nils-herrmann/clean_scirepeval huggingface dataset:
Establishing a framework for Open Geographic Information science
Venue: Int. J. Geogr. Inf. Sci.

When conducting research within a framework of Geographic Information Science (GISc) the scientific validity of this work can be argued as highly dependent upon the extent to which the methods employed are reproducible, and that, in the strictest sense, can only be fully achieved by implementing transparent workflows that utilize both open source software and openly available data. After considering the scientific implications of non reproducible methods, we provide a review of both open source Geographic Information Systems (GIS) and openly available data, before describing an integrated model for Open GISc. We conclude with a critical review of this embryonic paradigm, with directions for future development in supporting spatial data infrastructure.
Crowdsourcing, Citizen Science or Volunteered Geographic Information? The Current State of Crowdsourced Geographic Information
Venue: ISPRS Int. J. Geo Inf.

Citizens are increasingly becoming an important source of geographic information, sometimes entering domains that had until recently been the exclusive realm of authoritative agencies. This activity has a very diverse character as it can, amongst other things, be active or passive, involve spatial or aspatial data and the data provided can be variable in terms of key attributes such as format, description and quality. Unsurprisingly, therefore, there are a variety of terms used to describe data arising from citizens. In this article, the expressions used to describe citizen sensing of geographic information are reviewed and their use over time explored, prior to categorizing them and highlighting key issues in the current state of the subject. The latter involved a review of ~100 Internet sites with particular focus on their thematic topic, the nature of the data and issues such as incentives for contributors. This review suggests that most sites involve active rather than passive contribution, with citizens typically motivated by the desire to aid a worthy cause, often receiving little training. As such, this article provides a snapshot of the role of citizens in crowdsourcing geographic information and a guide to the current status of this rapidly emerging and evolving subject.
The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases.
Venue: Nature chemical biology

Lytic polysaccharide monooxygenases (LPMOs) are copper containing enzymes that oxidatively break down recalcitrant polysaccharides such as cellulose and chitin. Since their discovery, LPMOs have become integral factors in the industrial utilization of biomass, especially in the sustainable generation of cellulosic bioethanol. We report here a structural determination of an LPMO oligosaccharide complex, yielding detailed insights into the mechanism of action of these enzymes. Using a combination of structure and electron paramagnetic resonance spectroscopy, we reveal the means by which LPMOs interact with saccharide substrates. We further uncover electronic and structural features of the enzyme active site, showing how LPMOs orchestrate the reaction of oxygen with polysaccharide chains.
Polysaccharide based nanoparticles for theranostic nanomedicine.
Venue: Advanced drug delivery reviews

Polysaccharides are natural biological molecules that have numerous advantages for theranostics, the integrated approach of therapeutics and diagnostics. Their derivable reactive groups can be leveraged for functionalization with a nanoparticle enabling conjugate, therapeutics (small molecules, proteins, peptides, photosensitizers) and/or diagnostic agents (imaging agents, sensors) In addition, polysaccharides are diverse in size and charge, biodegradable and abundant and show low toxicity in vivo. Polysaccharide based nanoparticles are increasingly being used as platforms for simultaneous drug delivery and imaging and are therefore becoming popular theranostic nanoparticles. The review focuses on the method of nanoparticle formation (self assembled, physical or chemical cross linked) when engineering polysaccharide based nanoparticles for theranostic nanomedicine. We highlight recent examples of polysaccharide based theranostic systems from literature and their potential for use in the clinic, particularly chitosan and hyaluronic acid based NPs.
Sulfated modification, characterization and antioxidant activities of polysaccharide from Cyclocarya paliurus

In this study, polysaccharide extracted from Cyclocarya paliurus was chemically modified to obtain its sulfated derivatives. The physicochemical characterizations and antioxidant properties of these sulfated polysaccharide derivatives were comparatively investigated by chemical methods, circular dichroism spectra, high performance anion exchange chromatography, high performance gel permeation chromatography, fourier transform infrared spectrometry, and hydroxyl radical assay, DPPH radical assay, superoxide radical assay and b carotene linoleic acid assay, respectively. Results showed that these modifications were successful, and the physicochemical and antioxidant properties of polysaccharides were changed after sulfation. Among these sulfated polysaccharides, the S CP1 8 with relatively the lowest degree of substitution (DS) molecular weight (Mw) and the highest protein content exhibited excellent antioxidant activities in hydroxyl, superoxide, DPPH radical assay and b carotene linoleic acid assay. These results indicated that the in vitro antioxidant activities of the sulfated polysaccharides from Cyclocarya paliuru may be related to combined effects of DS, Mw, sulfate content, protein and uronic acid content.
Isocyperol, isolated from the rhizomes of Cyperus rotundus, inhibits LPS induced inflammatory responses via suppression of the NF kB and STAT3 pathways and ROS stress in LPS stimulated RAW 264.7 cells.
Venue: International immunopharmacology

The rhizomes of Cyperus rotundus (cyperaceae) have been used in Korean traditional medicines for treating diverse inflammatory diseases. However, little is known about the biological activities of isocyperol, a sesquiterpene isolated from C. rotundus, and their associated molecular mechanisms. In this study, we found that isocyperol significantly inhibited lipopolysaccharide (LPS) induced production of nitrite oxide (NO) and prostaglandin E2 (PGE2) and suppressed LPS induced expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase 2 (COX 2) at the mRNA and protein levels in RAW 264.7 macrophages. In addition, isocyperol downregulated the LPS induced expression of several proinflammatory cytokines, such as interleukin 1beta (IL 1b) IL 6, and monocyte chemotactic protein 1 (MCP 1) Isocyperol treatment suppressed the LPS induced nuclear translocation and transcriptional activation of nuclear factor kappaB (NF kB) in macrophages. Moreover, the activation of STAT3, another proinflammatory signal, was suppressed by isocyperol in LPS stimulated RAW 264.7 cells. Isocyperol pretreatment also induced heme oxygenase 1 (HO 1) expression and reduced LPS stimulated reactive oxygen species (ROS) accumulation in macrophages. Furthermore, isocyperol significantly increased the survival rate and attenuated serum levels of NO, PGE2, and IL 6 in LPS induced septic shock mouse model. Taken together, these data indicate that isocyperol suppress septic shock through negative regulation of pro inflammatory factors through inhibition of the NF kB and STAT3 pathways and ROS. To our knowledge, this is the first report on the biological activity of isocyperol and its molecular mechanism of action.
The Impact of Optimal Respiratory Gating and Image Noise on Evaluation of Intratumor Heterogeneity on 18F FDG PET Imaging of Lung Cancer
Venue: The Journal of Nuclear Medicine

Accurate measurement of intratumor heterogeneity using parameters of texture on PET images is essential for precise characterization of cancer lesions. In this study, we investigated the influence of respiratory motion and varying noise levels on quantification of textural parameters in patients with lung cancer.  We used an optimal respiratory gating algorithm on the list mode data of 60 lung cancer patients who underwent 18F FDG PET. The images were reconstructed using a duty cycle of 35% (percentage of the total acquired PET data) In addition, nongated images of varying statistical quality (using 35% and 100% of the PET data) were reconstructed to investigate the effects of image noise. Several global image derived indices and textural parameters (entropy, high intensity emphasis, zone percentage, and dissimilarity) that have been associated with patient outcome were calculated. The clinical impact of optimal respiratory gating and image noise on assessment of intratumor heterogeneity was evaluated using Cox regression models, with overall survival as the outcome measure. The threshold for statistical significance was adjusted for multiple comparisons using Bonferroni correction.  In the lower lung lobes, respiratory motion significantly affected quantification of intratumor heterogeneity for all textural parameters (P 0.007) except entropy (P 0.007) The mean increase in entropy, dissimilarity, zone percentage, and high intensity emphasis was 1.3% 1.5% (P 0.02) 11.6% 11.8% (P 0.006) 2.3% 2.2% (P 0.002) and 16.8% 17.2% (P 0.006) respectively. No significant differences were observed for lesions in the upper lung lobes (P 0.007) Differences in the statistical quality of the PET images affected the textural parameters less than respiratory motion, with no significant difference observed. The median follow up time was 35 mo (range, 7 39 mo) In multivariate analysis for overall survival, total lesion glycolysis and high intensity emphasis were the two most relevant image derived indices and were considered to be independent significant covariates for the model regardless of the image type considered.  The tested textural parameters are robust in the presence of respiratory motion artifacts and varying levels of image noise.
An Investigation of Semantic Interlingual Errors in the Writing of Libyan English as Foreign Language Learners

The aim of this paper is to investigate some semantic interlingual errors in the writing performance of Libyan English as Foreign Language Learners (LEFLLS) The study seeks to analyze these errorsthat appear in the learners' written production. The data was gathered from 25 essays written by 25 Libyan postgraduates majoring in different fields. It was collected and organized according to the errors committed. Errors taxonomy adapted from James' (1998) and Al Shormani and Al Sohbani's (2012) was used in identifying and analyzing these errors. Semantic errors were classified into five categories namely formal mis selection, formal misformation, lexical choice, collocation and lexico grammatical choice. The semantic errors identified were 346. These errors were classified into four categories namely, formal misformation (46.7% distortion due to spelling (32.4% lexical choice (40.6% and lexicogrammatical choice (2.4% The results show that direct translation from the first language (L1) assumed synonym and misselection of letters sub categories score the highest number of the errors, i.e.14.2% 13.08% and 12.08% respectively. While the sub category, both collocations incorrect error was the lowest (0.52% The other errors take the form of paraphrase (11.5% and Idiomacity (8.5% Two main sources have been found to be the cause behind these errors namely, L1 influence and insufficient knowledge about the second language (L2) Moreover, cultural differences between L1 and L2 had its impact in the written products of Libyan students.
EFL Teachers' Productive Skills Errors and their Effects on Students English Language Proficiency: The Case of Selected Preparatory Schools in East Wollega Zone

The objective of this descriptive study was to investigate the types of oral and written errors EFL teachers make, the sources of the errors and their potential effects on students' English language proficiency. Qualitative and quantitative data were collected from 16 teachers found in 4 preparatory schools in East Wollega Zone. The schools were selected purposively according to their locations and the teachers were selected by availability sampling technique. To get the quantitative and the qualitative data on the types of written and the oral errors, essays and interviews were used. The sources and effects of the written and oral errors were found through classroom observations, dictation of English words and interview. The written errors were grouped as grammatical, lexical, semantics and mechanics, and the oral ones were grouped as grammatical, lexical and semantic. The findings indicated that the teacher participants made 380 written errors which occurred in 19 categories 360 oral errors which occurred in 16 categories. The analysis of the interview data attributed sources of the teachers' written errors to the grammatical, lexical, semantics and mechanics errors made as intralingual transfer. From the dictation of 30 English words made by the researchers. It was found out that the teacher participants' primary school experiences had an interlanguage error transfer on them such that their spelling errors were due to a lack of appropriate pronunciation teaching by their primary and secondary school teachers. The other source of teachers' written errors was the mismatch between their English language learning experiences with their current teaching experiences. The findings also indicated that the fact that teachers made oral and written errors undeservedly, posed problems on their students language proficiency. Thus, it could be concluded that the targeted teachers need lots of trainings and workshops not to let them spoil their students' language proficiency.
Antecedents of ERP systems implementation success: a study on Jordanian healthcare sector
Venue: J. Enterp. Inf. Manag.

Most small and medium sized enterprises (SMEs) use some business management software to manage their daily operations. Ultimately they consider transitioning to an enterprise resources planning (ERP) system. However, implementing ERP system successfully is costly and complex, and often shows high disappointment rates or even abandonment due to need of fit with the business or social culture. In Jordan, large businesses have been using the ERP system for a long time, but SMEs usage of the system is relatively new. The purpose of this paper is to study the effect of ERP implementation success antecedents which consists of training, supportive leadership and ease of use on ERP implementation success itself through a mediating effect of user satisfaction.  Empirical data were collected using a survey questionnaire which was distributed to ERP users in Jordanian healthcare organizations. A total of 175 responses were collected and analyzed using structure equation modeli.
A thousand splendid suns
Venue: Indian journal of ophthalmology

Born a generation apart and with very different ideas about love and family, Mariam and Laila are two women brought jarringly together by war, by loss and by fate. As they endure the ever escalating dangers around them in their home as well as in the streets of Kabul they come to form a bond that makes them both sisters and mother daughter to each other, and that will ultimately alter the course not just of their own lives but of the next generation. With heart wrenching power and suspense, Hosseini shows how a woman's love for her family can move her to shocking and heroic acts of self sacrifice, and that in the end it is love, or even the memory of love, that is often the key to survival.
Locus: Locating bugs from software changes
Venue: 2016 31st IEEE/ACM International Conference on Automated Software Engineering (ASE)

Various information retrieval (IR) based techniques have been proposed recently to locate bugs automatically at the file level. However, their usefulness is often compromised by the coarse granularity of files and the lack of contextual information. To address this, we propose to locate bugs using software changes, which offer finer granularity than files and provide important contextual clues for bug fixing. We observe that bug inducing changes can facilitate the bug fixing process. For example, it helps triage the bug fixing task to the developers who committed the bug inducing changes or enables developers to fix bugs by reverting these changes. Our study further identifies that change logs and the naturally small granularity of changes can help boost the performance of IR based bug localization. Motivated by these observations, we propose an IR based approach Locus to locate bugs from software changes, and evaluate it on six large open source projects. The results show that Locus outperforms existing techniques at the source file level localization significantly. MAP and MRR in particular have been improved, on average, by 20.1% and 20.5% respectively. Locus is also capable of locating the inducing changes within top 5 for 41.0% of the bugs. The results show that Locus can significantly reduce the number of lines needing to be scanned to locate the bug compared with existing techniques.
Generative Adversarial Imitation Learning
Venue: NIPS

Consider learning a policy from example expert behavior, without interaction with the expert or access to reinforcement signal. One approach is to recover the expert's cost function with inverse reinforcement learning, then extract a policy from that cost function with reinforcement learning. This approach is indirect and can be slow. We propose a new general framework for directly extracting a policy from data, as if it were obtained by reinforcement learning following inverse reinforcement learning. We show that a certain instantiation of our framework draws an analogy between imitation learning and generative adversarial networks, from which we derive a model free imitation learning algorithm that obtains significant performance gains over existing model free methods in imitating complex behaviors in large, high dimensional environments.
Coupled Generative Adversarial Networks
Venue: NIPS

We propose coupled generative adversarial network (CoGAN) for learning a joint distribution of multi domain images. In contrast to the existing approaches, which require tuples of corresponding images in different domains in the training set, CoGAN can learn a joint distribution without any tuple of corresponding images. It can learn a joint distribution with just samples drawn from the marginal distributions. This is achieved by enforcing a weight sharing constraint that limits the network capacity and favors a joint distribution solution over a product of marginal distributions one. We apply CoGAN to several joint distribution learning tasks, including learning a joint distribution of color and depth images, and learning a joint distribution of face images with different attributes. For each task it successfully learns the joint distribution without any tuple of corresponding images. We also demonstrate its applications to domain adaptation and image transformation.
Energy based Generative Adversarial Network
Venue: ArXiv

We introduce the "Energy based Generative Adversarial Network" model (EBGAN) which views the discriminator as an energy function that attributes low energies to the regions near the data manifold and higher energies to other regions. Similar to the probabilistic GANs, a generator is seen as being trained to produce contrastive samples with minimal energies, while the discriminator is trained to assign high energies to these generated samples. Viewing the discriminator as an energy function allows to use a wide variety of architectures and loss functionals in addition to the usual binary classifier with logistic output. Among them, we show one instantiation of EBGAN framework as using an auto encoder architecture, with the energy being the reconstruction error, in place of the discriminator. We show that this form of EBGAN exhibits more stable behavior than regular GANs during training. We also show that a single scale architecture can be trained to generate high resolution images.
Anthocyanin Extraction from Purple Sweet Potato Cultivar Antin 3 (Ipomoea batatas L. using Maceration, Microwave Assisted Extraction, Ultrasonic Assisted Extraction and Their Application as Anti Hyperglycemic Agents in Alloxan Induced Wistar Rats

Purple sweet potato (PSP) cultivar Antin 3 was reported has higher anthocyanin content than other cultivars that had been circulating in Indonesia. Anthocyanins contained in the PSP has positive health effects. The antioxidant properties of anthocyanin play a role in reducing oxidative stress in the body due to conditions of hyperglycemia. Diabetes Mellitus (DM) is a metabolic disease characterized by high blood glucose levels exceed the normal level (hyperglycemia) Anthocyanins extract from PSP was expected to help reduce the progression of the diabetes by lowering blood glucose. Three types of extraction methods used in this study (Microwave Assisted Extraction, Ultrasonic Assisted Extraction and maceration) Anthocyanin extracts from best method was tested to alloxan induced Wistar rats to determine their effects in lowering blood glucose levels. The results showed that the extraction method significantly affect on the levels of anthocyanin, antioxidant activity DPPH IC50, antioxidant activity FIC IC50, total phenol, pH, and redness level of anthocyanin extracts from PSP cultivar Antin 3. The best treatment obtained from MAE extraction method where levels of anthocyanin reached 687.58 ppm, DPPH IC50 antioxidant activity 61.91 ppm, FIC IC50 antioxidant activity 199.31 ppm, totalphenolic content 5186.51 ppm GAE, pH 3.00, and redness level 39.5. Anthocyanin extract at dose of 40mg/200gr body weight for 4 weeks to the experimental animals could lower blood glucose levels by 33.23% and had effect on improvement histopathological pancreatic b cells.
Antioxidant activities and polyphenols of sweet potato (Ipomoea batatas L. leaves extracted with solvents of various polarities

Sweet potato Ipomoea batatas L. leaves are under utilized vegetables with abundant polyphenols. In this study, ten different solvents, including water, aqueous methanol, aqueous ethanol and aqueous acetone were used to investigate the effect of solvents on the recovery and antioxidant activities of polyphenols from sweet potato leaves. Results indicated that the total phenolic content in extracts ranged from 23.3 to 43.8 mg CAE/g DM, and 70% ethanol extract had the highest total flavonoid (3.4 mg QE/g DM) and total anthocyanin (36.5 mg c 3 gE/100 g DM) content. While, 50% acetone extract exhibited the highest crude extract yield (33.4% in dry materials) total phenolic content (43.8 mg CAE/g DM) as well as the strongest in vitro antioxidant activities. The best correlation with antioxidant activities was observed on total phenolics. Totally 14 phenolics were identified or tentatively identified in 50% acetone extract, caffeoylquinic acid (CQA) and quercetin derivatives were indicated as the most abundant phenolics. HPLC analysis also revealed that the extraction efficiency of 3 CQA, caffeic acid, 3,4 3,5 and 4,5 diCQA varied with the polarity of tested solvent, and 70% acetone showed the highest extraction capacity for 3,4 3,5 and 4,5 diCQA. All these data demonstrated that the types of extracting solvents impact the recovery and antioxidant activities of sweet potato leaf polyphenols greatly, and 50% (v/v) acetone is quite an efficient solvent to recover polyphenols and antioxidants from sweet potato leaves.