SIRIS-Lab/unlabelled-sti-corpus huggingface dataset:
Predicting metabolic pathways from bacterial operons and regulons

The pathway extraction tool predicts metabolic pathways from sets of functionally related enzyme-coding genes [Faust, et al., Bioinformatics 2010, 26:1211]. In contrast to pathway projection approaches, pathway discovery does not rely on any assumption of pathway conservation. This approach can detect variants, super-pathways, and “cross-map” paths. It can be applied to organisms whose metabolism is unknown, but for which enzyme-coding genes have been identified in the genome, and some information is available about their functional grouping (co- expression, operons, gene fusion, ....). Materials and Methods To extract a pathway, we connect query compounds or reactions in the metabolic network using various algorithms: the random walk based kWalks algorithm, three approaches based on k-shortest path finding and combinations of kWalks with the latter. When predicting pathways from genes, we have to link enzyme-coding genes to reactions. In case of broad-specificity enzymes, this yields a large number of reactions, only a few of which are relevant in the pathway. To address this problem, reactions catalyzed by the same EC number are merged into equivalence groups. Results We evaluated the pathway extraction algorithms on 71 MetaCyc pathways and found that a combination of kWalks with a shortest-paths based approach yields the highest accuracy (77%). The pathway extraction tool has been integrated in the Network Analysis Tools (NeAT, http://rsat.ulb.ac.be/neat/), and can be accessed via a web interface, as stand-alone application or as SOAP/WSDL Web services. The seed nodes for subgraph extraction can be provided as reactions, (partial) compound names as well as EC numbers or genes. Pathways can be extracted from KEGG, MetaCyc or custom networks. Discussion We will present a selection of study cases illustrating the way to combine operon prediction, phylogenetic footprint discovery and pathway extraction in order to infer metabolic pathways from bacterial genomes. In future, this strategy will be systematically applied on bacterial genomes in the framework of the MICROME project (EU FP7).
Hybrid drug delivery systems upon mesoporous materials, self assembled therapeutics and virosomes

HYMADE focuses on the development of capsules and engineered colloidal particles for drug delivery combining mesoporous colloids, the Layer by Layer (LbL) technique and virosomes. The capsules and particles have potential applications in cancer and inflammatory diseases such as rheumatoid arthritis and uveitis. 
The project is based on the secondments of Early Stage Researchers and Experienced Researchers and networking and training activities between European and non European academic institutions. 
HYMADE aims to profit from the combination of hybrid materials to fabricate advanced drug delivery systems with controlled release and targeting efficiency of biological entities. The project also aims to gain understanding of the self assembly process of hybrid materials and the transport properties of the drug delivery systems.The biological fate, drug release, degradation and therapeutical efficiency of the drug delivery systems will be studied in vitro and in vivo with state of the art imaging techniques. To achieve these goals we have  gathered an international multidisciplinary team with scientists at the forefront of Material Science, Self assembly, Physics, Chemistry, Biophysics and Imaging from Germany, Austria, France and Spain on the European side and from  United States of America, Argentina and Armenia on the non European side.
INVESTMENT SUPPORT FUND

The main objective of the planned project is to support entrepreneurs in creating and expanding advanced capacities for the development of products and services, which will contribute to the achievement of the specific objective of facilitating the stabilisation of the SME sector in the new economic conditions resulting from the COVID-19 outbreak. The project will be implemented in partnership by entities classified as part of the so-called. Business Environment Institution (IOB). These entities are located in the territory of Kujawsko-Pomorskie voivodship, have staff with the appropriate knowledge and experience to implement the project. The project will be implemented by:1. Toruń Regional Development Agency S.A. (PW),2. Kujawsko-Pomorski Fundusz Poloczkowy Sp. z o.o. (P1). The project plans to provide support in the form of grants for:1. investments related to the support of entrepreneurs participating in the supply chains of products and services relevant to countering and limiting the impact of COVID-19.2 investments related to the diversification of the company’s activities by introducing new products/services or introducing a new method of production/service provision for entrepreneurs affected by COVID-19.3 investments related to equipping retail outlets, such as residential stores, bakeries, etc. into air filtering equipment. The co-financed project must be carried out in the Kujawsko-Pomorskie voivodship. Deadline for implementation of the project: 05.2020-06.2022. Calls for proposals are expected to be published cyclically, with priority support to those companies most affected by the COVID-19 pandemic (highest decrease in gross income).
Compression Using Context Free Grammers

The emergence of computers and their operating systems caused the transmition and storing huge amounts of data, which operating system can manage. We are limited with memory space and also with the transfer data time. This was the reason for invention of first algorithms for compression data to small packages, intended for the storage and transmission. Such packages can be later extended in the source data, which means that they are intended to lower consumption of available resources, either space or time. 
The main theme is the comparison of a handful of existing compression algorithms 
based on context-free grammar. It will identify one of them in selected file formats behave optimally. For comparison I took a basic version of the LZW algorithm, the Re-Pair algorithm and the bisection algorithm. All algorithms are used for core compression context-free grammar and dictionary. I also implemented algorithms in the Pascal programming language, with Delphi development environment and made the user interface for testing. I chose to compare the time (speed) and compression ratio between the source and the compressed file. The main purpose was to determine behavior of algorithms on the selected files of different formats: graphic BMP (bitmap) format, TXT format, PostScript format, and Java source.
Autoxidation of anthropogenic volatile organic compounds (avoc) as a source of urban air pollution

Previous efforts to raise living standards have been based on relentlessly increasing combustion, causing environmental destruction at all scales. In addition to climate-warming CO2, fossil fuel combustion also produces a large number of organic compounds and particulate matter, which deteriorate air quality.

The atmosphere is cleansed from such pollutants by gas-phase oxidation reactions, which are invariably mediated by peroxy radicals (RO2). Oxidation transforms initially volatile and water-insoluble hydrocarbons into water-soluble forms (ultimately CO2), enabling scavenging by liquid droplets. A minor but crucially important alternative oxidation pathway leads to oxidative molecular growth, and formation of atmospheric aerosols. Aerosols impart a huge influence on the atmosphere, from local air quality issues to global climate forcing, yet their formation mechanisms and structures of organic aerosol precursors remains elusive.

In a paradigm change, RO2 was recently found to undergo autoxidation, enabling rapid aerosol precursor formation even at sub-second time-scales – in stark contrast to the long processing times (days - weeks) previously assumed to be necessary. We have shown how abundant biogenic hydrocarbons (BVOC) autoxidize, but due to key structural differences, the same pathways are not available for anthropogenic hydrocarbons (AVOC), and thus they were not expected to autoxidize. My preliminary experiments reveal that AVOCs do autoxidize, but the mechanism enabling this remain unknown. Crucially, the co-reactants shown to inhibit BVOC seem to enforce AVOC autoxidation – potentially explaining the recent mysterious discovery of new-particle formation in polluted megacities. In ADAPT, I will use a combination of novel mass spectrometric detection methods fortified by theoretical calculations, to solve the mechanism of AVOC autoxidation. This will directly assist both air quality management, and the design of cleaner fuels and engines.
Educational Systems and Inequalities in Educational Attainment in Central and Eastern European Countries

Before exploring the selectivity of educational attainment in detail, this article extensively describes the contours of educational systems in Central and Eastern European (CEE) countries. These countries provide an interesting setting in view of their post-secondary education expansion and differentiation, as well as their variation in the degree of vocational orientation at the secondary level. Drawing on high quality, national micro data, we find that students from disadvantaged family backgrounds who manage to enter post-secondary education are ‘diverted’ to second-tier post-secondary institutions, while longterm university programs are more likely to be dominated by students whose parents have an academic background. At the secondary level, we confirm the patterns of negative selection among students from lower social backgrounds into lower vocational programs. This diversion effect at the secondary level is especially pronounced in CEE countries that inherited a strong secondary vocational system and reinstalled early tracking.
Project drafting techniques in the field of cross-border cooperation - Adrijana Šonc Može and Adriana Longo

In the vast scenario of opportunities and challenges following EU enlargement, the need is emerging in the Italian-Slovenian cross-border area for a joint, coordinated, harmonious and sustainable development, to strengthen integration and increase territorial competitiveness. The project, falling within the field of vocational training and integration in the labour market, offers two work experiences targeting two unemployed persons, residing one in Italy and one in Slovenia, in the eligible areas of Community Initiative Programme INTERREG IIIA Italy-Slovenia 2000-2006. The traineeship - lasting for eight months - intends to train professionals who are able to recognize and manage the socio-economic processes afoot (both at public administration level and among enterprises) and who possess the necessary technical and specialist knowledge to draft cooperation projects functional to the joint and integrated development of the territory. During the period of training - under the close supervision of tutors who are experts in cross-border cooperation - the two trainees will learn, specifically, the techniques required in the various phases of project design, management and accounting.
Alpine space industrial Clusters’ networks: paving the way for Europe 2020

The Alpine Space economy is largely based on manufacturing SMEs and clusters are a powerful tool to enhance competitiveness. The establishment of transnational clusters networks is a step forward to favour cross-border cooperation although poor awareness of the potentialities from the addressees and the lack of self-sustainability in the medium and long term are still real barriers. AlpClusters2020 aims to contribute to the design of an integrated policy approach for the support of transnational clusters networks at ALPINE space level, in order to: -facilitate the emergence of new industries, enhancing the resilience of Alpine industrial ecosystem -track and valorise the achievements of the previous supported initiatives, assessing their impact -animate a deep and intense participatory process through which private and public relevant actors can take part in the design of future actions -support policy development process, exploring the synergies and suggesting joint actions toward 2020.
What can we learn from high-resolution numerical simulations of single- and multi-phase fluid flow in fractured outcrop analogues?

Naturally fractured reservoirs (NFR), such as the large carbonate reservoirs in the Middle East, contain a major part of the world's remaining conventional oil reserves, but recovering these is especially challenging as the fractures only constitute fluid conduits while the oil is trapped in a low-permeability rock matrix. Recovery factors are therefore difficult to estimate, permeability anisotropy is high, size and shape of drainage areas are difficult to constrain, early water breakthrough is likely to be associated with a high and irreversible water cut, and secondary recovery behaviour is unusual. Outcrop-analogue model-based discrete fracture and matrix (DFM) simulations have emerged recently, helping us to disentangle and rationalize this erratic production behaviour. They allow us to understand the emergent flow behaviour and resulting saturation patterns in NFRs. Thus, classical simulation approaches, such as dual-continua conceptualizations, can be critically evaluated and improved where they fail to capture the flow behaviour of interest. This paper discusses recent advances in DFM simulation of single- and multi-phase flow processes in geologically realistic outcrop-analogue models, and solved with finite-element (FE) and finite-volume (FV) methods. It also reviews key results from recent DFM simulation studies, in particular how new measures such as the fracture-matrix flux ratio and velocity spectra can provide new means to analyse flow behaviour in heterogeneous domains or how results from outcrop-based simulations can be used to test the suitability of conventional upscaling approaches for NFR and guide the development of new ones. We close by enlisting outstanding challenges in outcrop-based flow simulations such as the need to capture the fracture-matrix transfer processes due to capillary, gravity and viscous forces accurately, which often implies detailed grid refinement at the fracture-matrix interface and small time-steps to resolve the physical processes adequately. Thus, we explore how outcrop-based flow simulation could be applied more routinely in NFR reservoir characterization and simulation workflows.
Horizontally-structured CAD/CAM modeling for virtual concurrent product and process design

Disclosed herein is a method of horizontally structured CAD/CAM modeling and manufacturing for concurrent product and process design, comprising: selecting a blank for machining into an actual part establishing a coordinate system (6); and creating a master product and process concurrent model (40) comprising: a virtual blank (10) corresponding to the blank; a manufacturing feature (12a - 12j); virtual machining of the manufacturing feature (12a - 12j) into the virtual blank (10); where the manufacturing feature (12a - 12j) exhibits an associative relationship with the coordinate system (6). The method also includes generating a product drawing (44) of the actual part; and generating machining instructions to create the actual part by machining the manufacturing feature (12a - 12j) into the blank. Also disclosed herein is a horizontally structured CAD/CAM model for concurrent product and manufacturing processes comprising: a blank for machining into an actual part; a coordinate system (6); and a master product and process concurrent model (40) comprising: a virtual blank (10) corresponding to the blank; a manufacturing feature (12a - 12j); the manufacturing feature (12a - 12j) virtual machined into the virtual blank (10); and the manufacturing feature (12a - 12j) exhibiting an associative relationship with the coordinate system (6). Further disclosed is a storage medium encoded with a machine-readable computer program code for horizontally structured CAD/CAM modeling. The storage medium including instructions for causing a computer to implement the method of horizontally structured CAD/CAM modeling and manufacturing for concurrent product and process design. Additionally disclosed is a computer data signal for horizontally structured CAD/CAM modeling. The computer data signal comprising code configured to cause a processor to implement a method of horizontally structured CAD/CAM modeling and manufacturing for concurrent product and process design.
HEAT TRANSFER SYSTEM AND ELECTRIC OR OPTICAL COMPONENT

A novel heat transfer system (100) is herein proposed involving a coupler which, when attached to a heat sink (110), defines at least a part of a vapor chamber (130) inside the heat transfer system (100). The coupler (120) attaches component heat source (203) to the header (117) to a thermally transferring connection with the heat sink (110).
The hunt for brain Aβ oligomers by peripherally circulating multi-functional nanoparticles: Potential therapeutic approach for Alzheimer disease

We previously showed the ability of liposomes bi-functionalized with phosphatidic acid and an ApoE-derived peptide (mApoE-PA-LIP) to reduce brain Aβ in transgenic Alzheimer mice. Herein we investigated the efficacy of mApoE-PA-LIP to withdraw Aβ peptide in different aggregation forms from the brain, using a transwell cellular model of the blood-brain barrier and APP/PS1 mice. The spontaneous efflux of Aβ oligomers (Aβo), but not of Aβ fibrils, from the 'brain' side of the transwell was strongly enhanced (5-fold) in presence of mApoE-PA-LIP in the 'blood' compartment. This effect is due to a withdrawal of Aβo exerted by peripheral mApoE-PA-LIP by sink effect, because, when present in the brain side, they did not act as Aβo carrier and limit the oligomer efflux. In vivo peripheral administration of mApoE-PA-LIP significantly increased the plasma Aβ level, suggesting that Aβ-binding particles exploiting the sink effect can be used as a therapeutic strategy for Alzheimer disease. From the Clinical Editor: Alzheimer disease (AD) at present is an incurable disease, which is thought to be caused by an accumulation of amyloid-β (Aβ) peptides in the brain. Many strategies in combating this disease have been focused on either the prevention or dissolving these peptides. In this article, the authors showed the ability of liposomes bi-functionalized with phosphatidic acid and with an ApoE- derived peptide to withdraw amyloid peptides from the brain. The data would help the future design of more novel treatment for Alzheimer disease.
Structural insights into the dual substrate specificities of mammalian and Dictyostelium dihydropteridine reductases toward two stereoisomers of quinonoid dihydrobiopterin

Up to now, d-threo-tetrahydrobiopterin (DH(4), dictyopterin) was detected only in Dictyostelium discoideum, while the isomer L-erythro-tetrahydrobioterin (BH(4)) is common in mammals. To elucidate the mechanism of DH(4) regeneration by D. discoideum dihydropteridine reductase (DicDHPR), we have determined the crystal structure of DicDHPR complexed with NAD(+) at 2.16 Å resolution. Significant structural differences from mammalian DHPRs are found around the coenzyme binding site, resulting in a higher K(m) value for NADH (K(m)=46.51±0.4 μM) than mammals. In addition, we have found that rat DHPR as well as DicDHPR could bind to both substrates quinonoid-BH(2) and quinonoid-DH(2) by docking calculations and have confirmed their catalytic activity by in vitro assay.
GAARs and Treaties: From the Guiding Principle to the Principal Purpose Test. What Have We Gained from BEPS Action 6?

The issue of General Anti-Avoidance Rules (GAARs) and treaties is a legal problem as old as double tax conventions themselves. However, the Base Erosion and Profit Shifting (BEPS) Project, materialized in fifteen Actions and particularly in the Final Report of BEPS Action 6, involves a radical change in the very physiognomy of the problem. Apart from the inclusion of a Limitation-on-benefits rule in the OECD Model, the most groundbreaking innovation arising from BEPS Action 6 would be the incorporation, also to the Model, of a GAAR (the Principal Purpose Test). This article will examine the pros and cons of the Principal Purpose Testvis á vis the old paradigm. It also seeks to analyse some new problems originating from the very existence of the PPT.
Surfactant mediated enhanced biodegradation of hexachlorocyclohexane (HCH) isomers by Sphingomonas sp. NM05

Environmental biodegradation of several chlorinated pesticides is limited by their low solubility and sorption to soil surfaces. To mitigate this problem we quantified the effect of three biosurfactant viz., rhamnolipid, sophorolipid and trehalose-containing lipid on the dissolution, bioavailability, and biodegradation of HCH-isomers in liquid culture and in contaminated soil. The effect of biosurfactants was evaluated through the critical micelle concentration (CMC) value as determined for each isomer. The surfactant increased the solubilization of HCH isomers by 3-9 folds with rhamnolipid and sophorolipid being more effective and showing maximum solubilization of HCH isomers at 40 μg/mL, compared to trehalose-containing lipid showing peak solubilization at 60 μg/mL. The degradation of HCH isomers by Sphingomonas sp. NM05 in surfactant-amended liquid mineral salts medium showed 30% enhancement in 2 days as compared to degradation in 10 days in the absence of surfactant. HCH-spiked soil slurry incubated with surfactant also showed around 30-50% enhanced degradation of HCH which was comparable to the corresponding batch culture experiments. Among the three surfactants, sophorolipid offered highest solubilization and enhanced degradation of HCH isomers both in liquid medium and soil culture. The results of this study suggest the effectiveness of surfactants in improving HCH degradation by increased bioaccessibility.