nils-herrmann/clean_scirepeval huggingface dataset:
Comparison of phenotype,genotype and drug resistance genes of Acinetobacter baumunnii isolated from clinic

To investigate the genotypes and encoding resistance genes differences of Acinetobacter baumannii and analyze their interrelations with multi-drug resistance. A total of 77strains Acinetobacter baumannii were collected random from the second Xiangya Hospital during September 2008 to September 2009.The K-B method which was WHO recommended was adopted to Acinetobacter baumannii drug sensitivity test to 15 kinds of antibiotics to establish susceptibility spectrum.At the same time,random amplified polymorphic DNA(RAPD)technique was used to establish DNA fingerprinting.The genes of β-lactamase(TEM-1,IMP,OXA-23,OXA-24,AmpC),aminoglycoside-modifying enzymes[aac(3')-Ⅰ ,aac(6')-Ⅰ ,ant(3")-Ⅰ]and 16S rRNA methylase(armA,rmtA,rmtB)were detected by PCR and sequenced,and find the relationship between the gene encoding and multi-drug resistance.In addition,we compared the rates of resistance genes of Acinetobacter baumannii and the relations with the genotype and the multi-resistance. Thirty-one sensitive strains and 46 multi-drug resistance strains(10 Pan-drug resistances)were isolated.Seventeen types from A to Q were separated using RAPD technique.E genotype widely popular in the ICU was the advantage type in multi-drug resistance strains,and the rate was 47.1%.While the various types scattered in sensitive strains.The positive rates of TEM-1,IMP,ant(3")-Ⅰ ,armA in the multi-drug resistance strains and the sensitive strains were 95.7%,39.1%,84.8% ,54.3%,87.0%,89.1%,84.8%,45.7%,63.0% and 58.1%,9.7%,32.3%,48.4%,48.4%,29.0%,45.2%,12.9%,9.7%,respectively,and there was significant difference except for OXA-24 using the X2 test(P ＜ 0.05).All isolates were negative for rmtA gene and rmtB gene.Drug susceptibility analysis showed that the resistant rate was significantly higher of the strains carrying resistant genes than that of the resistance negative strains.When the strains were resistant to gentamicin and amikacin,the rate of three aminoglycoside genes positive was 34.8%.The trains containing all the measured β-lactamase genes were all resistant strains. Compared with the sensitive Acinetobacter baumannii strains,a broad resistance spectrum and a high drug resistance rate were showed in multidrug resistance strains isolated from clinic,which harboring many kinds of β-lactamase genes and aminoglycosides genes with a high separation rate,and the same clone of multiple drug-resistant strains may be transmitted in and among wards. 
 
 
Acinetobacter baumannii; Drug resistance,multiple; Phenotype ; Genotype; Genes

Field of study: Biology
Use of non-crystallographic symmetry in protein structure refinement.

Several methods to assess the (dis)similarity of protein structures objectively are described, some of which, when applied to non-crystallographically related protein models, are able to discriminate between significant differences and 'random noise'. Some of these methods have been used to investigate a sample of several hundred protein structures which have been solved by means of X-ray crystallography in order to investigate the extent to which non-crystallographically related protein models differ from one another. It is shown that the extent of such differences is largely dependent on the resolution of the data used for the determination and refinement of the structure and, measured by some statistics, even varies essentially linearly with the resolution. The implications of these findings for the strategies used to refine structures with non-crystallographic symmetry, in particular at low resolution, are discussed. Finally, two examples are given of recent structure determinations from this laboratory in which the presence (and employment) of non-crystallographic symmetry was crucial to the solution and refinement of the structure.

Field of study: Chemistry
Interleukin-27 is elevated in sepsis-induced myocardial dysfunction and mediates inflammation.

Interleukin (IL)-27 is an important cytokine involved in many human inflammatory diseases. In this study, we investigated its role in the pathogenesis of sepsis-induced myocardial dysfunction (SIMD).



Twenty patients with SIMD and 24healthy donors were prospectively enrolled. Expression of IL-27 was detected in serum from SIMD patients by ELISA. Cardiac dysfunction was induced by administration of Escherichia coli lipopolysaccharide (LPS) to C57BL/6 (wild type) or IL-27R-/- mice. IL-27 mRNA in the myocardium was measured by RT-PCR. Cytokine levels in serum were determined by ELISA.



Expression of IL-27 in the serum was markedly increased in patients with SIMD compared with that in controls. Serum IL-27 levels and cardiac IL-27 mRNA expression were significantly increased after LPS injection compared with control specimens. Compared with wild-type mice, IL-27R-/- mice had higher expression of brain natriuretic peptide, cardiac troponin I, IL-6, IL-12, tumor necrosis factor-α and transforming growth factor-β.



IL-27 is an important protective mediator of SIMD.

Field of study: Medicine
Impact of Supply Voltage and Frequency on the Soft Error Rate of Logic Circuits

Alpha particle irradiations of 28-nm combinational logic and flip-flop circuits under different supply voltage and frequency operating conditions are investigated. Results indicate that while the supply voltage has a strong impact on the alpha particle soft error rate of flip-flops, the combinational logic error rate is relatively unaffected by supply voltage variation. Simulations are used to explain the results and highlight the differences between low-LET alpha particle irradiation and heavy-ion irradiation as far as voltage dependence of the logic soft error rate is concerned. Moreover, frequency has a much stronger impact on the logic soft error rate as compared to the flip-flop soft error rate. As a result, the frequency at which soft errors from combinational logic circuits will exceed errors from flip-flops decreases as the voltage increases. The impact of these observations is discussed in the context of soft-error mitigation strategies.

Field of study: Physics
The Lobbying of London Quakers for Pennsylvania Friends

The Lobbying of London Quakers for Pennsylvania Friends IN THE EIGHTEENTH CENTURY LONDON QUAKERS developed a highly effective political lobby, the London Meeting for Sufferings, capable of exerting political pressure on behalf of Quakers throughout the British Isles and the Empire—in the provinces as well as the metropolis, in the American provinces as well as the English. Since Pennsylvania was the American province most clearly dominated by Friends closely tied to the London Meeting, one would have expected it to be consistently the main American beneficiary of the Londoners' attention throughout the eighteenth century. In fact, however, London lobbying for Pennsylvania Friends was uneven over the years. In the quarter century from 1730 to 1755 Pennsylvania did become the strongest American concern of the London Meeting for Sufferings, but immediately after that London lobbying for all the colonies, Pennsylvania included, dropped off abruptly. By the eve of the American Revolution there was almost no lobbying.

Field of study: History
Study and Enlightenment on Zhang Jian’s Thoughts of Agricultural Science

Zhang Jian is a modern industrialist and reformer in our country. He put forward a series of ideas of developing agricultural science, among which developing farming coordinately, promoting the sustainable development of society, promoting agriculture through talents, science and education, managing system of innovative agriculture, farming in large scale and developing agriculture by making use of foreign capital, etc. are useful references and enlightenment to our modernization and the present newcountryside program.

Field of study: Agricultural and Food sciences
Strebel Differentials and stable Matrix Factorizations

We study the connection between quadratic Strebel differentials on punctured surfaces and the construction of moduli spaces of matrix factorizations for dimer models using GIT-quotients. We show that for each consistent dimer model and each nondegenerate stability condition $\theta$ we can find a Strebel differential for which the horizontal trajectories correspond to the $\theta$-stable matrix factorizations and the vertical trajectories correspond to the arrows of the dimer quiver. We give explicit expressions for the $\theta$-stable matrix factorizations that can be deduced from these horizontal trajectories. 
Following ideas by Pascaleff and Sybilla we show that each nondegenerate stability condition gives rise to a sheaf of curved algebras coming from consistent dimer models. The corresponding categories of matrix factorizations can be glued together to form the category of matrix factorizations of the original dimer.

Field of study: Mathematics
Health care in the EC member states.

Acknowledgements 1.  Chapter I. Actual Services 1. Present coverage 2. Coverage of benefits in kind 2.1 Costs and health status 2.1.1 Diversity of costs 2.1.2 Diversity of life expectancy and mortality 2.2 Prevention 2.3 Ambulatory medical services 2.4 Dental services 2.5 Paramedical services 2.6 Hospital services 2.7 Drugs 2.8 Nursing homes 2.9 Home care 2.10 Rehabilitation 3. Cash benefits 3.1 Sickness benefits 3.2 Maternity benefits 3.3 Death benefit Chapter II Health Care Reform Acts in Selected Member States 1. Overview 2. Federal Republic of Germany 3. Ireland 4. Netherlands 5. United Kingdom Chapter III Feasible Scenarios for European Health Care Baskets 1. Health insurance dimensions of the Single Market 2. Organizational principles of health care systems 2.1 Market vs non-market principles 2.1.1 Market approach 2.1.2 Health care as public good 2.1.3 The public-private mix of health care 2.2 Principles of subsidiarity and solidarity 3. Hypothetic pathways for the future 3.1 Status quo 3.2 Harmonization 3.3 Deregulation 3.4 Synchronization 3.5 Realization of pathways Chapter IV. Synchronization of the European Health Care Baskets 1. Demand side sychronization 1.1 Coinsurance 1.2 Financial aspects 1.3 Subsidies 1.4 Insurers 2. Synchronization on the supply side 2.1 Contracts with doctors 2.2 Contracts with hospitals 2.3 Medical goods 2.4 Health care planning 3. Quality assurance 4. Minimum health care baskets 5. Information systems 6.

Field of study: Medicine, Political science
Effects of sodium butyrate on the expression of sodium channels by neuronal cell lines derived from the rat CNS.

We have studied the effects of sodium butyrate on cell morphology and the expression of mRNAs encoding voltage-gated sodium channels in five neuronal cell lines, B35, B50, B65, B103 and B104, all derived from the rat CNS. The cells were grown in medium supplemented with 2.5 mM sodium-n-butyrate and examined daily by phase-contrast microscopy. Sodium butyrate caused slowing of cell division and the formation of longer and more highly branched cytoplasmic processes than were present in untreated cells. Expression of sodium channel mRNA was analysed by PCR with primers that allow the transcripts encoding the different types of sodium channel to be distinguished according to the lengths of the PCR products. The identity of the PCR products was confirmed by restriction enzyme digestion. Southern blotting and hybridization with internal radiolabelled probes. Prior to sodium butyrate treatment, expression of sodium channel mRNA was largely restricted to B50 and B104 cells: B50 cells showed expression of rat brain types I and II sodium channel and B104 cells expressed rat brain type III sodium channel. After treatment for 5 days with sodium butyrate, sodium channel mRNA was detected in all five cell lines. In addition to type I and type II sodium channel, B50 cells expressed rat brain type III sodium channel. These three types of sodium channel were also expressed by B35, B65 and B103 cells. Even after butyrate treatment, B104 cells expressed only type III sodium channel. The treatment also induced expression of rat skeletal muscle SkM1 sodium channel in B35 cells but only trace amounts in the other neuronal cell lines.

Field of study: Biology
How well can hillslope evolution models “explain” topography? Simulating soil transport and production with high-resolution topographic data

The morphology of hillslopes is a direct refl ection of tectonic forcing and climatic and biologic processes that drive soil production, mobilization, and transport. Soil transport on hillslopes affects river incision by providing tools for channel abrasion and controls the distribution of sediment that infl uences aquatic habitat. Although numerous hillslope transport relationships have been proposed over the past 60+ years, a comprehensive analysis of model predictions for a real landscape has not been performed. Here, we use high-resolution topographic data obtained via airborne laser swath mapping (ALSM) to simulate the long-term evolution of Oregon Coast Range hillslopes and test three published transport models and a new model that accounts for nonlinear depth- and slopedependent transport. Analysis of one-dimensional, steady-state solutions for these four models suggests that plots of gradient-curvature may be diagnostic for distinguishing model predictions. To evaluate two-dimensional model predictions for our fi eld site, we assumed local steady-state erosion for a 72,000 m 2 sequence of hillslopes and valleys. After calibrating each of the four models, we imposed constant base-level lowering for cells within the valley network, simulated 500,000 yr of soil production and transport, and determined which transport model best preserved morphologic patterns that describe the current landscape form. Models for which fl ux varies proportionally with hillslope gradient generated broadly convex hilltops inconsistent with the sharp-crested, steep-sided slopes of our study site, whereas the two nonlinear slope-dependent models produced convex-planar slopes consistent with current hillslope form. Our proposed nonlinear slope- and depth-dependent model accounts for how soil thickness controls the magnitude of biogenic disturbances that drive transport; this model best preserved the current landscape form, particularly the narrow, sharply convex hilltops characteristic of the Oregon Coast Range. According to our formulation, which provides an explicit linkage for relating the distribution of biota to hillslope processes, the degree of hilltop convexity varies nonlinearly with the ratio of erosion rate to maximum soil production rate, highlighting the profound infl uence of soil depth on hillslope evolution.

Field of study: Geology
Intermeshing Passive and Active Learning Strategies in Teaching Biochemistry.

Case studies and student presentations to the class were intermeshed with lectures and demonstrations into a three-semester hour, required biochemistry course in the first professional year of the entry level PharmD curriculum. The resulting course structure, made possible in part through the use of computer-assisted lecture presentations and lecture handouts, combined the high efficiency of information transfer of the lecture format with the high effectiveness of more active learning formats. This approach increased the motivation of the students to learn the material by helping them to see the relevance of biochemistry to the practice of pharmacy. Simultaneously, it made assimilation of the mass of information embodied in the course more manageable.

Field of study: Education, Medicine
CFD SIMULATIONS OF LIQUID PHASE FLOW IN STRUCTURED PACKED COLUMN

Liquid flow behavior, such as velocity distribution, in the packed column is of considerable importance in determining column performance. Using the volume-averaged method, a computational fluid dynamics(CFD) model was proposed to describe the liquid flow behavior in a structured packing column where the gas phase is stationary.A column packed with Mellapak 350Y had an inside diameter of 150 mm and a height of 1000 mm was simulated by solving the flow equations.A commercial CFD code, PHOENICS 3.3, was used to predict the fluid dynamics behavior of the liquid phase flow.The simulated profiles of pressure, velocity and concentration of the tracer were presented.The axial backmixing coefficients evaluated by the CFD results were presented and compared with the experimental data and the relative deviation was 3.8%—36.8%.

Field of study: Chemistry, Environmental science
Four-photon parametric frequency selection in wide stimulated emission lines

It is shown theoretically that the interaction between coherent light waves may give rise to periodic structures of parameters such as the refractive index, the absorption, and population inversion, etc. These structures can act as frequency-selection elements of the diffraction grating or the multilayer mirror type. Numerical estimates are obtained for some cases which satisfy formally the phase matching conditions for the four-photon interaction. Particular consideration is given to the case of coherent pumping of a dye-solution laser in which the frequency of the laser emission within a wide line can sometimes be altered.

Field of study: Engineering, Physics
Variable linear polarization from an X-ray undulator.

A new X-ray undulator has been designed and constructed which produces linearly polarized X-rays in which the plane of polarization can be oriented to a user selectable angle, from horizontal to vertical. Based on the Apple-II elliptically polarizing undulator (EPU), the undulator rotates the angle of the linear polarization by a simple longitudinal motion of the undulator magnets. Combined with the circular and elliptical polarization capabilities of the EPU operating in the standard mode, this new undulator produces soft X-ray radiation with versatile polarization control. This paper describes the magnetic structure of the device and presents an analysis of the magnetic field with varying undulator parameters. The variable linear polarization capability is then exhibited by measuring the X-ray absorption spectrum of an oriented polytetrafluoroethylene thin film. This experiment, which measures the linear dichroism of the sample at two peaks near the C 1s absorption edge, demonstrates the continuous polarization rotation capabilities of the undulator.

Field of study: Physics
Reducing uncertainty in nitrogen budgets for African livestock systems

Livestock is poorly represented in N budgets for the African continent although some studies have examined livestock-related N flows at different levels. Livestock plays an important role in N cycling and therefore on N budgets including livestock-related flows. This study reviews the literature on N budgets for Africa to identify factors contributing to uncertainties. Livestock densities are usually modelled because of the lack of observational spatial data. Even though feed availability and quality varies across seasons, most studies use constant livestock excretion rates, and excreta are usually assumed to be uniformly distributed onto the land. Major uncertainties originate in the fraction of manure managed, and emission factors which may not reflect the situation of Africa. N budgets use coarse assumptions on production, availability, and use of crop residues as livestock feed. No flows between croplands–livestock and rangelands reflect the lack of data. Joint efforts are needed for spatial data collection of livestock data, crowdsourcing appears to be a promising option. The focus of the assessment of N budgets must go beyond croplands to include livestock and crop–livestock flows. We propose a nested systems definition of livestock systems to link local, regional level, and continental level and to increase the usefulness of point measurements of N losses. Scientists working at all levels should generate data to calibrate process-based models. Measurements in the field should not only concentrate on greenhouse gas emissions, but need to include crop and livestock production measurements, soil stock changes and other N loss pathways such as leaching, run-off and volatilization to assess management practices and trade-offs. Compared to the research done in other continents on N flows in livestock systems, there are few data for Africa, and therefore concerted effort will be needed to generate sufficient data for modelling. S Online supplementary data available from stacks.iop.org/ERL/9/105008/mmedia

Field of study: Environmental science
Crystallization and preliminary crystallographic analyses of pokeweed antiviral protein from seeds.

Pokeweed antiviral protein from seeds (PAP-S) is a ribosome inactivating protein which has lowest toxicity and highest inhibition activity as opposed to other pokeweed antiviral proteins and its three potential glycosylation sites (10, 44, 255) were shown to bind to N-acetylglucosamine. Good quality crystals of PAP-S were grown at high protein concentration (100 mg ml-1) and high temperature (306 K). The crystals have space group I222 and cell parameters a = 78.7, b = 85.2 and c = 93.0 A. An X-ray diffraction data set with resolution up to 1.8 A was collected. This high-resolution data will help to locate the sugars bound to the protein and provide accurate structural data for understanding structure-function relationships of PAP-S.

Field of study: Chemistry
Online Kernel-Based Classification Using Adaptive Projection Algorithms

The goal of this paper is to derive a novel online algorithm for classification in reproducing kernel hilbert spaces (RKHS) by exploiting projection-based adaptive filtering tools. The paper brings powerful convex analytic and set theoretic estimation arguments in machine learning by revisiting the standard kernel-based classification as the problem of finding a point which belongs to a closed halfspace (a special closed convex set) in an RKHS. In this way, classification in an online setting, where data arrive sequentially, is viewed as the problem of finding a point (classifier) in the nonempty intersection of an infinite sequence of closed halfspaces in the RKHS. Convex analysis is also used to introduce sparsification arguments in the design by imposing an additional simple convex constraint on the norm of the classifier. An algorithmic solution to the resulting optimization problem, where new convex constraints are added every time instant, is given by the recently introduced adaptive projected subgradient method (APSM), which generalizes a number of well-known projection-based adaptive filtering algorithms such as the classical normalized least mean squares (NLMS) and the affine projection algorithm (APA). Under mild conditions, the generated sequence of estimates enjoys monotone approximation, strong convergence, asymptotic optimality, and a characterization of the limit point. Further, we show that the additional convex constraint on the norm of the classifier naturally leads to an online sparsification of the resulting kernel series expansion. We validate the proposed design by considering the adaptive equalization problem of a nonlinear channel, and by comparing it with classical as well as with recently developed stochastic gradient descent techniques.

Field of study: Engineering