SIRIS-Lab/unlabelled-sti-corpus huggingface dataset:
Substituent effects and local molecular shape correlations

Using a detailed electron density shape analysis methodology, a new method is proposed for studying the main components of substituent effects in a series of disubstituted benzenes, in correlation with their activating and deactivating characteristics as observed by the induced shape changes of a local electron density cloud. The numerical measures obtained for the extent of shape changes can be correlated with known and with some unexpected effects of various substituents. The insight obtained from the shape analysis provides a theoretical, electron density based justification for some well-known trends, but it also provides new explanations for some of the unexpected features of these substituent effects.
A tool for the automatic generation and analysis of regular analog layout modules

This paper describes the characteristics of a new CAD tool that enables the creation of layout libraries of selected analog modules. This Analog Modules Generator (AMG) automatically creates multiple layout versions of two commonly used analog structures: the differential pair and arrays of series-connected or stacked devices, for the subsequent generation of layout libraries. Based on the number of devices and rows defined by the user for the layout implementation, the tool validates all possible implementations, which are later saved in a database with their corresponding characteristics, such as area and parasitics information. Additionally, an extraction process can be optionally executed over all the layout views saved in the database. The AMG generates several reports with all the characteristics of the implemented layouts, including area and parasitic components, facilitating further statistical processing. We describe the features and capabilities of the proposed AMG tool, and several test cases are presented. Results show that optimal layout implementations can be achieved by layout and circuit designers in a reduced amount of time.
Cells and giant viruses: a win-win co-evolution

The discovery of Mimivirus, the first icosahedral virus visible by light microscopy, was followed by the characterization of many other relatives. Its aquatic relative Megavirus chilensis, has a 1.2 Mb genome and encodes more than 1000 proteins, 2/3 unique to the Mimiviridae. Their infectious cycle is cytoplasmic. During the last 10 years, my laboratory discovered three other giant virus families: -the pandoraviridae, with their unique amphora-shaped 1µm long virion morphologies, genome sizes reaching 3Mb and encoding thousands of proteins, most of which without homologues in the cellular or the viral world – the mollivirus, which was isolated from a 30,000 years old Siberian permafrost sample, presents common features with the pandoraviruses. They share 60 unique genes and the roughly spherical (0.6µm) mollivirions present an external tegument resembling the pandoravirions. Both viruses have an early nuclear phase – the pithovirus, despite its amphora-shaped virions, has a fully cytoplasmic cycle. Our work raised questions on the origin of these intriguing viral families and their position in the tree of life.  My project is unique as it will address the coevolution of these viruses and their amoebal hosts by focusing on specific features of the virions in two overall aims. 1) Promising preliminary results led us to hypothesize that a progressive transition from the rigid icosahedral virions to the more plastic amphora-shaped particles was made possible through hijacking of the host cellulose synthesis pathway by the ancestor of pandoraviruses. 2) The icosahedral mimivirus package its genome in a complex rod-shaped structure. My team will investigate this structure to unveil possible evolutionary links with the genome packaging systems in the cellular world. We will characterize the machinery responsible for such organization. These two high-risk/high-gain aims will continue to revisit the concept of virus and their evolutionary trajectory in the living world.
Noa, a disruptive portable device to monitor asthma

In Europe, about 30 million children and adults under 45 years old have asthma. There is no cure for asthma, it is a chronic disease. Asthma can have a very negative impact on the quality of life of those people who suffer from it. However, it can be diagnosed and effectively controlled at an early stage. The total cost of the disease for the European population aged between 15 and 64 was EUR 19.3 billion per year.
We have developed the NOA device, that monitors asthma in a simple, painless, non-invasive and precise way, with accurate and immediate results. The NOA is useful for both preventive and post-treatment monitoring.
The basis of the NOA device is its ability to measure the Fraction of Exhaled Nitric Oxide (FeNO) of human breath, which is a marker that indicates the existence and extent of inflammation to the upper airways caused by asthma.
The NOA is the only portable device able of monitoring asthma with high accuracy, and is easy to use and very fast (5 seconds) because of an innovative patent-protected technological development that combines electronics and pneumatics, sensors and mathematical algorithms. Our solution is based on studies carried out with high scientific rigor, which allows us to guarantee the validity of the NOA. The NOA device has been successfully tested by more than 100 people and 35 doctors.
Our client’s segments are hospitals with departments of allergology and/or pneumology and pharmacies. The NOA has important advantages in regard to convenience, speed of the test, price and business model, making it feasible for pharmacies to offer a service that has, up to now, not been on offer.
The general objective of the Innovation Project is to bring the NOA device to the European market. Phase 1 of SME Instrument represents an opportunity to get a thorough business plan to minimize risks.
Vattu — Virtual products of manufacturing industry

The aim of the project is to produce and implement new information for companies to utilise gaming engine technology in their production and operations through research, studies and experiments. In particular, the study will focus on the cost-effective translation of design models, i.e. 3D CADs, with the most automated processes possible for gaming engine platforms, as this is the most costly and burdensome phase made by traditional methods. For example, when involving users in the design and prototype phase, marketing non-finished products or training users in the product, 3D CAD models do not work on different devices or formats, such as mobile devices or AR/VR platforms, and are not visually realistic for the above-mentioned usage needs. The biggest strengths of the game engines are increased functionality, a more realistic visual look and a versatile development for different platforms. These are not offered by any other solution as a whole.The aim of the project is also:- Providing information on the topic to education so that they can renew their education programmes with future needs remarks. In addition, participate in the curriculum reform work on this theme.- Increase the procurement skills of companies in the region in order to obtain solutions in accordance with the themes of the project and lower the threshold for companies to carry out rapid experimentation and provide support.The project measures are divided into the following työpaketteihin:TP1: Production of the latest knowledge through research, studies and experimentsTP2: Identification of needs and opportunitiesTP3: Implementation of pilotsTP4: Dissemination and Stakeholder CooperationTP5: Project management The result of the project is 2 concrete pilots, studies, reports and publications, thesis and new knowledge and expertise in the area, which can be utilised in the network of operators.
MONITORING OF HEALTH CARE DATA

The invention provides an apparatus for gathering and/or representing health data. The apparatus includes means for prompting a user to respond to one or more healthcare-related queries, said one or more queries being selectable from a memory containing a plurality of healthcare-related queries; means for receiving data in response to the queries; and means for processing at least a subset of the received data. The invention also provides corresponding systems and methods.
Nitrogen Removal over Nitrite by Aeration Control in Aerobic Granular Sludge Sequencing Batch Reactors

This study investigated the potential of aeration control for the achievement of N-removal over nitrite with aerobic granular sludge in sequencing batch reactors. N-removal over nitrite requires less COD, which is particularly interesting if COD is the limiting parameter for nutrient removal. The nutrient removal performances for COD, N and P have been analyzed as well as the concentration of nitrite-oxidizing bacteria in the granular sludge. Aeration phase length control combined with intermittent aeration or alternate high-low DO, has proven to be an efficient way to reduce the nitrite-oxidizing bacteria population and hence achieve N-removal over nitrite. N-removal efficiencies of up to 95% were achieved for an influent wastewater with COD:N:P ratios of 20:2.5:1. The total N-removal rate was 0.18 kgN·m-3·d-1. With N-removal over nitrate the N-removal was only 74%. At 20 °C, the nitrite-oxidizing bacteria concentration decreased by over 95% in 60 days and it was possible to switch from N-removal over nitrite to N-removal over nitrate and back again. At 15 °C, the nitrite-oxidizing bacteria concentration decreased too but less, and nitrite oxidation could not be completely suppressed. However, the combination of aeration phase length control and high-low DO was also at 15 °C successful to maintain the nitrite pathway despite the fact that the maximum growth rate of nitrite-oxidizing bacteria at temperatures below 20 °C is in general higher than the one of ammonium-oxidizing bacteria.
Phantom energy accretion and primordial black holes evolution in Brans–Dicke theory

In this work, we study the evolution of primordial black holes within the context of Brans-Dicke theory by considering the presence of a dark energy component with a super-negative equation of state called phantom energy as a background. Besides Hawking evaporation, here we consider two type of accretions - radiation accretion and phantom energy accretion. We found that radiation accretion increases the lifetime of primordial black holes whereas phantom accretion decreases the lifespan of primordial black holes. Investigating the competition between the radiation accretion and phantom accretion, we got that there is an instant during the matter-dominated era beyond which phantom accretion dominates radiation accretion. So the primordial black holes which are formed in the later part of radiation dominated era and in matter dominated era are evaporated at a quicker rate than the Hawking evaporation. But for presently evaporating primordial black holes, radiation accretion and Hawking evaporation terms are dominant over phantom accretion term and hence presently evaporating primordial black holes are not much affected by phantom accretion.
Information from symbols and illustrations: how to get it without vision

In everyday life individuals are bombarded with symbols and illustrations: ‘poisonous’, ‘flammable’, ‘fire evacuation route’ etc.; however this life-saving information is not accessible to all of us.

One in 30 Europeans experiences sight loss, including one in three individuals over 65 years of age. These individuals cannot recognise a face, or read a symbol or an illustration: they rely on their sense of touch.

Those who use touch mix up angles and curves over 50% of the time which makes interpreting tactile symbols and illustrations problematic: the Euro symbol (€) may be mistaken for the capital E; the Pythagorean triangle may have no right angle. This mix-up has serious consequences:
– Lack of awareness of important, sometimes life-saving information. This is a particular problem for individuals with low tactile sensibility (often caused by age, diabetes or stroke). Marie Sklodowska-Curie herself experienced this double disability (blindness and low tactile sensibility);
– Shortcomings in school, e.g. in science, where teaching relies on symbols and illustrations

The objective of the InSIght project is to investigate in what configuration(s) of shape features angles are perceived as angles, curves as curves and straight lines as straight lines – and if misperceived, why. These results will be the basis for a visionary project to develop a checklist and teaching guide on tactile symbols and illustrations. Through this strategy InSIght will improve awareness of important, potentially life-saving, information and reduce shortcomings in school, e.g., in science; thus the environment’s costs for special needs education. Finally, InSIght will reduce the environment’s costs by leading to development of universal design standards for tactile symbols and illustrations.

InSIght will produce four academic and non-academic articles, and develop a non-academic booklet with the checklist and teaching guide. It will set up a European conference and an interactive webpage.
Novel imaging of the heart for new structural and metabolic diagnosis

Each year cardiovascular disease (CVD) causes over 4 million deaths in Europe. Predictions suggest that 80% of premature heart disease and stroke is preventable, but ~20% of CVDs are misdiagnosed, and in elderly patients up to 60% of CVDs remain undiagnosed. We need to develop new technologies and strategies for early and accurate diagnosis of the biggest killer in western society.

Currently, diagnosis of CVD is based on assessment of macro-anatomy, whole heart function, and whole body metabolic markers. Early CVD processes begin in heart cells, before evolving to the ’macro’ pathology recognisable by traditional techniques. Clinicians desire a non-invasive technique that can provide high-resolution 3D micro-anatomy, and organ specific regional metabolic assessment. However the intricate micro-anatomy of the heart and its dynamic relationship with cardiac function is still fiercely debated.

To elucidate the true micro-anatomy of the heart, and understand its correlation with both pump- and metabolic function in health and disease, I will investigate the following questions:
1)What is the true micro-anatomy of the heart, and how is it remodelled in disease?
2)What is the role of 3D micro-anatomy in 4D pump function?
3)Does micro-anatomical remodelling correlate with regional changes in metabolism?

Using novel state-of-the-art non-invasive 3D and 4D ex-vivo and in-vivo imaging methodologies, I will answer these questions. We will finally understand the micro-anatomy of the heart in 3D, and its relationship with cardiac contraction and metabolism in disease. I hypothesise detecting and correlating novel morphological and metabolic changes upstream of the macro-anatomical and non-specific metabolic changes identifiable by traditional techniques, will offer the foundation for a step-wise change in diagnosis of CVD.

Working with world-renowned researchers, I will develop interdisciplinary skills in functional cardiac imaging to support a productive career in academia.
Construction of a twin-pier platform for biological sensing

This paper describes the successful construction of a twin-pier platform for use in biological sensing applications. The two piers are inline and have a tunable gap between them, with gap distance varying between 60–200 nm. The proximal ends of the piers are contiguous with a Co-Planar Waveguide structure that allows for testing. The basic pier structure was created by ablation of a customized MMA/PMMA stack using a JEOL laser system. A layer of Ti-Au was then deposited on silicon using standard electron beam deposition techniques. Electromagnetic testing of the structures was correlated with SEM imagery for characterization of electrical properties and gap integrity. The overall design is to create a biological sensing bridge by tethering molecules across the distal ends of the piers thereby completing the circuit. The type and composition of biological bridge provides sensor selectivity and sensitivity.
Assessment of RNA Stability in Postmortem Tissue from New-Born Lambs

The recovery of high quality RNA from postmortem tissue is crucial to gene expression analyses. The acquisition of postmortem tissue has inherent time delays and, hence, understanding the temporal variation in the stability of total RNA is imperative. This experiment aimed: ( 1 ) to qualitatively and quantitatively assess the integrity of total RNA derived from a range of new-born ovine tissues (liver, spleen, thyroid, skeletal muscle, ileum, and perirenal adipose tissue) which were stored at ambient temperature until extraction at 0, 3, 6, and 9 h postmortem; and ( 2 ) to analyze the stability of the reference gene(s) and expression of specific target genes in these tissues. Postmortem sampling time resulted in variable reductions in the relative integrity number (RIN) values across the tissues, ranging from 0.9 to 1.8% in liver, spleen, skeletal muscle, and ileum to 5.7-11.1% in the thyroid and perirenal adipose tissues, respectively (P < 0.05). In conclusion, tissues with small reductions in RIN value can exhibit disproportionately large differences in the normalization factor used to calculate the target gene expression. Hence, changes in transcript abundance due to RNA degradation are not always sufficiently buffered through normalization with reference genes. The normalization factor should be presented alongside the RIN value in postmortem tissue studies.
New chemical synthetic methods for reacting phenols selectively with different molecules and with itself: use of electricity as a sustainable, economic and traceless reagent.

Inventing new green and inexpensive synthetic methods for relevant chemical compounds is one of the ways how organic chemist can contribute to the well-being of humans and Earth.  One of the most promising chemical method for this is synthetic organic electrochemistry. It can replace chemical reducing agents and oxidizers with sole cheap electrons or electron-holes and, at the same time, reduce both the amount of waste and the expense of chemical synthesis. Syntheses are easily controllable as they can be ‘switched-off’ and they are implementable on a large industrial scale with ease. Interestingly, organic electrosynthesis can be used to stabilize electrical grids as fluctuating electric currents are tolerated in certain reactions. 

The aim of this project is to develop new sustainable, selective and economic electro-organic synthetic methods for the functionalization of phenols. Particularly, we will concentrate on our efforts for finding new ways to form C-heteroatom bonds between phenols and different substrates. At first, we will study the conversion of phenols to diarylethers and dibenzofurans that are important building blocks and core structures of natural products and biologically active substances. Later, we will try to extend the reactivity for phenol-analogues as wll. On the next step, we will study the cross-coupling between phenols and benzoxazoles and its analogues. In this way, we also obtain important synthetic intermediates for organic chemistry in a sustainable and ecologic manner. The proposed action is divided in two research and three additional work packages. 

The project will be implemented at the Institute of Organic Chemistry of Johannes-Gutenberg-University in Mainz in the research group of Professor Siegfried Waldvogel. He has been one of the driving forces of electro-organic synthesis already for 18 years and made seminal contributions during that time. It is therefore the top laboratory worldwide for performing the proposed action.
Een-Innovate pt

The main goal of this project is to contribute to greater economic impact from innovation activities in SMEs, by reinforcing their innovation management capacity and contributing to establish more effective and efficient links between actors through all the innovation chain. In order to achieve the above objective, 2 main target groups and 2 specific objectives are defined: i) SMEs beneficiaries of Horizon 2020 SME Instrument (Phase 1 and Phase 2) the specific objectives of this service (KAM) consist in identifying bottlenecks to the creation of economic impact in companies benefitting from grants and address these bottlenecks with the help of capable coaches. ii) SMEs with significant innovation activities and a high potential for internationalisation, which could potentially become beneficiaries of European research and innovation programmes but without effective access to consulting services for innovation management. The objective of this service (EIMC) is to increase the efficiency and effectiveness of innovation processes in those companies. For the WP 2017-2018, we propose to deliver a 3rd service to a new target group iii) SMEs awarded with a Seal of Excellence from H2020 SME Instrument, the objective is to take advantage of the work made by the EU and try to create synergies between investment in the framework of Horizonte 2020 and other sources of national and international funding; we intend to develop a signaling service forwarding them to services of advice and support in the scope of activity 1 of EEN – PORTUGAL Consortium. This objective will be developed in close collaboration with relevant stakeholders. In summary, the partners participating in this project (IAPMEI, ADI, CEC and INESC) expect to deliver a total of 119 services covering all the country. The project respects the excellence, 'no wrong door', proximity, subsidiarity and additionally principles as well as the mechanisms of signposting and follow-up of target audience inside the Network.
Cationic Poly([R]‐3‐hydroxybutyrate) Copolymers as Antimicrobial Agents

Poly([R]-3-hydroxybutyrate) (PHB), a natural biodegradable polyester, has attracted much attention as a new biomaterial because of its sustainability and good biocompatibility. In this study, it is discovered that PHB can be conveniently functionalized to obtain a number of platform chain architectures that may provide a wide range of functional copolymers. In a transesterification reaction, linear (di-hydroxylated) and star shaped (tri- and tetra-hydroxylated) PHB oligomers are synthesized, followed by copolymerization with 2-(dimethylamino)ethyl methacrylate and quaternization with benzyl bromide to afford antimicrobial properties. The antimicrobial activities of the quaternary salts against clinically relevant pathogens on the interactions with outer and cytoplasmic membranes, lethal mechanisms, multipassage resistance, and synergy effect with antibiotics are investigated. Cationic PHB copolymers show effectiveness as antimicrobial agents, with minimum inhibitory concentration values 0.24-0.65 µm (or µmol dm-3 ) (or 32-128 µg mL-1 ) against Gram-positive and Gram-negative bacteria. Modifying the copolymer architectures into star shapes results in enhanced effectiveness to disrupt the membrane integrity. Synergistic effects are attained for all the quaternized PHB derivatives when they are used together with tobramycin. Multipassage resistance does not occur in both the linear and star derivatives against Gram-negative bacteria after 20 passages.