nils-herrmann/clean_scirepeval huggingface dataset:
Applications of Discrete Molecular Dynamics in biology and medicine.
Venue: Current opinion in structural biology

Discrete Molecular Dynamics (DMD) is a physics based simulation method using discrete energetic potentials rather than traditional continuous potentials, allowing microsecond time scale simulations of biomolecular systems to be performed on personal computers rather than supercomputers or specialized hardware. With the ongoing explosion in processing power even in personal computers, applications of DMD have similarly multiplied. In the past two years, researchers have used DMD to model structures of disease implicated protein folding intermediates, study assembly of protein complexes, predict protein protein binding conformations, engineer rescue mutations in disease causative protein mutants, design a protein conformational switch to control cell signaling, and describe the behavior of polymeric dispersants for environmental cleanup of oil spills, among other innovative applications.
Integrating Topic and Latent Factors for Scalable Personalized Review based Rating Prediction
Venue: IEEE Transactions on Knowledge and Data Engineering

Personalized review based rating prediction, a newly emerged research problem, aims at inferring users' ratings over their unrated items using existing reviews and corresponding ratings. While some researchers proposed to learn topic factor from review text to obtain interpretability for rating prediction, they often overlooked the fact that the learned topic factors are limited to review text and cannot fully reveal the complicated relations between reviews and ratings. Moreover, topic modeling based solutions for this problem usually utilize Gibbs sampling algorithms to learn topics and word distributions, resulting in non negligible computational overload. To address the above challenges, we propose an integrated topic and latent factor model (ITLFM) which combines topic and latent factors in a linear way to make them complement each other for better accuracies in rating prediction tasks. In addition, ITLFM models review text through an additive topic model to reveal user's and item's topic factors simultaneously. To ensure high learning efficiency, we design a hybrid stochastic learning algorithm for ITLFM. We evaluate ITLFM on several standard benchmarks and compare with representative approaches. The experimental results demonstrate that the proposed ITLFM method is computationally efficient and accurate, as well as scalable for large scale applications.
Design, Fabrication, and Evaluation of Superhydrophobic (SHPo) Surfaces for Drag Reduction in Turbulent Boundary Layer Flows

Author(s) Xu, Muchen Advisor(s) Kim,  Sustaining a gas layer on them in liquid, superhydrophobic (SHPo) surfaces have attracted enormous attention due to the possibility of reducing friction drag in numerous flow applications. Although many SHPo surfaces proved to reduce drag significantly (e.g. g 10% in microchannel flows and certain SHPo surfaces proved to have an unprecedentedly large slip length (e.g. g 100 microns) a significant drag reduction is still elusive in turbulent flows that reflect most applications, such as watercraft in marine environment. Recognizing the gas layer (called plastron) as the key and studying its robustness under water of varying depths, we first conclude that the SHPo surfaces capable of a significant drag reduction cannot maintain the plastron indefinitely if submerged deeper than a few centimeters. By developing a high resolution shear sensor for centimeters size sample surfaces and using silicon SHPo surfaces that keep plastron more robust than others, we obtain up to ~25% drag reduction in turbulent boundary layer flows at Reynolds numbers up to 1.1x107. Obtained at a high speed water tunnel and a high speed tow tank, the results also indicate that the drag reduces more with increasing Reynolds number, corroborating the numerical studies in the literature. Moreover, we develop and conduct SHPo drag experiments using a real boat in marine conditions for the first time, achieving ~20% drag reduction. Finally, a scalable fabrication process is developed for scale up manufacturing of both passive and semi active SHPo surfaces. For the semi active SHPo surfaces, i.e. SHPo surfaces with self regulating gas restoration capability, we propose and demonstrate a gas generation mechanism that does not require any external power input.
Professional Development of Preceptors Improves Nurse Outcomes
Venue: Journal for nurses in professional development

This hospital preceptor program includes processes to recruit, select, and provide ongoing evaluation of preceptor function. After volunteering, candidates are chosen by peer vote. A blended training program includes online, commercially available modules and nursing professional development practitioner led sessions that engage preceptors in reflection and problem solving. Preceptor education allows nurses to further develop their skills over 2 years. Formal evaluation found that preceptors gained efficiency in their role with low turnover rate and positive patient outcomes.
An exploration of role model influence on adult nursing students' professional development: A phenomenological research study.
Venue: Nurse education today

Patients' expectations of being cared for by a nurse who is caring, competent, and professional are particularly pertinent in current health and social care practice. The current drive for NHS values based recruitment serves to strengthen this. How nursing students' development of professionalism is shaped is not fully known, though it is acknowledged that their practice experience strongly shapes behaviour. This study (in 2013 14) explored twelve adult nursing students' lived experiences of role modelling through an interpretive phenomenological analysis approach, aiming to understand the impact on their development as professional practitioners. Clinical nurses influenced student development consistently. Some students reported that their experiences allowed them to learn how not to behave in practice; a productive learning experience despite content. Students also felt senior staff influence on their development to be strong, citing 'leading by example. The impact of patients on student professional development was also a key finding. Through analysing information gained, identifying and educating practice based mentors who are ready, willing, and able to role model professional attributes appear crucial to developing professionalism in nursing students. Those involved in nurse education, whether service providers or universities, may wish to acknowledge the influence of clinical nurse behaviour observed by students both independent of and in direct relation to care delivery and the impact on student nurse professional development. A corollary relates to how students should be guided and briefed/debriefed to work with a staff to ensure their exposure to a variety of practice behaviours.
Linking Entities for Enriching and Structuring Social Media Content
Venue: WWW

Social media platforms such as Twitter, Facebook or LinkedIn become a reliable source of news and play a key role for being aware of events around the world. Using social media to recognize, enrich or summarize events is however very challenging. In the first part of this talk, we will present ADEL, a novel hybrid architecture for an adaptive entity linking system, that combines methods from the natural language processing, information retrieval and semantic fields. The framework enables to link all the mentions occurring in a text to their entity counterparts in a knowledge base. It is modular and adaptive since it enables to process text written in different languages and of different kind (newswire, tweets, blog posts, etc. while entities can be of common types (PERSON, LOCATION and ORGANIZATION) or specific ones (dates, numbers) and be disambiguated in generic or specialized knowledge bases. We will show how ADEL can outperform the state of the art systems on the reference NEEL challenges that happens in the yearly #Micropost workshop (2014 2016) In the second part of this talk, we will present a framework that can collect microposts from more than 12 social platforms and that contain media items, as a result of a query for example a trending event. We will then show how we can automatically create different visual storyboards that reflect what users have shared about this particular event. The visualization emphasizes the different aspects of storyboards. A graph view shows the relationships between microposts and topics that we automatically extract, while the timeline view emphasizes the time dimension. The user can watch and interact with the summarized view of all the topics or select a particular one with the additional details. In addition, the states of different views are persistent through the URLs which makes easy sharing possible.
Testing a Habitat Suitability Index Model for Boreal Owls in Western Newfoundland, Canada
Venue: Journal of Raptor Research

Boreal Owls (Aegolius funereus) rely on mature forests and, consequently, are negatively affected by timber harvesting strategies that alter the composition and structure of these forests. We tested an existing Boreal Owl habitat suitability index (HSI) model created using data from across the species' North American breeding distribution, plus a modified Newfoundland version that incorporated local data. We assessed the applicability of these models to a population on the periphery of the species' North American range in Newfoundland, Canada. We also conducted habitat composition analyses and evaluated the Boreal Owl HSI model values associated with forest cover projections under three different forest harvesting scenarios. Overall output from both HSI models indicated low levels of suitability for locations across the study area. Long term persistence in Newfoundland demonstrates that suitable habitat for Boreal Owls exists, but what constitutes suitable habitat for populations in other parts of North America may differ from that in our study area. Boreal Owls in Newfoundland occupied locations with a greater proportion of disturbed cover, and lesser proportions of deciduous and mixed coniferous and deciduous stands =60 yr old, compared to what was available in the surrounding region, as measured in randomly selected plots. Whereas Boreal Owl habitat use in Newfoundland was similar to that described for other populations, the limited use of deciduous and mixed stands was distinct. Forward projection modeling of forest cover indicated that there were no differences in the overall suitability of habitat available to Boreal Owls under the three harvesting scenarios. Our study highlights the importance of adjusting forest management strategies to account for differences in habitat use among populations.
The Combined Effects of Healthy Lifestyle Behaviors on All Cause Mortality: The Golestan Cohort Study.
Venue: Archives of Iranian medicine

Most studies that have evaluated the association between combined lifestyle factors and mortality outcomes have been conducted in populations of developed countries.  The aim of this study was to examine the association between combined lifestyle scores and risk of all cause and cause specific mortality for the first time among Iranian adults.  The study population included 50,045 Iranians, 40 75 years of age, who were enrolled in the Golestan Cohort Study, between 2004 and 2008. The lifestyle risk factors used in this study included cigarette smoking, physical inactivity, and Alternative Healthy Eating Index. The lifestyle score ranged from zero (non healthy) to 3 (most healthy) points. From the study baseline up to analysis, a total of 4691 mortality cases were recorded. Participants with chronic diseases at baseline, outlier reports of calorie intake, missing data, and body mass index of less than 18.5 were excluded from the analyses. Cox regression models were fitted to establish the association between combined lifestyle scores and mortality outcomes.  After implementing the exclusion criteria, data from 40,708 participants were included in analyses. During 8.08 years of follow up, 3,039 cases of all cause mortality were recorded. The adjusted hazard ratio of a healthy lifestyle score, compared with non healthy lifestyle score, was 0.68 (95% CI: 0.54, 0.86) for all cause mortality, 0.53 (95% CI: 0.37, 0.77) for cardiovascular mortality, and 0.82 (95% CI: 0.53, 1.26) for mortality due to cancer. When we excluded the first two years of follow up from the analysis, the protective association between healthy lifestyle score and cardiovascular death did not change much 0.55 (95% CI: 0.36, 0.84) but the inverse association with all cause mortality became weaker 0.72 (95% CI: 0.55, 0.94) and the association with cancer mortality was non significant 0.92 (95% CI: 0.58, 1.48) In the gender stratified analysis, we found an inverse strong association between adherence to healthy lifestyle and mortality from all causes and cardiovascular disease in either gender, but no significant relationship was seen with mortality from cancer in men or women. Stratified analysis of BMI status revealed an inverse significant association between adherence to healthy lifestyle and mortality from all causes, cardiovascular disease and cancer among non obese participants.  We found evidence indicating that adherence to a healthy lifestyle, compared to non healthy lifestyle, was associated with decreased risk of all cause mortality and mortality from cardiovascular diseases in Iranian adults.
Association of Age at Onset of Menopause and Time Since Onset of Menopause With Cardiovascular Outcomes, Intermediate Vascular Traits, and All Cause Mortality: A Systematic Review and Meta analysis.
Venue: JAMA cardiology

As many as 10% of women experience natural menopause by the age of 45 years. If confirmed, an increased risk of cardiovascular disease (CVD) and all cause mortality associated with premature and early onset menopause could be an important factor affecting risk of disease and mortality among middle aged and older women.  To systematically review and meta analyze studies evaluating the effect of age at onset of menopause and duration since onset of menopause on intermediate CVD end points, CVD outcomes, and all cause mortality. Data Sources Medical databases (ie, Medline, EMBASE, and Web of Science) until March 2015. Study Selection Studies (ie, observational cohort, case control, or cross sectional) that assessed age at onset of menopause and/or time since onset of menopause as exposures as well as risk of cardiovascular outcomes and intermediate CVD end points in perimenopausal, menopausal, or postmenopausal women.  Extraction and Synthesis Studies were sought if they were observational cohort, case control, or cross sectional studies; reported on age at onset of menopause and/or time since onset of menopause as exposures; and assessed associations with risk of CVD related outcomes, all cause mortality, or intermediate CVD end points. Data were extracted by 2 independent reviewers using a predesigned data collection form. The inverse variance weighted method was used to combine relative risks to produce a pooled relative risk using random effects models to allow for between study heterogeneity.  Cardiovascular disease outcomes (ie, composite CVD, fatal and nonfatal coronary heart disease [CHD] and overall stroke and stroke mortality) CVD mortality, all cause mortality, and intermediate CVD end points.  Of the initially identified references, 32 studies were selected that included 310 329 nonoverlapping women. Outcomes were compared between women who experienced menopause younger than 45 years and women 45 years or older at onset; the relative risks (95% CIs) were 1.50 (1.28 1.76) for overall CHD, 1.11 (1.03 1.20) for fatal CHD, 1.23 (0.98 1.53) for overall stroke, 0.99 (0.92 1.07) for stroke mortality, 1.19 (1.08 1.31) for CVD mortality, and 1.12 (1.03 1.21) for all cause mortality. Outcomes were also compared between women between 50 and 54 years at onset of menopause and women younger than 50 years at onset; there was a decreased risk of fatal CHD (relative risk, 0.87; 95% CI, 0.80 0.96) and no effect on stroke. Time since onset of menopause in relation to risk of developing intermediate cardiovascular traits or CVD outcomes was reported in 4 observational studies with inconsistent results.  The findings of this review indicate a higher risk of CHD, CVD mortality, and overall mortality in women who experience premature or early onset menopause.
Recent automatic text summarization techniques: a survey
Venue: Artificial Intelligence Review

As information is available in abundance for every topic on internet, condensing the important information in the form of summary would benefit a number of users. Hence, there is growing interest among the research community for developing new approaches to automatically summarize the text. Automatic text summarization system generates a summary, i.e. short length text that includes all the important information of the document. Since the advent of text summarization in 1950s, researchers have been trying to improve techniques for generating summaries so that machine generated summary matches with the human made summary. Summary can be generated through extractive as well as abstractive methods. Abstractive methods are highly complex as they need extensive natural language processing. Therefore, research community is focusing more on extractive summaries, trying to achieve more coherent and meaningful summaries. During a decade, several extractive approaches have been developed for automatic summary generation that implements a number of machine learning and optimization techniques. This paper presents a comprehensive survey of recent text summarization extractive approaches developed in the last decade. Their needs are identified and their advantages and disadvantages are listed in a comparative manner. A few abstractive and multilingual text summarization approaches are also covered. Summary evaluation is another challenging issue in this research field. Therefore, intrinsic as well as extrinsic both the methods of summary evaluation are described in detail along with text summarization evaluation conferences and workshops. Furthermore, evaluation results of extractive summarization approaches are presented on some shared DUC datasets. Finally this paper concludes with the discussion of useful future directions that can help researchers to identify areas where further research is needed.
Calculation of a building's life cycle carbon emissions based on Ecotect and building information modeling

Buildings are responsible for more than 40% of global energy usage and as much as 33% of global greenhouse gas emissions in both developed and developing countries. However, the study of carbon emissions over a building's life cycle based on Ecotect and building information modeling in developing areas of Nanjing has yet to be conducted. Therefore, the results and recommendations of this paper represent a contribution to the literature on this topic. The scientific value of this paper is that Ecotect and building information modeling can be helpful in simplifying the estimation of carbon emissions over a building's life cycle because they can provide a majority of the information and calculation tools necessary for performing an life cycle assessment (LCA) which may alleviate the problem of insufficient information when executing an LCA of a building. A sensitivity analysis was performed by changing several parameters to identify the parameters that have the largest impacts on the performance a building. A comparison of the life cycle carbon emissions for each stage showed that the operational stage is the largest contributor to carbon emissions. Approximately 85.4% of the total carbon emissions were generated during operation. The construction stage accounted for 12.6% of the total carbon emissions. Approximately 2% of the total carbon emissions occurred during the demolition stage. Compared to the total carbon emissions over the entire life cycle of the building, carbon sequestration by vegetation was minimal. Thus, these findings indicate that governments can achieve the greatest reductions in carbon emissions by targeting the operational phase of buildings. However, the opportunity for addressing non operational phases should not be ignored because the average carbon emissions per working area per year of non operational stages are far greater than those of the use phase.
Changing trends and emissions of hydrochlorofluorocarbons and their hydrofluorocarbon replacements

18 High frequency, in situ global observations of HCFC 22 (CHClF2) HCFC 141b (CH3CCl2F) 19 HCFC 142b (CH3CClF2) and HCFC 124 (CHClFCF3) and their main HFC replacements HFC 134a 20 (CH2FCF3) HFC 125 (CHF2CF3) HFC 143a (CH3CF3) and HFC 32 (CH2F2) have been used to 21 determine their changing global growth rates and emissions in response to the Montreal Protocol and its 22 recent amendments. The 2007 adjustment to the Montreal Protocol required the accelerated phase out of 23 HCFCs with global production and consumption capped in 2013, to mitigate their environmental impact 24 as both ozone depleting substances and important greenhouse gases. We find that this change has 25 coincided with a reduction in global emissions of the four HCFCs with aggregated global emissions in 26 2015 of 444 75 Gg/yr, in CO2 equivalent units (CO2 e) 0.75 0.1 Gt/yr, compared with 483 70 Gg/yr 27 (0.82 0.1 Gt/yr CO2 e) in 2010. (All quoted uncertainties in this paper are 1 sigma) About 80% of the 28 total HCFC atmospheric burden in 2015 is HCFC 22, where global HCFC emissions appear to have been 29 relatively constant in spite of the 2013 cap on global production and consumption. We attribute this to a 30 probable increase in production and consumption of HCFC 22 in Montreal Protocol Article 5 31 (developing) countries and the continuing release of HCFC 22 from the large banks which dominate 32 HCFC global emissions. Conversely, the four HFCs all show increasing annual growth rates with 33 aggregated global HFCs emissions in 2015 of 329 70 Gg/yr (0.65 0.12 Gt/yr CO2 e) compared to 34 2010 with 240 50 Gg/yr (0.47 0.08 Gt/yr CO2 e) As HCFCs are replaced by HFCs we investigate the 35 impact of the shift to refrigerant blends which have lower global warming potentials (GWPs) We also 36 Atmos.  2016 Manuscript under review for journal Atmos.  15 December 2016 c (c) Author(s) 2016. CC BY 3.0 License.
Experimental simulation of solid state phenomena using photonic lattices

The propagation of light waves across a periodic array of evanescently coupled optical waveguides can be described by a Schrodinger like equation for a particle in a periodic potential. This mapping allows us to investigate the dynamics of electrons in a crystalline solid using an artificial crystal of optical waveguides, known as a photonic lattice. The unique capabilities of ultrafast laser inscription enable us to design, fabricate and precisely control various properties of a photonic lattice. Here, we focus on the experimental construction of the Hamiltonians associated with various complex quantum systems using engineered photonic lattices, and then measure the time evolution of a given input state. In this photonic platform, we experimentally observe various single particle effects known from solid state physics, such as the localised states associated with flat band lattice geometries, localised Wannier Stark states, photon assisted tunnelling and the anomalous topological edge modes in slowly driven lattices. Specific phenomena associated with particle interactions, such as the dynamics of two interacting particles in a one dimensional lattice with static and sinusoidally driven Hubbard Hamiltonian, is also investigated. The experimental results presented here will be of interest to a large community, including physicists working on photonics, quantum optics, cold atomic gases, and condensed matter physics. To my parents, Shantwana and Sambit Mukherjee.