nils-herrmann/clean_scirepeval huggingface dataset:
Microbial Biofilms on the Sandstone Monuments of the Angkor Wat Complex, Cambodia
Venue: Current Microbiology
Year: 2011

Discoloring biofilms from Cambodian temples Angkor Wat, Preah Khan, and the Bayon and West Prasat in Angkor Thom contained a microbial community dominated by coccoid cyanobacteria. Molecular analysis identified Chroococcidiopsis as major colonizer, but low similarity values <95% suggested a similar genus or species not present in the databases. In only two of the six sites sampled were filamentous cyanobacteria, Microcoleus, Leptolyngbya, and Scytonema, found; the first two detected by sequencing of 16S rRNA gene library clones from samples of a moist green biofilm on internal walls in Preah Khan, where Lyngbya (possibly synonymous with Microcoleus) was seen by direct microscopy as major colonizer. Scytonema was detected also by microscopy on an internal wall in the Bayon. This suggests that filamentous cyanobacteria are more prevalent in internal (high moisture) areas. Heterotrophic bacteria were found in all samples. DNA sequencing of bands from DGGE gels identified Proteobacteria (Stenotrophomonas maltophilia and Methylobacterium radiotolerans) and Firmicutes (Bacillus sp. Bacillus niacini, Bacillus sporothermodurans, Lysinibacillus fusiformis, Paenibacillus sp. Paenibacilluspanacisoli, and Paenibacillus zanthoxyli) Some of these bacteria produce organic acids, potentially degrading stone. Actinobacteria, mainly streptomycetes, were present in most samples; algae and fungi were rare. A dark pigmented filamentous fungus was detected in internal and external Preah Khan samples, while the alga Trentepohlia was found only in samples taken from external, pink stained stone at Preah Khan. Results show that these microbial biofilms are mature communities whose major constituents are resistant to dehydration and high levels of irradiation and can be involved in deterioration of sandstone. Such analyses are important prerequisites to the application of control strategies.
Pregnancy and Breast Cancer: when They Collide
Venue: Journal of Mammary Gland Biology and Neoplasia
Year: 2009

Women of childbearing age experience an increased breast cancer risk associated with a completed pregnancy. For younger women, this increase in breast cancer risk is transient and within a decade after parturition a cross over effect results in an ultimate protective benefit. The post partum peak of increased risk is greater in women with advanced maternal age. Further, their lifetime risk for developing breast cancer remains elevated for many years, with the cross over to protection occurring decades later or not at all. Breast cancers diagnosed during pregnancy and within a number of years post partum are termed pregnancy associated or PABC. Contrary to popular belief, PABC is not a rare disease and could affect up to 40,000 women in 2009. The collision between pregnancy and breast cancer puts women in a fear invoking paradox of their own health, their pregnancy, and the outcomes for both. We propose two distinct subtypes of PABC: breast cancer diagnosed during pregnancy and breast cancer diagnosed post partum. This distinction is important because emerging epidemiologic data highlights worsened outcomes specific to post partum cases. We reported that post partum breast involution may be responsible for the increased metastatic potential of post partum PABC. Increased awareness and detection, rationally aggressive treatment, and enhanced understanding of the mechanisms are imperative steps toward improving the prognosis for PABC. If we determine the mechanisms by which involution promotes metastasis of PABC, the post partum period can be a window of opportunity for intervention strategies.
Numerical evaluation of a compact generator design for steam driven H2O/LiBr absorption chiller application
Year: 2018

The objectives of this study are to analyze effects of design parameters of a generator with a steam heat source on condensation heat transfer and flow characteristics inside tubes and to design optimum configuration of the generator with minimum volume that satisfies design constraints for H2O/LiBr absorption chiller application. To that end, the heat transfer and flow characteristics of a straight pipe tube and a tube with return bends were analyzed through numerical analysis according to the tube diameter, number of tubes, and the diameter of return bends. It was found that the minimum tube volume satisfying the design constraints was obtained for N t u b e 2 and D t u b e 12 m m in the case of the straight tube. The smaller the diameter of the return bend was, the greater the flow separation area, which caused a large local flow velocity. In the case of the return bend tubes, the smallest tube volume that satisfies both the flow and pressure drop constraints was obtained for N t u b e 2 and D t u r n D t u b e 1.0. In the case D t u r n D t u b e 1.5 where the pressure drop was the smallest, the pressure drop was higher by 9% compared to the pressure drop constraint (1 bar) but the tube volume that satisfies the flow constraints decreased by 49%
A review on current status of municipal solid waste management in India.
Venue: Journal of environmental sciences
Year: 2015

Municipal solid waste management is a major environmental issue in India. Due to rapid increase in urbanization, industrialization and population, the generation rate of municipal solid waste in Indian cities and towns is also increased. Mismanagement of municipal solid waste can cause adverse environmental impacts, public health risk and other socio economic problem. This paper presents an overview of current status of solid waste management in India which can help the competent authorities responsible for municipal solid waste management and researchers to prepare more efficient plans.
Decoupled Energy Stable Schemes for a Phase Field Model of Three Phase Incompressible Viscous Fluid Flow
Venue: J. Sci. Comput.
Year: 2017

We develop a numerical approximation for a hydrodynamic phase field model of three immiscible, incompressible viscous fluid phases. The model is derived from a generalized Onsager principle following an energetic variational formulation and is consisted of the momentum transport equation and coupled phase transport equations. It conserves the volume of each phase and warrants the total energy dissipation in time. Its numerical approximation is given by a set of easy to implement, semi discrete, linear, decoupled elliptic equations at each time step, which can be solved efficiently using fast solvers. We prove that the scheme is energy stable. Mesh refinement tests and three numerical examples of three phase viscous fluid flows in 3D are presented to benchmark the effectiveness of the model as well as the efficiency of the numerical scheme.
HySAR: Hybrid Material Rendering by an Optical See Through Head Mounted Display with Spatial Augmented Reality Projection
Venue: IEEE Transactions on Visualization and Computer Graphics
Year: 2018

Spatial augmented reality (SAR) pursues realism in rendering materials and objects. To advance this goal, we propose a hybrid SAR (HySAR) that combines a projector with optical see through head mounted displays (OST HMD) In an ordinary SAR scenario with co located viewers, the viewers perceive the same virtual material on physical surfaces. In general, the material consists of two components: a view independent (VI) component such as diffuse reflection, and a view dependent (VD) component such as specular reflection. The VI component is static over viewpoints, whereas the VD should change for each viewpoint even if a projector can simulate only one viewpoint at one time. In HySAR, a projector only renders the static VI components. In addition, the OST HMD renders the dynamic VD components according to the viewer's current viewpoint. Unlike conventional SAR, the HySAR concept theoretically allows an unlimited number of co located viewers to see the correct material over different viewpoints. Furthermore, the combination enhances the total dynamic range, the maximum intensity, and the resolution of perceived materials. With proof of concept systems, we demonstrate HySAR both qualitatively and quantitatively with real objects. First, we demonstrate HySAR by rendering synthetic material properties on a real object from different viewpoints. Our quantitative evaluation shows that our system increases the dynamic range by 2.24 times and the maximum intensity by 2.12 times compared to an ordinary SAR system. Second, we replicate the material properties of a real object by SAR and HySAR, and show that HySAR outperforms SAR in rendering VD specular components.
Parameter Tuning and Confidence Limits of Malware Clustering
Venue: CODASPY
Year: 2019

The growing number of new malware and the sophisticated obfuscation techniques used by malware authors are causing major problems in identifying, managing, and releasing anti malware products to the consumers. Clustering malware variants based on their behavior has the potential to ease this problem of scale and conveniently lend itself to better, faster, and efficient prioritization of malware analysis. In this paper, we cluster real world malware and expand on commonly used algorithms through fine grained testing. Results of top performing algorithms are discussed.
Designing a multi epitope vaccine against blood stage of Plasmodium falciparum by in silico approaches.
Venue: Journal of molecular graphics modelling
Year: 2020

Plasmodium falciparum causes the most severe form of malaria disease and is the major cause of infection related mortalities in the world. Due to increasing in P. falciparum resistance to the first line antimalarial drugs, an effective vaccine for the control and elimination of malaria infection is urgent. Because the pathogenesis of malaria disease results from blood stage infection, and all of the symptoms and clinical illness of malaria occur during this stage, there is a strong rationale to develop vaccine against this stage. In the present study, different structural vaccinology and immuno informatics tools were applied to design an effective antibody inducing multi epitope vaccine against the blood stage of P. falciparum. The designed multi epitope vaccine was composed of three main parts including B cell epitopes, T helper (Th) cell epitopes, and two adjuvant motives (HP91 and RS09) which were linked to each other via proper linkers. B cell and T cell epitopes were derived from four protective antigens expressed on the surface of merozoites, which are critical to invade the erythrocytes. HP91 and RS09 adjuvants and Th cell epitopes were used to induce, enhance and direct the best form of humoral immune response against P. falciparum surface merozoite antigens. The vaccine construct was modeled, and after model quality evaluation and refinement by different software, the high quality 3D structure model of the vaccine was achieved. Analysis of immunological and physicochemical features of the vaccine showed acceptable results. We believe that this multi epitope vaccine can be effective for preventing malaria disease caused by P. falciparum.
A critical review of published research literature reviews on nursing and healthcare ageism
Venue: Journal of clinical nursing
Year: 2017

To establish how common and impactful nursing and healthcare ageism is and whether proven interventions or prevention methods exist.  Ageism has been a concern since 1969 when it was first introduced as a concept for social reform. As ageism has been linked to lower quality health services and reduced health care access, it is imperative that healthcare and nursing ageism is prevented or identified and reduced or eliminated.  A qualitative narrative review of published research literature reviews using a scoping design to map all published reviews was undertaken. The EBSCO Discovery Service (providing access to articles in 271 databases, including MEDLINE and CINAHL) and Directory of Open Access Journals (providing access to over 9,000 open access journals) were used to find review articles. Using predetermined inclusion and exclusion criteria, and limited by English language and peer review publications, 12 eligible reviews were identified and information from them was systematically identified, assessed and synthesised.  The 12 reviews did not provide clear and convincing information to determine how common and impactful nursing or healthcare ageism is, nor what can best be done to prevent or address it. Although each review had value since research literature was collected and discussed on nursing or healthcare ageism, the array of literature search and analysis methods, and diversity in conclusions reached about the evidence is highly problematic.  Research literature reviews offering a more balanced perspective and demonstrating greater care in finding and using quality evidence are needed.  TO CLINICAL PRACTICE At this point in time, there is no clear understanding of how widespread and impactful nursing or healthcare ageism is, and what can best be done to prevent or address it. Nurses need to be aware that ageism may be common and impactful, and guard against it.
Design Considerations for Collaborative Visual Analytics
Venue: Inf. Vis.
Year: 2008

Visualizations leverage the human visual system to support the process of sensemaking, in which information is collected, organized, and analyzed to generate knowledge and inform action. Although most research to date assumes a single user focus on perceptual and cognitive processes, in practice, sensemaking is often a social process involving parallelization of effort, discussion, and consensus building. Thus, to fully support sensemaking, interactive visualization should also support social interaction. However, the most appropriate collaboration mechanisms for supporting this interaction are not immediately clear. In this article, we present design considerations for asynchronous collaboration in visual analysis environments, highlighting issues of work parallelization, communication, and social organization. These considerations provide a guide for the design and evaluation of collaborative visualization systems.
A hydrogel based antifouling solar evaporator for highly efficient water desalination
Year: 2018

Solar desalination is a promising method for large scale water purification by utilizing sustainable energy. However, current high rate solar evaporation often relies on optical concentration due to the diffusion of natural sunlight, which leads to inadequate energy supply. Here we demonstrate a hydrogel based solar evaporator that is capable of generating vapor at a high rate of ~2.5 kg m 2 h 1 under one sun irradiation (1 kW m 2) among the best values reported in the literature. Such highly efficient solar evaporation is achieved by a hybrid hydrogel composed of a hydrophilic polymer framework (polyvinyl alcohol, PVA) and solar absorber (reduced graphene oxide, rGO) which has internal capillary channels. The PVA can greatly facilitate the water evaporation owing to the reduced water evaporation enthalpy in the hydrogel network. The rGO penetrating into the polymeric network enables efficient energy utilization. The capillary channels sustain an adequate water supply for continuous solar vapor generation at a high rate. This hydrogel based solar evaporator also exhibits promising antifouling properties, enabling long term water desalination without recycling. The high efficiency hydrogel based solar vapor generators open significant opportunities to enhance solar water evaporation performance and reduce the cost of solar desalination systems.
Formalization of the Resolution Calculus for First Order Logic
Venue: ITP
Year: 2016

A formalization in Isabelle/HOL of the resolution calculus for first order logic is presented. Its soundness and completeness are formally proven using the substitution lemma, semantic trees, Herbrand's theorem, and the lifting lemma. In contrast to previous formalizations of resolution, it considers first order logic with full first order terms, instead of the propositional case.
Substantial Motion and Self aware Soul: Does Mulla Sadra's "Substantial Motion" theory provide a reliable framework for the Explanation of the Relationship between Body and Soul?
Year: 2019

One of the major challenges that humankind have not properly dealt with is Mindbody problems. Through which ways, an immaterial entity (Soul) emerges out of a material body, and the relationship that exists between these two entities have constantly stimulated proposed explanations to find novel models in this regard. Mulla Sadra"s "substantial motion theory" suggests providing an extensive explanation concerning the relationship between mind and soul. Sadra considered "change" as an all pervasive reality running through the entire universe including the category of substance. According to Sadra, in certain circumstances that have the potential to occur only in humans, for the aforementioned reason, matter changes essentially and converts to the soul. Mutational changes occur in the substance of matter like the emergence of life out of unliving matter, and self aware soul"s appearance out of unaware matter. Based on Mulla Sadra"s perspective, contemplating, along with investigating the situations based on this fundamental transformation, endorses sufficient perception of the relation between spirit and body.
Sexual Surrogate Partner Therapy: Legal and Ethical Issues
Year: 2013

The Ben Lewin film The Sessions has drawn attention again to the potential role for sexual surrogate partners and sex workers in enabling persons with disabilities and impairments to give expression to their sexual needs and desires. However, away from the big screen, the ethics of registered health practitioners in themselves engaging in such therapies are highly problematic. Difficult too is the role of such practitioners in being 'the therapist' responsible for enabling or brokering sexual contact between their patients and those offering such services for financial reward. In some jurisdictions, arrangements involving sexual surrogate therapy (especially where the therapist benefits from it financially) may not be lawful. Further, in spite of many assertions one way and the other, there are no data enabling evaluation of the success rates of the interventions of sexual surrogates or sex workers. Whether positive outcomes to such interactions are likely in most circumstances, given that the provision of services is predicated upon idealised attachments, is questionable. It is also unclear whether sexual surrogates' adherence to an ethical code effectively ameliorates the potential for counter therapeutic consequences from the commodification of intimacy, and it is far from straightforward to identify what steps should be taken by the referring health practitioner to select a suitable provider of sexual services to their patient or client, and then to monitor whether the arrangement is achieving its objectives.
Using Risk Group Profiles as a Lightweight Qualitative Approach for Intervention Development: An Example of Prevention of Tick Bites and Lyme Disease
Venue: JMIR research protocols
Year: 2013

Many public health campaigns use a one size fits all strategy to achieve their desired effect. Public health campaigns for tick bites and Lyme disease (LD) in many countries convey all relevant preventive measures to all members of the public. Although preventing tick bites (eg, by wearing protective clothing or using repellants) and checking for tick bites after visiting a risk area are effective and cost efficient methods to prevent an individual from contracting a tick borne disease, public compliance to these methods is low.  We aimed to identify the group of individuals within the general Dutch population that are at high risk of being bitten by a tick or developing LD and to describe their characteristics, knowledge, and perceptions. The incidence of patients visiting their general practitioner for tick bites and erythema migrans (the first sign of LD) has increased tremendously in the last decades in the Netherlands and other European countries; therefore, our efforts can be used to counter this troubling trend.  We conducted in depth semi structured interviews to identify individuals belonging to the average risk group. Participants were recruited in two ways. Patients who visited two municipal health services travel health clinics (one in a high endemic area and one in a low endemic area) were asked to participate. This resulted in 18 interviews. Further, parents were recruited using the convenience sampling method, which resulted in 7 interviews. We discontinued interviewing when the point of data saturation was reached. We analyzed the results immediately after each interview to identify the point of data saturation. Data saturation is when the new interviews provided no new information compared to the previous interviews. The interviews were transcribed and analyzed using inductive thematic analysis.  We identified four groups at risk of being bitten by ticks and developing LD among the general Dutch population. The groups were as follows: (1) outdoor people that check for tick bites, (2) outdoor people that do not check for tick bites, (3) parents that check their children for tick bites, and (4) parents that do not check their children for tick bites. Previous experience with ticks or LD was the main denominator between the groups. Checking for tick bites is a more easily adopted measure than preventing tick bites. Therefore, for all groups, public health efforts in the future should primarily emphasize on the importance of checking for tick bites.  The lightweight qualitative approach presented in this paper is highly relevant in tailoring public health efforts toward specific groups. The profiles of members in each risk group and the motivations underlying the behaviors of the members in each risk group can be used to determine the features and content of a targeted communication strategy about ticks and LD.
Clustering with Bregman Divergences: an Asymptotic Analysis
Venue: NIPS
Year: 2016

Clustering, in particular $k$ means clustering, is a central topic in data analysis. Clustering with Bregman divergences is a recently proposed generalization of $k$ means clustering which has already been widely used in applications. In this paper we analyze theoretical properties of Bregman clustering when the number of the clusters $k$ is large. We establish quantization rates and describe the limiting distribution of the centers as $k\to \infty$ extending well known results for $k$ means clustering.
Quem e Esse Pokemon? Uma Analise do Jogo de Cartas Pokemon a Luz da Teoria dos Campos Conceituais
Year: 2020

This article presents a discussion about the potencial of the ficcional entertainment universe of Pokemon in the educational scope. Such universe presents the characteristics of the transmedia work presented by Jenkins (2009) amongst them the capacity of expanding itself through a great deal of media platforms, providing multiple interaction experiences between its fans. Starting from the premise it is possible to utilize games, drawings and comic books in the benefit of learning, our main goal is to discuss the contributions of a particular element of this universe, the collectible cards game, under the perspective of Mathematical Education, in light of the Theory of Conceptual Fields, by Gerard Vergnaud. For this study, we analyze five Pokemon card decks, in which some cards present problem situations involving additive and multiplicative structures. After that analysis, it was possible to recognize in the commands existent in some of the cards of the game, additive problem situations that correspond to transformation and multiplicative problems involving simple proportion. Although the problems explored in the cards are specifically of two types, it is necessary to highlight the importance of the game for mathematical work. In developing relational calculations and numerical calculations during matches, players are encouraged to develop mathematical reasoning.