Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-dimensional human head modelling: a systematic review

ABSTRACT Human head is one of the most important parts of the body, as it houses brain and other sensory organs, which controls functioning and working of the whole body. The products used for head and face are designed for functions like protection, information transfer, healthcare or to improve the aesthetic appearance. In order for them to serve their purpose, they need a close fit and in order to make it more ergonomic, user's comfort also needs to be addressed, thereby making it necessary to acquire accurate anthropometric data for ergonomic product design. Traditional techniques involve manual measurement using tapes, callipers and scales which normally have low reliability and low accuracy. With the advancement in image processing and computer aided designing and modelling techniques it has become possible to develop highly accurate and reliable 3D head and face model. Following paper presents a systematic review of different approaches that have been proposed for developing 3D head and face model and also the techniques used in processing and analysis of 3D data and their limitations. The paper also presents application of head and face models for ergonomic product design.
Preliminary trials of the gold nanoparticles conjugated chrysin: An assessment of anti-oxidant, anti-microbial, and in vitro cytotoxic activities of a nanoformulated flavonoid

Abstract Chrysin (CHR), a dihydroxy flavone, exhibits several bioactivities, i.e., anti-oxidant, anti-inflammatory, and anti-cancer, and is known to possess limited aqueous solubility causing lowered bioavailability, and compromised therapeutic efficacy. Gold nanoparticles (AuNPs) conjugated chrysin (CHR–AuNPs) were prepared and characterized by UV-Vis, Fourier transform infra-red, X-ray diffraction, energy dispersive X-ray (EDX), and zeta potential analyses. The nanoformulated CHR–AuNPs were primarily examined on trial scale for their cytotoxic, anti-oxidant, and anti-microbial activity in comparison to the unformulated CHR. The CHR–AuNPs effectively scavenged the 2,2-diphenyl-1-picrylhydrazyl free radicals, also in comparison to CHR and AuNPs. The CHR–AuNPs also exhibited potential cytotoxic effects in a dose-dependent manner and demonstrated significant reduction (P = 0.05) of the cells proliferation, and growth of the human breast cancer cell lines, AMJ13, which were measured by 3-(4,5-dimethylthiazal-z-yl)-2,5-diphenyltetrazolium, and crystal violet assays, respectively. When compared with the pure CHR and free-AuNPs, the CHR–AuNPs exerted highest anti-microbial bioactivity against Staphylococcus aureus and Escherichia coli. The strong anti-oxidant, anti-microbial, as well as cytotoxic activity of the CHR–AuNPs preparation has the potential for clinical use after considerable appropriate developments. Graphical abstract
Measuring the Impact of the Coviid-19 Crisis on the Foreign Tourist Receipts

Abstract Tourism is a significant economic activity for developing any national economy and the world economy as well. Revenues generated through tourism services affect GDP and directly stimulate economic growth. The revenues are important for the national economies, i.e. the foreign exchange inflow, generated through tourist services export. However, many factors directly impact on the volume of foreign tourist arrivals, and thus directly affect both foreign exchange inflows and GDP. Government measures taken for various reasons that have a straight impact on the movement of people significantly reduce tourist travels. It can cause numerous and robust adverse effects on the national economy. The health crisis caused by the pandemic COVID – 19 has led to restrictive governmental measures that had a negative impact on tourist travels, and thus on the revenues generated from the export of tourist services. The paper aims to measure the effect of the COVID - 19 crises on the income generated by the foreign tourists’ arrivals in Ohrid, as a case study destination in North Macedonia. The research results will show the losses this economic sector has suffered from the “lockdown” caused by the pandemic.
Senescent macrophages alter fibroblast fibrogenesis in response to SARS-CoV-2 infection

Abstract SARS-CoV-2 has, since its emergence in 2019, become a global pandemic. Disease outcomes are worsened in older patients who are infected. The causes for this is multifactorial, but one potential cause for this disparity is increased rates of cellular senescence in older individuals, particularly in immune cells. Cellular senescence, the accumulation of factors resulting in cell growth arrest and apoptosis resistance, increases as individuals age. In immune cells, senescence is associated with increased inflammation, and alterations in immune response. We utilized a co-culture system consisting of senescent or non-senescent macrophages directly cultured with fibroblasts, and infected with SARS-CoV-2. We assessed the expression of collagen and fibronectin, important molecules in the extracellular matrix, as well as a number of fibrogenic factors. We observed that infection with SARS-CoV-2 induced collagen production in co-cultures with senescent, but not non-senescent macrophages. Fibronectin expression was decreased in both co-culture conditions. While significant results were not observed, concentrations of other fibrogenic molecules were consistent with the collagen results. These data demonstrate that senescence in macrophages alters the production of fibrotic molecules from fibroblasts in a SARS-CoV-2 infection model. As collagen and fibronectin expression are generally directly correlated, this suggests that senescence dysregulates fibrogenesis in response to infection with SARS-CoV-2. There is a need to further investigate the mechanisms for these changes.
A geographical and content-based approach to prioritize relevant and reliable tweets for emergency management

ABSTRACT Tweets posted by the general public during disaster events represent timely, up-to-date, and on-site data that may be useful for emergency responders. However, since Twitter data has been deemed to be unverifiable and untrustworthy, it is challenging to identify those reliable and relevant tweets that can inform emergency response operations. Although computational methods exist both to classify overwhelming amounts of tweets and to filter those relevant to emergency response, using contextual geographic information regarding the disaster event to filter tweets has been overlooked. We review the existing research on the quality of data contributed by the general public from a geographical perspective, and then propose an approach to prioritize tweets for emergency response based on their relevance and reliability. The novelty of the approach is twofold: a) the use of both authoritative data such as hazard-related information and on-the-ground reports provided by weather spotters and validated by the National Weather Service; and b) the fact that it leverages tweets content as well as their geographical context and location. Using Hurricane Harvey in 2017 as a case study, results show that by following the proposed approach 79% of tweets sent from post-identified flooded areas were classified as of high or medium relevance and reliability. This suggests that the proposed approach can provide an accurate prioritization of tweets to be used for real time emergency management.
Application of Wireless Power Transfer to Railway Parking Functionality: Preliminary Design Considerations with Series-Series and LCC Topologies

There is a wide literature concerning the application of inductive power transfer (IPT) to light railway systems. In this work, proposed application is innovative with respect to existing literature: static current collection on conventional railway lines is proposed in order to replace the functionalities implemented by conventional battery chargers and the so-called railway “parking” system. According to standards in force, current collection in standstill conditions is limited since pantograph contact shoes and catenary wires have to be protected by thermal overload. These limitations have to be considered since power demand for all the services installed on modern coaches should be higher than 20-40kW. This is a critical technical issue especially for long compositions that have to be prepared for service by activating on-board subsystems such as heating and air conditioning. Additional possible applications should be related to refrigerated wagons in freight compositions. In all these cases the availability of a simple, safe, and compact system should be useful to ensure a wireless power collection to on-board equipment. In this work authors introduce the proposed application and perform some preliminary design considerations. With respect to current literature on IPT systems, authors also introduce some innovative design criteria based on the analogy between resonant electrical system and corresponding mechanical ones. In this way, sizing of the proposed IPT system can be performed using modal methods that are also used for the proper sizing of mechanical vibrating systems, such as example, vehicle suspensions, or pantograph systems.
Analysis of Lower-Grade Gliomas in MRI Through Segmentation and Genomic Cluster-Shape Feature Correlation

Gliomas, which originate from glial cells, are considered the most aggressive type of brain tumors. Currently, glioma research efforts are focused mainly on high-grade gliomas. This project aims to analyze lower-grade gliomas (LGG) in MRI and extend the understanding of LGGs. LGG segmentation, which outlines tumors in MRIs, is crucial to developing effective treatment plans. However, segmentation performed manually by radiologists is tedious, time-consuming, and often leads to inter-observer variability. Another unexplored area of LGG research is genomic subtypes. These subtypes can play a large factor in how LGGs can be treated, however there is currently no noninvasive method of identifying these subtypes. Recent studies suggest that LGG shape features have a correlation with genomic subtypes and should be investigated as a viable factor in LGG treatment options. This presents a need for additional research as most LGGs eventually develop into high-grade gliomas. The specific aims of this project include analyzing LGGs through deep learning-based segmentation, shape feature extraction, and statistical analysis to identify correlation between selected shape features and genomic subtypes. To realize these goals, programs were written and run using a publicly available LGG dataset. In terms of automatic segmentation, two models were created using different convolutional neural networks (CNN). The highest performing model used U-Net with a ResNeXt-50 backbone and yielded a 91.4% accuracy in terms of mean intersection over union (IoU) after testing. Shape feature extraction included three geometric features and 4 radiomic features which quantified tumor shape in 2D and 3D. Angular Standard Deviation (ASD), Margin Fluctuation (MF), Bounding Ellipsoid Volume Ratio (BEVR), Elongation, Major and Minor Axis Length, and Volume were tested for correlation with genomic subtype data using 49 Pearson’s chi-squared tests. P-values less than or equal to 0.05 suggested correlation. Statistical analysis found 16 statistically significant associations. The strongest associations were between MF and the RNASeq cluster (p < 0.00003), ASD and the RNASeq Cluster (p < 0.0005), and volume and the RPPA cluster (p < 0.0035).
Specific targeting of inflammatory osteoclastogenesis by the probiotic yeast S. boulardii CNCM I-745 reduces bone loss in osteoporosis

Bone destruction is a hallmark of chronic inflammation, and bone-resorbing osteoclasts arising under such a condition differ from steady-state ones. However, osteoclast diversity remains poorly explored. Here, we combined transcriptomic profiling, differentiation assays and in vivo analysis in mouse to decipher specific traits for inflammatory and steady state osteoclasts. We identified and validated the pattern-recognition receptors (PRR) TLR2, Dectin-1 and Mincle, all involved in yeast recognition as major regulators of inflammatory osteoclasts. We showed that administration of the yeast probiotic Saccharomyces boulardi CNCM I-745 (Sb) in vivo reduced bone loss in OVX but not sham mice by reducing inflammatory osteoclasts. This beneficial impact of Sb is mediated by the regulation of the inflammatory environment required for the generation of inflammatory osteoclasts. We also showed that Sb derivatives as well as agonists of TLR2, Dectin-1 and Mincle specifically inhibited directly the differentiation of inflammatory but not steady state osteoclasts in vitro. These findings demonstrate a preferential use of the PRR-associated costimulatory differentiation pathway by inflammatory osteoclasts, thus enabling their specific inhibition, which opens new therapeutic perspectives for inflammatory bone loss.
Modern human expansion from (southern?) Africa: Origin, non-African ancestry, and linearity

Previous research favours the idea that modern humans spread worldwide from Africa. For instance, through autosomal diversity, an area of origin for this worldwide expansion is indicated to entirely be within Africa. It remained to be seen if this indication happens for certain variables such as Y-chromosomal diversity. There is disagreement regarding where in Africa the origin is. Support for a region could reflect non-African ancestry rather than the expansion. The present research considered whether some genetic and cranial variables indicate the expansion, and, furthermore, where in Africa the expansion started. Variables included, for example, autosomal diversity (in sub-Saharan Africa) which was adjusted for non-African ancestry, Y-chromosomal diversity, and cranial sexual size dimorphism. For each, it was seen if the estimated area of origin was solely in Africa. Moreover, to generally estimate the origin, a centroid was calculated from potential origins which were obtained in the present, and past, research. The area of origin was completely within Africa for each variable except one – for Y-chromosomal diversity, the area was possibly in Asia only. The centroid of the potential origins was in southern Africa. The autosomal diversity of sub-Saharan African populations, adjusted for non-African ancestry, indicated a southern African origin. This adjusted diversity appeared to start declining from about 2,000-3,000 km away from the origin; the non-linearity may be explained by travels after the expansion, or the expansion entering locations in Africa which were already populated, to differing extents, by modern humans. Southern Africa is perhaps where the expansion began.
Ligand Binding Free Energy Evaluation by Monte Carlo Recursion

The correct evaluation of ligand binding free energies by computational methods is still a very challenging active area of research. The most employed methods for these calculations can be roughly classified into four groups: (i) the fastest and less accurate methods, such as molecular docking, designed to sample a large number of molecules and rapidly rank them according to the potential binding energy; (ii) the second class of methods use a thermodynamic ensemble, typically generated by molecular dynamics, to analyze the endpoints of the thermodynamic cycle for binding and extract differences, in the so-called ‘end-point’ methods; (iii) the third class of methods is based on the Zwanzig relationship and computes the free energy difference after a chemical change of the system (alchemical methods); and (iv) methods based on biased simulations, such as metadynamics, for example. These methods require increased computational power and as expected, result in increased accuracy for the determination of the strength of binding. Here, we describe an intermediate approach, based on the Monte Carlo Recursion (MCR) method first developed by Harold Scheraga. In this method, the system is sampled at increasing effective temperatures, and the free energy of the system is assessed from a series of terms W(b, T), computed from Monte Carlo (MC) averages at each iteration. We show the application of the MCR for ligand binding with datasets of guest-hosts systems (N=75) and we observed that a good correlation is obtained between experimental data and the binding energies computed with MCR. We also compared the experimental data with an end-point calculation from equilibrium Monte Carlo calculations that allowed us to conclude that the lower-energy (lower-temperature) terms in the calculation are the most relevant to the estimation of the binding energies, resulting in similar correlations between MCR and MC data and the experimental values. On the other hand, the MCR method provides a reasonable view of the binding energy funnel, with possible connections with the ligand binding kinetics, as well. The codes developed for this analysis are publicly available on GitHub as a part of the LiBELa/MCLiBELa project (https://github.com/alessandronascimento/LiBELa).
Prevalent regulation of GATA2/3 and MSX2 on endogenous retrovirus-derived regulatory elements in human trophoblast stem cells

The placenta is an organ with extraordinary phenotypic diversity in eutherian mammals. Recent evidence suggests that numerous human placental enhancers are evolved from lineage-specific insertions of endogenous retroviruses (ERVs), yet the transcription factors (TFs) underlying their regulation remain largely elusive. Here, by first focusing on MER41, a primate-specific ERV family previously linked to placenta and innate immunity, we uncover the binding motifs of multiple crucial trophoblast TFs (GATA2/3, MSX2, GRHL2) in addition to innate immunity TFs STAT1 and IRF1. Integration of ChIP-Seq data confirms the binding of GATA2/3, MSX2 and their related factors on the majority of MER41-derived enhancers in human trophoblast stem cells (TSCs). Notably, MER41-derived enhancers that are constitutively active in human TSCs are distinct from those activated upon interferon stimulation, which is determined by the binding of relevant TFs and their sub-family compositions. We further demonstrate that GATA2/3 and MSX2 have prevalent binding on numerous other ERV families – indicating their broad impact on ERV-derived enhancers. Functionally, the derepression of many syncytiotrophoblast genes after disruption of MSX2 is likely to be mediated by regulatory elements derived from ERVs – suggesting ERVs are also important for mediating transcriptional repression. Overall, this study characterized the prevalent regulation of GATA2/3, MSX2 and their co-factors on ERV-derived regulatory elements in human TSCs and provided mechanistic insights into the importance of ERVs in human trophoblast regulatory network.
Characterization of the Y Chromosome in Newfoundland and Labrador: Evidence of a Founder Effect

The population of Newfoundland and Labrador (NL) is largely derived from settlers who migrated primarily from England and Ireland in the 1700-1800s. Previously described as an isolated founder population, based on historical and demographic studies, data on the genetic ancestry of this population remains fragmentary. Here we describe the largest investigation of patrilineal ancestry in NL. To determine the paternal genetic structure of the population, 1,110 Y chromosomes from an NL based cohort were analyzed using 5,761 Y-specific markers. We identified 160 distinct paternal haplotypes, the majority of which (71.4%) belong to the R1b haplogroup. When NL is compared with global reference populations, the haplotype composition and frequencies of the NL paternal lineages primarily resemble the English and Irish ancestral source populations. There is also evidence for genetic contributions from Basque, French, Portuguese, and Spanish fishermen and early settlers that frequented NL. The population structure shows geographical and religious clustering that can be associated with the settlement of ancestral source populations from England and Ireland. For example, the R1b-M222 haplotype, seen in people of Irish descent, is found clustered in the Irish-settled Southeast region of NL. The clustering and expansion of Y haplotypes in conjunction with the geographical and religious clusters illustrate that limited subsequent in-migration, geographic isolation and societal factors have contributed to the genetic substructure of the NL population and its designation as a founder population.
Systematic Analysis of Autophagy Identifies Atg9 Vesicles as the Origin of the Phagophore

Autophagy is a catabolic pathway required for the clearance and recycling of cytoplasmic materials. Upregulation and dysfunction of autophagy contributes to the pathology of cancer and neurogenerative diseases, respectively. To define the molecular mechanisms that control autophagic flux it is critical to quantitatively characterize the dynamic behavior of autophagy factors in living cells. Using a panel of 9 cell lines expressing HaloTagged autophagy factors from their endogenous loci, we systematically analyze the abundance, single-molecule dynamics, and autophagosome association kinetics of a wide variety of autophagy proteins involved in the initiation and maturation of the autophagosome. Our results reveal that phagophores are initiated by the accumulation of autophagy factors on mobile ATG9 vesicles and tethering of these ATG9 vesicles to donor membranes by ATG2 is a key step in phagophore maturation. In addition, we demonstrate that the overall lifetime of an autophagosome is approximately 160 seconds and the majority of phagophore initiation events fail to produce mature autophagosomes. In total our work establishes a new experimental framework to quantitatively analyze autophagy and demonstrates that ATG9 vesicles are the seeds for autophagosome formation in human cells.
Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains

Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. Retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the novel nanoparticles we describe may be broadly useful in biotechnological applications.