Miracle-dz/UniFAR-FTUs huggingface dataset:
Conversion rate to the secondary conformation state in the binding mode of SARS-CoV-2 spike protein to human ACE2 may predict infectivity efficacy of the underlying virus mutant

Since its outbreak in 2019 SARS-CoV-2 has spread with high transmission efficiency across the world, putting health care as well as economic systems under pressure [1, 2]. During the course of the pandemic, the originally identified SARS-CoV-2 variant has been widely replaced by various mutant versions, which showed enhanced fitness due to increased infection and transmission rates [3, 4]. In order to find an explanation, why SARS-CoV-2 and its emerging mutated versions showed enhanced transfection efficiency as compared to SARS-CoV 2002, an improved binding affinity of the spike protein to human ACE has been proposed by crystal structure analysis and was identified in cell culture models [5-7]. Kinetic analysis of the interaction of various spike protein constructs with the human ACE2 was considered to be best described by a Langmuir based 1:1 stoichiometric interaction. However, we demonstrate in this report that the SARS-CoV-2 spike protein interaction with ACE2 is best described by a two-step interaction, which is defined by an initial binding event followed by a slower secondary rate transition that enhances the stability of the complex by a factor of ∼190 with an overall KD of 0.20 nM. In addition, we show that the secondary rate transition is not only present in SARS-CoV-2 wt but is also found in B.1. 1.7 where its transition rate is five-fold increased.
Learning Spatiotemporal Properties of Hippocampal Place Cells

Visual Abstract It is well known that hippocampal place cells have spatiotemporal properties, namely, that they generally respond to a single spatial location of a small environment, and they also display the temporal response property of theta phase precession, namely, that the phase of spiking relative to the theta wave shifts from the late phase to early phase as the animal crosses the place field. Grid cells in Layer II of the medial entorhinal cortex (MEC) also have spatiotemporal properties similar to hippocampal place cells, except that grid cells respond to multiple spatial locations that form a hexagonal pattern. Because the EC is the upstream area that projects strongly to the hippocampus, a number of EC-hippocampus learning models have been proposed to explain how the spatial receptive field properties of place cells emerge via synaptic plasticity. However, the question of how the phase precession properties of place cells and grid cells are related has remained unclear. This study shows how theta phase precession in hippocampal place cells can emerge from MEC input as a result of synaptic plasticity, demonstrating that a learning model based on non-negative sparse coding can account for both the spatial and temporal properties of hippocampal place cells. Although both MEC grid cells and other EC spatial cells contribute to the spatial properties of hippocampal place cells, it is the MEC grid cells that predominantly determine the temporal response properties of hippocampal place cells displayed here.
Electron cryo-tomography structure of axonemal doublet microtubule from Tetrahymena thermophila

By using electron cryo-tomography and subtomogram average, this study reveals the assembly of T. thermophila axonemal MT doublet in wild type and mutant, showing its structure conservation and diversity compared to other organisms. Doublet microtubules (DMTs) provide a scaffold for axoneme assembly in motile cilia. Aside from α/β tubulins, the DMT comprises a large number of non-tubulin proteins in the luminal wall of DMTs, collectively named the microtubule inner proteins (MIPs). We used cryoET to study axoneme DMT isolated from Tetrahymena. We present the structures of DMT at nanometer and sub-nanometer resolution. The structures confirm that MIP RIB72A/B binds to the luminal wall of DMT by multiple DM10 domains. We found FAP115, an MIP-containing multiple EF-hand domains, located at the interface of four-tubulin dimers in the lumen of A-tubule. It contacts both lateral and longitudinal tubulin interfaces and playing a critical role in DMT stability. We observed substantial structure heterogeneity in DMT in an FAP115 knockout strain, showing extensive structural defects beyond the FAP115-binding site. The defects propagate along the axoneme. Finally, by comparing DMT structures from Tetrahymena and Chlamydomonas, we have identified a number of conserved MIPs as well as MIPs that are unique to each organism. This conservation and diversity of the DMT structures might be linked to their specific functions. Our work provides structural insights essential for understanding the roles of MIPs during motile cilium assembly and function, as well as their relationships to human ciliopathies.
Adsorption of heavy metals using activated carbon produced from municipal organic solid waste

AbstractAdsorption of cadmium (Cd2+) and lead (Pb2+) was investigated using activated carbon (AC) produced from municipal organic solid waste (MOSW). The produced AC was characterized using Scanning Electron Microscopy, X-ray Diffraction, Fourier Transform Infrared spectroscopy, and Brunauer–Emmett–Teller. The results showed that an AC with a surface area of 790 m2/g was produced at carbonization temperature and time of 700°C and 2 h, respectively, and activation with phosphoric acid concentration of 30%. The effect of operational factors, namely, pH 3–7, contact time (0–480 min), metal concentration (25–300 mg/L), and adsorbent dosage (25–300 mg per 50 mL of metal solution) on the adsorption process was investigated. The results showed that optimum adsorption of Cd2+ and Pb2+ were obtained at pH of 5, contact time of 180 min, metal concentration of 100 mg/L, and adsorbent dose of 200 mg per 50 mL of metal solution. At optimum operational conditions, removal efficiencies of 78 and 94% for Cd2+ and Pb2+, r.
Prolactin and prolactin receptor expression in the HPG axis and crop during parental care in both sexes of a biparental bird (Columba livia)

During breeding, multiple circulating hormones, including prolactin, facilitate reproductive transitions in species that exhibit parental care. Prolactin underlies parental behaviors and related physiological changes across many vertebrates, including birds and mammals. While circulating prolactin levels often fluctuate across breeding, less is known about how relevant target tissues vary in their prolactin responsiveness via prolactin receptor (PRLR) expression. Recent studies have also investigated prolactin (PRL) gene expression outside of the pituitary (i.e., extra-pituitary PRL), but how PRL gene expression varies during parental care in non-pituitary tissue (e.g., hypothalamus, gonads) remains largely unknown. Further, it is unclear if and how tissue-specific PRL and PRLR vary between the sexes during biparental care. To address this, we measured PRL and PRLR gene expression in tissues relevant to parental care, the endocrine reproductive hypothalamic-pituitary-gonadal (HPG) axis and the crop (a tissue with a similar function as the mammalian mammary gland), across various reproductive stages in both sexes of a biparental bird, the rock dove (Columba livia). We also assessed how these genes responded to changes in offspring presence by adding chicks mid-incubation, simulating an early hatch when prolactin levels were still moderately low. We found that pituitary PRL expression showed similar increases as plasma prolactin levels, and detected extra-pituitary PRL in the hypothalamus, gonads and crop. Hypothalamic and gonadal PRLR expression also changed as birds began incubation. Crop PRLR expression correlated with plasma prolactin, peaking when chicks hatched. In response to replacing eggs with a novel chick mid-incubation, hypothalamic and gonadal PRL and PRLR gene expression differed significantly compared to mid-incubation controls, even when plasma prolactin levels did not differ. We also found sex differences in PRL and PRLR that suggest gene expression may allow males to compensate for lower levels in prolactin by upregulating PRLR in all tissues. Overall, this study advances our understanding of how tissue-specific changes in responsiveness to parental hormones may differ across key reproductive transitions, in response to offspring cues, and between the sexes.
Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye

Pattern formation of biological structures involves the arrangement of different types of cells in an ordered spatial configuration. In this study, we investigate the mechanism of patterning the Drosophila eye into a precise triangular grid of photoreceptor clusters called ommatidia. Previous studies had led to a long-standing biochemical model whereby a reaction-diffusion process is templated by recently formed ommatidia to propagate a molecular prepattern across the eye epithelium. Here, we find that the templating mechanism is instead, mechanical in origin; newly born columns of ommatidia serve as a template to spatially pattern cell flows that move the cells in the epithelium into position to form each new column of ommatidia. Cell flow is generated by a pressure gradient that is caused by a narrow zone of cell dilation precisely positioned behind the growing wavefront of ommatidia. The newly formed lattice grid of ommatidia cells are immobile, deflecting and focusing the flow of other cells. Thus, the self-organization of a regular pattern of cell fates in an epithelium is mechanically driven.
Allele-resolved single-cell multi-omics uncovers the dynamics and transcriptional kinetics of X-chromosome upregulation

X-chromosome inactivation (XCI) and upregulation (XCU) are the major opposing chromosome-wide modes of gene regulation that collectively achieve dosage compensation in mammals, but the regulatory link between the two remains elusive. Here, we use allele-resolved single-cell RNA-seq combined with chromatin accessibility profiling to finely dissect the separate effects of XCI and XCU on RNA levels during mouse development. We uncover that balanced X dosage is flexibly attained through expression tuning by XCU in a sex- and lineage-specific manner along varying degrees of XCI and across developmental and cellular states. Male blastomeres achieve XCU upon zygotic genome activation while females experience two distinct waves of XCU, upon imprinted- and random XCI, and ablation of Xist impedes female XCU. Contrary to widely established models of mammalian dosage compensation, naïve female embryonic cells carrying two active X chromosomes do not exhibit upregulation but express both alleles at basal level, yet collectively exceeding the RNA output of a single hyperactive allele. We show, in vivo and in vitro, that XCU is kinetically driven by X-specific modulation of transcriptional burst frequency, coinciding with increased compartmentalization of the hyperactive allele. Altogether, our data provide unprecedented insights into the dynamics of mammalian XCU, prompting a revised model of the chain in events of allelic regulation by XCU and XCI in unitedly achieving stable cellular levels of X-chromosome transcripts.
Multiple Access in Cognitive Radio Networks: From Orthogonal and Non-Orthogonal to Rate-Splitting

Due to the increasingly complicated communication scenarios and network architectures as well as growing traffic demands for high speed connectivity, dynamic spectrum allocation in fifth generation (5G) networks becomes insufficient to guarantee the satisfaction of main network requirements in terms of spectrum efficiency (SE), scalability, delay, and energy efficiency (EE). Enormous multiple access schemes and cognitive radio (CR) network scenarios come to fulfill these requirements and enhance network functionalities. With multiple access schemes, users are able to transmit their data streams simultaneously under maximum capacity constraints. On the other hand, vacant spectrum holes are exploited in an opportunistic manner via CR and software defined radio. In order to exploit these spectrum holes as well as meeting different network requirements, several multiple access techniques have been presented that have been initiated through the adoption of orthogonal multiple access (OMA) scheme. Additionally, non-orthogonal multiple access (NOMA) and space division multiple access (SDMA) are presented to achieve a promising multiplexing gain as well as to address the inefficient spectrum utilization incurred with OMA schemes. However, such multiplexing gain is limited as it depend on the channel conditions. Accordingly, a generalized multiple access scheme has been presented recently, namely rate splitting multiple access (RSMA), to further enhance the SE. In this paper, we provide a comprehensive study regarding the key multiple access schemes presented for CRNs to further enhance the use of spectral resources, and additionally highlights the key implementation challenges and the enabling techniques addressed to overcome it. We have given a special attention to the enhances provided by RSMA as compared with OMA, SDMA, and NOMA techniques. Finally, some open issues are spotted to shed lights on the need for further studies and future research efforts.
Exploiting Secrecy Performance of Uplink NOMA in Cellular Networks

We study the secrecy transmission of uplink non-orthogonal multiple access (NOMA) with single antenna and multi-antenna users in presence of an eavesdropper. Two phases are required for communications during each time frame between the users and the base station in cellular networks. We study the case where an eavesdropper overhears the relay and direct links from the users to the base stations. In terms of the secure performance analysis, we focus on two main metrics including secrecy outage probability (SOP) and strictly positive secrecy capacity (SPSC) with the assumption that the eavesdropper is able to detect the signals. Analytical closed-form expressions for the SOP and SPSC are derived to evaluate the system secure performance achieved by the proposed schemes. Furthermore, the asymptotic analysis is presented to gain further insights. The analytical and numerical results indicate that the proposed schemes can realize better secrecy performance once we improve the channel condition and signal-to-noise ratio (SNR) at the base station. Our results confirms that the secrecy performance gaps exist among the two users since different power allocation factors are assigned to these users.
Vehicle License Plate Detector in Compressed Domain

Data compression techniques allow data size to be reduced prior to data transmission and involve decompression upon transfer. This study shows for the first time that license plate (LP) detection can be accomplished without full decompression of the encoded data. Therefore, by determining in advance which images are required for LP recognition, computational costs of the system can be reduced. The proposed approach is realized on High Efficiency Video Coding (HEVC) based compressed video sequences. Two methods are provided that generate images from HEVC attributes. Fully decoded pixel domain images are also generated for comparative purposes from the same encoded data. The YOLO V3 Tiny Object Detector is used in order to detect LPs in the generated images. EnglishLP, a public dataset, is used to interpret the findings in terms of speed and precision and for comparison with previous studies. An additional contribution of the paper is that a new compressed domain LP database has been created and made publicly available, comprising images captured by a commercial license plate recognition system. Using at least two-orders-of-magnitude less amount of data, the proposed compressed domain LP detector achieved similar precision and recall values to those of the state-of-the-art LP detection schemes tested on both datasets. Moreover, the proposed method results in more than 30% saving in inference time. The results suggest that the proposed method can be utilized for rapid video archive searching applications.
Implementing circularity in the construction process: a case study examining the reorganization of multi-actor environment and the decision-making process

Abstract Circularity aims to make waste obsolete by both closing and narrowing resource loops and by extending the lifespan of materials and products. This fundamentally different approach to construction practices necessitates a completely different method of organising the construction process. The rounds of decision-making undertaken by different actors at particular moments in the construction process have a significant role to play in this regard. Consequently, this research aims to analyse current circular practices for both the multi-actor environment and the decision-making process. An analytical framework is developed based on the theoretically-informed assumption that actors are responsible for decision-making and that circular strategies are an effective means through which to integrate circularity within the construction process. This analytical framework is applied to three circular building cases in the Netherlands, by drawing upon stakeholder interviews and documentation. It can be concluded that: some conventional actors have acquired knowledge on circularity; and that there is an emergent group of expert actors specialising in circularity. Both types of actors are a prerequisite for implementing circular strategies at both the beginning and end-of-life phase of a building; and should be involved early on to influence decision-making on circularity, especially concerning the long-lived layers of a building.
Analysing the contribution of urban agriculture towards urban household food security in informal settlement areas

ABSTRACT Rapid urban growth due to unprecedented rural–urban migration is putting pressure on urban food systems. The general impression is that households engaged in urban agriculture experience improved nutritional status, higher health standards and provide towards income and employment. However, empirical research findings are limited and inconsistent. This study provides empirical knowledge on the urban agriculture–food security nexus. Data was gathered from a sample of 220 households comprising of those with small household (backyard) garden projects funded by the Department of Agriculture in the Western Cape, South Africa, and a control group. Propensity score matching was used to determine the contribution of urban agriculture to household food security. The findings indicated that households engaged in urban agriculture were benefiting from dietary diversity and the generation of income through the production of various food products. There was, however, no indication of a significant positive contribution of urban agriculture towards food security.
Accessible Maker-Based Approaches to Educational Robotics in Online Learning

Educational Robotics holds the potential to promote the development of important 21st century skills, such as creativity and problem-solving skills in addition to digital literacy. However, the emergence of the Covid-19 pandemic has posed particular obstacles that had to be overcome in order to allow Educational Robotics activities to be conducted in distance learning. In the first place, the obligation to work from home limited the access to required equipment for many students. Secondly, many teachers had to face the novel challenge of creating pedagogically meaningful activities in online learning formats. Aiming to address these challenges, this work explored maker-based approaches as a way to implement Educational Robotics activities in online learning. The devised tools and activities were evaluated in two case studies performed with (i) high school students participating in a mobile robotics summer school and (ii) in-service teachers attending a professional development course on Educational Robotics. The teachers’ and students’ perception of the proposed activities was analyzed using online surveys and video interviews. The findings showed that the combination of the devised tools and activities allowed teachers and students to explore the basics of mobile robotics while helping them develop a maker mindset. The use of ubiquitous construction materials and affordable electronic components promotes the accessibility of the approach. The proposed tools and activities may therefore provide an exemplary framework for more general applications of Educational Robotics in online learning that go beyond the context of emergency remote teaching.
Machine Learning Framework for Multi-Level Classification of Company Revenue

The planning and execution of a business strategy are important aspects of the strategic human resource management of a company. In previous studies, machine learning algorithms were used to determine the main factors correlating employees with company performance. In this study, we introduced a method based on machine-learning algorithms for the classification of company revenue. Both annual and integrated datasets were examined to evaluate the classification performance of the framework under both binary and multiclass conditions. The performance of the proposed method was validated using six evaluation metrics: accuracy, precision, recall, F1-score, receiver operating characteristic curve, and area under the curve. As the experimental results indicate, the XGBoost classifier displayed the best classification performance among the three algorithms (XGBoost classifier, stochastic gradient descent classifier, and logistic regression) used in this study. Moreover, we confirmed the important features of the trained XGBoost model in accordance with variables focusing on human resource management studies. These results demonstrate that the proposed framework has strength in terms of both classification and practical implementation. This study provides novel insights into the relationship between employees and the revenue levels of their employer.
Repeatability and reproducibility in the breathability measurement of surgical masks

The pandemic COVID-19 is still requiring several countermeasures to adopted in order to decrease the virus spread. Among others, face masks have shown their potentiality to reduce the person-to-person transmission. For this reason, several research groups and/or industries focused their supply chain in the production of innovative materials for the face mask design. Considering the surgical mask, several parameters have to be checked before their commercialization, as for example the breathability. This study aims at evaluating the repeatability and reproducibility of the breathability measurement in surgical masks, and at assessing the effects induced by the selected measurement points on the mask. Three samples for each type I, II and IIR masks were tested within the experimental protocol. Breathability was measured by following the UNI EN 14683:2019. Fifteen measurement points were identified for each mask and the measure was repeated five times per each point. Standard deviation across the repeated measures on the single point and across the different tested areas were used to evaluate the repeatability and reproducibility of the procedure, respectively. The measurement uncertainty was also computed. In addition, in order to verify the effects induced by the selection of five points out the available fifteen, as requested by the UNI EN 14683:2019, all combinations of points were tested. Results showed a high value of reproducibility error, leading to the consideration that different areas of the same mask are characterized by different values of breathability. Thus, the selection of the five measurement points to perform the breathability measurement according to the standard is a crucial aspect that can influence the result of mask compliance. The results of the present paper could provide useful information for the standardization of the breathability measurement.