nils-herrmann/clean_scirepeval huggingface dataset:
Spatial structure of a gastropod community in the litter of a beech forest of dentario glandulosae fagetum in the Tatra Mountains

The grid method was used in the present study of the spatial structure of a gastropod community. 2,474 specimens representing 29 species were collected from an area of 9 sq m. The numbers of species were higher in squares with higher densities of snails (rNS 0.9) Species diversity varied between the squares, ranging from about 2.6 to 4.1, and was not very closely correlated with increase in species number (rSH 0.6) Snail density was not correlated with average dry litter weight in a square (rNM 0.03) The values of the indices of Lexis and of Morista show that the distribution of snails in the studied forest patches was aggregated. The material suggests an obvious relation between snails and plants. key WordS: Gastropoda, mountain malacofauna, snail community structure, species composition, abundance, dominance, ecological parameters Folia Malacologica 3/1989 was originally published as No. 1216 of Scientific Bulletins of University of Mining and Metallurgy, Cracow. This digitalised version was prepared by the Association of Polish Malacologists and first published on line on December 30th, 2016. http:/dx.doi.org/10.12657/folmal.003.004 Folia Malacol. 3: 55 72
Late holocene molluscan assemblages from Czorsztyn (Pieniny Klippen Belt, southern Poland)

Rich molluscan assemblages occur in the Upper Holocene sediments of the Pasternik stream at Czorsztyn and in limestone soils on rocks at the castle of Czorsztyn. The older assemblage found in the muds of the upper terrace comprises a fauna with a big share of forest snails whereas the younger assemblage comes from the sediments of the lower terrace and contains mostly typical species of the open environment. The change of fauna is due to the deforestation of the catchment basin of the stream, which took place in the 13th and 14th centuries. In the initial limestone soil there are very numerous snail shells representing various ecologic groups and the diversification of the assemblages reflects the mosaic pattern of their habitats, which were being slightly changed by human impact.  Pieninski National Park, molluscan assemblages, fluvial deposits, ecological groups Folia Malacologica 5/1993 was originally published as No. 1462 of Scientific Bulletins of University of Mining and Metallurgy, Cracow. This digitalised version was prepared by the Association of Polish Malacologists and first published on line on December 30th, 2016. http:/dx.doi.org/10.12657/folmal.005.001 Folia Malacol. 5: 15 24
Nuclear charge radii: density functional theory meets Bayesian neural networks

The distribution of electric charge in atomic nuclei is fundamental to our understanding of the complex nuclear dynamics and a quintessential observable to validate nuclear structure models. The aim of this study is to explore a novel approach that combines sophisticated models of nuclear structure with Bayesian neural networks (BNN) to generate predictions for the charge radii of thousands of nuclei throughout the nuclear chart. A class of relativistic energy density functionals is used to provide robust predictions for nuclear charge radii. In turn, these predictions are refined through Bayesian learning for a neural network that is trained using residuals between theoretical predictions and the experimental data. Although predictions obtained with density functional theory provide a fairly good description of experiment, our results show significant improvement (better than 40% after BNN refinement. Moreover, these improved results for nuclear charge radii are supplemented with theoretical error bars. We have successfully demonstrated the ability of the BNN approach to significantly increase the accuracy of nuclear models in the predictions of nuclear charge radii. However, as many before us, we failed to uncover the underlying physics behind the intriguing behavior of charge radii along the calcium isotopic chain.
DEM simulation of different particle ejection mechanisms in a fluidized bed with and without cohesive interparticle forces

The discrete element method (DEM) is used to simulate three particle ejection mechanisms in a two dimensional (2D) bubbling fluidized bed. The aim of the study is to analyze the particle ejection mechanisms and to investigate the effects of externally imposed interparticle forces on particle ejection. The ejection mechanisms are observed to be highly dependent on the extent of bubble coalescence. Bulge burst, which is induced by an isolated bubble eruption at the free bed surface, exhibits a regular dome contour with a lower initial velocity; wake spike, which is caused by the coalescence of two bubbles, shows a form of a spike with a higher initial velocity; jet spray, which is induced by the coalescence of more bubbles, presents continuous and violent clouds of particles. The induction of cohesive interparticle force not only delays the onset of particle ejection but also weakens its strength. The effect increases with increasing cohesive force. When cohesive force is increased to a high value, the occurrence of particle agglomeration further weakens particle ejection. For three different mechanisms, bulge burst is most sensitive to cohesive interparticle force, followed by wake spike and jet spray.
Real time obstacle detection for mobile robot navigation using stereo vision
Venue: 2016 International Conference on Computing, Analytics and Security Trends (CAST)

Obstacle detection and avoidance is playing very important role in field of mobile robot navigation, space exploration and automation industries for safety of robot. In this study paper we are proposing a real time obstacle detection and avoidance algorithm using passive stereoscopic Kinect camera. The basic idea behind the obstacle detection method is to find a depth map of image captured by Kinect camera and map it with the real world coordinates. Camera can be used as non contact type of sensor for detection of obstacles unlike the classical sensors. The obstacle detection and avoidance is carrying out in both static and dynamic environment i.e. obstacles in environment can be stationary or moving. The proposed system is tested in indoor environment with raspberry pi 2 model with 640*480 pixels image size and with a frame rate of 30 fps. The system is simple, robust and efficient. By use of camera system as sensor the need for complex sensor arrangement can be avoided. By the experimental results we can conclude that the proposed system is robust and convenient.
Theme development in qualitative content analysis and thematic analysis

Sufficient knowledge is available about the definition, details and differences of qualitative content and thematic analysis as two approaches of qualitative descriptive research. However, identifying the main features of theme as the data analysis product and the method of its development remain unclear. The purpose of this study was to describe the meaning of theme and offer a method on theme construction that can be used by qualitative content analysis and thematic analysis researchers in line with the underpinning specific approach to data analysis. This methodological paper comprises an analytical overview of qualitative descriptive research products and the meaning of theme. Also, our practical experiences of qualitative analysis supported by relevant published literature informed the generation of a stage like model of theme construction for qualitative content analysis and thematic analysis.  This paper offers a conceptual clarification and a pragmatic step by step method of theme development that has the capacity of assisting nurse researchers understand how theme is developed. As nursing is a pragmatic discipline, nurse researchers have tried to develop practical findings and devise some way to "do something" with findings to enhance the action and impact of nursing. The application of a precise method of theme development for qualitative descriptive data analysis suggested in this paper helps yield meaningful, credible and practical results for nursing.
Blended Wing Body Aircraft: A Historical Perspective

A blended wing body aircraft, BWB in short, is an innovative radical configuration applicable to the conceptual design of future large transport aircraft. Realization of the BWB aims at a substantial step in the continuous process of improving their flight performance, reducing atmospheric emissions, and minimizing environmental noise production due to civil aviation. The BWB belongs to the category of flying wings, an airplane layout with high aerodynamic efficiency that until recently has been practiced operationally for long range bomber aircraft only. Applications of the BWB are foreseen primarily in high subsonic jetliners with a capacity between 250 and 1000 seats. The general arrangement of a BWB does neither feature a discrete fuselage body nor an empennage. The crew, passenger seats, cargo, and luggage compartments are integrated in a thick lift generating central wing segment with a large center body chord and approximately equal span. The narrow chord outboard wings of recently proposed BWBs together form a conventional moderately loaded high aspect ratio swept wing. Advanced designs for a BWB intended for commercial application were developed during the last decennium of the twentieth century in the United States by teams formed by NASA, the industry, and universities. Although various proposed concepts have quite different characteristics, they consistently indicate that a BWB can have acceptable flying qualities, improve the aerodynamic efficiency by 25% and the fuel efficiency and CO2 emissions by 35% relative to the conventional TAW. Further refinements of the concept, wind tunnel experiments and low speed flights with a remotely controlled flight test vehicle after the year 2000 have confirmed the promises of the advancements obtained by the project study teams.  Aircraft Design Technology; flying wings; fuel efficiency; tailless aircraft
Ruxolitinib is an effective treatment for CALR positive patients with myelofibrosis
Venue: British journal of haematology

Approximately 60 65% of patients with myelofibrosis carry mutations in the Janus kinase 2 gene (JAK2) and 5 10% carry mutations in the thrombopoietin receptor gene, MPL (Vainchenker et al, 2011) Recently, somatic mutations in the calreticulin gene (CALR) were identified in most patients lacking JAK2 or MPL mutations (Klampfl et al, 2013; Nangalia et al, 2013) In preclinical models, overexpression of CALR mutations resulted in cytokine independent proliferation of Ba/F3 cells and activation of signal transducer and activator of transcription 5 (STAT5) (Klampfl et al, 2013) Fedratinib, a JAK2 inhibitor, suppressed these effects in vitro (Klampfl et al, 2013) and reduced palpable spleen length and symptoms in two patients with myelofibrosis (Passamonti et al, 2014) These results suggest that inhibition of abnormal JAK/STAT signalling represents a therapeutic option for CALR mutated patients.
Daily events are important for age differences in mean and duration for negative affect but not positive affect.
Venue: Psychology and aging

Across midlife and into old age, older adults often report lower levels of negative affect and similar if not higher levels of positive affect than relatively younger adults. Researchers have offered a simple explanation for this result: Age is related to reductions in stressors and increases in pleasurable activities that result in higher levels of well being. The current study examines subjective reports of emotional experience assessed across 8 days in a large sample of adults (N 2,022) ranging from 35 to 84 years old. By modeling age differences before and after adjusting for daily positive uplifts and negative stressors, this article assesses the extent to which daily events account for age differences in positive and negative affect reports. Consistent with previous research, the authors found that older age is related to lower mean levels and shorter duration of a negative emotional experience in a model only adjusting for gender, education, and ethnicity. After adjusting for daily events, however, the linear age related effects were no longer significant. For positive affect, adjusting for daily events did not alter age related patterns of experiencing higher mean levels and longer positive experience duration, suggesting that other factors underlie age related increases in positive affect.
How computer science can help in understanding the 3D genome architecture
Venue: Briefings Bioinform.

Chromosome conformation capture techniques are producing a huge amount of data about the architecture of our genome. These data can provide us with a better understanding of the events that induce critical regulations of the cellular function from small changes in the three dimensional genome architecture. Generating a unified view of spatial, temporal, genetic and epigenetic properties poses various challenges of data analysis, visualization, integration and mining, as well as of high performance computing and big data management. Here, we describe the critical issues of this new branch of bioinformatics, oriented at the comprehension of the three dimensional genome architecture, which we call 'Nucleome Bioinformatics' looking beyond the currently available tools and methods, and highlight yet unaddressed challenges and the potential approaches that could be applied for tackling them. Our review provides a map for researchers interested in using computer science for studying 'Nucleome Bioinformatics' to achieve a better understanding of the biological processes that occur inside the nucleus.
A self powered amperometric lactate biosensor based on lactate oxidase immobilized in dimethylferrocene modified LPEI.
Venue: Biosensors bioelectronics

Lactate is an important biomarker due to its excessive production by the body during anerobic metabolism. Existing methods for electrochemical lactate detection require the use of an external power source to supply a positive potential to the working electrode of a given device. Herein we describe a self powered amperometric lactate biosensor that utilizes a dimethylferrocene modified linear poly(ethylenimine) (FcMe2 LPEI) hydrogel to simultaneously immobilize and mediate electron transfer from lactate oxidase (LOx) at the anode and a previously described enzymatic cathode. Operating as a half cell, the FcMe2 LPEI electrode material generates a jmax of 1.51 0.13 mAcm( 2) with a KM of 1.6 0.1 mM and a sensitivity of 400 20 mAcm( 2)mM( 1) while operating with an applied potential of 0.3 V vs. SCE. When coupled with an enzymatic biocathode, the self powered biosensor has a detection range between 0mM and 5mM lactate with a sensitivity of 45 6 mAcm( 2)mM( 1) Additionally, the FcMe2 LPEI/LOx based self powered sensor is capable of generating a power density of 122 5 mWcm( 2) with a current density of 657 17 mAcm( 2) and an open circuit potential of 0.57 0.01 V, which is sufficient to act as a supplemental power source for additional small electronic devices.
Conformational flexibility related to enzyme activity: evidence for a dynamic active site gatekeeper function of Tyr215 in Aerococcus viridans lactate oxidase
Venue: Scientific reports

L Lactate oxidase (LOX) belongs to a large family of flavoenzymes that catalyze oxidation of a hydroxy acids. How in these enzymes the protein structure controls reactivity presents an important but elusive problem. LOX contains a prominent tyrosine in the substrate binding pocket (Tyr215 in Aerococcus viridans LOX) that is partially responsible for securing a flexible loop which sequesters the active site. To characterize the role of Tyr215, effects of substitutions of the tyrosine (Y215F, Y215H) were analyzed kinetically, crystallographically and by molecular dynamics simulations. Enzyme variants showed slowed flavin reduction and oxidation by up to 33 fold. Pyruvate release was also decelerated and in Y215F, it was the slowest step overall. A 2.6 A crystal structure of Y215F in complex with pyruvate shows the hydrogen bond between the phenolic hydroxyl and the keto oxygen in pyruvate is replaced with a potentially stronger hydrophobic interaction between the phenylalanine and the methyl group of pyruvate. Residues 200 through 215 or 216 appear to be disordered in two of the eight monomers in the asymmetric unit suggesting that they function as a lid controlling substrate entry and product exit from the active site. Substitutions of Tyr215 can thus lead to a kinetic bottleneck in product release.
Layer by layer construction of ascorbate interference free amperometric lactate biosensors with lactate oxidase, ascorbate oxidase, and ceria nanoparticles
Venue: Microchimica Acta

AbstractWe report on the design of an ascorbate interference free lactate biosensor that takes advantage of the redox properties of ceria (CeO2) nanoparticles that make this material suitable to be used in electrochemical biosensors operating in low oxygen conditions. First, ceria free lactate biosensors were fabricated using a positively charged polymer, polyethylenimine (PEI) for the immobilization of lactate oxidase (LOx) and ascorbate oxidase (AOx) on Pt electrodes. When AOx was not immobilized on the electrode, the sensor was interfered by ascorbate. Immobilization of AOx on the electrode surface, however, resulted in a loss of interference by ascorbate due to the depletion of oxygen in the enzyme layer. To address this challenge, we exploited the oxygen storage capacity of ceria nanoparticles. Their introduction into the enzyme layer enabled the fabrication of lactate biosensors that are not interfered by ascorbate and yet can be operated under low oxygen conditions. The Pt/CeO2 3(PEI/LOx) 3(PEI/AOx) biosensors, if operated at a working voltage of 0.6 V (vs. Ag/AgCl) display a wide linear range (20 mM to 1 mM) a low detection limit (0.3 mM) and a sensitivity of 172.9 11.7 mAmM 1cm 2. Evidently, the layer by layer configuration eliminates interferences by common species such as ascorbic acid, uric acid, and glucose. The practical applicability of the sensors was evaluated by detecting lactate in human serum. Graphical abstractAscorbate interference free amperometric lactate biosensors were constructed using layer by layer deposition of ceria nanoparticles, polyethylenimine, lactate oxidase, and ascorbate oxidase.
Enzymatic Resolution by a d Lactate Oxidase Catalyzed Reaction for (S) 2 Hydroxycarboxylic Acids

Oxidase catalyzed kinetic resolution is important for the production of enantiopure 2 hydroxycarboxylic acids (2 HAs) which are versatile building blocks for the synthesis of many significant compounds. However, in contrast to that of (R) 2 HAs, the production of (S) 2 HA is challenging because of the lack of related oxidases. Herein, suitable enzymes were screened systematically through the analysis of numerous putative d lactate oxidase sequences and identification of several required properties. Finally, a d lactate oxidase from Gluconobacter oxydans 621H with advantageous characteristics, such as good solubility, broad substrate spectrum, and high stereoselectivity, was selected to resolve 2 HAs into (S) 2 HAs. A variety of (S) 2 HAs was produced successfully using this d lactate oxidase with excellent enantiomeric excess values >99 The presented screening criteria and approach for target biocatalysis suggested a guideline for the production of optically active chemicals such as (S) 2 HAs.
Pharmacodynamic Analysis of Morphine Time to Remedication Events in Infants and Young Children After Congenital Heart Surgery
Venue: Clinical Pharmacokinetics

ObjectiveThe aim of this study was to characterize the relationship between morphine plasma concentration and repeated time to postoperative remedication events in children undergoing cardiac surgery.MethodsData from our previously published study of morphine pharmacokinetics were utilized in this pharmacodynamic study. A population survival analysis based on hazard functions was undertaken in NONMEM(r).ResultsHazard was best described by a Gompertz function changing in steps over time. Concentration and age were the only predictors of the hazard function. Concentration producing 50 reduction in hazard was 19.6 (bootstrap 95 confidence interval 5.90 49.5 ng/ml) The hazard ratio for a 1 year old child to a 1 month old child was 1.91 (1.35 2.86) Sensitivity to morphine decreased with age and leveled off after 1 year of life. Morphine sulfate doses >0.1 mg/kg did not noticeably increase tolerable pain durations.ConclusionTime to remedication is a clinically useful endpoint for assessing opioid induced analgesia. Sensitivity to morphine treatment is age dependent. Morphine sulfate doses of 0.1 0.2 mg/kg are adequate for the management of postoperative pain in children. Our findings may help avoid unnecessary large morphine doses in children.
Learning Graph based POI Embedding for Location based Recommendation
Venue: CIKM

With the rapid prevalence of smart mobile devices and the dramatic proliferation of location based social networks (LBSNs) location based recommendation has become an important means to help people discover attractive and interesting points of interest (POIs) However, the extreme sparsity of user POI matrix and cold start issue create severe challenges, causing CF based methods to degrade significantly in their recommendation performance. Moreover, location based recommendation requires spatiotemporal context awareness and dynamic tracking of the user's latest preferences in a real time manner. To address these challenges, we stand on recent advances in embedding learning techniques and propose a generic graph based embedding model, called GE, in this paper. GE jointly captures the sequential effect, geographical influence, temporal cyclic effect and semantic effect in a unified way by embedding the four corresponding relational graphs (POI POI, POI Region, POI Time and POI Word)into a shared low dimensional space. Then, to support the real time recommendation, we develop a novel time decay method to dynamically compute the user's latest preferences based on the embedding of his/her checked in POIs learnt in the latent space. We conduct extensive experiments to evaluate the performance of our model on two real large scale datasets, and the experimental results show its superiority over other competitors, especially in recommending cold start POIs. Besides, we study the contribution of each factor to improve location based recommendation and find that both sequential effect and temporal cyclic effect play more important roles than geographical influence and semantic effect.