Golgi staining of neurons: Oxidation-state dependent spread of chemical reaction identifies a testable property of the connectome

Camillo Golgi observed reticular nature of the nervous system by his staining method. Ramon Cajal modified this protocol to obtain staining restricted to individual neurons, in support of the cell theory. Close examination shows that Golgi used an oxidizing agent to pre-treat the brain tissue before the staining reaction and Cajal used an additional oxidizing agent for the same step. It shows that oxidation state of the tissue has a crucial role in determining the spread of Golgi chemical reaction between neurons. The correct structure-function mechanism of brain functions may reveal the nature of the route through which the staining reaction spreads between neurons under decreasing oxidation states. Present work examines the chemical reaction behind the staining, explores the role of oxidizing agents in limiting the stain to individual neurons, and discusses a probable property of the connectome that can provide a gateway for an oxidation state-dependent spread of staining reaction.

Spectra to Structure: Deep Reinforcement Learning for Molecular Inverse Problem

Spectroscopy is the study of how matter interacts with electromagnetic radiations of specific frequencies that has led to several monumental discoveries in science. The spectra of any particular molecule is highly information-rich, yet the inverse relation from the spectra to the molecular structure is still an unsolved problem. Nuclear Magnetic Resonance (NMR) spectroscopy is one such critical tool in the tool-set for scientists to characterise any chemical sample. In this work, a novel framework is proposed that attempts to solve this inverse problem by navigating the chemical space to find the correct structure that resulted in the target spectra. The proposed framework uses a combination of online Monte- Carlo-Tree-Search (MCTS) and a set of offline trained Graph Convolution Networks to build a molecule iteratively from scratch. Our method is able to predict the correct structure of the molecule ∼80% of the time in its top 3 guesses. We believe that the proposed framework is a significant step in solving the inverse design problem of NMR spectra to molecule.

Error Analysis on the Malaysian Students’ Writing for ESL Classroom

English has been regarded as one of the core subjects in the Malaysian Certificate of Education or known as the Sijil Pelajaran Malaysia (SPM). There has been a concern over the writing components in English language papers at the SPM level. Writing requires students’ competence in syntax, coherence, developing and arranging ideas, mechanics in writing and appropriate use of vocabulary. A concern over students who produce very limited number of words in their essays has resulted in the lack of content to be assessed which then led to low scores. This paper presents an error analysis focusing on the types of errors found in students’ written test scripts to identify the weaknesses of students' writing abilities. The study adopts a qualitative approach where the students’ written assessment texts were collected. A total of 18 upper secondary Year Four students (aged 16 years old) were selected as the research participants. The selection of participants was carried out in a secondary school in one of the states in Malaysia. The students’ written tests were analysed to identify the emerging categories of language use, focusing on language and grammar inaccuracies. It is found that students have the idea on how to write the answers to the task but seem to have difficulties putting the ideas in the correct structure.

Synthesis and structure elucidation of the human tRNA nucleoside mannosyl-queuosine

Queuosine (Q) is a structurally complex, non‐canonical RNA nucleoside. It is present in many eukaryotic and bacterial species, where it is part of the anticodon loop of certain tRNAs. In higher vertebrates, including humans, two further modified queuosine-derivatives exist ‐ galactosyl‐ (galQ) and mannosyl-queuosine (manQ). The function of these low abundant hypermodified RNA nucleosides remains unknown. While the structure of galQ was elucidated and confirmed by total synthesis, the reported structure of manQ still awaits confirmation. By combining total synthesis and LC-MS-co-injection experiments, together with a metabolic feeding study of labelled hexoses, we show here that the natural compound manQ isolated from mouse liver deviates from the literature-reported structure. Our data show that manQ features an α‐allyl connectivity of its sugar moiety. The yet unidentified glycosylases that attach galactose and mannose to the Q‐base therefore have a maximally different constitutional connectivity preference. Knowing the correct structure of manQ will now pave the way towards further elucidation of its biological function.

Bracketing Paradoxes resolved

Bracketing Paradoxes (BPs) have been the subject of many different analyses since the 1970s. Each of these analyses have included BP-specific machinery to account for the apparent mismatch between the syntactico-semantic and morpho-phonological structures argued to be necessary for a complete analysis of this phenomenon. This article proposes that independently necessary operations and structures in the morpho-syntactic and phonological modules allow for an analysis of BPs that avoids postulating ad-hoc tools. Specifically, a system that includes cyclic (phasal) interpretation of the morpho-syntax in combination with a flat (CVCV) phonological framework avoids the emergence of paradoxical structures altogether. The discussion therefore includes both current morpho-syntactic and phonological analyses of each construction proposed to give rise to a BP; comparatives (unhappier), Level-ordering BPs (ungrammaticality), Phrasal BPs (modular grammarian), Compound BPs (particle physicist), Particle-verbs (podžëg ‘set fire’ [Russian]), and Reduplicated BPs (kwíita-kwíita ‘to pour a bit’ [Kihehe]). The proposal that a flat phonological framework is key in avoiding the paradoxical nature of BPs has implications for the correct structure of phonological representations generally.

Synthesis and Structure Elucidation of the Human tRNA Nucleoside Mannosyl-Queuosine

Queuosine (Q) is a structurally complex, non-canonical RNA nucleoside. It is present in many eukaryotic and bacterial species, where it is part of the anticodon loop of certain tRNAs. In higher vertebrates, including humans, two further modified queuosine-derivatives exist, galactosyl- (galQ) and mannosyl-queuosine (manQ). The function of these low abundant hypermodified RNA nucleosides remains unknown. While the structure of galQ was elucidated and confirmed by total synthesis, the reported structure of manQ still awaits confirmation. By combining total synthesis and LC-MS-co-injection, together with a metabolic feeding study of labelled hexoses, we show here that the natural compound manQ isolated from mouse liver deviates from the literature-reported structure. The chemical structure of the natural product manQ features a novel α-allyl connectivity. The data reported here shows that the yet unidentified glycosylases that attach galactose and mannose to the Q-base have different constitutional connectivity preferences. Knowing the correct structure of manQ will now pave the way towards further elucidation of its biological function.

Timed Automata Relaxation for Reachability

Timed automata (TA) have shown to be a suitable formalism for modeling real-time systems. Moreover, modern model-checking tools allow a designer to check whether a TA complies with the system specification. However, the exact timing constraints of the system are often uncertain during the design phase. Consequently, the designer is able to build a TA with a correct structure, however, the timing constraints need to be tuned to make the TA comply with the specification.In this work, we assume that we are given a TA together with an existential property, such as reachability, that is not satisfied by the TA. We propose a novel concept of a minimal sufficient reduction (MSR) that allows us to identify the minimal set S of timing constraints of the TA that needs to be tuned to meet the specification. Moreover, we employ mixed-integer linear programming to actually find a tuning of S that leads to meeting the specification.

The effect of added high-iron slag on the frost resistance of cement compositions

Currently, it is of particular importance to study the possibility of increasing the durability of composite building materials by regulating the chemical and mineralogical composition. In this aspect, it is rational to consider the issues of increasing the frost resistance of cement concrete. It is known that to improve this property in concrete, it is necessary to create the correct structure of the hardened cement stone. The work aims to study the process of clogging the pores of a cement stone due to the formation of finely dispersed phases - ferrihydrite - in the process of hydration of composite Portland cement with the addition of high-iron slag of the established chemical composition. The paper analyzes the chemical and phase composition of concretes obtained based on of slag-containing binders with high values of frost resistance. It is shown that, based on this slag, concrete with frost resistance of 500 cycles has been obtained. Analysis of the hydration products showed that finely dispersed ferrihydrite of ferric iron are formed in the cement stone, which increases the density of concrete, plugging the defects in the microstructure of the C-S-H gel.

Learning linear non-Gaussian graphical models with multidirected edges

In this article, we propose a new method to learn the underlying acyclic mixed graph of a linear non-Gaussian structural equation model with given observational data. We build on an algorithm proposed by Wang and Drton, and we show that one can augment the hidden variable structure of the recovered model by learning multidirected edges rather than only directed and bidirected ones. Multidirected edges appear when more than two of the observed variables have a hidden common cause. We detect the presence of such hidden causes by looking at higher order cumulants and exploiting the multi-trek rule. Our method recovers the correct structure when the underlying graph is a bow-free acyclic mixed graph with potential multidirected edges.

Метод восстановления моделей тепломассопереноса по пространственно-временным распределениям параметров

An algorithm of the generative design method for reconstruction of heat transfer models from the available data is proposed. The method is applied to generate a partial differential equation describing the process of heating and evaporation of a metal, the surface of which is heated by laser radiation. The high efficiency of the method was demonstrated for the purpose of reconstructing the correct structure of the equation, indicating additional processes accompanying heating as phase transitions, and also for determining the values of the temperature-dependent coefficients of the derivatives.