp. 356-362 ◽  
Author(s):  
J.M. Dumore
Keyword(s):  
Transition Zone ◽  
Viscous Fingering ◽  
Favorable Effect ◽  
Homogeneous Layer ◽  
Oil Viscosity ◽  
Critical Rate ◽  
Miscible Displacements ◽  
Viscous Fingers ◽  
The Stability ◽  
Definition Of

Abstract If, in a vertical, downward miscible displacement, the transition zone between the displacing and displaced fluids is neglected, a criterion for stable displacement can be obtained by considering a small hypothetical protrusion of one of the fluids into the other. This criterion leads to the definition of the well-known critical rate, uc = kg ??/?µ. The consideration is further extended by taking into account the transition zone that develops as a result of diffusion and mixing. A generalization of the previous criterion leads to the definition of another characteristic rate, the stable rate, which in actual miscible drives will be less than the critical rate. In such drives, the entire transition zone is stable at rates less than the stable rate. At rates between the stable and critical rates, the displacement is only partly stable, i.e. part of the transition zone adjacent to the displaced fluid is in an unstable position. From that part of the transition zone viscous fingers will develop. At rates greater than the critical rate the entire displacement is unstable and viscous fingers will develop more strongly. Results of laboratory experiments are in agreement with the expected behavior based on the theoretically deduced stability of the displacement. INTRODUCTION The simplest form of miscible drive in an oil-bearing formation is the injection of a fluid that is completely miscible* with the oil under reservoir conditions. In general, such a fluid, a solvent for example, is less dense and less viscous than the oil present in the formation. If it is injected into a horizontal homogeneous layer, gravitational forces will lead to the formation of a gravity tongue of solvent in the upper part of the layer and the adverse solvent-oil viscosity ratio will cause viscous fingers to develop. If, however, the solvent is injected up-structure into a dipping layer, gravity has a favorable effect, because it tends to keep the less dense solvent up-structure. Tongue formation and viscous fingering are consequently reduced and it is even possible that they will be suppressed completely. Viscous fingering and gravity tonguing are the consequences of the instability of the displacement. A stable displacement cannot result in growing viscous fingers and/or growing gravity tongues. Since large amounts of oil can be bypassed if there is viscous fingering and/or gravity tonguing, the stability of a miscible drive is very important with respect to the recovery efficiency of the drive. The stability is of particular importance in miscible-slug drives, as it determines how quickly the miscible slug between the displaced and displacing fluids will be distorted and broken up, after which the drive is no longer completely miscible. Stability is thus a most important factor in determining the success of a miscible drive, and it is considered that the aspects of stability considered in this paper will make a useful contribution to existing theories. Consideration is given only to vertical downward displacements, in which no gravity tongues can develop and which are therefore simpler than downward displacements in sloping layers.

scholarly journals Towards the determination of capabilities relevant for expert thinking

2006 ◽  
Vol 38 (1) ◽  
pp. 45-59
Author(s):  
Zora Krnjaic
Keyword(s):  
Complex Nature ◽  
Crystallized Intelligence ◽  
Domain Specific ◽  
Abstract Thought ◽  
Key Concepts ◽  
Definition Of ◽  
Systematic Education ◽  
Special Relevance ◽  
Complex Manner

The paper starts from the assumption that expert thinking is a complex manner of thinking of higher order, comprising higher mental functions and complex capabilities based on deep structures and knowledge patterns. It is a domain-determined and specialized thinking developed through systematic education. Particular aspects of ability, selected for this study, primarily concern the relation between abilities and knowledge and the relation between general and specific abilities. Particular emphasis was laid on the key concepts of the theories presented, relevant for the study of the complex nature of expert thinking. Special attention was paid to mediated intelligence and the process of systemogenesis of knowledge, Katel?s definition of crystallized intelligence, Gardener?s work on multiple intelligences in the context of knowledge and experience as well as Sternberg?s two-facet subtheory. The capability for abstract thought and the ability to select what is important as well as the domain of relevant specific capability are assumed to be of special relevance for understanding expert thinking and, as such, they were articulated and examined. Expert thinking-abstract, specialized and domain-specific, seems to be based on general and specific capabilities and their interaction.

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