Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of Joint Vector-space Embeddings from Heterogeneous Data Sources

Recent state-of-the-art approaches in Natural Language Processing and Graph Learning have shown to benefit from the combination of heterogeneous data sources, such as texts and graphs, as these can complement each other in terms of their content. Thus, in order to exploit the available complementary content, complex architectures need to be developed. In this context, semi-structured Knowledge Graphs, which consist of structured data (entities and relations) and unstructured data (literals), are an important information source. However, they are naturally incomplete, and at the same time often contain data of different data types as literals. My thesis proposes to jointly learn vector space embeddings from differently-structured sources to make the data accessible to established approaches without modification of their architecture. It is expected that data sources complement each other, which leads to reduced task training time and increased task performance and robustness. Applications range from Link Prediction in graphs to Named Entity Recognition. My thesis proposes two ways towards a jointly learned embedding space: one solution is to transform all data into a common representation before training, the other possibility is to combine the data during training through data type specific encoders or jointly optimized loss functions.
Exploring project managers’ perception of stress when working in increasingly complex construction projects

Stress is a recognised feature of the project managers’ life. Projects are becoming more complex with the uncertainty in the system contributing to the lack of control and added stress. This study explores a microcosm of 25 project managers in the South Australian construction industry, their perceived level of uncertainty and stress. The project managers interviewed provide their views on what their key stressors were and the mechanisms they use to manage effectively their stress. The results showed that structural, technical and directional complexity of projects was high, but this did not always convert into more stress for the project managers. The results indicate that stressors like the lack of resources; lack of control and increasing accountability were project managers’ primary concerns. Coping strategies included optimism, applying emotional intelligence and active planning strategies. In addition, they reduced their stress by working with good teams, using theirs and their team's experience, implementing sound systems and processes and effectively researching and gathering information.
The use of prevention through design as a management tool: a systematic review

The Prevention Through Design – PtD can be used as a project management and coordination tool, which aims to reduce the number of accidents in civil construction. Therefore, it is necessary to understand the occupational health and safety scenario to establish preventive control measures. In this sense, it is important that prevention is effective, whether in the concept design or execution phase. Thus, this study aims to investigate works that have addressed the PtD, seeking to analyze its usability as a management tool, also pointing out its positive and negative aspects. The methodology followed the guidelines of the Preferred Report Items for Systematic Reviews and Meta-Analysis (PRISMA), using keywords in agreement with the Boolean descriptor “AND” such as: “prevention through design”, “management”, “construction”, “occupational safety”, “design” and “design for safety”. Initially, 624 articles were found, but with the application of filters, 30 articles remained for full reading. After the complete reading, 14 articles were included for detailed analysis. It was observed that in underdeveloped countries, the tool is not applied. However, in more developed countries the Prevention Through Design – PtD tool is highly requested for accident prevention. Finally, it is understood that there is a cost linked to the accident management tool, however it is seen that when it is implemented, the number of accidents is reduced, which makes the tool effective.
BLUE MUSSEL MYTILUS EDULIS AS HABITAT PROVIDER ON OFFSHORE WIND TURBINE FOUNDATIONS

We compare the species composition of the early (mussels not prevalent) and mature (mussels prevalent) subtidal colonizing communities at offshore wind turbine foundations with special attention to the mobility and habitat preferences of the colonizing species. We identified 47 species belonging to nine different phyla from the samples of the mature community, including 21 species unique to the secondary substratum provided by the mussel shell, all of them are sessile species. Only 17 of the 37 species identified from the early subtidal colonizing community were present in the mature community. The main phyla present in both the early and mature samples were Mollusca, Arthropoda, and Annelida. Our findings confirm the hypothesis that mussels counteract the impoverishment of total species richness on wind turbines, caused by the abundant presence of Metridium senile in mature artificial hard substratum communities by providing secondary substratum for colonization by. sessile and hemi-sessile epifauna. The species assemblage found on these mussels is different from the one previously found on the piles, and only seven-teen species (~36%) present in the mature community were already present in the first year after installation. In 2020, all bryozoan species (7) were exclusively observed on the secondary substratum provided by the shells of the mussels. However, these species were previously encountered on the scour protection or on the shells of other bivalves. This may be due to the fact that the secondary substratum provided by the mussels differs in physical properties (e.g., microhabitat complexity) from the primary (vertical) substratum of the pile.
Nowcasting Indonesia’s GDP Growth: Are Fiscal Data Useful?

Since introduced by Giannone et al. (2008), GDP nowcasting models have been used in many countries, including Indonesia. Variables to select usually include housing and construction, income, manufacturing, labor, surveys, international trade, retails and consumptions. Interestingly, fiscal variables are excluded even though government expenditure is an integral part of the basic GDP identity. By employing the Bok et al. (2018)’s quarter -to-quarter real GDP growth nowcasting technique, this paper is aimed at testing the usefulness of inclusion of fiscal variables, in addition to 61 non-fiscal variables, in nowcasting Indonesia GDP. The results show, even though based on the fact that fiscal data have low correlation coefficients to GDP, the inclusion of fiscal data may help to produce a better early estimate of GDP growth.
Hate and Offensive Language Detection using BERT for English Subtask A

This paper presents the results and main findings of the HASOC-2021 Hate/Offensive Language Identification Subtask A. The work consisted of fine-tuning pre-trained transformer networks such as BERT and an ensemble of different models, including CNN and BERT. We have used the HASOC-2021 English 3.8k annotated twitter dataset. We compare current pre-trained transformer networks with and without Masked-Language-Modelling (MLM) fine-tuning on their performance for offensive language detection. Among different BERT MLM fine-tuned BERT-base, BERT-large, and ALBERT outperformed other models; however, BERT and CNN ensemble classifier that applies majority voting outperformed other models, achieving 85.1% F1 score on both hate/non-hate labels. Our final submission achieved 77.0 F1 in the HASOC-2021 competition.
A Sequential Algorithmic Pattern

This paper discuss the general class of algorithms that can be implemented using sequential constructions. Common characteristics of these algorithms are also described in order to provide a generic representation for sequential algorithms. In addition it descri bes the sequential pattern in terms of pixel scans and its relationship within mathematical morphology. Such a pattern is essential for the development of morphological operators and operations. Examples of pattern usage are the distance tranform, reconstruction, extrema detection, minima imposition and so on.
Digital Creativity and the Regional Museum: Experimental Collaboration at the Convergence of Immersive Media and Exhibition Design

This paper presents the findings of the Within the Walls of York Gaol, an interdisciplinary and collaborative practice-based research project which was established to examine the intersection between emerging forms of immersive media, game design, and contemporary archaeological exhibition design. The project was a collaboration between researchers and practitioners at York Museums Trust, The University of York, and the University of Glasgow and used co-design methods to design and produce two immersive installations in the prison cells at York Castle Museum in collaboration with community groups. The project sought to re-think the role of the museum within regional creative economies and to argue for the importance of the regional museum as a hub for digital design and innovation. Through innovative forms of collaborative research practice the project was able to develop new understandings of the ways in which collaborative approaches to the design and development of interactive digital media can be used to build skilled communities of practice around regional museums. The project took a critical stance to the use of immersive media technologies and led to the development of innovative and highly distinctive digital immersive installations which emerged in response to the specific opportunities and design requirements of museums and their audiences. This paper will set out the findings of this project as well as identify new creative directions and new forms of collaborative design practice which can be adopted and adapted for use across the museum sector.
Toward Multi-area Contactless Museum Visitor Counting with Commodity WiFi

Multi-area visitor counting plays a critical role in museum management, which can help administrative staff better study visitor flows and hotspots, so that they can ensure the quality and safety of visits. Internet of Things (IoT) techniques facilitate efficient recording and understanding of visitors’ spatial and temporal distribution in museums, and traditional visitor tracking applications use surveillance cameras or wireless connections with portable smart devices. However, these methods either involve privacy concerns or face the obstacle of getting natural behavioral data of all visitors. This article explores an IoT monitoring methodology in the field of museum studies, proposing a commodity WiFi-based head-counting framework that does not need the visitor to connect with any device. Our system analyzes the Channel State Information amplitude fluctuations at the fixed receiver caused when visitors cross the line-of-sight link. It enables multi-area visitor counting by achieving In-and-Out traffic detection at different sites with a convolutional neural network algorithm. The method also allows for a rough classification of visitor types based on body size, and an extra transfer module is presented to reduce training time for increasing sensing scenarios. Over 2,300 samples at five different sites were collected to test the usability. Experiment 1 implemented in three environments/deployments demonstrated that the proposed approach can be potentially implemented in variable sites of museums. It achieved high up to 95% and 99% accuracies for identifying the number and direction of people crossing, respectively. Experiment 2 sampled adults, children, and adult-child groups at a science museum and achieved approximately 89% classification accuracy of visitor types. Experiment 3 collected data for all cases in which up to three targets entered and exited simultaneously, and reached a recognition accuracy of around 88% for nine different cases. The potential and limitations for the practical application of wireless contactless sensing to cultural spaces are discussed.
Nuanced role for dendritic cell intrinsic IRE1 RNase in the regulation of antitumor adaptive immunity

The IRE1/XBP1s axis of the unfolded protein response (UPR) plays divergent roles in dendritic cell (DC) biology in steady state versus tumor contexts. Whereas tumor associated DCs show dysfunctional IRE1/XBP1s activation that curtails their function, the homeostasis of conventional type 1 DCs (cDC1) in tissues requires intact IRE1 RNase activity. Considering that cDC1s are key orchestrators of antitumor immunity, it is relevant to understand the functional versus dysfunctional roles of IRE1/XBP1s in tumor DC subtypes. Here, we show that cDC1s constitutively activate IRE1 RNase within subcutaneous B16 melanoma and MC38 adenocarcinoma tumor models. Mice lacking XBP1s in DCs display increased melanoma tumor growth, reduced T cell effector responses and accumulation of terminal exhausted CD8+ T cells. Transcriptomic studies revealed that XBP1 deficiency in tumor cDC1s decreased expression of mRNAs encoding XBP1s and regulated IRE1 dependent decay (RIDD) targets. Finally, we find that the dysregulated melanoma growth and impaired T cell immunity noticed in XBP1 deficient mice are attributed to RIDD induction in DCs. This work indicates that IRE1 RNase activity in melanoma/MC38-associated DCs fine tunes aspects of antitumor immunity independently of XBP1s, revealing a differential role for the UPR axis that depends on the DC subtype and cancer model.
Reassessing the Abundance of miRNAs in the Human Pancreas and Rodent Cell Lines and Its Implication

miRNAs are critical for pancreas development and function. However, we found that there are discrepancies of pancreatic miRNA abundance in published datasets. To obtain a more relevant profile that is close to the true profile, we profiled small RNAs from human islets cells, acini, and four rodent pancreatic cell lines routinely used in diabetes and pancreatic research using a bias reduction protocol for small RNA sequencing. In contrast to the previous notion that miR-375-3p is the sole dominant pancreatic miRNA, we found that miR-148a-3p and miR-7-5p were equally abundant in islets. In silico studies using predicted and validated targets of these three miRNAs revealed that they possibly work in cooperation to modulate cell differentiation in endocrine and exocrine cells. Our results also suggest, compare to the well characterized miR-375, both miR-148a-3p and miR-7-5p may play more critical roles in human pancreas development and function. Moreover, according to in silico predicted targets, we found that miR-375-3p had a much broader target spectrum by targeting the coding sequence and the 5’ untranslated region rather than the conventional 3’ untranslated region, suggesting additional unexplored roles for miR-375-3p beyond pancreas. Our study provides a valuable resource for studying miRNAs in pancreas.
What drives prey selection? Assessment of tiger food habits across the Terai-Arc landscape, India

Large carnivores strongly shape ecological interactions within their respective ecosystems, but experience significant conflicts with human across their range due to their specific ecological resource requirements. The tiger (Panthera tigris) typifies the challenges faced by the large carnivore communities globally. India retains majority of the global tiger population with significant numbers outside protected areas (PAs) that are involved in conflicts from livestock predation and human/tiger death. To understand the prey selection patterns and spatio-temporal patterns of livestock predation-related conflict issues we investigated tiger food habits across the Indian part of the Terai-Arc Landscape (TAL), a globally-important tiger conservation landscape in India. We used 510 genetically-confirmed tiger faeces collected across the landscape and ascertained 10 wild and livestock as major prey species. Large-bodied species (sambar, swamp deer, nilgai, chital, wild pig and livestock) comprised ~94% of tiger diet, with sambar, chital and livestock were the major prey species. Habitat-specific (Shivalik-Bhabar and Terai) analyses show significantly different pattern of prey selections determined by abundance and prey body weight. Results also suggest that PA and non-PAs of Terai habitat are more prone to livestock depredation-related conflicts, and careful management interventions and community involvements are required to reduce such threats. We suggest long-term plans including population estimation of tigers and prey outside PAs, reducing grazing pressures and cattle enumeration, detailed investigation of tiger deaths etc. to ensure future tiger sustainability across this habitat.
Fixing reference errors efficiently improves sequencing results

The GRCh38 reference is the current standard in human genomics research and clinical applications, but includes errors across 33 protein-coding genes, including 12 with medical relevance. Current studies rely on the correctness of this reference genome and require an accurate and cost-effective way to improve variant calling and expression analysis across these erroneous loci. We identified likely artifacts in GTEx, gnomAD, 1000 Genomes Project, and other important genomic resources leading to wrong interpretations for these genes. Here, we present FixItFelix together with a modified GRCh38 version that improves the subsequent analysis across these genes within minutes for an existing BAM/CRAM file. We showcase these improvements over multi-ethnic control samples across short and long-read DNA-, and RNA-sequencing. Furthermore, applying our approach across thousands of genomes demonstrates improvements for population variant calling as well as eQTL studies. Still, some genes e.g., DUSP22 indicate mixed results due to their complexity.
DNA-binding mechanism and evolution of replication protein A

Here the authors present the structure of Replication Protein A (RPA) in Archaea. The RPA structure from P. abyssi has been determined in presence and absence of DNA, providing insights into the evolution of this replication factor in eukaryotes Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD ( A cidic R pa1 O B-binding D omain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
Relationship between salmon egg subsidy and the distribution of an avian predator

As a spatial subsidy, which is the phenomenon of transferring resources from a donor system to a recipient system, anadromous salmonids contribute to the supply of marine-derived nutrients to freshwater and terrestrial systems. Live salmon and salmon carcasses and eggs are utilized by various organisms and affect their abundance and distribution. However, the evaluation of the effect of salmon subsidies on the abundance and distribution of terrestrial animals is biased towards predators or scavengers that utilize spawning adults and carcasses, and few studies have focused on the effect of salmon eggs as a subsidy. To avoid underestimating the function of salmon subsidies, the response to the availability of salmon eggs in various systems should be investigated. Here, we investigated the abundance and feeding behaviour of the brown dipper Cinclus pallasii, as salmon egg a consumer, based on the hypothesis that the availability of salmon eggs affects the diet composition and stream distribution of this small predator. In addition, to test whether changes in the abundance of brown dippers are determined by salmon spawning or by other factors, their abundance was compared upstream and downstream of the dam. Brown dippers used salmon eggs during the spawning season (63% of diet composition), and their abundance increased as the number of spawning redds increased. In contrast, this pattern was not observed upstream of the dam. These results suggested that the abundance and stream distribution of brown dippers vary according to the variation in the spatiotemporal availability of salmon eggs.
Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing

Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence. First, an RNA three-way junction harbouring the split system was assembled in an E. coli based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a ‘bio-orthogonal’ hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect femtomoles of a Campylobacter spp. DNA target sequence. Potential applications of our system include real-time monitoring of the self-assembly of nucleic acid-based devices in vivo and of intracellular delivery of therapeutic nanostructures, as well as in vitro and in vivo detection of different DNA/RNA target.