Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryo-Electron Tomography of the Herpesvirus Procapsid Reveals Interactions of the Portal with the Scaffold and a Shift on Maturation

Herpes simplex virus 1 (HSV-1) infects a majority of humans, causing mostly mild disease but in some cases progressing toward life-threatening encephalitis. Understanding the life cycle of the virus is important to devise countermeasures. ABSTRACT Herpes simplex virus 1 (HSV-1) requires seven proteins to package its genome through a vertex in its capsid, one of which is the portal protein, pUL6. The portal protein is also thought to facilitate assembly of the procapsid. While the portal has been visualized in mature capsids, we aimed to elucidate its role in the assembly and maturation of procapsids using cryo-electron tomography (cryoET). We identified the portal vertex in individual procapsids, calculated a subtomogram average, and compared that with the portal vertex in empty mature capsids (A-capsids). The resulting maps show the portal on the interior surface with its narrower end facing outwards, while maintaining close contact with the capsid shell. In the procapsid, the portal is embedded in the underlying scaffold, suggesting that assembly involves a portal-scaffold complex. During maturation, the capsid shell angularizes with a corresponding outward movement of the vertices. We found that in A-capsids, the portal translocates outward further than the adjacent capsomers and strengthens its contacts with the capsid shell. Our methodology also allowed us to determine the number of portal vertices in each capsid, with most having one per capsid, but some none or two, and rarely three. The predominance of a single portal per capsid supports facilitation of the assembly of the procapsid. IMPORTANCE Herpes simplex virus 1 (HSV-1) infects a majority of humans, causing mostly mild disease but in some cases progressing toward life-threatening encephalitis. Understanding the life cycle of the virus is important to devise countermeasures. Production of the virion starts with the assembly of an icosahedral procapsid, which includes DNA packaging proteins at a vertex, one of which is the dodecameric portal protein. The procapsid then undergoes maturation and DNA packaging through the portal, driven by a terminase complex. We used cryo-electron tomography to visualize the portal in procapsids and compare them to mature empty capsids. We found the portal located inside one vertex interacting with the scaffold protein in the procapsid. On maturation, the scaffold is cleaved and dissociates, the capsid angularizes, and the portal moves outward, interacting closely with the capsid shell. These transformations may provide a basis for the development of drugs to prevent HSV-1 infections.
The Impact of Institutional Features on R&D in Business Enterprise Sector and Sustainable Growth

Abstract The main goal of our study is to theoretically and empirically contribute to the analysis of relation between institutional features and R&D in business enterprise sector and consequently on sustainable economic growth. We exploited the available measures of institutional quality from World Government Indicators of World Bank and data on R&D in business enterprise sector. We employed First-Differencing GMM method to estimate the model on the balanced panel data including the following European countries: Bulgaria, Croatia, the Czech Republic, Hungary, Poland, Romania, Serbia and the Slovak Republic, for the time span of 2007-2017. The institutional features are statistically significant factor of R&D in business enterprise sector. We found that Government effectiveness and Control of corruption in particular are very important in supporting the R&D. These measures of institutional quality are key institutional determinants of R&D in business enterprise sector. R&D in business enterprise sector is one of the crucial parts of the overall R&D, and therefore policymakers have to develop favourable conditions for those activities in private firms. Institutional features should be an important variable in explanation of R&D intensity. The presented analysis empirically contributes to the body of knowledge on determinants of R&D for European countries that have to develop their institutions further in order to grow sustainably. This study is using contemporary methods for testing the underlying problem.
A novel regulatory element upstream of TNFAIP3 promoter may be influenced by SLE risk variants

Almost all of Genome Wide Association Studies (GWAS) hits come from non-coding DNA elements. Data from chromatin interaction analyses suggest a long-range interaction with a putative enhancer upstream of TNFAIP3. Disrupting the enhancer may impair TNFAIP3 expression and enhance SLE risk. Two variants, rs10499197 and rs58905141 carried on the SLE risk haplotype are situated near this enhancer and could affect its function. Cloning the regulatory region surrounding rs10499197 into an expression plasmid containing a CRISPR-Cas9 backbone, and then performing a genome editing assay, we found that the variant is located near an enhancer. And any changes to the SNP region might impair enhancer and its ability to regulate TNFAIP3 expression.
The Giardia lamblia ribosome structure reveals divergence in translation and quality control pathways

Giardia lamblia is a human pathogen of worldwide importance with limited treatment options. Its unusual molecular biology presents targets for new therapies and the opportunity to explore the fundamental features of important biological mechanisms. We determined the structure of the G. lamblia 80S ribosome by cryoelectron microscopy, revealing how it combines eukaryotic and bacterial features. The structure reveals regions that are rapidly evolving, including depletion of A and U bases from its rRNA. Specific features of the G. lamblia ribosome suggest it is less prone to stall on problematic peptide sequences, and that the organism uses altered ribosome quality control pathways compared to other eukaryotes. Examination of translation initiation factor binding sites suggests these interactions are conserved despite a divergent initiation mechanism. This work defines key new questions regarding ribosome-centric biological pathways in G. lamblia and motivates new experiments to explore potential targetable mechanisms.
An evaluation of machine learning and latent semantic analysis in text sentiment classification

Abstract In this paper, we compare the following machine learning methods as classifiers for sentiment analysis: k – nearest neighbours (kNN), artificial neural network (ANN), support vector machine (SVM), random forest. We used a dataset containing 5,000 movie reviews in which 2,500 were marked as positive and 2,500 as negative. We chose 5,189 words which have an influence on sentence sentiment. The dataset was prepared using a term document matrix (TDM) and classical multidimensional scaling (MDS). This is the first time that TDM and MDS have been used to choose the characteristics of text in sentiment analysis. In this case, we decided to examine different indicators of the specific classifier, such as kernel type for SVM and neighbour count in kNN. All calculations were performed in the R language, in the program R Studio v 3.5. 2. Our work can be reproduced because all of our data sets and source code are public.
A New Six-DoF Parallel Mechanism for Captive Model Test

Abstract In order to obtain the hydrodynamic coefficients that can save cost and meet the accuracy requirements, a new hydrodynamic test platform based on a 6DoF (six degrees of freedom) parallel mechanism is proposed in this paper. The test platform can drive the ship to move in six degrees of freedom. By using this experimental platform, the corresponding hydrodynamic coefficients can be measured. Firstly, the structure of the new device is introduced. The working principle of the model is deduced based on the mathematical model. Then the hydrodynamic coefficients of a test ship model of a KELC tank ship with a scale of 1:150 are measured and 8 typical hydrodynamic coefficients are obtained. Finally, the measured data are compared with the value of a real ship. The deviation is less than 10% which meets the technical requirements of the practical project. The efficiency of measuring the hydrodynamic coefficients of physical models of ships and offshore structures is improved by the device. The method of measuring the hydrodynamic coefficients by using the proposed platform provides a certain reference for predicting the hydrodynamic performance of ships and offshore structures.
Accessing Mitochondrial Protein Import in Living Cells by Protein Microinjection

Mitochondrial protein biogenesis relies almost exclusively on the expression of nuclear-encoded polypeptides. The current model postulates that most of these proteins have to be delivered to their final mitochondrial destination after their synthesis in the cytoplasm. However, the knowledge of this process remains limited due to the absence of proper experimental real-time approaches to study mitochondria in their native cellular environment. We developed a gentle microinjection procedure for fluorescent reporter proteins allowing a direct non-invasive study of protein transport in living cells. As a proof of principle, we visualized potential-dependent protein import into mitochondria inside intact cells in real-time. We validated that our approach does not distort mitochondrial morphology and preserves the endogenous expression system as well as mitochondrial protein translocation machinery. We observed that a release of nascent polypeptides chains from actively translating cellular ribosomes by puromycin strongly increased the import rate of the microinjected preprotein. This suggests that a substantial amount of mitochondrial translocase complexes were involved in co-translational protein import of endogenously expressed preproteins. Our protein microinjection method opens new possibilities to study the role of mitochondrial protein import in cell models of various pathological conditions as well as aging processes.
A super-resolution protocol to correlate structural underpinnings of fast second-messenger signalling in primary cell types

Nanometre-scale cellular information obtained through super-resolution microscopies are often unaccompanied by functional information, particularly transient and diffusible signals through which life is orchestrated in the nano-micrometre spatial scale. We describe a correlative imaging protocol which allows the ubiquitous intracellular second messenger, calcium (Ca2+), to be directly visualised against nanoscale patterns of the ryanodine receptor (RyR) Ca2+ channels which give rise to these Ca2+ signals in wildtype primary cells. This was achieved by combining total internal reflection fluorescence (TIRF) imaging of the elementary Ca2+ signals, with the subsequent DNA-PAINT imaging of the RyRs. We report a straightforward image analysis protocol of feature extraction and image alignment between correlative datasets and demonstrate how such data can be used to visually identify the ensembles of Ca2+ channels that are locally activated during the genesis of cytoplasmic Ca2+ signals.
Sex robot technology and the Narrative Policy Framework (NPF): A relationship in the making?

Abstract The use of sex robots is expected to become widespread in the coming decades, not only for hedonistic purposes but also for therapy, to keep the elderly company in care homes, for education, and to help couples in long-distance relationships. As new technological artifacts are introduced to society, they play a role in shaping the societal norms and belief systems while also creating tensions between various approaches and relationships, resulting in a range of policy-making proposals that bring into question traditional disciplinary boundaries that exist between the technical and the social. The Narrative Policy Framework attempts to position policy studies in such a way so as to better describe, explain, and predict a wide variety of processes and outcomes in a political world increasingly burdened by uncertain reporting, capitalistic marketing, and persuasive narratives. Through content analysis, this study identifies coalitions in the scientific community, based on results gathered from Scopus, to develop insights into the manner in which liberal, utilitarian, and conservative influences alike are shaping narrative elements and content both in favor of and against sex robot technology.
Approximate State–Space and Transfer Function Models for 2×2 Linear Hyperbolic Systems with Collocated Boundary Inputs

Abstract Two approximate representations are proposed for distributed parameter systems described by two linear hyperbolic PDEs with two time- and space-dependent state variables and two collocated boundary inputs. Using the method of lines with the backward difference scheme, the original PDEs are transformed into a set of ODEs and expressed in the form of a finite number of dynamical subsystems (sections). Each section of the approximation model is described by state-space equations with matrix-valued state, input and output operators, or, equivalently, by a rational transfer function matrix. The cascade interconnection of a number of sections results in the overall approximation model expressed in finite-dimensional state-space or rational transfer function domains, respectively. The discussion is illustrated with a practical example of a parallel-flow double-pipe heat exchanger. Its steady-state, frequency and impulse responses obtained from the original infinite-dimensional representation are compared with those resulting from its approximate models of different orders. The results show better approximation quality for the “crossover” input–output channels where the in-domain effects prevail as compared with the “straightforward” channels, where the time-delay phenomena are dominating.
Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia

A severe lack of distribution data for aquatic reptiles in northern Australia leaves many taxa vulnerable to extirpation and extinction. Environmental DNA (eDNA) technologies offer sensitive and non-invasive genetic alternatives to trapping and visual surveys and are increasingly employed for the detection of aquatic and semi-aquatic reptiles. However, at present, these studies have largely applied species-specific primers which do not provide a cost-effective avenue for the simultaneous detection of multiple reptilian taxa. Here, we present a 16S rRNA metabarcoding assay for the broad detection of aquatic and semi-aquatic reptile species. This assay is tested on water samples collected at multiple sampling sites at two tropical locations: 12 marine/estuarine sites in Roebuck Bay, Western Australia, and 4 estuarine sites in Cooktown, Queensland, Australia. A total of nine reptile taxa were detected from 10 of the 16 sampled sites, including marine and freshwater turtles, aquatic and semi-aquatic/terrestrial snakes, and terrestrial skinks. However, inconsistencies in the detection of previously observed aquatic reptiles at our sampled sites, such as saltwater crocodile and sea snakes, indicates that further research is required to assess the reliability, strengths and limitations of eDNA methods for aquatic reptile detection before it can be integrated as a broad-scale bioassessment tool.
BCR-induced protein dynamics and the emerging role of SUMOylation revealed by proximity proteomics

Successful B cell activation, critical for high-affinity antibody production, is controlled by the B cell antigen receptor (BCR). However, we still lack a comprehensive protein-level view of the very dynamic multi-branched cellular events triggered by antigen binding. Here, we employed APEX2 proximity biotinylation to study antigen-induced changes, 5-15 min after receptor activation, at the vicinity of the plasma membrane lipid rafts, wherein BCR enriches upon activation. The data reveals dynamics of signaling proteins, as well as various players linked to the subsequent processes, such as actin cytoskeleton remodelling and endocytosis. Interestingly, our differential expression analysis identified dynamic responses in various proteins previously not linked to early B cell activation. We demonstrate active SUMOylation at the sites of BCR activation in various conditions and report its functional role in BCR signaling through Akt and MAPK axes.
Investigations of the Working Process in a Dual-Fuel Low-Emission Combustion Chamber for an FPSO Gas Turbine Engine

Abstract This investigation is devoted to an analysis of the working process in a dual-fuel low-emission combustion chamber for a floating vessel’s gas turbine. The low-emission gas turbine combustion chamber with partial pre-mixing of fuel and air inside the outer and inner radial-axial swirlers was chosen as the object of research. When modelling processes in a dual-flow low-emission gas turbine combustion chamber, a generalized method is used, based on the numerical solution of the system of conservation and transport equations for a multi-component chemically reactive turbulent system, taking into consideration nitrogen oxides formation. The Eddy-Dissipation-Concept model, which incorporates Arrhenius chemical kinetics in a turbulent flame, and the Discrete Phase Model describing the interfacial interaction are used in the investigation. The obtained results confirmed the possibility of organizing efficient combustion of distillate liquid fuel in a low-emission gas turbine combustion chamber operating on the principle of partial preliminary formation of a fuel-air mixture. Comparison of four methods of liquid fuel supply to the channels of radial-axial swirlers (centrifugal, axial, combined, and radial) revealed the advantages of the radial supply method, which are manifested in a decrease in the overall temperature field non-uniformity at the outlet and a decrease in nitrogen oxides emissions. The calculated concentrations of nitrogen oxides and carbon monoxide at the flame tube outlet for the radial method of fuel supply are 32 and 9.1 ppm, respectively. The results can be useful for further modification and improvement of the characteristics of dual-fuel gas turbine combustion chambers operating with both gaseous and liquid fuels.
Sirt1 mediated regulation of p107 mitochondrial function controls muscle stem cell proliferative fates

Muscle wasting diseases and aging are associated with impaired myogenic stem cell self-renewal and a diminished number of their proliferating and differentiating committed muscle progenitor cells (MPs). Importantly, distinct metabolic states govern how MPs proliferate and differentiate. Central to this is the regulation of energy generation between glycolysis in the cytoplasm and oxidative phosphorylation (Oxphos) in the mitochondria. However, the mechanisms that connect these energy provisioning centers to control cell behaviour remain obscure. Herein, our results reveal a mechanism by which mitochondrial-localized transcriptional co-repressor p107 governs MP proliferative capacity, under the control of NAD+ dependent Sirt1 deacetylase. We found p107 directly interacts at the mitochondrial DNA promoter leading to repression of mitochondrial-encoded genes. This reduces the mitochondrial ATP generation capacity, by limiting the electron transport chain complex formation. Importantly, the amount of ATP generated by the mitochondrial function of p107 is directly associated to the cell cycle rate in vivo and in vitro. In vivo, p107 genetically deleted MPs had a faster proliferative capacity, whereas forced expression of p107 in the mitochondria blocked cell cycle progression. Sirt1, whose activity is dependent on the cytoplasmic by-product of glycolysis, NAD+, directly interacts with p107 impeding its mitochondrial localization and function. Deletion of Sirt1 increased p107 mitochondrial localization, decreased MP mitochondrial Oxphos generation, concomitant with dampened cell cycle progression. Increasing the activity of Sirt1 had the opposite effect on p107 function. This metabolic control of cell cycle progression, driven by differential p107 mitochondrial function based on Sirt1 activity, establishes a new paradigm to manipulate muscle cell proliferative fates that is likely to extend to most other dividing cell types.
Synaptic correlates of associative fear memory in the lateral amygdala

Successful adaptation to the environment requires accurate responding to external threats by recalling specific memories. However, elucidating underlying neural substrates of associative fear memory was limited due to the difficulties in direct examination of extinction-induced changes of specific synapses that encode an auditory fear memory. Using dual-eGRASP (enhanced Green Fluorescent Protein Reconstitution Across Synaptic Partners), we found that synapses between engram cells or synaptic engram showed a significantly larger spine morphology at auditory cortex (AC) to lateral amygdala (LA) projections after auditory fear conditioning. Fear extinction reversed the enhanced synaptic engram spines while re-conditioning with the same tone and shock restored the size of the synaptic engram. Taken together, we suggest that the synaptic engram may represent a different state of fear memory. One Sentence Summary Associative fear memory enlarged the spine morphology of synapses between engram neurons in the amygdala, which was diminished by memory extinction and restored by re-conditioning, suggesting that connections between engram cells represent a different state of fear memory.
REEP4 is recruited to the inner nuclear membrane by ELYS and promotes nuclear pore complex formation

Nuclear pore complexes (NPCs) are channels within the nuclear envelope that mediate nucleocytoplasmic transport. NPCs assemble either into the closed nuclear envelope during interphase or concomitantly with nuclear envelope reformation during anaphase. Both, interphase and post-mitotic NPC biogenesis require local deformation of membrane. Yet, the factors that control proper membrane remodeling for post-mitotic NPC assembly are unknown. Here, we report that the reticulon homology domain-protein REEP4 localizes not only to high-curvature membrane of the cytoplasmic endoplasmic reticulum (ER) but also to the inner nuclear membrane (INM). We show that REEP4 is recruited to the INM by the NPC biogenesis factor ELYS and promotes NPC assembly. REEP4 contributes mainly to anaphase NPC assembly, suggesting that REEP4 has an unexpected role in coordinating nuclear envelope reformation with post-mitotic NPC biogenesis.
Characterization of microalgae species from Qatar coastal waters for animal feed production

Microalgae have a great potential to be used in animal feeding due to its significant amount of protein and essential fatty acids secreted in their cells. Two strains of microalgae were selected from Qatar University Culture Collection of Cyanobacteria and Microalgae (QUCCCM) isolated from the Qatari coasts and subjected to different cultural conditions (salinities and CO2) and the biomass produced is further analyzed for protein, lipids, and mineral composition. Result shows that Tetraselmis sp. under optimum condition of 35 psu and 5% CO2 enriched air is a promising candidate for feedstock production containing higher amount of calcium. Additionally, Nannochloris sp. isolate contains high amount of fatty acids, especially PUFA and contains high amount of potassium. We suggest using a blend of Tetraselmis sp. and Nannochloris sp. to provide adjustable diet for animals depending on their dietary requirements.