nils-herrmann/clean_scirepeval huggingface dataset:
NPInter v3.0: an upgraded database of noncoding RNA associated interactions
Venue: Database J. Biol. Databases Curation

Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs' functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs) especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs) In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high throughput technologies. In addition, we also curated lncRNA miRNA interactions from in silico predictions supported by AGO CLIP seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria) NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available at http:/www.bioinfo.org/NPInter/ Database URL: http:/www.bioinfo.org/NPInter/
ATtRACT a database of RNA binding proteins and associated motifs
Venue: Database J. Biol. Databases Curation

RNA binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available at http:/attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand curated experimentally validated data from CISBP RNA, SpliceAid F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discovering de novo motifs enriched in a set of related sequences and compare them with the motifs included in the database.  attract. cnic.
HPIDB 2.0: a curated database for host pathogen interactions
Venue: Database J. Biol. Databases Curation

Identification and analysis of host pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http:/www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016) Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources.  http:/www.agbase.msstate.edu/hpi/main.html
Solid lipid nanoparticles as a drug delivery system for the treatment of neurodegenerative diseases
Venue: Expert opinion on drug delivery

The failure of many molecules as CNS bioactive compounds is due to many restrictions: poor water solubility, intestinal absorption, in vivo stability, bioavailability, therapeutic effectiveness, side effects, plasma fluctuations, and difficulty crossing physiological barriers, like the brain blood barrier (BBB) to deliver the drug directly to the site of action.  Nanotechnology based approaches with the employment of liposomes, micelles, dendrimers, and solid lipid nanoparticles (SLN) as drug delivery systems, are used to overcome the above reported limitations. Here, we focus on the delivery of drugs based on SLN formulation to treat neurodegenerative diseases. Notably, SLN have the ability to protect drugs from chemical and enzymatic degradation, direct the active compound towards the target site with a substantial reduction of toxicity for the adjacent tissues, and pass physiological barriers increasing bioavailability without resorting to high dosage forms.  We believe that SLN could represent a suitable tool to pass the BBB and permit drugs to reach damaged areas of the CNS in patients affected by neurodegenerative pathologies, such as Alzheimer's and Parkinson's diseases.
Long term monitoring of soil management effects on runoff and soil erosion in sloping vineyards in Alto Monferrato (North West Italy)

Long term runoff and soil erosion data have been collected from differently managed field scale vineyard plots within the "Tenuta Cannona Experimental Vine and Wine Center of Regione Piemonte" located in the Alto Monferrato vine production area (NW Italy) The primary intent of the program was to evaluate the effects of agricultural management practices on the hydrologic, soil erosion, nutrient transport and soil compaction processes in vineyards. Field runoff data have been collected for every event since the year 2000 until now. Sediment and nutrient concentrations in water have been also monitored. Regarding soil properties and initial conditions, surveys have been carried out to investigate spatial and temporal variability of soil bulk density, soil saturated conductivity, soil water content, and penetration resistance. The Cannona Data Base (CDB) includes data for more than 300 runoff events and over 90 soil loss events; moreover, periodic measurements for soil physical characteristics are included for the three plots. Runoff and sediment yield showed high annual and seasonal variability and were strongly affected by the adoption of different soil management in the vineyard inter rows, especially after some years of observation. Grass cover reduced runoff by at least 37% in comparison with management by tillage, and average annual sediment yield ranged from 1.8 Mg ha 1 year 1 to 20.7 Mg ha 1 year 1 respectively for the "grass covered" and the "reduced tillage" vineyards. Furthermore, results showed the effect of the adopted soil management on soil properties. The Cannona Data base (CDB) can be accessed via a website http:/sustag.to.cnr.it/index.php/cannona db supported by the IMAMOTER CNR.
Monitoring daily evapotranspiration over two California vineyards using Landsat 8 in a multi sensor data fusion approach

California's Central Valley grows a significant fraction of grapes used for wine production in the United States. With increasing vineyard acreage, reduced water availability in much of California, and competing water use interests, it is critical to be able to monitor regional water use and evapotranspiration (ET) over large areas, but also in detail at individual field scales to improve water management within these viticulture production systems. This can be achieved by integrating remote sensing data from multiple satellite systems with different spatiotemporal characteristics. In this research, we evaluate the utility of a multi scale system for monitoring ET as applied over two vineyard sites near Lodi, California during the 2013 growing season, leading into the drought in early 2014. The system employs a multi sensor satellite data fusion methodology (STARFM: Spatial and Temporal Adaptive Reflective Fusion Model) combined with a multi scale ET retrieval algorithm based on the Two Source Energy Balance (TSEB) land surface representation to compute daily ET at 30 m resolution. In this system, TSEB is run using thermal band imagery from the Geostationary Environmental Operational Satellites (GOES; 4 km spatial resolution, hourly temporal sampling) the Moderate Resolution Imaging Spectroradiometer (MODIS) data (1 km resolution, daily acquisition) and the new Landsat 8 satellite (sharpened to 30 m resolution, 16 day acquisition) Estimates of daily ET generated in two neighboring fields of Pinot noir vines of different age agree with ground based flux measurements acquired in field during most of the 2013 season with relative mean absolute errors on the order of 19 23% (root mean square errors of approximately 1 mm d 1 reducing to 14 20% at the weekly timestep relevant for irrigation management 5 mm wk 1 A model overestimation of ET in the early season was detected in the younger vineyard, perhaps relating to an inter row grass cover crop. Spatial patterns of cumulative ET generally correspond to measured yield maps and indicate areas of variable crop moisture, soil condition, and yield within the vineyards that could require adaptive management. The results suggest that multi sensor remote sensing observations provide a unique means for monitoring crop water use and soil moisture status at field scales over extended growing regions, and may have value in supporting operational water management decisions in vineyards and other high value crops.
Water footprint assessment of some Italian wines: a territorial perspective

The main intent of this paper is to examine the potential typical wine production specialisation in some Italian geographical areas regarding virtual water consumption. The second purpose is to analyse and evaluate the water footprint data of two DOC wines from in vineyards in the North and South and Islands of Italy with the intent of showing that typical wines have a lower water footprint. The principle reason behind this can be found in the fact that the main component of virtual water tied to DOC or DOCG wine production is green water, as irrigation and fertilisation are banned for these categories of wine production. Moreover, growing good crops in the traditional areas of cultivation lets these typical wines be made in an even more sustainable way, in spite the fact that the yield of litres per hectares are limited to precise levels.
Research on quality of red wine varieties obtained at Bujoru Vineyard Dealu Bujorului Wine Center Romania

The ecoclimatic conditions advantageous for the grapevine growth fall into two categories: indispensable conditions and critical natural conditions. The indispensable conditions have negative influences on the growth and fruition of grapevine, resulting in a decreased production both for quantitative and qualitative respects. The purpose of this paper was to trace the influence of the ecoclimatic conditions of 2013 2014 2015 over the quality of grapevine varieties used for high quality wines. The used biological material was represented by Merlot, Cabernet Sauvignon and Feteasca Neagra. Determination was conducted in accordance with international standards for determining wine quality (O.I.V) The alcohol content varies in large limits 12.5% vol. in Feteasca Neagra (2013) and 16.37% vol. in 2015. Regarding the total acidity, Merlot variety, recorded the lowest value 6.07 g/L tartaric acid (2015) while the Feteasca Neagra variety has recorded the highest value 7.60 g/L tartaric acid. Volatile acidity to Feteasca Neagra (2013) was 0.34 g/L acetic acid, the highest value was recorded at Merlot (2015) of 0.65 g/L acetic acid. Free SO2 content and the total recorded in the normal range, the highest values were recorded Cabernet Sauvignon (2014) 26.33 mg/L (free SO2) and Merlot (2013) 121.67 mg/L (total SO2) in contrast with the lowest values were recorded in Feteasca Neagra (2015) 16.0 mg/L (free SO2) and 59.67 (total SO2) the Feteasca Neagra (2014) Potassium recorded values between 778.67 mg/L Merlot (2013) and 1179.67 mg/L to Feteasca Neagra (2015) Calcium content values ranged between 77.87 mg/L Merlot (2013) and 115.30 mg/L Cabernet Sauvignon (2013) The largest iron content was recorded at Feteasca Neagra (2015) 0.54 mg/L, and the opposite with the lowest concentration was recorded at Merlot (2013) 0.36 mg/L, while copper and lactic acid was below the detection limit. The ecoclimatic conditions studied in Dealu Bujorului distinguished the exceptional viticultural character of this wine area and the nature of authenticity present in the large variety of wines produced in the areas studied. Regarding the qualitative assessment of the eight varieties taken under testing, based on the results can be observed that the varieties have good suitability in the studied area and in terms of quality assessment, they show the particularities of the varieties and also the influence of the eco climatic and ecopedological conditions on wine quality. The results of the research indicate very good ecoclimatic conditions for the cultivation of grapevines in the Dealu Bujorului Vineyard, as well as a good suitability for the tested varieties in order to be cultivated as to achieve a superior quality wine.
Under Review as a Conference Paper at Iclr 2017 Delving into Transferable Adversarial Ex Amples and Black box Attacks

An intriguing property of deep neural networks is the existence of adversarial examples, which can transfer among different architectures. These transferable adversarial examples may severely hinder deep neural network based applications. Previous works mostly study the transferability using small scale datasets. In this work, we are the first to conduct an extensive study of the transferability over large models and a large scale dataset, and we are also the first to study the transferability of targeted adversarial examples with their target labels. We study both non targeted and targeted adversarial examples, and show that while transferable non targeted adversarial examples are easy to find, targeted adversarial examples generated using existing approaches almost never transfer with their target labels. Therefore, we propose novel ensemble based approaches to generating transferable adversarial examples. Using such approaches, we observe a large proportion of targeted adversarial examples that are able to transfer with their target labels for the first time. We also present some geometric studies to help understanding the transferable adversarial examples. Finally, we show that the adversarial examples generated using ensemble based approaches can successfully attack Clarifai.com, which is a black box image classification system.
Human Detection from Aerial Imagery for Automatic Counting of Shellfish Gatherers
Venue: VISIGRAPP

Automatic human identification from aerial image time series or video sequences is a challenging issue. We propose here a complete processing chain that operates in the context of recreational shellfish gatherers counting in a coastal environment (the Gulf of Morbihan, South Brittany, France) It starts from a series of aerial photographs and builds a mosaic in order to prevent multiple occurrences of the same objects on the overlapping parts of aerial images. To do so, several stitching techniques are reviewed and discussed in the context of large aerial scenes. Then people detection is addressed through a sliding window analysis combining the HOG descriptor and a supervised classifier. Several classification methods are compared, including SVM, Random Forests, and AdaBoost. Experimental results show the interest of the proposed approach, and provides directions for future research.
Pedestrian Detection and Tracking from Low Resolution Unmanned Aerial Vehicle Thermal Imagery
Venue: Sensors

Driven by the prominent thermal signature of humans and following the growing availability of unmanned aerial vehicles (UAVs) more and more research efforts have been focusing on the detection and tracking of pedestrians using thermal infrared images recorded from UAVs. However, pedestrian detection and tracking from the thermal images obtained from UAVs pose many challenges due to the low resolution of imagery, platform motion, image instability and the relatively small size of the objects. This research tackles these challenges by proposing a pedestrian detection and tracking system. A two stage blob based approach is first developed for pedestrian detection. This approach first extracts pedestrian blobs using the regional gradient feature and geometric constraints filtering and then classifies the detected blobs by using a linear Support Vector Machine (SVM) with a hybrid descriptor, which sophisticatedly combines Histogram of Oriented Gradient (HOG) and Discrete Cosine Transform (DCT) features in order to achieve accurate detection. This research further proposes an approach for pedestrian tracking. This approach employs the feature tracker with the update of detected pedestrian location to track pedestrian objects from the registered videos and extracts the motion trajectory data. The proposed detection and tracking approaches have been evaluated by multiple different datasets, and the results illustrate the effectiveness of the proposed methods. This research is expected to significantly benefit many transportation applications, such as the multimodal traffic performance measure, pedestrian behavior study and pedestrian vehicle crash analysis. Future work will focus on using fused thermal and visual images to further improve the detection efficiency and effectiveness.
What Leads to Customer Satisfaction and Repurchase Intention in Taobao.com

The purpose of this paper is to investigate the Taobao.com's consumer behavior and to find out the effects of Taobao.com's service quality, product factor and price factor on customer satisfaction and repurchase intention. For the purpose we collected and analyzed data via a Web based questionnaire survey. This paper also investigates the moderating effect of online shopping experience on the way. The results reveal that: first, customer satisfaction positively affects repurchase intention in Taobao.com; second, online shopping experience has a moderating effect on relationship between service and customer satisfaction; service and repurchase intention; and satisfaction and repurchase intention.
A Study on the Relationship Among Trust, Satisfaction and Repurchase Intention Towards E Shopping

The shift in the shopping behavior towards online shopping in particular has encouraged many organizations to launch e store businesses. Trust is considered to be the most crucial factor for the success of e shopping. Customer's trust has generally been identified in terms of beliefs and behavior/behavioral intention. Customer satisfaction is determined by emotional reactions. In general, satisfaction leads to positive results such as increase in customer loyalty and customer repurchase intention. In India online shopping is expected to grow to 65 million by end of 2015 with better infrastructure in terms of logistics, broadband and Internet ready devices.
The value of express delivery services for cross border e commerce in European Union markets

Further growth of cross border e commerce in the European Union markets requires improved express delivery services. The framework presented in this paper identifies relevant contextual factors that affect express delivery adoption rates in European cross border e commerce. This framework leads to a set of hypotheses, both on the effects of express deliveries on financial performance indicators (order incidence, order size, and repurchase rate) and on the factors that drive demand for express deliveries (consumer income, logistic costs, and lead time benefits) A case study provides empirical tests of the hypotheses, using data on about forty thousand sales transactions from a consumer electronics manufacturer's cross border online shop. The findings are that express delivery has positive effects on financial performance, as it leads to higher order incidence, larger order size, and higher repurchase rates in cross border transactions. Demand for express delivery services increases with higher income, larger lead time benefits, and lower logistic costs. Managers can employ the presented framework to formulate and analyse their own targets for performance and express delivery services.
Towards direct numerical simulations of low Mach number turbulent reacting and two phase flows using immersed boundaries

Most reacting and two phase flows of practical interest are turbulent but take place at low Mach numbers or under incompressible conditions. In order to investigate the properties of such complex flows with high accuracy but acceptable computing times, a suitable tool for Direct Numerical Simulations (DNS) called DINOSOARS, has been developed. The present article describes the numerical components and methods implemented in this code, together with a detailed verification and validation phase, and finishes with two examples of full scale simulations. We hope it might be useful as a "verification and validation guideline" for other researchers working on DNS of reacting flows. Since applications of growing complexity are considered by DNS, a Direct Boundary Immersed Boundary Method (DB IBM) has been implemented, allowing a description of arbitrary geometries on a fixed, but possibly refined, Cartesian mesh. A direct force IBM is implemented as well in DINOSOARS in order to resolve large moving spherical particles (much larger than the Kolmogorov scale) on the grid. Particles below the Kolmogorov scale are treated as point particles, taking into account additionally heat and mass transfer with the continuous flow. The efficient parallelization of the code relies on the open source library 2DECOMP&FFT. The underlying Poisson equation is solved in a fast and accurate manner by FFT, even for non periodic boundary conditions. The flexibility of DINOSOARS makes it a very promising tool for analyzing a variety of problems and applications involving turbulent reacting and/or two phase flows.