nils-herrmann/clean_scirepeval huggingface dataset:
In silico methods for drug repurposing and pharmacology
Venue: Wiley interdisciplinary reviews. Systems biology and medicine
Year: 2016

Data in the biological, chemical, and clinical domains are accumulating at ever increasing rates and have the potential to accelerate and inform drug development in new ways. Challenges and opportunities now lie in developing analytic tools to transform these often complex and heterogeneous data into testable hypotheses and actionable insights. This is the aim of computational pharmacology, which uses in silico techniques to better understand and predict how drugs affect biological systems, which can in turn improve clinical use, avoid unwanted side effects, and guide selection and development of better treatments. One exciting application of computational pharmacology is drug repurposing finding new uses for existing drugs. Already yielding many promising candidates, this strategy has the potential to improve the efficiency of the drug development process and reach patient populations with previously unmet needs such as those with rare diseases. While current techniques in computational pharmacology and drug repurposing often focus on just a single data modality such as gene expression or drug target interactions, we argue that methods such as matrix factorization that can integrate data within and across diverse data types have the potential to improve predictive performance and provide a fuller picture of a drug's pharmacological action.  2016, 8:186 210. doi: 10.1002/wsbm.1337
Phase contrast time lapse microscopy datasets with automated and manual cell tracking annotations
Venue: Scientific data
Year: 2018

Phase contrast time lapse microscopy is a non destructive technique that generates large volumes of image based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer aided cell tracking and analysis, 48 time lapse image sequences, each spanning approximately 3.5 days, were generated with accompanying ground truths for C2C12 myoblast cells cultured under 4 different media conditions, including with fibroblast growth factor 2 (FGF2) bone morphogenetic protein 2 (BMP2) FGF2 BMP2, and control (no growth factor) The ground truths generated contain information for tracking at least 3 parent cells and their descendants within these datasets and were validated using a two tier system of manual curation. This comprehensive, validated dataset will be useful in advancing the development of computer aided cell tracking algorithms and function as a benchmark, providing an invaluable opportunity to deepen our understanding of individual and population based cell dynamics for biomedical research.
Reasoning with vectors: A continuous model for fast robust inference
Venue: Log. J. IGPL
Year: 2015

This paper describes the use of continuous vector space models for reasoning with a formal knowledge base. The practical significance of these models is that they support fast, approximate but robust inference and hypothesis generation, which is complementary to the slow, exact, but sometimes brittle behavior of more traditional deduction engines such as theorem provers. The paper explains the way logical connectives can be used in semantic vector models, and summarizes the development of Predication based Semantic Indexing, which involves the use of Vector Symbolic Architectures to represent the concepts and relationships from a knowledge base of subject predicate object triples. Experiments show that the use of continuous models for formal reasoning is not only possible, but already demonstrably effective for some recognized informatics tasks, and showing promise in other traditional problem areas. Examples described in this paper include: predicting new uses for existing drugs in biomedical informatics; removing unwanted meanings from search results in information retrieval and concept navigation; type inference from attributes; comparing words based on their orthography; and representing tabular data, including modelling numerical values. The algorithms and techniques described in this paper are all publicly released and freely available in the Semantic Vectors open source software package.
Mediation role of responsible innovation between CSR strategy and competitive advantage: Empirical evidence for the case of Saudi Arabia enterprises
Year: 2020

September 5 2019 Received in revised format: September 8 2019  October 23, 2019  2019 This study examines whether responsible innovation can be an important channel through which the corporate social responsibility (CSR) strategy influences the competitive advantage of the firm. Specifically, we tried to test the role of firm size and activity sector as conditional factors in the mediation of responsible innovation between CSR strategy and the competitive advantage for the case of Saudi Arabia enterprises. Based on structural equation modelling (SEM) our results show that responsible innovation is a key element of the sustainable business model since it determines the success of CSR strategy in boosting the competitive advantage of firms. In this model, the mediation of responsible innovation is moderated differently by the firm size and the activity sector, and it is dependent on the choice between strategic or reactive CSR strategy. Within this context, we also find that the indirect effects of the CSR strategy on competitive advantage are moderated by the firm size in the case of reactive CSR, whereas by the activity sector in case of strategic CSR. The originality of this paper is that it examines whether the competitive advantage of firms in a developing country is more dependent on the reactive CSR strategy or the strategic CSR strategy. It also proposes an empirical investigation into the conditional factors of responsible innovation and their effects on the relationship between CSR strategy and competitive advantage.
NR IQA for noise affected images using singular value decomposition
Venue: IET Signal Process.
Year: 2019

This study presents an efficient no reference image quality assessment (NR IQA) technique to assess the quality of images affected by noise. The proposed technique is based on two characteristics of the human eye (retina) namely the presence of centre surround receptive field and visualisation utilising different spatial frequency channels. In the proposed technique, the authors model centre surround receptive field using difference of Gaussians (DoG) whereas to mimic multiple frequencies in the centre surround receptive field, they compute multiple DoG images of different values of standard deviations generated for different frequencies. Furthermore, the singular value decomposition based features are obtained from the generated DoG images to estimate the image quality. The proposed technique does not require any training, neither based on distorted/original images nor based on subjective human scores, to assess the image quality. The performance of the proposed technique is being analysed on LIVE, TID08, CSIQ and SD IVL databases and it shows that the proposed technique outperforms recently proposed NR and no training/training based IQA techniques. Experimental validation of the proposed technique in the big data scenario of 10,000 noisy images also shows encouraging results.
Schulbasierte Achtsamkeitsprogramme mit Kindern und Jugendlichen
Year: 2020

School based Mindfulness Programs for Children and Adolescents Mindfulness is a mental state achieved by focusing one's awareness on the present moment, while calmly acknowledging and accepting one's bodily sensations, sensory feedback, thoughts, and feelings. Mindfulness interventions can improve proprioception, direction of attention, and emotion regulation. An accepting attitude towards thoughts and feelings reduces the experience of stress so that it is easier to cope with stressful situations. The regular practice of mindfulness exercises affects neurobiological mechanisms, which can lead to an improvement of executive functions as well as psychological health. Metaanalyses provide evidence of small effects of mindfulness interventions in schools, both in cognitive areas (executive functions, concentration, memory) and in emotional areas (anxiety, depressivity, wellbeing) The focus of this review article is on German and English language mindfulness programmes for children and adolescents in schools, which have already been the subject of initial evaluation studies. This study presents the programmes Paws b, Mind Up, and Mehr Ruhe for children, and .b, Mind Up, AISCHU, and 8sam for adolescents, together with their evaluation results. The conclusion discusses open questions concerning conceptual and methodological issues.
When Is Blockchain Worth It? A Case Study of Carbon Trading
Year: 2020

Blockchain, as an emerging technology and a disruptive innovation, has attracted attention from both academia and industry. However, there are many potential risks associated with it, such as the technical risk, the legal risk and the privacy risk. A comprehensive risk analysis is crucial for cost effective deployment of blockchain technology. Important adoption decisions, including when to deploy blockchain, how to plan the investment, how to transfer current businesses onto blockchain, and how to price the blockchain service depend on this risk analysis. Yet very little study exists concerning the blockchain adoption planning with risks analysis. This research presents a cost and risk analysis framework and an adoption planning method for the case of blockchain application in carbon trading. Design requirements implied by the analysis are inferred and the architecture of a novel hybrid blockchain system is proposed. The system leverages the advantages of blockchain technology and incorporates institutional risk control framework. The optimal adoption strategy of this system is derived through modelling of users' and the organizer's behavior.
Use of Electrochemistry in the Synthesis of Heterocyclic Structures.
Venue: Chemical reviews
Year: 2018

The preparation and transformation of heterocyclic structures have always been of great interest in organic chemistry. Electrochemical technique provides a versatile and powerful approach to the assembly of various heterocyclic structures. In this review, we examine the advance in relation to the electrochemical construction of heterocyclic compounds published since 2000 via intra and intermolecular cyclization reactions.
Financing Japan's World War II Occupation of Southeast Asia
Venue: The Journal of Economic History
Year: 2013

This article analyzes how Japan financed its World War II occupation of Southeast Asia, the market purchased transfer of resources to Japan, and the monetary and inflation consequences of Japanese policies. Occupation was financed principally by printing large quantities of money. While some Southeast Asian countries had high inflation, hyperinflation hardly occurred because of a sustained transactions demand for money and because of Japan's strong enforcement of monetary monopoly. Highly specialized Southeast Asian economies and loss of Japanese merchant shipping limited resource extraction.
GPU Powered Malware
Year: 2008

There is an increasing interest in Graphics Processing Units for general purpose programming, due to their processing power and massively parallel design. Therefore, most consumer graphics hardware are now fully programmable using either Nvidia's CUDA toolkit or AMD/ATI Stream SDK. This presentation will give an analysis of how the GPU can be used by malware as an anti reverse engineering platform, with examples using the CUDA technology. With CUDA, the GPU is fully programmable in C, but the resulting device program can't be debugged because Nvidia's GPUs do not support this feature natively. As a result, a malware analyst has to use static analysis against the device code in order to understand the malware. But this task is harder with GPU code than with traditional binaries since the source of a CUDA program is compiled to undocumented microcode (and therefore unsupported by standard disassemblers such as IDA Pro) Finally, this presentation will also assess the technical feasability of an unpacker written fully in device code.
Correction to: Impact of an electronic monitoring device and behavioural feedback on adherence to multiple sclerosis therapies in youth: results of a randomized trial
Venue: Quality of Life Research
Year: 2017

The clinicaltrials.gov identifying number for the article titled "Impact of an electronic monitoring device and behavioral feedback on adherence to multiple sclerosis therapies in youth: results of a randomized trial" is NCT02234713 (https:/clinicaltrials.gov/ct2/show/NCT02234713)
Colorectal cancer metastases to the thyroid gland a systematic review
Venue: Hormones
Year: 2020

Despite its rich vasculature, the thyroid gland is a rare site of metastatic disease. We present a systematic review of colorectal cancer (CRC) thyroid metastases, with emphasis on diagnosis, therapeutic management, and oncological outcomes.  A systematic review of the English literature (1990 to 2019) was performed, using the PubMed, Embase, and Google Scholar bibliographic databases. For each patient, epidemiological, surgical, histopathological, and oncological data were extracted.  A total of 111 patients (40% males, mean age 61 12 years) were included in the final analysis. The primary CRC was locally advanced (T3 T4) in 83% had positive lymph nodes (N+ in 65% and had distant metastases (M+ in 28% Thyroid metastases were synchronous in 15% and metachronous in 80% with a mean interval of 51 31 months from primary tumor treatment. Thyroid metastatic disease was diagnosed clinically (60% radiologically (33% biochemically (2% or postmortem (5% When performed, FNA biopsy was diagnostic in 73% and highly suspicious in 13% A total of 63% of patients had additional distant metastases, usually in the liver or lungs, while 68% of patients underwent surgical excision (total or subtotal thyroidectomy 58% lobectomy 42% and 43% received adjuvant chemotherapy or radiotherapy. Mean overall survival after primary CRC was 55.5 34.7 months, with mean disease free survival of 31.3 27.2 months. Following diagnosis or treatment of thyroid metastases, 1 2 and 3 year survival rates were 79, 66, and 60% respectively. Mean survival following diagnosis of thyroid metastases was 11.3 months.  CRC thyroid metastasis is a relatively uncommon event, usually associated with locoregionally advanced tumors. Prognosis is poor, mainly due to multimetastatic disease.
Determining Code Words in Euphemistic Hate Speech Using Word Embedding Networks
Venue: ALW
Year: 2018

While analysis of online explicit abusive language detection has lately seen an ever increasing focus, implicit abuse detection remains a largely unexplored space. We carry out a study on a subcategory of implicit hate: euphemistic hate speech. We propose a method to assist in identifying unknown euphemisms (or code words) given a set of hateful tweets containing a known code word. Our approach leverages word embeddings and network analysis (through centrality measures and community detection) in a manner that can be generalized to identify euphemisms across contexts not just hate speech.
Transmitarray based Metasurface Lens Antenna
Venue: 2019 IEEE International Symposium on Antennas and Propagation and USNC URSI Radio Science Meeting
Year: 2019

A transmitarray metasurface design is proposed to function as an integrated lens antenna within the frequency range of 11.6 GHz to 13.25 GHz. A finite periodic array of three layer metallo dielectric discrete unit cells is used to form the transmitarray lens. The transmitarray is used in front of an open ended waveguide to obtain more directive radiation. The transmitarray lens is shown to provide at least 3.75 dB higher gain than a comparable standard horn antenna whilst occupying about half of the physical space.
Quality Evaluation for Indoor Mobile Data Customers in Addis Ababa Business Area Using Data from Network Management System, Walk Test, Crowdsourcing and Subjective Survey
Venue: ICT4DA
Year: 2019

Introduction and penetration of high speed and innovative mobile data services including social media and video services have been increasing significantly across the globe. This growth is driven by deployment and availability of capable and affordable mobile networks and smartphones. These trends have also been observed in Ethiopia as the country's sole incumbent operator ethio telecom has expanded coverage and capacity of its mobile data network, especially for universal mobile telecommunications system (UMTS) network. The successful provision of these innovative services requires mobile operators to have continuous monitoring of the quality of their networks and customer satisfaction. To that end, this monitoring allows the operator to make timely network optimization, marketing and other relevant decisions that enhance service quality. Traditionally measurement and analysis of network quality of service (QoS) is performed using data from network management system (NMS) and drive/walk test (DT/WT) In recent times, the usage QoS data from crowdsourcing (CS) is also emerging as useful monitoring tool. However, all these methods do not fully capture users' quality of experience (QoE) which is a function of not only network QoS but also other factors including subjective users' technical literacy and opinion. As a result, operators have recently provided attention not only for QoS but also QoE. Yet, most quality related analyses are performed using data from only subjective survey, NMS, DT/WT, or CS. It is not straightforward to find quality investigation based on data from all the methods. More importantly, such quality investigation has not been made in the context of Ethiopia's mobile market. In this paper, we perform QoS and QoE evaluation for UMTS mobile data service based on quality data from all NMS, WT, CS and subjective survey for a business area in Addis Ababa. The evaluation is made using downlink user throughput and mean opinion score (MOS) metrics. The obtained 50th percentile throughput results from NMS, WT and CS are good enough for web browsing and offline video streaming but not for high definition (HD) video calls and live HD video streaming. Furthermore, CS provides optimistic results compared to NMS and WT and its 90th percentile throughput is very good even for live HD video streaming. Moreover, the obtained MOS results from subjective survey almost fit to the QoS results, thus indicating that the network QoS is a significant contributor to users' perceived QoE.
Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster
Venue: The ISME Journal
Year: 2017

Animals are routinely colonized by microorganisms. Despite many studies documenting the microbial taxa associated with animals, the pattern and ecological determinants of among animal variation in microbial communities are poorly understood. This study quantified the bacterial communities associated with natural populations of Drosophila melanogaster. Across five collections, each fly bore 16 78 OTUs, predominantly of the Acetobacteraceae, Lactobacillaceae, and Enterobacteriaceae. Positive relationships, mostly among related OTUs, dominated both the significant co occurrences and co association networks among bacteria, and OTUs with important network positions were generally of intermediate abundance and prevalence. The prevalence of most OTUs was well predicted by a neutral model suggesting that ecological drift and passive dispersal contribute significantly to microbiome composition. However, some Acetobacteraceae and Lactobacillaceae were present in more flies than predicted, indicative of superior among fly dispersal. These taxa may be well adapted to the Drosophila habitat from the perspective of dispersal as the principal benefit of the association to the microbial partners. Taken together, these patterns indicate that both stochastic processes and deterministic processes relating to the differential capacity for persistence in the host habitat and transmission between hosts contribute to bacterial community assembly in Drosophila melanogaster.
Efterarets aroma, historien om en lugt
Year: 2011

"Hvilket blad? Hvilken svamp?" Komponisten John Cages oversaettelse af Matsuo Bachos klassiske haiku digt. Kao rakte mig svampen. Det var forste gang, jeg oplevede lugten. Lugten er ikke nem at definere eller beskrive. Den minder hverken om blomster eller laekker mad, men er foruroligende. Mange mennesker vaenner sig aldrig til den. Nogle mennesker sammenligner den med radne ting, og andre med naturlig skonhed. Ved denne forste duft var jeg bare foruroliget.
Senescence Associated MCP 1 Secretion Is Dependent on a Decline in BMI1 in Human Mesenchymal Stromal Cells.
Venue: Antioxidants redox signaling
Year: 2016

Cellular senescence and its secretory phenotype (senescence associated secretory phenotype [SASP] develop after long term expansion of mesenchymal stromal cells (MSCs) Further investigation of this phenotype is required to improve the therapeutic efficacy of MSC based cell therapies. In this study, we show that positive feedback between SASP and inherent senescence processes plays a crucial role in the senescence of umbilical cord blood derived MSCs (UCB MSCs)  We found that monocyte chemoattractant protein 1 (MCP 1) was secreted as a dominant component of the SASP during expansion of UCB MSCs and reinforced senescence via its cognate receptor chemokine (c c motif) receptor 2 (CCR2) by activating the ROS p38 MAPK p53/p21 signaling cascade in both an autocrine and paracrine manner. The activated p53 in turn increased MCP 1 secretion, completing a feed forward loop that triggered the senescence program in UCB MSCs. Accordingly, knockdown of CCR2 in UCB MSCs significantly improved their therapeutic ability to alleviate airway inflammation in an experimental allergic asthma model. Moreover, BMI1, a polycomb protein, repressed the expression of MCP 1 by binding to its regulatory elements. The reduction in BMI1 levels during UCB MSC senescence altered the epigenetic status of MCP 1, including the loss of H2AK119Ub, and resulted in derepression of MCP 1.  Our results provide the first evidence supporting the existence of the SASP as a causative contributor to UCB MSC senescence and reveal a so far unappreciated link between epigenetic regulation and SASP for maintaining a stable senescent phenotype.  Senescence of UCB MSCs is orchestrated by MCP 1, which is secreted as a major component of the SASP and is epigenetically regulated by BMI1.
Predicting Purchase Decisions Using Autoencoders in a High Dimensional Setting
Year: 2019

To be able to serve customers with personalized product recommendations or shopping lists, it is important for retailers to accurately predict the purchase behaviour of their customers. In this study, we propose an autoencoder based model for next basket prediction. The goal of next basket prediction is to accurately predict the set of items a customer will buy at his next moment of purchase. Our model consists of three main steps. First, we train an autoencoder, which encodes high dimensional baskets into low dimensional codes. Next, this code is used to predict the code of the next basket, which is decoded in the third step to obtain basket predictions. Our model clearly outperforms the benchmark model in a wide range of performance measure and is able to deal with high dimensionality of the retailer's assortment.