Bottom-up Reconstruction Research Articles

Is there an ‘Italian’ school of Spinoza studies? Some present and future perspectives

This paper sketches a bottom-up reconstruction of the panorama of Italian Spinoza studies over the past three decades. It tries to capture the self-representation of the Italian scholarly community starting from the analysis of collective volumes, and then exploring the results of a survey among the members of the newly established Italian Societas Spinozana, complemented by individual interviews with leading Spinoza scholars. What emerges is a past heritage centered on historical and philological research, but also deeply interested in political themes and in bringing Spinoza into dialogue with contemporary issues. Today, Spinoza studies in Italy seem to be in a transitional phase, in which a solid bridge must be built between older and younger generations of scholars, negotiating how to handle the heritage of the former and orienting the new perspectives of the latter.

Methodological issues in Rma etymology

Abstract This paper examines the state-of-the-art for the historical study of the Rma (Qiang) language (< Trans-Himalayan/Sino-Tibetan) and points out some methodological issues in earlier work. The paper discusses how vowel correspondences have been obfuscated by loanwords, onomatopoeic forms, and analogical levelling. It also discusses the analysis of compound forms and points out how certain compound forms have been incorrectly etymologized. It deals with broader, more fundamental issues in prior work such as top-down rather than bottom-up reconstructions, and problematic conceptualizations of what constitutes reconstructions. The article offers potential solutions to the issues discussed and points out where future work would be most profitable.

Bottom-up reconstruction and phase change over nickel–iron layered double hydroxides for boosted electrocatalytic oxygen evolution reaction

To improve electrochemical water splitting, it is essential to develop efficient electrocatalysts. While the incorporation of sulfur atom (S) into nickel–iron electrocatalysts has demonstrated a critical role in boosting oxygen evolution reaction (OER), the detailed mechanism remains ambiguous and elusive. In this study, bottom-up monitoring is employed to deeply investigate the role of sulfur atoms in the OER performance. To achieve this, the nickel–iron oxyhydroxide, after a two-step sulfurization and electrochemical activation process, was converted to activated nickel–iron oxyhydroxide. It was found that the metal–sulfur bond in the new intermediate NiSO4·xH2O underwent reconstruction and phase changes along with enhanced crystallinity, resulting in the appearance of a new metal–oxygen active site. After the reconstruction step, the major phase of the pre-catalyst consisting of Ni(OH)2/FeOOH becomes NiOOH/Fe2O3. The presence of S atoms facilitates the reconstruction of P − NiFeOxHy towards a new catalyst that only requires (242 and 273) mV overpotentials to reach a current density of (10 and 50) mA·cm−2, respectively. This shows a low Tafel slope of 39 mV·dec−1 with long-term durability. Density functional theory (DFT) calculation reveals that the ΔEads values of O* and OOH* on the NiOOH − Fe2O3 are more negative than on the Ni(OH)2–FeOOH, facilitating OER reaction on the former electrocatalyst under the practical test conditions.

Matter bounce scenario in extended symmetric teleparallel gravity

In this paper, we have shown the matter bounce scenario of the Universe in an extended symmetric teleparallel gravity, the f(Q) gravity. Motivated from the bouncing scenario and loop quantum cosmology (LQC), the form of the function f(Q) has been obtained at the backdrop of Friedmann–Lema{hat{i}}tre–Robertson Walker (FLRW) space time. Considering the background cosmology dominated by dust fluid, the e-folding parameter has been expressed, which contains the nonmetricity term. Since the slow roll criterion in the bouncing context is not valid, we used a conformal equivalence between f(Q) and scalar-tensor model to apply the bottom-up reconstruction technique in the bouncing model. The dynamics of the model has been studied through the phase space analysis, where both the stable and unstable nodes are obtained. Also, the stability analysis has been performed with the first order scalar perturbation of the Hubble parameter and matter energy density to verify the stability of the model.

The structure of dimensions of psychopathology in normative and clinical samples: Applying causal discovery to MMPI-2-RF scales to investigate clustering of psychopathology spectra and p-factors.

We applied a Bayesian Constraint-based Causal Discovery method (BCCD) to examine the hierarchical structure of the Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF) Restructured Clinical (RC) scales. Two different general psychopathology super spectra (p-factor) scales were extracted from (1) all RC scales and (2) all RC scales except the RCd (Demoralization) scale. These p-factor scales were included in separate models to investigate the structure of dimensions of psychopathology in a normative (n = 3,242) and clinical (n = 2,466) sample, as well as the combined normative/clinical sample (N = 5,708), by applying the BCCD algorithm to obtain a data-driven reconstruction of the internal hierarchical structure of the MMPI-2-RF. Research on the underlying structure of the MMPI-2-RF has clinical relevance as well as conceptual relevance in the context of the HiTOP model. Results demonstrated that the syndromes measured with the RC-scales-in presence of a p-factor-cluster into six spectra: internalizing, disinhibited-externalizing, antagonistic-externalizing, thought disorder, detachment, and somatoform. These results may support a super spectrum construct, as it was necessary for obtaining a bottom-up reconstruction of this six-spectrum structure. We found support for superiority of a broad super spectrum with additional variance over and above demoralization, as it resulted in the clearest structure (i.e., clustering of the RC scales). Furthermore, our results indicate independent support for the bifactor structure model of psychopathology.

Bottom-up reconstruction of smart textiles with hierarchical structures to assemble versatile wearable devices for multiple signals monitoring

Wearable smart textiles based on natural biocompatible materials have attracted considerable interests due to the promising use for healthcare management, human-machine interactions, and remote monitoring. However, assembling conductive yarns into smart textiles and wearable sensing devices based on silks is hardly investigated. Herein, a bottom-up and scalable strategy of constructing smart fabric from conductive yarns units is presented. Specifically, silk yarns are functionalized by customized conductive paints consisted of polyaniline (PANI) and carbon nanotubes (CNT), which selectively etches the interface of yarns without damage of their internal structures. The as-prepared sensing units not only maintain the characters of silk, PANI and CNT, with robust mechanical performances and high conductivity, but also can efficiently monitor a series of critical signals, such as strain, temperature and harmful gas. The sensing units can be sewed into fabric to integrate flexible smart textiles, and the obtained smart textiles preserve the structural integrity and detection capacity under deformations, frictions and water exposure. An integrated textile device is also shown, which consists of display and warning can serve as a health butler, demonstrating the system’s potential within the “internet of things” in various areas, including motion monitoring and smart home.

Coupled MD simulations and NMR reveal that the intrinsically disordered domain of the breast-cancer susceptibility 1 protein (BRCA1) binds head-on to DNA double-strand ends

Mutations of the breast cancer susceptibility 1 (BRCA1) gene are associated with high risks of breast and ovarian cancer, not least due to the vital role of the BRCA1 gene product in DNA double-strand repair. Strikingly, little is known about the structural dynamics of BRCA1-DNA complexes, despite their importance for maintaining a healthy cell cycle and the potential boost for rational targeting of BRCA1 by their detailed understanding. Aiming to address this shortcoming, we present a model resulting from the direct binding of the intrinsically disordered region (IDR) of BRCA1 to DNA oligomers. To this end, we developed a workflow combining in-silico structural predictions, computational docking, and molecular dynamics simulations with chemical shift perturbations in 1H-31P crosspeaks obtained by nuclear magnetic resonance spectroscopy of a binding DNA oligomer. Our data show that the BRCA1-DNA complexes are stabilized, mainly through ‘head-on’ interaction between BRCA1 and the DNA double-strand ends. ‘Side-on’ binding to the DNA major grove was insufficient to form stable complexes. When bound to the nucleic acid, the IDR maintained high degrees of flexibility in our simulations reminiscent of ‘fuzzy’ complexes. Illustrating the structural dynamics underlying BRCA1-DNA complexes is essential for the bottom-up reconstruction of the role BRCA1 plays in DNA double-strand break repair. The presented work makes a step in this direction, aiming to complement existing assays with models that can assist in the functional screening of hereditary breast and ovarian cancer (HBOC)-relevant mutations.

Bottom-up reconstruction of viable GW170817 compatible Einstein–Gauss–Bonnet theories

In this work we shall use a bottom-up approach for obtaining viable inflationary Einstein–Gauss–Bonnet models which are also compatible with the GW170817 event. Specifically, we shall use a recently developed theoretical framework in which we shall specify only the tensor-to-scalar ratio, in terms of the e-foldings number. Starting from the tensor-to-scalar ratio, we shall reconstruct from it the Einstein–Gauss–Bonnet theory which can yield such a tensor-to-scalar ratio, finding the scalar potential and the Gauss–Bonnet coupling scalar function as functions of the e-foldings number. Accordingly, the calculation of the spectral index of the primordial scalar perturbations, and of the tensor spectral index easily is greatly simplified and these observational indices can easily be found. After presenting the general formalism for the bottom-up reconstruction, we exemplify our findings by presenting several Einstein–Gauss–Bonnet models of interest which yield a viable inflationary phenomenology. These models have also an interesting common characteristic, which is a blue tilted tensor spectral index. We also investigate the predicted energy spectrum of the primordial gravitational waves for these Einstein–Gauss–Bonnet models, and as we show, all the models yield a detectable primordial wave energy power spectrum.

Learning to Predict Superquadric Parameters From Depth Images With Explicit and Implicit Supervision

Reconstruction of 3D space from visual data has always been a significant challenge in the field of computer vision. A popular approach to address this problem can be found in the form of bottom-up reconstruction techniques which try to model complex 3D scenes through a constellation of volumetric primitives. Such techniques are inspired by the current understanding of the human visual system and are, therefore, strongly related to the way humans process visual information, as suggested by recent visual neuroscience literature. While advances have been made in recent years in the area of 3D reconstruction, the problem remains challenging due to the many possible ways of representing 3D data, the ambiguity of determining the shape and general position in 3D space and the difficulty to train efficient models for the prediction of volumetric primitives. In this article, we address these challenges and present a novel solution for recovering volumetric primitives from depth images. Specifically, we focus on the recovery of superquadrics, a special type of parametric models able to describe a wide array of 3D shapes using only a few parameters. We present a new learning objective that relies on the superquadric (inside-outside) function and develop two learning strategies for training convolutional neural networks (CNN) capable of predicting superquadric parameters. The first uses explicit supervision and penalizes the difference between the predicted and reference superquadric parameters. The second strategy uses implicit supervision and penalizes differences between the input depth images and depth images rendered from the predicted parameters. CNN predictors for superquadric parameters are trained with both strategies and evaluated on a large dataset of synthetic and real-world depth images. Experimental results show that both strategies compare favourably to the existing state-of-the-art and result in high quality 3D reconstructions of the modelled scenes at a much shorter processing time.

ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.

The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype-phenotype relationships. Accordingly, genome-scale metabolic models (GEMs) can be used to predict the response of organisms to genetic and environmental variations. A bottom-up reconstruction procedure typically starts by generating a draft model from existing annotation data on a target organism. For model species, this part of the process can be straightforward, due to the abundant organism-specific biochemical data. However, the process becomes complicated for non-model less-annotated species. In this paper, we present a draft liver reconstruction, ReCodLiver0.9, of Atlantic cod (Gadus morhua), a non-model teleost fish, as a practicable guide for cases with comparably few resources. Although the reconstruction is considered a draft version, we show that it already has utility in elucidating metabolic response mechanisms to environmental toxicants by mapping gene expression data of exposure experiments to the resulting model.

Bottom-up reconstruction of non-singular bounce in F(R) gravity from observational indices

We apply the bottom-up reconstruction technique in the context of bouncing cosmology in F(R) gravity, where the starting point is a suitable ansatz of observable quantity (like spectral index or tensor to scalar ratio) rather than a priori form of Hubble parameter. In inflationary scenario, the slow roll conditions are assumed to hold true, and thus the observational indices have general expressions in terms of the slow-roll parameters, as for example the tensor to scalar ratio in F(R) inflation can be expressed as r=48ϵF2 with ϵF=−1HF2dHFdtF and HF, tF are the Hubble parameter, cosmic time respectively. However, in the bouncing cosmology (say in F(R) gravity theory), the slow-roll conditions are not satisfied, in general, and thus the observable quantities do not have any general expressions that will hold true irrespective of the form of F(R). Thus, in order to apply the bottom-up reconstruction procedure in F(R) bouncing model, we use the conformal correspondence between F(R) and scalar-tensor model where the conformal factor in the present context is chosen in a way such that it leads to an inflationary scenario in the scalar-tensor frame. Due to the reason that the scalar and tensor perturbations remain invariant under conformal transformation, the observable viability of the scalar-tensor inflationary model confirms the viability of the conformally connected F(R) bouncing model. Motivated by these arguments, here we construct a viable non-singular bounce in F(R) gravity directly from the observable indices of the corresponding scalar-tensor inflationary model.

Complexity in Biological Organization: Deconstruction (and Subsequent Restating) of Key Concepts.

The “magic” word complexity evokes a multitude of meanings that obscure its real sense. Here we try and generate a bottom-up reconstruction of the deep sense of complexity by looking at the convergence of different features shared by complex systems. We specifically focus on complexity in biology but stressing the similarities with analogous features encountered in inanimate and artefactual systems in order to track an integrative path toward a new “mainstream” of science overcoming the actual fragmentation of scientific culture.

ReConvPy: Modeling Local Field Potentials of Cerebellum Granule Neurons using Repetitive Convolutions in Python

Abstract One of the main goals in today’s computational neuroscience laboratories is the ability to construct ensemble population responses from bottom-up reconstructions that involve computationally-detailed single neuron models. As a modeler’s tool, local field potentials are population responses that abstract information from an ensemble of neurons connecting single neuron response to a circuit function. In this paper, we have developed a new implementation of reproducing the local field potentials (LFP) using the repetitive convolution technique in Python adding on to the tool set library already developed for mathematically modeling cerebellar local field potentials. The LFP tool accurately reproduces the in vitro negative N2a, N2b waves and in vivo T and C waves generated by 200 to 700 cerebellar granule neurons and replicates pharmacological changes and induced plasticity properties.

Common Law Confrontations

This symposium essay contends that the image of the common law drawn by the Supreme Court in the Confrontation Clause context is both distorted and incomplete. In particular, the Court and scholars defending originalist positions rely almost entirely on English sources in their reconstruction of the common law basis for the Confrontation Clause, thereby neglecting the diversity of American common laws from the time of the Founding, a diversity that has already been unearthed by a number of legal historians. By drawing on hitherto untapped sources to furnish a bottom-up reconstruction of how testimony was treated in local criminal courts within mid- to late-eighteenth-century New Jersey, this essay demonstrates that, in at least some jurisdictions, the originalist vision of common law did not apply. The common law cannot, therefore, furnish a univocal answer to questions about the original meaning of the Confrontation Clause.

Modeling fMRI BOLD signals and temporal mismatches in the cerebellar cortex

To understand brain activity relating neurons to circuits to learning and behavior, we explored a bottom-up computational reconstruction of population signals arising from cerebellum granular layer. As a first implementation, using bio-realistic computational models of cerebellum granule cell, in vivo spike train patterns were computed and then translated into functional Magnetic Resonance Imaging, Blood Oxygen-Level Dependent (BOLD) signals. The BOLD response was generated from averaged activity arising from center-surround organization modeled by using excitatory-inhibitory ratios related to experimental data. The averaged responses were converted to BOLD signals using the balloon and modified Windkessel models. Although both models generated BOLD responses corresponding to neural activity, the temporal mismatch was attributed to the response by the delayed compliance parameter in the Windkessel model. The modeling suggests that experimental variability observed in the cerebellar micro-zones could be related to compliance chances, activation patterns and number of neurons. Although detailed neuro-vasculature information was not modeled, the advantage in this methodology is that cerebellar cortex may allow seemingly linear transformations of underlying spiking that could be then used to validate network reconstructions.

Proto-Ong-Be Initials and Finals

This study is the first to provide a bottom-up reconstruction of Proto-Ong-Be initials and finals using the comparative method. Thirty-four initials (labelled with tone series) and nine finals that can be reconstructed with confidence are postulated. This paper shows that the early voicing contrast associated with initials cannot be directly reconstructed based on the internal evidence, although the loss of the contrast is compensated for at the suprasegmental level. This study also demonstrates that Proto-Ong-Be finals remain intact in modern Ong-Be varieties. In addition, this paper serves as a testing ground and a demonstration for doing linguistic reconstruction from different angles.

Viable inflation in scalar-Gauss-Bonnet gravity and reconstruction from observational indices

In this paper the focus is on inflationary dynamics in the context of Einstein Gauss-Bonnet gravitational theories. We investigate the implications of the slow-roll condition on the slow-roll indices and we investigate how the inflationary dynamical evolution is affected by the presence of the Gauss-Bonnet coupling to the scalar field. For exemplification of our analysis we investigate how the dynamics of inflationary cubic, quartic order and also exponential scalar potentials are affected by the non-trivial Gauss-Bonnet coupling to the scalar field. As we demonstrate it is possible to obtain a viable phenomenology compatible with the observational data, although the canonical scalar field theory with cubic and quartic order potentials does not yield phenomenologically acceptable results. In addition, with regard to the exponential potential example, the Einstein Gauss-Bonnet extension of the single canonical scalar field model has an inherent mechanism that can trigger the graceful exit from inflation. Furthermore we introduce a bottom-up reconstruction technique, in the context of which by fixing the tensor-to-scalar ratio and the Hubble rate as a function of the $e$-foldings number, one is capable of reproducing the Einstein Gauss-Bonnet theory which generates the aforementioned quantities. We illustrate how the method works by using some relatively simple examples.

Viable inflationary evolution from Einstein frame loop quantum cosmology

In this work we construct a bottom-up reconstruction technique for Loop Quantum Cosmology scalar-tensor theories, from the observational indices. Particularly, the reconstruction technique is based on fixing the functional form of the scalar-to-tensor ratio as a function of the $e$-foldings number. The aim of the technique is to realize viable inflationary scenarios, and the only assumption that must hold true in order for the reconstruction technique to work is that the dynamical evolution of the scalar field obeys the slow-roll conditions. We shall use two functional forms for the scalar-to-tensor ratio, one of which corresponds to a popular inflationary class of models, the $\alpha$-attractors. For the latter, we shall calculate the leading order behavior of the spectral index and we shall demonstrate that the resulting inflationary theory is viable and compatible with the latest Planck and BICEP2/Keck-Array data. In addition, we shall find the classical limit of the theory, and as we demonstrate, the Loop Quantum Cosmology corrected theory and the classical theory are identical at leading order in the perturbative expansion quantified by the parameter $\rho_c$, which is the critical density of the quantum theory. Finally, by using the formalism of slow-roll scalar-tensor Loop Quantum Cosmology, we shall investigate how several inflationary potentials can be realized by the quantum theory, and we shall calculate directly the slow-roll indices and the corresponding observational indices. In addition, the $f(R)$ gravity frame picture is presented.

Attractor cosmology from nonminimally coupled gravity

By using a bottom-up reconstruction technique for non-minimally coupled scalar-tensor theories, we realize the Einstein frame attractor cosmologies in the $\Omega (\phi)$-Jordan frame. For our approach, what is needed for the reconstruction method to work is the functional form of the non-minimal coupling $\Omega(\phi)$ and of the scalar-to-tensor ratio, and also the assumption of the slow-roll inflation in the $\Omega (\phi)$-Jordan frame. By appropriately choosing the scalar-to-tensor ratio, we demonstrate that the observational indices of the attractor cosmologies can be realized directly in the $\Omega (\phi)$-Jordan frame. We investigate the special conditions that are required to hold true in for this realization to occur, and we provide the analytic form of the potential in the $\Omega (\phi)$-Jordan frame. Also, by performing a conformal transformation, we find the corresponding Einstein frame canonical scalar-tensor theory, and we calculate in detail the corresponding observational indices. The result indicates that although the spectral index of the primordial curvature perturbations is the same in the Jordan and Einstein frames, at leading order in the $e$-foldings number, the scalar-to-tensor ratio differs. We discuss the possible reasons behind this discrepancy, and we argue that the difference is due to some approximation we performed to the functional form of the potential in the Einstein frame, in order to obtain analytical results, and also due to the difference in the definition of the $e$-foldings number in the two frames, which is also pointed out in the related literature. Finally, we find the $F(R)$ gravity corresponding to the Einstein frame canonical scalar-tensor theory.

The reconstruction of f(ϕ)R and mimetic gravity from viable slow-roll inflation

In this work, we extend the bottom-up reconstruction framework of F(R) gravity to other modified gravities, and in particular for f(ϕ)R and mimetic F(R) gravities. We investigate which are the important conditions in order for the method to work, and we study several viable cosmological evolutions, focusing on the inflationary era. Particularly, for the f(ϕ)R theory case, we specify the functional form of the Hubble rate and of the scalar-to-tensor ratio as a function of the e-foldings number and accordingly, the rest of the physical quantities and also the slow-roll and the corresponding observational indices can be calculated. The same method is applied in the mimetic F(R) gravity case, and in both cases we thoroughly analyze the resulting free parameter space, in order to show that the viability of the models presented is guaranteed and secondly that there is a wide range of values of the free parameters for which the viability of the models occurs. In addition, the reconstruction method is also studied in the context of mimetic F(R)=R gravity. As we demonstrate, the resulting theory is viable, and also in this case, only the scalar-to-tensor ratio needs to be specified, since the rest follow from this condition. Finally, we discuss in brief how the reconstruction method could function for other modified gravities.