nils-herrmann/clean_scirepeval huggingface dataset:
Sinogram denoising via simultaneous sparse representation in learned dictionaries.
Venue: Physics in medicine and biology

Reducing the radiation dose in computed tomography (CT) is highly desirable but it leads to excessive noise in the projection measurements. This can significantly reduce the diagnostic value of the reconstructed images. Removing the noise in the projection measurements is, therefore, essential for reconstructing high quality images, especially in low dose CT. In recent years, two new classes of patch based denoising algorithms proved superior to other methods in various denoising applications. The first class is based on sparse representation of image patches in a learned dictionary. The second class is based on the non local means method. Here, the image is searched for similar patches and the patches are processed together to find their denoised estimates. In this paper, we propose a novel denoising algorithm for cone beam CT projections. The proposed method has similarities to both these algorithmic classes but is more effective and much faster. In order to exploit both the correlation between neighboring pixels within a projection and the correlation between pixels in neighboring projections, the proposed algorithm stacks noisy cone beam projections together to form a 3D image and extracts small overlapping 3D blocks from this 3D image for processing. We propose a fast algorithm for clustering all extracted blocks. The central assumption in the proposed algorithm is that all blocks in a cluster have a joint sparse representation in a well designed dictionary. We describe algorithms for learning such a dictionary and for denoising a set of projections using this dictionary. We apply the proposed algorithm on simulated and real data and compare it with three other algorithms. Our results show that the proposed algorithm outperforms some of the best denoising algorithms, while also being much faster.
Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development
Venue: Scientific reports

Using transcriptome data to mine microsatellite and develop markers has growingly become prevalent. However, characterizing the possible function of microsatellite is relatively rare. In this study, we explored microsatellites in the transcriptome of the brown alga Sargassum thunbergii and characterized the frequencies, distribution, function and evolution, and developed primers to validate these microsatellites. Our results showed that Tri nucleotide is the most abundant, followed by di and mono nucleotide. The length of microsatellite was significantly affected by the repeat motif size. The density of microsatellite in the CDS region is significantly lower than that in the UTR region. The annotation of the transcripts containing microsatellite showed that 573 transcripts have GO terms and can be categorized into 42 groups. Pathways enrichment showed that microsatellites were significantly overrepresented in the genes involved in pathways such as Ubiquitin mediated proteolysis, RNA degradation, Spliceosome, etc. Primers flanking 961 microsatellite loci were designed, and among the 30 pairs of primer selected randomly for availability test, 23 were proved to be efficient. These findings provided new insight into the function and evolution of microsatellite in transcriptome, and the identified microsatellite loci within the annotated gene will be useful for developing functional markers in S. thunbergii.
Environmental effects on arsenosugars and arsenolipids in Ectocarpus (Phaeophyta)

Seaweeds have recently been shown to contain a significant proportion of arsenic in the form of arsenolipids (AsLp) Three strains of the filamentous brown alga Ectocarpus species were grown in the laboratory with different simulationsofenvironmentalstress:controlconditions(1/2Provasoli enrichedseawater),lownitrate(30%oftheamount ofnitratesinthecontrol),lowphosphate(30%ofthe amountofphosphateinthecontrol)andunderoxidativestresslevels (2 mM H2O2) Generally, the major AsLp was an arsenic containing hydrocarbon, AsHC360 (50 80% but additionally, several arsenic containing phospholipids (AsPL) were identified and quantified using high performance liquid chroma tography inductivelycoupledplasmamassspectrometryandelectrosprayionisationmassspectrometry(HPLC ICP MS/ ESI MS).TheAsLpsincultureswerecomparedwithAsLpsinEctocarpusfoundinitsnaturalhabitataswellaswithother brown filamentous algae. The AsLp and arsenosugar profiles differed depending on the experimental conditions. Under low phosphate conditions, a significant reduction of phosphorus containing arsenosugars was noticed, and a significant increaseofphosphate containingAsLpswasfoundwhencomparedwiththecontrols.Strainsgrownunderoxidativestress showed a significant increase in AsLps as well as clear physiological changes.  chloroplasts, cultures, HPLC ESIMS, HPLC ICP MS, lipid soluble arsenic, speciation.  October 2014, accepted 2 March 2015,
Bioprospecting for lipophilic like components of five Phaeophyta macroalgae from the Portuguese coast
Venue: Journal of Applied Phycology

Lipophilic compounds present in dichloromethane extracts of five brown macroalgae from the Portuguese coast were analyzed by gas chromatography mass spectrometry (GC MS) Their dicarboxylic acids, long chain aliphatic alcohols, and monoglyceride profile are reported for the first time. Additionally, other new compounds were also first reported: 24 methylene cholesterol in Himanthalia elongata, Laminaria ochroleuca, and Undaria pinnatifida; desmosterol and brassicasterol in H. elongata, L. ochroleuca, Sargassum muticum, and U. pinnatifida; fucosterol and campesterol in S. muticum; and cholest 5 en 3 ol (3b) 3 phenyl 2 propenoate in Cystoseira tamariscifolia. Brown macroalgae dichloromethane extracts are mainly composed of fatty acids (463.4 3089.0 mg kg 1 of dry material) and sterols (75.5 442.7 mg kg 1 of dry material) High amounts of polyunsaturated fatty acids were found, with the o 6/o 3 ratios of all species lower than 3. Cystoseira tamariscifolia, H. elongata, and S. muticum showed to be also promising sources of fucosterol. These results seem to uphold the incorporation of these macroalgae in a more balanced diet, as well as their use in the nutraceutical industry, as long as they are coupled with sustainable management of these natural resources.
Screening of Endophytic Fungi from Chlorophyta and Phaeophyta for Antibacterial Activity

Chlorophyta and Phaeophyta macroalgae are important sources of secondary metabolites with pharmaceutically relevant antibacterial, antifungal and antiviral bioactivities. Oftentimes, these algae derived compounds are, in fact, produced by endophytic fungi living inside the macroalgal tissue. Numerous studies have shown that endophytic fungi can produce a broad range of active metabolites such as terpenes, alkaloids, and quinones. The aim of the present study was to screen fungal strains isolated from a variety of Caulerpa spp. Halimeda spp. and Sargassum spp. for antibacterial activity against Staphylococcus aureus and Escherichia coli. Thirteen morphologically different isolates were tested. Two of them showed pronounced activity against S. aureus in agar diffusion assays.
Context sensitive reward shaping for sparse interaction multi agent systems
Venue: The Knowledge Engineering Review

Potential based reward shaping is a commonly used approach in reinforcement learning to direct exploration based on prior knowledge. Both in single and multi agent settings this technique speeds up learning without losing any theoretical convergence guarantees. However, if speed ups through reward shaping are to be achieved in multi agent environments, a different shaping signal should be used for each context in which agents have a different subgoal or when agents are involved in a different interaction situation. This paper describes the use of context aware potential functions in a multi agent system in which the interactions between agents are sparse. This means that, unknown to the agents a priori, the interactions between the agents only occur sporadically in certain regions of the state space. During these interactions, agents need to coordinate in order to reach the global optimal solution. We demonstrate how different reward shaping functions can be used on top of Future Coordinating Q learning (FCQ learning) an algorithm capable of automatically detecting when agents should take each other into consideration. Using FCQ learning, coordination problems can even be anticipated before the actual problems occur, allowing the problems to be solved timely. We evaluate our approach on a range of gridworld problems, as well as a simulation of air traffic control.
Coagulation and Flocculation in Water and Wastewater Treatment Third Edition

Coagulation and Flocculation in Water and Wastewater Treatment provides a comprehensive account of coagulation and flocculation techniques and technologies in a single volume covering theoretical principles to practical applications. Thoroughly revised and updated this new edition has been progressively modified and increased in scope to cater for the requirements of practitioners involved with water and wastewater treatment. New topics in this new edition include: The book presents the subject logically and sequentially from theoretical principles to practical applications. Successive chapters deal with, in turn, properties of materials present in waters and wastewaters; characteristics and types of coagulants commonly in use; mechanisms and practical implications of destabilization of waterborne material using metal coagulants and polyelectrolytes; considerations and requirements for coagulant addition at the rapid mixing stage; theoretical and practical considerations of flocculation; and details of experimental procedures for assessing primary coagulants, flocculant aids, sludge conditioners, and flocculation parameters. Numerous examples are included as appropriate. Treatment and disposal of sludges resulting from coagulation flocculation related operations is dealt with in an Appendix. This important topic has been separated from the main text to avoid disturbing the continuum of the presentation. Coagulation and Flocculation in Water and Wastewater Treatment is a readable and useful resource for the water scientist and engineer. It is a convenient reference handbook providing numerous examples and appended information and it is a vital text for course material for undergraduate and postgraduate students.  9781780407500 (eBook) ISBN: 9781780407494 (Print)
Relation Classification via Multi Level Attention CNNs
Venue: ACL

Relation classification is a crucial ingredient in numerous information extraction systems seeking to mine structured facts from text. We propose a novel convolutional neural network architecture for this task, relying on two levels of attention in order to better discern patterns in heterogeneous contexts. This architecture enables endto end learning from task specific labeled data, forgoing the need for external knowledge such as explicit dependency structures. Experiments show that our model outperforms previous state of the art methods, including those relying on much richer forms of prior knowledge.
STUDY OF WATER MIST SYSTEM FOR PRE COOLING THE ENTERING AIR OF AN AIR COOLED CHILLER CONDENSER

February 2016  2016 A practical method for improving the COP of an air cooled chiller is pre cooling the air entering its condenser via a water mist system. This article studies a water mist system with hollow cone spray nozzles and investigates the effects of water flow rate, water droplet diameter and the number of spray nozzles on system performance. Simulations were run by FLUENT software, applying EulerianLagrangian method. Solution grid independency was obtained and was validated with experimental data. According to the results, in a constant air flow rate of 8.3 (kg/s) with increasing the water flow rate from 0.05 to 0.4 (kg/s) percent increase of COP increases from 3 to about 14, but the percentage of evaporated water decreases from 12.13 to 7.62 (however the value of evaporated water increases) Besides, decreasing the water droplets diameter from 200 to 50 micrometer, results in percent increase of COP from 4 to 24. Due to less water evaporation in higher flow rates, the number of spray nozzles was raised in a constant total flow rate which, according to the results, increasing the number of nozzles improves the system performance. Also, with other simulations it was observed that increasing the number of nozzles is more effective in higher flow rates and less drop diameters. Finally, the case study demonstrated that using sufficient number of nozzles, it is possible to achieve higher COPs in lower flow rates and therefore in addition to energy consumption, the water consumption could be reduced.
Effect of gas temperature on the capture of charged particles by oppositely charged water droplets

This work reports experimental results on the effects of temperature (25, 45, and 65degC at different relative humidity) on the scrubbing of charged submicron particles by means of cold (25degC) droplets charged with opposite polarity. The aim of the study is to experiment how the capture of particles is influenced by the simultaneous presence of electrostatic and phoretic forces related to the occurrence of thermal and water vapor gradients close to the droplet surface. This information plays an important role in the development of wet electrostatic scrubbing (WES) an emerging technology for submicron and ultrafine particle capture. Tests were performed in a lab scale system in which the particle laden gas was scrubbed by a train of identic droplets. Particles were charged by a corona source while droplets are generated by electrospraying. Experiments revealed that for particles larger than about 250 300 nm, there were higher removal efficiencies in nonisothermal conditions, with limited differences between 45 and 65degC tests. For particles finer than about 150 nm, we sometimes observed lower removal efficiencies for higher gas temperatures, probably due to the difficulties in controlling particle charging for these particles. The experiments were interpreted with a consolidated stochastic model that predicted successfully the data at isothermal conditions, but was less effective for tests at higher gas temperatures. In our opinion, this discrepancy relies on synergies among the fluid dynamic field induced by droplet evaporation/condensation, the phoretic and the electrostatic forces, which are not considered in the model.
The Effect of Geothermal Water on Skin Condition and Body Fat

Balneotherapy for therapeutic purposes has been used since ancient times, and was based on empirical experience carried forward from generation to generation. There is scientific evidence about the positive effects of the thermal water on the skin and on body weight, but studies with the mineral water from a borehole are missing.  To investigate the effect of high mineralisation geothermal water on the skin and body fat.  The study included 50 women who received geothermal water baths for 15 20 min (34degC, 27,6 g/l mineralisation and a pH of 7,24) The participants' subjective and objective skin state and body fat were assessed after the procedure, as well as 1 and 4 months after the procedure. The statistical software package SPSS 20 was used for the analysis.  There were reductions in the overall number of skin complaints (p=0,001) usage of skincare products (p=0,001) limb volume (p<0,05) cutaneous fold thickness (p<0,001) and BMI (p=0,015) whereas there was an increase in the moisture content of the skin (p=0,047) after a 15minute balneotherapy treatment. After 1 month following the treatment, there remained a reduction in the cutaneous fold (p<0,05) limb volume (p<0,05) itching, networks of veins, cellulite (p=0,046) and usage of skincare products (p=0,001) After 4 months following the treatment, there remained fewer skin complaints (p=0.01) itching and cellulitis (p=0,046) and furthermore, a positive impact on the volume of the limbs was observed (p<0,05) and the cutaneous fold was significantly lower Original Research Article Rapoliene; BJMMR, 18(10) xxx xxx, 2016; Article no.BJMMR.29892 2 than before the treatment (p<0,01) After 20 minutes of balneotherapy treatment, there were fewer skin complaints (p=0,003) a decreased BMI (p<0,001) and a lower body fat percentage (p=0,017) as well as greater skin moisture (p<0,05) and skin elasticity (p=0,016)  High mineralisation geothermal baths of a duration of 15 20 minutes will improve the skin condition and reduce the amount of fat in the body; the effect lasts up to 4 months after the treatment. As a result, geothermal water treatments should be integrated into the treatment programmes for skin diseases and should take a significant place among beauty procedures.
The normative power of food promotions: Australian children's attachments to unhealthy food brands
Venue: Public Health Nutrition

The formation of food brand associations and attachment is fundamental to brand preferences, which influence purchases and consumption. Food promotions operate through a cascade of links, from brand recognition, to affect, and on to consumption. Frequent exposures to product promotions may establish social norms for products, reinforcing brand affect. These pathways signify potential mechanisms for how children's exposure to unhealthy food promotions can contribute to poor diets. The present study explored children's brand associations and attachments for major food brands.  A cross sectional online survey was conducted. Fourteen study brands were used, with each child viewing a set of seven logos. The questionnaire assessed perceptions of food brands and perceptions of users of brands, using semantic differential scales, and perceived brand 'personalities' using Likert scales.  New South Wales, Australia, October November 2014.  Children aged 10 16 years (n 417)  Children demonstrated strong positive affect to certain brands, perceiving some unhealthy food brands to have positive attributes, desirable user traits and alignment to their own personality. Brand personality traits of 'smart' and 'sporty' were viewed as indicators of healthiness. Brands with these traits were ranked lower for popularity.  Children's brand associations and attachments indicate the potential normative social influences of promotions. While children are aware of brand healthiness as an attribute, this competes with other brand associations, highlighting the challenge of health/nutrition messaging to counter unhealthy food marketing. Restricting children's exposure to unhealthy food marketing and the persuasive nature of marketing is an important part of efforts to improve children's diet related health.
Prediction Model of The Net Asset Returns of Indian Equity Fund of Mutual Funds With Application of Ar

As return is the central focus of any investment,finance researchers all the times have shown interest in doing modeling and forecasting of assets returns. Fund of Mutual funds are fast growing as India's investment vehicle of choice. As there are a variety ofinvestors in all types fund of fund schemes, the competition among them is very intense and the investors choose fundson the forecasting of NAV returns and thus there is a need to identify right model for forecasting. Among various forecasting methods, ARMA method is considered one of the most usefulextrapolation methods for forecasting the stock returns. In this paper, some of the Fund of Mutual Funds in India has been modeled using Box Jenkins autoregressive moving average (ARMA) methodology. The modeling has been attempted on daily returns of four Growth oriented schemes. The NAV data from 1 st April 2007 to 29 th February 2015 have been collected from the respective AMC websites. Validity of the models was tested using the future NAV returns of the fund of mutual funds with that of forecasted. The analysisshowed that all the schemes in the forecasted sample showed the sustainable return.
Targeting Inflammation in Cancer Prevention and Therapy
Venue: Cancer Prevention Research

Inflammation is associated with the development and malignant progression of most cancers. As most of the cell types involved in cancer associated inflammation are genetically stable and thus are not subjected to rapid emergence of drug resistance, the targeting of inflammation represents an attractive strategy both for cancer prevention and for cancer therapy. Tumor extrinsic inflammation is caused by many factors, including bacterial and viral infections, autoimmune diseases, obesity, tobacco smoking, asbestos exposure, and excessive alcohol consumption, all of which increase cancer risk and stimulate malignant progression. In contrast, cancer intrinsic or cancer elicited inflammation can be triggered by cancer initiating mutations and can contribute to malignant progression through the recruitment and activation of inflammatory cells. Both extrinsic and intrinsic inflammation can result in immunosuppression, thereby providing a preferred background for tumor development. In clinical trials, lifestyle modifications including healthy diet, exercise, alcohol, and smoking cessation have proven effective in ameliorating inflammation and reducing the risk of cancer related deaths. In addition, consumption of certain anti inflammatory drugs, including aspirin, can significantly reduce cancer risk, suggesting that common nonsteroidal anti inflammatory drugs (NSAID) and more specific COX2 inhibitors can be used in cancer prevention. In addition to being examined for their preventative potential, both NSAIDs and more potent anti inflammatory antibody based drugs need to be tested for their ability to augment the efficacy of more conventional therapeutic approaches on the basis of tumor resection, radiation, and cytotoxic chemicals. Cancer Prev Res; 9(12) 895 905. (c)2016 AACR.
Targeting Signal Transducer and Activator of Transcription 3 for Colorectal Cancer Prevention and Treatment with Natural Products

Signal transducers and activators of transcription 3 (STAT3) a transcription factor, plays key role in regulating the signal transduction events mediated by cytokines and growth factors. STAT3 is involved in many activities including survival, proliferation, differentiation, and apoptosis. Persistent activation of STAT3 has been demonstrated to be closely correlated to tumor cell proliferation, apoptosis, invasion, metastasis, and angiogenesis. Recent studies indicate that treatment with STAT3 inhibitor or silencing the expression of STAT3 can significantly reduce the progression/incidence of colorectal cancer (CRC) partly through regulating inflammation. Therefore, STAT3 offers a promising therapy. This review evaluates the evidence linking STAT3 with CRC development and analyzes the molecular mechanisms involved, specifically focusing on discussing the roles of natural products or herbal medicines on CRC progression by targeting STAT3. STAT3 activity suppresses tumor development and progression in part by regulating inflammation.
Dataflow matrix machines as programmable, dynamically expandable, self referential generalized recurrent neural networks
Venue: ArXiv

Dataflow matrix machines are a powerful generalization of recurrent neural networks. They work with multiple types of linear streams and multiple types of neurons, including higher order neurons which dynamically update the matrix describing weights and topology of the network in question while the network is running. It seems that the power of dataflow matrix machines is sufficient for them to be a convenient general purpose programming platform. This paper explores a number of useful programming idioms and constructions arising in this context.