SIRIS-Lab/unlabelled-sti-corpus huggingface dataset:
A graph-based approach for designing extensible pipelines

In bioinformatics, it is important to build extensible and low-maintenance systems that are able to deal with the new tools and data formats that are constantly being developed. The traditional and simplest implementation of pipelines involves hardcoding the execution steps into programs or scripts. This approach can lead to problems when a pipeline is expanding because the incorporation of new tools is often error prone and time consuming. Current approaches to pipeline development such as workflow management systems focus on analysis tasks that are systematically repeated without significant changes in their course of execution, such as genome annotation. However, more dynamism on the pipeline composition is necessary when each execution requires a different combination of steps.We propose a graph-based approach to implement extensible and low-maintenance pipelines that is suitable for pipeline applications with multiple functionalities that require different combinations of steps in each execution. Here pipelines are composed automatically by compiling a specialised set of tools on demand, depending on the functionality required, instead of specifying every sequence of tools in advance. We represent the connectivity of pipeline components with a directed graph in which components are the graph edges, their inputs and outputs are the graph nodes, and the paths through the graph are pipelines. To that end, we developed special data structures and a pipeline system algorithm. We demonstrate the applicability of our approach by implementing a format conversion pipeline for the fields of population genetics and genetic epidemiology, but our approach is also helpful in other fields where the use of multiple software is necessary to perform comprehensive analyses, such as gene expression and proteomics analyses. The project code, documentation and the Java executables are available under an open source license at http://code.google.com/p/dynamic-pipeline. The system has been tested on Linux and Windows platforms.Our graph-based approach enables the automatic creation of pipelines by compiling a specialised set of tools on demand, depending on the functionality required. It also allows the implementation of extensible and low-maintenance pipelines and contributes towards consolidating openness and collaboration in bioinformatics systems. It is targeted at pipeline developers and is suited for implementing applications with sequential execution steps and combined functionalities. In the format conversion application, the automatic combination of conversion tools increased both the number of possible conversions available to the user and the extensibility of the system to allow for future updates with new file formats.
Cobalt, nickel, wolfram, cadmium, selenium, silver and gold-bearing mercurian tetrahedrite from the Saski Rad barite-siderite deposit in the Mid-Bosnian Schist Mts.

In the Saski Rad barite-siderite ore deposit, Hg-tetrahedrite is the main ore mineral, pyrite and some others are only accessories. Two tetrahedrite samples (fresh and weathered) have been analysed in detail: major and minor components, constituent trace elements, REE, and δ34SCDT values. The following microconstituents have been detected: Ni 71 ppm (in fresh sample) and 70 ppm (in weathered sample); Co 113 and 90 ppm; Cd 27 and 20 ppm; W 20 and 5 ppm, Bi 2500 and 1613 ppm; Se >100 and 72 ppm and Au 11 and 9 ppm. These values have been compared with the only currently available analysis of Hg-tetrahedrite from the Duboki Vagan near Kresevo in the Mid-Bosnian Schist Mts. (MBSM) carried out by JURKOVIC et al. (2010): Ni 266.2 ppm; Co 63.5 ppm, Cd 319.6 ppm; Bi 1466.0 ppm; Au 38.96 ppm which also agrees with our analysis of Hg-tetrahedrite from the Brixlegg barite deposit in Tyrol, Austria: Co 234.4 ppm; Cd 160.5 ppm; W 6.7 ppm; Sn 1.0 ppm; Bi 909.1 ppm; Se > 100 ppm and Au 2.3 ppm. The δ34SCDT isotope values of six tetrahedrites from the Saski Rad are on average –10.11‰, those of three tetrahedrites from the Duboki Vagan –10,05‰ and of the tetrahedrite from the Brixlegg deposit –1.60‰. The ΣREE content is lower in two analysed tetrahedrites from the Saski Rad deposit (10 ppm) compared to the tetrahedrite from Duboki Vagan (15 ppm) and the tetrahedrite from Brixlegg (17.4 ppm). The analysed barite sample from the Saski Rad deposit does not contain microconstituents typical of Hg-tetrahedrite. The distribution and genetic signifi cance of some trace elements, tetrahedrite microconstituents, REE and siderite isomorphic components in the seven most important genetic and paragenetic types of ore deposits in the MBSM and South-Eastern Bosnia have been commented upon.
WATERBORNE POLYURETHANE COATING COMPOSITIONS

Aqueous polyurethane coating compositions are disclosed in this specification. The aqueous polyurethane coating compositions contain a polycarbonate-polyurethane resin component, an aminopiast resin component, and a polyacrySic polyol component.
INNOVAZIONE TECNOLOGICA MEDIANTE INSERIMENTO NUOVA PRESSA AD INIEZIONE FULL ELECTRIC NEL CICLO DI STAMPA

INTRODUZIONE DI INNOVATIVA PRESSA AD INIEZIONE FULL ELECTRIC E DEL RELATIVO SISTEMA DI ALIMENTAZIONE ROBOTIZZATO, IN SOSTITUZIONE DI UNA PRESSA IDRAULICA,IN OTTICA DI INNOVAZIONE TECNOLOGICA DEL PROCESSO MEDIANTE AMMODERNAMENTO DEI MACCHINARI DEL REPARTO
Unravelling the mechanisms of competence induction by antibiotic stress in streptococcus pneumoniae

Despite the introduction of several vaccines, the human pathogen Streptococcus pneumoniae remains one of the leading bacterial causes of mortality worldwide, killing 1 million of children each year. In developed countries, the rise of multi-drug resistance in S. pneumoniae during last decade is a serious cause of concern, since the patient is more likely to require hospitalization consuming high health resources, and increasing the risk of death.
The main mechanism by which S. pneumoniae acquire and spread antibiotic resistance is by activation of the competence state that allows the uptake of exogenous DNA. Strikingly, competence is induced by several antibiotics, but the molecular mechanisms driving competence development are poorly understood. 
Our approach integrates the use of promoter-luciferase fusions to competence genes, transposon-mutagenesis and -sequencing, total RNA sequencing, knockout strains constructions and time-lapse fluorescence microscopy, to identify clinical antimicrobials that induce competence and unravel its underlying molecular mechanisms. Data generated in this project will provide a better understanding of the mode of action of these antibiotics and give valuable molecular insights into the evolution of antibiotic resistance in S. pneumoniae. 
Finally, we will test thousands of pairwise drug combinations in a novel high-throughput screen to identify inhibitors of the competence process. This highly relevant project will provide new pre-clinical data for future novel treatment strategies against bacterial infections and the mitigation of the spread of antibiotic resistance.
MOVABLE OCULAR PROSTHETIC AND RELATED SYSTEMS AND METHODS THEREOF

A movable ocular prosthetic apparatus and related systems and methods for moving an ocular prosthetic include a support member. An ocular prosthetic is mounted to the support member, wherein the ocular prosthetic is movable about the at least two axes of rotation. A control system controls a movement of the ocular prosthetic based on a sensed movement of a pupil of an eyeball of a human being.
Magnetic sensors based on two-dimensional materials/si

Magnetoresistance sensors based on the change in electrical resistance upon an external magnetic field are widely used in day to day applications. The magnetic sensor industry sells billions of dollars worth of sensors every year and there is an ever-growing demand for magnetic sensors with high sensitivity, small size, low power consumption and low cost with compatibility with existing electronic systems. The project aims to develop a new class of highly sensitive magnetoresistance sensors based on doped Si and two dimensional (2D) layered materials, with a focus on single layer graphene and single layer WS2 which could be easily extended to other low dimensional layered materials. This plan will utilize the advantages of tunnelling through SiO2, gate tunability of 2D materials and the geometry of Si to obtain highly sensitive magnetic sensors from Si, which is very unique and novel. The large magnetoresistance observed in graphene by the applicant's group (Gopinadhan et al. Phys. Rev. B 88, 195429 (2013)) can be utilized to get an additional positive change in total resistance per unit applied magnetic field for higher sensitivity. Si can be integrated monolithically, in contrast, 2D layered materials such as graphene possess excellent electrical, thermal and mechanical properties. Its high mobility of carriers are very attractive for high speed applications. The interface between Si and 2D materials are little explored, however there is an enormous technological interest for applications such as graphene-based transparent electrodes in Si solar cells, high speed non-volatile flash memory, microwave switches, voltage controlled diodes, logic devices etc. Furthermore, most of the existing magnetic sensors are electron based and the possibility of both n and p type magnetic sensors due to the electric field tunability of 2D materials may provide new applications such as magnetic sensor and diode (p-n junction) in one active device.
3-bromopyruvate (3BP) a fast acting, promising, powerful, specific, and effective “small molecule” anti-cancer agent taken from labside to bedside: introduction to a special issue

Although the "Warburg effect", i.e., elevated glucose metabolism to lactic acid (glycolysis) even in the presence of oxygen, has been recognized as the most common biochemical phenotype of cancer for over 80 years, its biochemical and genetic basis remained unknown for over 50 years. Work focused on elucidating the underlying mechanism(s) of the "Warburg effect" commenced in the author's laboratory in 1969. By 1985 among the novel findings made two related most directly to the basis of the "Warburg effect", the first that the mitochondrial content of tumors exhibiting this phenotype is markedly decreased relative to the tissue of origin, and the second that such mitochondria have markedly elevated amounts of the enzyme hexokinase-2 (HK2) bound to their outer membrane. HK2 is the first of a number of enzymes in cancer cells involved in metabolizing the sugar glucose to lactic acid. At its mitochondrial location HK2 binds at/near the protein VDAC (voltage dependent anion channel), escapes inhibition by its product glucose-6-phosphate, and gains access to mitochondrial produced ATP. As shown by others, it also helps immortalize cancer cells, i.e., prevents cell death. Based on these studies, the author's laboratory commenced experiments to elucidate the gene basis for the overexpression of HK2 in cancer. These studies led to both the discovery of a unique HK2 promoter region markedly activated by both hypoxic conditions and moderately activated by several metabolites (e.g., glucose), Also discovered was the promoter's regulation by epigenetic events (i.e., methylation, demethylation). Finally, the author's laboratory turned to the most important objective. Could they selectively and completely destroy cancerous tumors in animals? This led to the discovery in an experiment conceived, designed, and conducted by Young Ko that the small molecule 3-bromopyruvate (3BP), the subject of this mini-review series, is an incredibly powerful and swift acting anticancer agent. Significantly, in subsequent experiments with rodents (19 animals with advanced cancer) Ko led a project in which 3BP was shown in a short treatment period to eradicate all (100%). Ko's and co-author's findings once published attracted global attention leading world-wide to many other studies and publications related to 3BP and its potent anti-cancer effect. This Issue of the Journal of Bioenergetics and Biomembranes (JOBB 44-1) captures only a sampling of research conducted to date on 3BP as an anticancer agent, and includes also a Case Report on the first human patient known to the author to be treated with specially formulated 3BP. Suffice it to say in this bottom line, "3BP, a small molecule, results in a remarkable therapeutic effect when it comes to treating cancers exhibiting a "Warburg effect". This includes most cancer types.
Midfrontal cortex theta oscillations: causes and consequences

While reading this text, pat your head and rub your stomach (if someone sees you, tell them it's OK; you're doing science). Right now you are engaging in an action that must be actively monitored and quickly adjusted to avoid making mistakes. Over the past five years, my collaborators and I discovered that there is a specific pattern of brain electrical activity that occurs during response conflict—competition between multiple conflicting actions when a mistake could be made. This brain activity is observed over the midfrontal cortex (MFC) and is characterized by oscillations at around 6 cycles per second (the theta band). MFC theta is a highly statistically robust marker of the neural networks involved in action monitoring and behavior adjustments, correlates with single-trial reaction time, and predicts how well people learn from mistakes. Despite these robust findings linking MFC theta to action monitoring, the significance of MFC theta for how neural microcircuits actually implement action monitoring and adjustments is unknown. In the ERC research we will use computer simulations and rodent models to understand how different types of neurons in different cortical layers might use action potentials and oscillations to implement action monitoring. The results will help us understand how the brain monitors behavior and avoids mistakes, and will also give insight into neural microcircuit organization as it relates to higher cognitive function. While developing these computer simulations and rodent models, we will also take our human research to the next level by asking: If action monitoring in the MFC is supported by theta oscillations, does this mean that our actions, and our ability to monitor and adjust them, occur with theta rhythmicity? To answer this question, we will develop new tasks combining data-gloves and EEG to test how the timing of human sequenced actions during keyboard typing (typists type in “theta”) corresponds to temporal dynamics of MFC theta.
METHOD OF DISTINGUISHING GENOTYPES

The present invention relates to a method of distinguishing genotypes using PCR-PHFA including: a nucleic acid amplification step in which a mutation site-including region of a gene is amplified by a nucleic acid amplification reaction, thereby obtaining an amplification reaction solution; and a distinction step in which the amplification reaction solution obtained from the nucleic acid amplification step is mixed with a reference double-stranded nucleic acid having a specific genotype on the mutation site as well as being labeled with a labeling substance, and the mixture is subjected to a competitive strand displacement reaction, and the level of the occurrence of strand displacement is assessed so as to distinguish the identity; and the competitive strand displacement reaction is performed under a condition to suppress a polymerase extension reaction, and a genotype distinguishing kit for use in the distinct of genotypes by this method.
A compact, unmanned, renewables-powered and self-sufficient vessel able to pick up marine litter and to treat it on board for volume reduction and energy recovery

The project intends to explore the feasibility of introducing to the market Sea Litter Critters, a compact, unmanned, renewables-powered and self sufficient marine litter collection and treatment vessel based on a patent pending device treating waste thermally with plasma technology and no harmful emissions. This device is designed to operate near the shores especially nearer tourist facilities substituting the mechanical collection of litter currently adopted. By picking up litter (plastic debris mostly) near the point of entry, Sea Litter Critters contribute to minimising the pollution risks linked to plastic in the sea, where plastic items become brittle and break down into small particles, but basically never dissolve. Such particles can be eaten by zooplankton thus enter the foodchain. Therefore picking up plastic debris while still intact and as soon as possible after their disposal supports and complement in the short term all the high level policy actions for litter prevention (minimisation of waste, use of biodegradable plastic, awareness raising, beach clean up days etc.). This study aims to check the attractiveness of the innovation to the market involving potential customers (coast towns, associations of tourist and fishing ports and marinas, representatives from the cruise and hotels industry, marine natural reserves authorities). The first markets identified are on the Mediterranean Sea, which is at the center of a very highly populated area of the World with many Countries relying mostly on tourism. Studies confirm that the Med has mostly marine litter derived from this economic activity and up to 80% of it originating from land. Italy, with its over 7600km long coastline and a strong dependency upon tourism, will be the first market, followed suit by France and Croatia and then Spain and Greece. After a 3 year phase to cover development, industrialisation and commercialisation, production is expected to start in 2019, with employment of 17 new staff.
Industrial micro electrochemical cell sensors for real-time quantification of h2s in wastewater

Danish SME Unisense A/S has developed an industrial Micro Electrochemical Cell sensor (iMEC) for automatically quantifying dissolved gasses in liquids. In this project, Unisense will optimize their existing handmade sensors, customized for each client, to an auto-calibrated industrial version, targeting wastewater utility companies.
In the sewer systems, the prevalence of the toxic H2S gas (sewage gas) causes sewer corrosion and collapse, while at the same time entailing odour nuisances for the population living nearby. The robust iMEC sensor can be installed directly in the sewer network to accurately map H2S contents in real-time, and provide feedback to pumping stations to adjust the chemicals dosed accordingly. This will allow utilities to effectively control H2S levels in wastewater, thereby avoiding corrossion and toxic H2S leaks, and bringing significant economical savings to utilities and municipalities.
Microvehicle for stand-alone and shared mobility  - leonardo

The objectives of LEONARDO are: 
1) to develop a new microvehicle based on the smart fusion of the concepts of monowheel and scooter. The monowheel and the scooter have the best characteristics to be used as a means of daily transport and to fully exploit the intermodality. The new microvehicle will take the best features of these two vehicles and eliminate the disadvantages, obtaining a silent, clean, energy efficient and safe vehicle, as well as attractive and affordable to the public so that the barriers for adopting it are minimized. The development includes a) the consolidation of already outlined conpects, through analysis of functionality and comparison with existing vehicles, on the basis of an extensive analysis of user's needs and safety and regulamentary aspects b) structural and electrical / electronic design c) in-house testing
2) to do an extensive demonstration and re-design activity. The vehicle will be tested in a real environment in 4 European cities: Rome, Eilat and 2 others that will be identified with a tender. In these demonstration tests, a fleet of vehicle will be tested for free by hundreds of users, on a rotating basis. Each vehicle can be used in stand alone mode or in battery sharing mode, through a system already developed by UNIFI, made available for the project. Operating data will be automatically collected through a platform and users will be asked to give feedback weekly. The pilot in Rome will start with 50 vehicles and will be used for a revision and re-design process, to arrive up to a TRL 7. Afterwards, the other pilots will start, in sequence, for 3 months in each city, in which 100 vehicles will be tested. These tests will be used to refine the vehicle up to the TRL8-9 and to do a physical demonstration of the technical and economic feasibility. During the pilots, pre-orders will be accepted. A detailed exploitation strategy and a draft business plan for the vehicle will be draft with the data collected.
Religion, politics and the arts in early medieval italy against the background of the ‘image struggle’ (680-850)

This project will specifically focus firstly on the development and dissemination of the theological matters that affected the policies of the Roman Catholic Church between the late seventh-mid ninth century, and secondly on the ‘translation’ of these theological matters into a literary and visual imagery. In the period 680-850 a great debate about the cult of sacred images – the Byzantine ‘image struggle’ or iconoclasm – engaged monks, emperors, popes.  Sacred images have for different reasons ispired devotion or spurred iconoclastic reactions and cultural opposition world-wide and often in human history – unfortunately also in the last fifteen years. The place of sacred image in the actual Christian religious mentality – i.e. the way in which cult images stimulate reactions, are perceived, venerated, chosen as personal ‘talismans’ and intercessors with the divine in contemporary culture – was radically shaped by the intense period of the Byzantine ‘image struggle’. The political, cultural, and artistic interactions and the developments of Christian mentality between the West and the East during this phase are actually still a ‘grey area’ in Medieval and Byzantine studies, having been dealt with only occasionally and compartimentally. By using literary as well as visual evidence, 'ICONOPHILIA' will explore this ‘grey area’ and prove to be significant to a range of scholarly disciplines, while being appealing also to a wider global audience interested in religious mentality, Church history, history of monasticism, cultural policies, visual thinking, art production and consumption as socio-political statements. The Centre for Byzantine, Ottoman and Modern Greek Studies in Birmingham will provide the ideal intellectual environment for the development of this interdisciplinary project.
Transnational and Borderland Studies in Mathematics Education

Preface by Richard S. Kitchen and Marta Civil 1. Ecological Approaches to Transnational Research on Mathematical Reasoning: A Focus on Latino/a Mathematics Learners in the Borderlands by Judit Moschkovich 2. Crossing the Border between Home and School: Dominican Parents' Perspectives on the Teaching and Learning of Mathematics by Mary Q. Foote 3. Impressions of Mexican Immigrant Families on their Early Experiences with School Mathematics in Arizona by Marta Civil & Jose Maria Menendez 4. Becoming a Liberal Math Learner: Expanding Secondary School Mathematics to Support Cultural Connections, Multiple Mathematical Identities and Engagement by Lisa M. Jilk 5. Engaging Underprivileged Mexican students in Reform-Oriented Mathematics Instruction by Jose Luis Cortina 6. Considering Mexican and U.S. Teachers' Views on the Teaching and Learning of Mathematics Through a Teaching for Diversity Lens by Richard S. Kitchen 7. Teachers' Task Management Practices in the Context of Routine and Non-Routine Mathematics Problems: A Descriptive Analysis by Guadalupe I. Lozano Teran 8. Teachers' Conceptions of Mathematics and Mathematics Teaching and Learning: The Case of Two Elementary Teachers in Northern Mexico by Jesus Acosta-Iriqui 9. Looking Forward: Establishing a Research Agenda for Transnational and Borderland Studies in Mathematics Education by Richard S. Kitchen & Marta Civil Epilogue by Olimpia Figueras