nils-herrmann/clean_scirepeval huggingface dataset:
Dynamic cross talk between host primary metabolism and viruses during infections in plants.
Venue: Current opinion in virology

Upon infection plant viruses modulate cellular functions and resources to survive and reproduce. Plant cells in which the virus is replicating are transformed into strong metabolic sinks. This conversion gives rise to a massive reprogramming of plant primary metabolism. Such a metabolic shift involves perturbations in carbohydrates, amino acids and lipids that eventually lead to increase respiration rates, and/or decrease in photosynthetic activity. By doing so, plants provide metabolic acclimation against cellular stress and meet the increased demand for energy needed to sustain virus multiplication and defense responses against viruses. This review will highlight our current knowledge pertaining to the contribution of primary metabolism to the outcome of viral infections in plants.
Siderophore Cephalosporin Cefiderocol Utilizes Ferric Iron Transporter Systems for Antibacterial Activity against Pseudomonas aeruginosa
Venue: Antimicrobial Agents and Chemotherapy

Cefiderocol (S 649266) is a novel parenteral siderophore cephalosporin conjugated with a catechol moiety at the third position side chain. The in vitro activity of cefiderocol against Pseudomonas aeruginosa was enhanced under iron depleted conditions, whereas that of ceftazidime was not affected. The monitoring of [thiazole 14C]cefiderocol revealed the increased intracellular accumulation of cefiderocol in P. aeruginosa cells incubated under iron depleted conditions compared with those incubated under iron sufficient conditions. Cefiderocol was shown to have potent chelating activity with ferric iron, and extracellular iron was efficiently transported into P. aeruginosa cells in the presence of cefiderocol as well as siderophores, while enhanced transport of extracellular ferric iron was not observed when one of the hydroxyl groups of the catechol moiety of cefiderocol was replaced with a methoxy group. We conclude that cefiderocol forms a chelating complex with iron, which is actively transported into P. aeruginosa cells via iron transporters, resulting in potent antibacterial activity of cefiderocol against P. aeruginosa.
Shifting Clade Distribution, Reassortment, and Emergence of New Subtypes of Highly Pathogenic Avian Influenza A(H5) Viruses Collected from Vietnamese Poultry from 2012 to 2015
Venue: Journal of Virology

Whole genome sequences of representative highly pathogenic avian influenza A(H5) viruses from Vietnam were generated, comprising samples from poultry outbreaks and active market surveillance collected from January 2012 to August 2015. Six hemagglutinin gene clades were characterized. Clade 1.1.2 was predominant in southern Mekong provinces throughout 2012 and 2013 but gradually disappeared and was not detected after April 2014. Clade 2.3.2.1c viruses spread rapidly during 2012 and were detected in the south and center of the country. A number of clade 1.1.2 and 2.3.2.1c interclade reassortant viruses were detected with different combinations of internal genes derived from 2.3.2.1a and 2.3.2.1b viruses, indicating extensive cocirculation. Although reassortment generated genetic diversity at the genotype level, there was relatively little genetic drift within the individual gene segments, suggesting genetic stasis over recent years. Antigenically, clade 1.1.2, 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c viruses remained related to earlier viruses and WHO recommended prepandemic vaccine strains representing these clades. Clade 7.2 viruses, although detected in only low numbers, were the exception, as indicated by introduction of a genetically and antigenically diverse strain in 2013. Clade 2.3.4.4 viruses (H5N1 and H5N6) were likely introduced in April 2014 and appeared to gain dominance across northern and central regions. Antigenic analyses of clade 2.3.4.4 viruses compared to existing clade 2.3.4 candidate vaccine viruses (CVV) indicated the need for an updated vaccine virus. A/Sichuan/26221/2014 (H5N6) virus was developed, and ferret antisera generated against this virus were demonstrated to inhibit some but not all clade 2.3.4.4 viruses, suggesting consideration of alternative clade 2.3.4.4 CVVs.  Highly pathogenic avian influenza (HPAI) A(H5) viruses have circulated continuously in Vietnam since 2003, resulting in hundreds of poultry outbreaks and sporadic human infections. Despite a significant reduction in the number of human infections in recent years, poultry outbreaks continue to occur and the virus continues to diversify. Vaccination of poultry has been used as a means to control the spread and impact of the virus, but due to the diversity and changing distribution of antigenically distinct viruses, the utility of vaccines in the face of mismatched circulating strains remains questionable. This study assessed the putative amino acid changes in viruses leading to antigenic variability, underscoring the complexity of vaccine selection for both veterinary and public health purposes. Given the overlapping geographic distributions of multiple, antigenically distinct clades of HPAI A(H5) viruses in Vietnam, the vaccine efficacy of bivalent poultry vaccine formulations should be tested in the future.
Sphingosine kinase 2 deficient mice exhibit reduced experimental autoimmune encephalomyelitis: Resistance to FTY720 but not ST 968 treatments
Venue: Neuropharmacology

The immunomodulatory drug FTY720 is presently approved for the treatment of relapsing remitting multiple sclerosis. It is a prodrug that requires activation by sphingosine kinase 2 (SK 2) to induce T cell homing to secondary lymphoid tissue. In this study, we have investigated the role of SK 2 in experimental autoimmune encephalomyelitis (EAE) in C57BL/6 mice. We show that SK 2 deficiency reduced clinical symptoms of EAE. Furthermore, in SK 2 deficient mice, the protective effect of FTY720 on EAE was abolished, while the non prodrug FTY720 derivative ST 968 was still fully active. Protection was paralleled by reduced numbers of T lymphocytes in blood and a reduced blood brain barrier leakage. This correlated with reduced mRNA expression of ICAM 1, VCAM 1, but enhanced expression of PECAM 1. A similar regulation of permeability and of PECAM 1 was seen in primary cultures of isolated mouse brain vascular endothelial cells and in a human immortalized cell line upon SK 2 knockdown. In summary, these data demonstrated that deletion of SK 2 exerts a protective effect on the pathogenesis of EAE in C57BL/6 mice and that SK 2 is essential for the protective effect of FTY720 but not of ST 968. Thus, ST 968 is a promising novel immunomodulatory compound that may be a valuable alternative to FTY720 under conditions where SK 2 activity is limited.
Oxo biodegradable Plastics: Who They Are and to What They Serve Present Status and Future Perspectives

The worldwide annual consumption of polymeric materials and relevant plastic items is nowadays well above 300 million Tons, of which less than 2 million Tons is represented by polymeric materials from renewable resources. These last materials, when converted to relevant plastic manufactured goods, are identified under the ambiguous chimeric "bioplastics" terminology as evidenced in official EU documents [1, 2]
Wolbachia: A biological control strategy against arboviral diseases.
Venue: Journal of vector borne diseases

Vector borne diseases particularly those transmitted by mosquitoes like Dengue are among the leading causes of mortality and morbidity in human population. There are no effective vaccines or treatment against dengue fever till date and the control methods are limited. So, new approaches are urgently in need to reverse these trends. Vector control is currently the primary intervention tool. Strategies that reduce or block pathogen transmission by mosquitoes have been proposed as a means of augmenting current control measures to reduce the growing burden of vector borne diseases. Wolbachia an endosymbiont of arthropod vectors is being explored as a novel ecofriendly control strategy. Studies in Drosophila have shown that Wolbachia can confer resistance to diverse RNA viruses and protect flies from virus induced mortality. This review was focused on biology of the Wolbachia and its implication as a control measure for arboviral diseases mainly Dengue and Chikungunya.
Nosocomial infection control in healthcare settings: Protection against emerging infectious diseases
Venue: Infectious Diseases of Poverty

The Middle East respiratory syndrome (MERS) outbreak in Korea in 2015 may be attributable to poor nosocomial infection control procedures implemented. Strict infection control measures were taken in the hospital where an imported case with MERS was treated in southern China and 53 health care workers were confirmed to be MERS CoV negative. Infection control in healthcare settings, in which patients with emerging infectious diseases such as MERS, Ebola virus disease, and the severe acute respiratory syndrome (SARS) are diagnosed and treated, are often imperfect. When it comes to emerging or unknown infectious diseases, before the imported case was finally identified or community transmission was reported, cases have often occurred in clusters in healthcare settings. Nosocomial infection control measures should be further strengthened among the workers and inpatients in designated healthcare settings that accommodate suspected cases suffering from emerging or unknown infectious diseases.
Flight control for a quadrotor of attitude control based on android system and using optimal tuning design
Venue: Comput. Electr. Eng.

This paper proposes the research and development of an Android based mobile platform with a quadrotor control and quadrotor flight controller. The proposed Android based mobile platform has the following advantages: (1) with Android remote controller has a bidirectional transmission function, which can transmit flight directives to the quadrotor and receive the feedback information to achieve the desired control. Additionally, the Android remote controller is designed on a mobile platform for convenient carrying. (2) The flight controller is designed with Proportional Integral Derivative (PID) Control and Sliding Mode Control methods to obtain optimum operations. Finally, parameters of optimum control are built and implemented by using Genetic and Tabu Search Algorithms. Experimental results are presented to verify the performance and the feasibility of the proposed Android based mobile platform with a quadrotor control and quadrotor flight controller.
Design and development of a ubiquitous healthcare monitoring system based on Android platform and ISO/IEEE 11073 standards
Venue: 2016 IEEE International Conference on Information and Automation (ICIA)

With the growth of aging populations in both developed and developing countries and the increase of noncommunicable disease, the contradiction between increasing healthcare demands and the shortage of medical specialists have become more and more serious. Wearable personal health devices (PHDs) provide a good solution to this problem. But due to the proprietary interface and data protocol, the compatibility and extensibility problem among different PHDs producers strongly influenced the spread adoption of the wearable PHDs in the field of telemedicine. So we designed and implemented a ubiquitous health monitoring system based on Android tablet, which can not only acquire and process the physiological signals from non standard laboratory developed multi function wearable health monitoring sensors, but also acquire and process the physiological signals from standard PHDs comply with Continua Alliance or/and ISO/IEEE 11073 standards. The preliminary results demonstrate that this system can not only receive data from standard and non standard PHDs, but also do the arrhythmia classification and heart rate variability analysis in real time.
Design on mobile health service system based on Android platform
Venue: 2016 IEEE Advanced Information Management, Communicates, Electronic and Automation Control Conference (IMCEC)

The system combines the wireless communication technology and medical sensor detection technology, to realize the remote medical monitoring of multiple physiological parameters. As the basis of the Android platform, the mobile health platform construct a health report with physical examination, health guidance for every members in family. After using the corresponding physiological data acquisition sensor module to collect physiological data, the mobile intelligent terminal will send the collected results to the background center server with Bluetooth. The central server is responsible for storing the patient's medical information and providing the data sharing service for other subsystems in the system. Android mobile data collection terminal and server connect together each other with Wifi network, and data services through implementation based on HTTP web server interface. The external terminal get medical information through accessing to the web server. Data storage in the client using SQLite database, server using MySQL database. It mainly record the daily health conditions of the family members, which can effectively manage various chronic diseases and the prevention of disease. At the same time, for some of the family members who have been suffering from chronic diseases, it can help patients manage their daily diet and treatment.
On the choice of covariance specifications for portfolio selection problems

Two crucial aspects to the problem of portfolio selection are the specification of the model for expected returns and their covariances, as well as the choice of the investment policy to be adopted. A common trade off is to consider dynamic covariance specifications vis a vis static models such as those based on shrinkage methods. This work empirically shows that these two aspects are intrinsically attached to the impact of transaction costs. To address this question, we implement a broad range of covariance specifications to generate a set of 16 portfolio selection policies in a high dimensional sample composed by the 50 most traded stocks of the S\&P100 index. We find that GARCH type dynamic covariances yield portfolios with superior risk adjusted performance only in the absence of transaction costs. In more realistic scenarios involving alternative levels of transaction costs, portfolios based on static covariance models outperform. In particular, we find that a risk averse investor with quadratic utility function is willing to pay an annualized fee of 368 basis points (bp) on average in order to switch from the dynamic covariance models to a static covariance specification when the level of transaction costs is 20 bp. Finally, portfolio policies that seek to alleviate estimation error by ignoring off diagonal covariance elements as those proposed in \citet{kirby2012s} are more robust specially in scenarios with higher transaction costs.
Fitting Unstructured Finite Mixture Models in Longitudinal Design: A Recommendation for Model Selection and Estimation of the Number of Classes

In longitudinal design, investigating interindividual differences of intraindividual changes enables researchers to better understand the potential variety of development and growth. Although latent growth curve mixture models have been widely used, unstructured finite mixture models (uFMMs) are also useful as a preliminary tool and are expected to be more robust in identifying classes under the influence of possible model misspecifications, which are very common in actual practice. In this study, large scale simulations were performed in which various normal uFMMs and nonnormal uFMMs were fit to evaluate their utility and the performance of each model selection procedure for estimating the number of classes in longitudinal designs. Results show that normal uFMMs assuming invariance of variance covariance structures among classes perform better on average. Among model selection procedures, the Calinski Harabasz statistic, which has a nonparametric nature, performed better on average than information criteria, including the Bayesian information criterion.
On portfolio optimization: forecasting asset covariances and variances based on multi scale risk models

The purpose of this paper is to show how investors can incorporate the multi scale nature of asset and factor returns into their portfolio decisions and to evaluate the out of sample performance of such strategies.  The authors decompose daily return series of common risk factors and of all stocks listed in the Dow Jones Industrial Index (DJI) from 2000 to 2015 into different time scales to separate short term noise from long run trends. Then, the authors apply various (multi scale) factor models to determine variance covariance matrices which are used for minimum variance portfolio selection. Finally, the portfolios are evaluated by their out of sample performance.  The authors find that portfolios which are constructed on variance covariance matrices stemming from multi scale factor models outperform portfolio allocations which do not take the multi scale nature of asset and factor returns into account.  The results of this paper provide evidence that accounting for the multi scale nature of return distributions in portfolio decisions might be a promising approach from a portfolio performance perspective.  The authors demonstrate how investors can incorporate the multi scale nature of returns into their portfolio decisions by applying wavelet filter techniques.
Insights into the Nature of the Chemical Bonding in Thiophene 2 thiol from X ray Absorption Spectroscopy.
Venue: The journal of physical chemistry. A

Thiophenes are the simplest aromatic sulfur containing compounds; they are widespread in fossil fuels and a variety of natural products, and they have vital roles in determining characteristic aromas that are important in food chemistry. We used a combination of sulfur K edge X ray absorption spectroscopy and density functional theory to investigate the chemical bonding in the novel sulfur containing heterocycle thiophene 2 thiol. We show that solutions of thiophene 2 thiol contain significant quantities of the thione tautomer, which may be the energetically preferred 5H thiophene 2 thione or the more accessible 3H thiophene 2 thione.
A Phenomenological Study: Examining the Experiences of High School Graduates Who Participated in a Career and Technical Education Program of Study

Career and Technical Education (CTE) programs are designed to help prepare students to become effective workers by equipping them with college and career readiness skills needed for the 21st century workplace. Students who participate in a CTE Program of Study (POS) have the potential for greater success during and after high school because they have achieved academic success in meeting the college and career readiness targets that lead to success in postsecondary and career training. The purpose of this phenomenological study was to describe the experiences of graduates from one high school in the southwest region of North Carolina who participated in a CTE POS. Through the use of documents, interviews, and a focus group the perceptions from 10 participants who participated in a CTE POS during high school were examined. The data gathered in this study was analyzed using the procedures of a hermeneutical phenomenology to gain a thick, rich understanding of participant experiences. Four themes emerged during the research process. The four themes were (a) The learning process was enhanced; (b) Influences on decision making; (c) Learning with understanding supports knowledge use in new situations; and (d) Guidance and advisement needs to be purposeful. This study found that the participant's learning process was enhanced through participation in a CTE POS, they were able to transfer learning to a variety of context that increased their readiness for college and their future career. The implications are discussed and recommendations are provided to educators along with recommendations for further research.
A Phenomenological Study

Career and Technical Education (CTE) programs are designed to help prepare students to become effective workers by equipping them with college and career readiness skills needed for the 21st century workplace. Students who participate in a CTE Program of Study (POS) have the potential for greater success during and after high school because they have achieved academic success in meeting the college and career readiness targets that lead to success in post secondary and career training. The purpose of this phenomenological study was to describe the experiences of graduates who participated in a CTE POS. Through the use of documents, interviews, and a focus group, the perceptions from 10 participants who participated in a CTE POS during high school were examined. The data gathered in this study was analyzed using the procedures of a hermeneutical phenomenology and four themes emerged during the research process. This study found that the participant's learning process was enhanced through participation in a CTE POS and they were able to transfer learning to a variety of contexts that increased their readiness for college and their future career.
Perception of nursing students on high fidelity practices: a phenomenological study

High fidelity simulation is a teaching/learning strategy increasingly used by nursing schools. Students undergo simulated clinical experiences very similar to the real context, developing technical and non technical skills. The objective of this study is to identify the perceptions of students of the Bachelor's Degree in Nursing regarding their participation in simulated clinical experiences with high fidelity simulation.  Qualitative study of phenomenological approach according to the seven procedural steps of methodological interpretation presented by Amadeo Giorgi.  From the analysis of interviews with 13 students participating in the study, an essential structure of the phenomenon emerged which reflects these students' perception of simulated clinical experiences on high fidelity simulation, consisting offour components: "Being a student with high fidelity simulation" "Relationship with peers in the simulation" "High fidelity simulated practice" and "Future expectations after high fidelity simulation"  The students are satisfied with their experience of high fidelity simulation. Despite moments of great stress and anxiety, it helps broaden their knowledge and prepares them for the real context.