SIRIS-Lab/unlabelled-sti-corpus huggingface dataset:
Characterisation of dna double-strand break repair by alternative end-joining:  potential targets for cancer therapy

DNA repair pathways evolved as an intricate network that senses DNA damage and resolves it in order to minimise genetic lesions and thus preventing tumour formation. Gaining in recognition the last few years, the alternative end-joining (alt-EJ) DNA repair pathway was recently shown to be up-regulated and required for cancer cell viability in the absence of homologous recombination-mediated repair (HR). Despite this integral role, the alt-EJ repair pathway remains poorly characterised in humans. As such, its molecular composition, regulation and crosstalk with HR and other repair pathways remain elusive. Additionally, the contribution of the alt-EJ pathway to tumour progression as well as the identification of a mutational signature associated with the use of alt-EJ has not yet been investigated. Moreover, the clinical relevance of developing small-molecule inhibitors targeting players in the alt-EJ pathway, such as the polymerase Pol Theta (Polθ), is of importance as current anticancer drug treatments have shown limited effectiveness in achieving cancer remission in patients with HR-deficient (HRD) tumours.

 Here, we propose a novel, multidisciplinary approach that aims to characterise the players and mechanisms of action involved in the utilisation of alt-EJ in cancer. This understanding will better elucidate the changing interplay between different DNA repair pathways, thus shedding light on whether and how the use of alt-EJ contributes to the pathogenic history and survival of HRD tumours, eventually paving the way for the development of novel anticancer therapeutics.

 For all the abovementioned reasons, we are convinced this project will have important implications in: 1) elucidating critical interconnections between DNA repair pathways, 2) improving the basic understanding of the composition, regulation and function of the alt-EJ pathway, and 3) facilitating the development of new synthetic lethality-based chemotherapeutics for the treatment of HRD tumours.
Long-term changes in soil salinity as influenced by subsoil thickness in a reclaimed coal mine in east-central Alberta

Olatuyi, S. O. and Leskiw, L. A. 2014. Long-term changes in soil salinity as influenced by subsoil thickness in a reclaimed coal mine in east-central Alberta. Can. J. Soil Sci. 94: 605–620. Elevated salinity and sodicity are major challenges to reclamation of surface-mined coal sites in the Alberta Plains region. Research plots were established in 1981 at the Battle River Coal Mine near Forestburg, AB, to determine an optimum depth of subsoil replacement over sodic mine spoil required to sustain agricultural capability. Subsoil thickness was varied at 0, 25, 65, 135, 165 and 335 cm, overlain with 15 cm topsoil. The plots were monitored annually from 1982 to 1986 and were seeded to forage from 1987. Plots were resampled in 2013 to examine long-term changes in soil quality by comparing the results with the historical means for the 1980s. Key soil parameters measured are pH, electrical conductivity (EC), total dissolved salts (TDS), sodium adsorption ratio (SAR) and soluble Na. The soil quality of the root zone (0–40 cm) improved over time in all treatments as EC, TDS, SAR and concentration of Na decreased significantly between the 1980s and 2013. Amounts of EC and soluble Na consistently increased with depth, suggesting salt accumulation was predominantly by downward leaching, but with contribution by upward migration of Na from the underlying spoil. Relative to the native soils in 2013, the root zone quality ratings for EC and SAR in the topsoil/spoil treatment were better than in the shallow-bedrock Solonetzic soil. Ratings for the 25-cm subsoil treatment were also comparable with the local Chernozemic soil, but better than the fine till Solonetzic soil. This study demonstrates that a minimum of 25 cm subsoil and 15 cm topsoil are required for mitigating salinity and sodicity in these reconstructed soils. The resampling in 2013 demonstrates that long-term monitoring is essential to obtain a better understanding of reclamation outcomes.
Lancing device with decoupled lancet

A lancing device having a low-mass, high-velocity lancet decoupled from a drive mechanism when piercing a user's skin. The drive mechanism includes a spring-driven piston that impacts the lancet on firing to propel the lancet from a retracted position towards an extended position. After impact, but before the lancet reaches the extended position, a stop limits the travel of the piston to separate the piston from the lancet. Precise guidance of the lancet minimizes lateral movement of the lancet.
Energy and exergy analysis of a hybrid photovoltaic thermal double pass air collector

In this paper an attempt has been made to analyze the performance of semi transparent hybrid PVT double pass air collector. Based on the first law of thermodynamics, energy balance equations are for-mulated to derive the analytical expression for air temperature at the outlet, as a function of the design and climatic parameters for investigating the performance of semi transparent hybrid PVT air collector. The analysis is based on quasi-steady state condition. This paper shows the detailed analysis of energy and exergy of a semi transparent hybrid PVT double pass air collector and its comparison with single pass air collector for four weather conditions (a, b, c and d type) for five different cities (New Delhi, Bangalore, Mumbai, Srinagar, and Jodhpur) of India. It has been analyzed that if such systems are installed only at 10% of the total residential houses in Delhi, then the total carbon credits earned by the system is found to be Rs. 1767 millions in terms of thermal energy and Rs. 493 millions in terms of exergy for double pass air collector whereas Rs. 1528 millions in terms of thermal energy and Rs. 446 millions in terms of exergy for single pass air collector. The results clearly shows that hybrid PVT double pass air collector have better performance as compared to single pass air collector.
DEVICE, METHOD AND COMPUTER PROGRAM FOR MAKING AVAILABLE INFORMATION ABOUT AN END OF A TRAFFIC JAM VIA A VEHICLE-TO-VEHICLE INTERFACE

Exemplary embodiments relate to devices, methods and computer programs for making available information about an end of a traffic jam via a vehicle-to-vehicle interface. The device (10) for a vehicle (100) comprises an apparatus (12) designed to receive indicators about an end of a traffic jam. The indicators comprise at least one element of the group of kinetic information of the vehicle (100) or of vehicles in an area surrounding the vehicle (100) and traffic jam warnings. The device (10) also comprises an apparatus (14) designed to determine information about an end of a traffic jam on the basis of the indicators. The information about the end of a traffic jam indicates that the vehicle (100) will reach the end of a traffic jam in the near future. The device (10) also comprises a vehicle-to-vehicle interface (16) designed to make available information about the end of a traffic jam to one or more other vehicles (200) via a vehicle-to-vehicle communication link.
P-67 * INTERNET ADDICTION AND MENTAL HEALTH: A CROSS-SECTIONAL ONLINE SURVEY OF ADULTS IN JAPAN

Internet Addiction Disorder (IAD) can be broadly conceptualized as an inability to control one's use of the Internet which leads to negative consequences in daily life. In recent years, internet addiction began to be dealt with as mental illness in the world of science by relating to various psychological issues. The aim of this study was to investigate depressive symptoms in adults of addictive internet use, and to assess the effect of the various internet applications use on the IAD severity. A cross-sectional online survey was carried out among participants registered for the opinion poll survey of Osaka City University Graduate School of Medicine, Japan. The questionnaire contained demographic information, the use of various internet applications, Self-rating Depression Scale (SDS), and Japanese version of Internet Addiction Test (JIAT). Of the 310 respondents, the mean age was 40.1 (SD = 12.4). Mean JIAT score was 50.06 (SD = 15.21), and mean SDS score was 40.04 (SD = 6.40). Correlation coefficients of SDS score with JIAT score was 0.212 (P < 0.001). Multiple linear regression analysis showed that JIAT score was associated with hours spent on web browsing (P < 0.001) and online chat (P = 0.033). More research is needed to clarify the issue.
Fruits of eurasia: domestication and dispersal

Plant and animal domestication and dispersal is one of the most heavily debated topics in the social and biological sciences. However, a focus on the cereals has dramatically overshadowed other scholarship in the field, resulting in a shocking lack of scientific data relating to the origins of many crops. In contrast to annual crops, the domestication of long-generation perennials appears to have taken different biological trajectories and required significant cultural and ideological shifts. The FEDD project will study the origins and spread of many of the world’s most popular fruits by contrasting art historical, historical, archaeological, and linguistic data with the results from archaeobotanical, genomics modelling, and ancient proteomics analyses. My team will focus on the broad geographic region of Central Eurasia, where several of the most cultivated fruits in the world are thought to have originated. Furthermore, many other economically important fruits spread across Eurasia in antiquity along exchange routes colloquially called the Silk Road. Contrasting the results of these multidisciplinary studies will allow us to look at biological changes in the fruits and cultural changes among their cultivators during the domestication process. My unique ability to conduct this research rests in access to archaeobotanical material from collaborations with archaeological excavations (n=15) spanning the late Pleistocene to the medieval period and crossing seven different countries. The project represents an international endeavour, incorporating collaborators working in many of the least-studied areas of Eurasia, and will pull together team members interested in approaching plant domestication studies from different methodological perspectives. The FEDD project seeks to uncover the enigmatic journey of some of the most beloved items on our kitchen tables; from apples to peaches and pistachios to walnuts, we will explore the domestication and spread of arboreal crops.
Vaccines as a remedy for antimicrobial resistant bacterial infections

Antimicrobial Resistance (AMR) is perhaps the most emerging alarm in health. It already causes 700,000 deaths per year and the forecast for 2050 is 10 million deaths, more than cancer today. WHO, UN General Assembly, World Bank, G20,  EU, UK and USA governments call  for new antibiotics, but  the pipeline for new antibiotics is not very promising.  Here we propose to use new technologies to develop human monoclonal antibodies and vaccines against three AMR  bacteria such as gonococcus, pneumococcus and E.coli.  The technology defined as reverse vaccinology 2.0, already successful for viral infections, will be used for bacterial vaccines.  Taking advantage of the recent possibility of high throughput cloning of human B cells from convalescent or vaccinated people we aim to find targets difficult or impossible to be discovered using conventional technologies.  B cells will be cloned from people convalescent from target infections  and from people vaccinated with Men B vaccine which confers some protection against gonococcus. The antibodies produced by the clones will be screened for their ability to bind, intoxicate  or kill bacteria using a novel high-throughput microscopy platform that rapidly captures digital images  and also with conventional,  lower throughput technologies such as bactericidal, opsono-phagocytosis and FACS assays. The selected  antibodies, will be expressed as full length and used for passive immunization in animal models and tested for protection in vivo.  Finally, those antibodies that will provide the best protection in the above assays, will be used to identify the recognized antigens. Selected antigens will be expressed and tested in vaccine formulations. Fab fragments can be used to make co-crystals with the antigen and determine the crystal structure of the new antigens, for the development of structure-based antigen design. In conclusion we expect to enable development of human monoclonal antibodies and vaccines against AMR.
Resolving the tussle in the internet: mapping, architecture, and policy making

The Internet has revolutionalized the way people and corporations communicate, publish, access, and search for information. As our globally-connected digital civilization increasingly relies on its smooth operation any disruption has a direct negative impact on both the economy and society. However, the Internet was not designed to serve its current role nor was foreseen to be a public good. On the contrary, it was designed to be fully decentralized and thus administrated by the owners of independent networks. Today, the various Internet players have diverse and often conflicting objectives. Indeed, the tussle between Internet players or between them and governments hit the news and the negative externalities affect the life of potentially billions of Internet users worldwide and harm innovation in the Internet.

We propose a research agenda to resolve the tussle in the Internet. First, we propose the use of sophisticated techniques to collect and analyze massive network data to unveil the complex interactions among the various Internet players that lead to disputes and to identify the conditions under which conditions a resolution is possible. Second, we utilize additional degrees of freedom to resolve the tussle in the Internet by enabling coordination of the various Internet players. To this end, we introduce expressiveness of all the involved parties in existing and emerging protocols and enable agile deployment of third-party services and applications inside operational networks. Third, we contribute to the Internet policy making debate by providing an unbiased view of the state and health of the Internet as well as providing recommendations on how to resolve the Internet tussle. This is an interdisciplinary effort to foster a dialogue for Internet's future and sustainability in light of its ever-increasing growth and competitiveness.
Computational Extractors and Pseudorandomness

Computational extractors are efficient procedures that map a source of sufficiently high min-entropy to an output that is computationally indistinguishable from uniform. By relaxing the statistical closeness property of traditional randomness extractors one hopes to improve the and entropy parameters of these extractors, while keeping their utility for cryptographic applications. In this work we investigate computational extractors and consider questions of existence and inherent complexity from the theoretical and practical angles, with particular focus on the relationship to pseudorandomness.

An obvious way to build a computational extractor is via the method: apply a statistical extractor and use its output to seed a PRG. This approach carries with it the entropy cost inherent to implementing statistical extractors, namely, the source entropy needs to be substantially higher than the PRG's seed length. It also requires a PRG and thus relies on one-way functions.

We study the necessity of one-way functions in the construction of computational extractors and determine matching lower and upper bounds on the black-box efficiency of generic constructions of computational extractors that use a one-way permutation as an oracle. Under this measure we prove a direct correspondence between the complexity of computational extractors and that of pseudorandom generators, showing the optimality of the extract-then-prg approach for generic constructions of computational extractors and confirming the intuition that to build a computational extractor via a PRG one needs to make up for the entropy gap intrinsic to statistical extractors.

On the other hand, we show that with stronger cryptographic primitives one can have more entropy- and computationally-efficient constructions. In particular, we show a construction of a very practical computational extractor from any weak PRF without resorting to statistical extractors.
Resource value flow analysis of paper-making enterprises: A Chinese case study

Abstract Papermaking enterprises are currently under both environmental pressure and economic pressure for sustainable development in China. Thus, the efficiency, effectiveness, and benefits of resource utilization need to be improved. High-consumption and high-pollution companies should manufacture paper using sustainable methods. This study highlights a resource value flow analysis from the circular economy perspective, developing an extension of material flow cost accounting and modifying it by accounting for environmental damage as well as economic benefits. With reference to the Plan-Do-Check-Act cycle, this specific case study was conducted to verify the comprehensive utility of resource value flow analysis by establishing decision-making prioritization according to the dualistic diagnosis of “internal resource loss–external environmental damage costs.” In general, applying a resource value flow analysis can both reduce resource consumption and minimize environmental damage, enhancing the sustainable development of a process industry with limited resources.
Strong CP and SUZ2

Solutions to the strong CP problem typically introduce new scales associated with the spontaneous breaking of symmetries. Absent any anthropic argument for small $\bar\theta$, these scales require stabilization against ultraviolet corrections. Supersymmetry offers a tempting stabilization mechanism, since it can solve the "big" electroweak hierarchy problem at the same time. One family of solutions to strong CP, including generalized parity models, heavy axion models, and heavy $\eta^\prime$ models, introduces $\mathbb{Z}_2$ copies of (part of) the Standard Model and an associated scale of $\mathbb{Z}_2$-breaking. We review why, without additional structure such as supersymmetry, the $\mathbb{Z}_2$-breaking scale is unacceptably tuned. We then study "SUZ$_2$" models, supersymmetric theories with $\mathbb{Z}_2$ copies of the MSSM. We find that the addition of SUSY typically destroys the $\mathbb{Z}_2$ protection of $\bar\theta=0$, even at tree level, once SUSY and $\mathbb{Z}_2$ are broken. In theories like supersymmetric completions of the twin Higgs, where $\mathbb{Z}_2$ addresses the little hierarchy problem but not strong CP, two axions can be used to relax $\bar\theta$.
Urinary Mineral Concentrations in European Pre-Adolescent Children and Their Association with Calcaneal Bone Quantitative Ultrasound Measurements

This study investigates differences and associations between urinary mineral concentrations and calcaneal bone measures assessed by quantitative ultrasonography (QUS) in 4322 children (3.1-11.9 years, 50.6% boys) from seven European countries. Urinary mineral concentrations and calcaneal QUS parameters differed significantly across countries. Clustering revealed a lower stiffness index (SI) in children with low and medium urinary mineral concentrations, and a higher SI in children with high urinary mineral concentrations. Urinary sodium (uNa) was positively correlated with urinary calcium (uCa), and was positively associated with broadband ultrasound attenuation and SI after adjustment for age, sex and fat-free mass. Urinary potassium (uK) was negatively correlated with uCa but positively associated with speed of sound after adjustment. No association was found between uCa and QUS parameters after adjustment, but when additionally adjusting for uNa, uCa was negatively associated with SI. Our findings suggest that urinary mineral concentrations are associated with calcaneal QUS parameters and may therefore implicate bone properties. These findings should be confirmed in longitudinal studies that include the food intake and repeated measurement of urinary mineral concentrations to better estimate usual intake and minimize bias.
Cell division and the origin of embryonic aneuploidy in preimplantation mouse development

Cell division is fundamental for development. In the early mammalian embryo it drives the rapid proliferation of totipotent cells, the basis for forming the fetus. Given its crucial importance, it is surprising that cell division is particularly error-prone at the beginning of mammalian life, resulting in spontaneous abortion or severe developmental retardation, the incidence of which is increasing with age of the mother. Why aneuploidy is so prevalent and how early embryonic development nevertheless achieves robustness is largely unknown. The goal of this project is a comprehensive analysis of cell divisions in the mouse preimplantation embryo to determine the molecular mechanisms underlying aneuploidy and its effects on normal development. Recent technological breakthroughs, including light sheet microscopy and rapid loss-of-function approaches in the mouse embryo will allow us for the first time to tackle the molecular mechanisms of aneuploidy generation and establish the preimplantation mouse embryo as a standard cell biological model system. For that purpose we will develop next generation light sheet microscopy to enable automated chromosome tracking in the whole embryo. Mapping of cell division errors will reveal when, where, and how aneuploidy occurs, what the fate of aneuploid cells is in the embryo, and how this changes with maternal age. We will then perform high resolution functional imaging assays to identify the mitotic pathways responsible for aneuploidy and understand why they do not fully function in early development. Key proteins will be functionally characterised in detail integrating light sheet imaging with single molecule biophysics in embryos from young and aged females to achieve a mechanistic understanding of the unique aspects of cell division underlying embryonic aneuploidy. The achieved knowledge gain will have an important impact for our understanding of mammalian, including human infertility.
Distributed biological algorithms

This project proposes a new application for computational reasoning. More specifically, the purpose of this interdisciplinary project is to demonstrate the usefulness of an algorithmic perspective in studies of complex biological systems. We focus on the domain of collective behavior, and demonstrate the benefits of using techniques from the field of theoretical distributed computing in order to establish algorithmic insights regarding the behavior of biological ensembles. The project includes three related tasks, for which we have already obtained promising preliminary results. Each task contains a purely theoretical algorithmic component as well as one which integrates theoretical algorithmic studies with experiments. Most experiments are strategically designed by the PI based on computational insights, and are physically conducted by experimental biologists that have been carefully chosen by the PI. In turn, experimental outcomes will be theoretically analyzed via an algorithmic perspective. By this integration, we aim at deciphering how a biological individual (such as an ant) “thinks”, without having direct access to the neurological process within its brain, and how such limited individuals assemble into ensembles that appear to be far greater than the sum of their parts. The ultimate vision behind this project is to enable the formation of a new scientific field, called algorithmic biology, that bases biological studies on theoretical algorithmic insights.