nils-herrmann/clean_scirepeval huggingface dataset:
Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils.

Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.

Field of study: Biology, Environmental science
Analysis of Small Molecular Selenium Species in Serum Samples from Mercury-Exposed People Supplemented With Selenium-Enriched Yeast by Anion Exchange-Inductively Coupled Plasma Mass Spectrometry

A hyphenated technique was optimized to simultaneously determine different selenium species, including Se(IV), Se(VI), selenocysteine (SeCys), and selenomethionine (SeMet), by anion exchange chromatography (AEC)-inductively coupled plasma mass spectrometry (ICP-MS). Ammonium citrate and methanol were used as mobile phase. Mobile phase A is composed of 0.5 mM ammonium citrate + 2% ( V/V ) methanol, and mobile phase B is 100 mM ammonium citrate + 2% ( V/V ) methanol. When 93% A + 7% B were used, the four Se species can be separated in 7.5 min. The detection limits for SeCys, Se(IV), SeMet and Se(VI) were 0.34, 0.67, 1.38 and 0.63 μg L −1 , respectively, according to three times standard deviation of the blank criterion. The recoveries of spiked Se(IV) in serum samples were between 93% and 107%, and the RSDs were less than 9% ( n = 3). This method was applied to analyze serum samples from long-term mercury-exposed people supplemented with selenium-enriched yeast. The concentrations of total Se and Se(IV) in serum samples were found to be increased after Se supplementation. The method is simple, rapid, sensitive, repeatable, and suitable for speciation analysis of small molecular weight seleno-compounds in different biological samples.

Field of study: Chemistry
GEOLOGY OF THE ELKHORN MOUNTAINS, NORTHEASTERN OREGON: PART 2. WILLOW LAKE INTRUSION

The Willow Lake intrusion is funnel-shaped with contacts inclined inward at 60°-70° and has a sheetlike appendage to the southwest, inclined northwest at 50°. The pluton lies athwart the southern contact of the Bald Mountain batholith and was emplaced before the main batholithic phases. It contains normal metagabbroic rocks, rhythmically layered rocks similar to those described from the Stillwater and Skaergaard intrusions, and abnormal banded rocks in which the minerals are elongated and arranged with their longer axes at high angles to the banding. Similar abnormal banded rocks have been found in a number of localities in Oregon and California, invariably in steep-walled intrusions of small size, including dikes a foot or less in width. The Willow Lake type of rhythmical layering cannot have been formed by a process combining gravitative sedimentation of crystals with convection currents in the magma, such as accounts for Skaergaard-type layered rocks. The Willow Lake-type layered rocks probably formed by undercooling and crystallization in the oversaturated (metastable) region, combined with intermittent convective and turbulent currents, in a magma near a univariant condition. Banded rocks of this type may be expected in epizonal metamorphic regions in steep-walled mafic intrusions, emplaced late in the regional metamorphic cycle. Criteria for so-called gravity stratification are examined; the various features of density stratification may in part be due to processes other than those operating under the influence of gravity. The perpendicular feldspar rock of the Skaergaard intrusion and the harrisite structure of layered periodotites from the island of Rhum are cited as products of moderate undercooling of magma in a bivariate condition. Translation-gliding effects and a set of conjugate shears developed in Willow Lake banded rocks are attributed to stresses in the crystal mush resulting from magma movements past surfaces of crystallization. The role of diffusion in the interstitial melt is discussed, and the formation of mono-mineralic layers in the Willow Lake banded rocks is attributed to diffusion between interstitial melts of adjacent bands of contrasting mineralogy and reactions between the melts and the surrounding solid phases.

Field of study: Geology
The role of interfacial reactions in Pt/CdTe contact formation

The reactions at the interface between CdTe and the contact metal platinum have been studied using various approaches including theoretical and experimental ternary phase diagram determination, bulk and thin film diffusion couples and electrical characterization of elemental and compound contacts on p- and n-Cd0.95Zn0.05Te (CZT). At the interface of Pt/CdTe diffusion couples a non-planar reaction layer of the intermetallics PtCd and PtTe is formed. This is consistent with the studied ternary phase diagram. Additional compounds which are stable in direct contact to CdTe can also be identified using these data. The contact barrier heights of pure Pt and of alloys with Cd or Te on CZT substrates and their variation after various annealing procedures were determined both on etched (Te-rich) and on virtually stoichiometric CZT surfaces. All the Pt-based contacts on the etched CZT surface showed a similar behaviour, determined by the Te excess and the ensuing formation of PtTe in direct contact to CZT. In contrast to that, a wide range of electrical properties can be achieved on the stoichiometric surface by deposition of Pt with or without additional Cd or Te interlayers due to the variety of phases forming in direct contact to CZT after deposition and annealing.

Field of study: Materials science
Authenticated Encryption in the Face of Protocol and Side Channel Leakage

Authenticated encryption schemes in practice have to be robust against adversaries that have access to various types of leakage, for instance decryption leakage on invalid ciphertexts (protocol leakage), or leakage on the underlying primitives (side channel leakage). This work includes several novel contributions: we augment the notion of nonce-base authenticated encryption with the notion of continuous leakage and we prove composition results in the face of protocol and side channel leakage. Moreover, we show how to achieve authenticated encryption that is simultaneously both misuse resistant and leakage resilient, based on a sufficiently leakage resilient PRF, and finally we propose a concrete, pairing-based instantiation of the latter.

Field of study: Computer science, Mathematics
Not All Flipped Classes Are the Same: Using Learning Science to Design Flipped Classrooms.

The flipped classroom has recently become a popular method used in both higher education and K-12 classrooms, yet research has not consistently demonstrated clear benefits of flipping a classroom. Also, any benefits seen might not be from the flipped design itself, but instead from the individual aspects of a flipped classroom (e.g., more active learning in class, more feedback on homework). This suggests that research focused on how to develop the activities and components of the flipped classroom, instead of simply flipping the traditional in-class and out-of-class activities, is critical to flipped pedagogy. These activities (both in and out of the classroom) should be designed based on a theory of learning. We draw upon the Practicing-Connections (PC) Hypothesis, supported by contemporary theories and research in the cognitive sciences, to design instructional activities to promote learning by having students practice making connections between concepts and situations. This paper examines a flipped class based on a theory-driven design versus a basic flipped classroom. The results of this work offer suggestions as to what dimensions of flipping may be important and how to design and evaluate flipped classrooms based on theories of learning.

Field of study: Education
Plant hormone effects on isoprene emission from tropical tree in Ficus septica.

Plant hormones and the circadian rhythm have been implicated in coordinated control of isoprene emission in plants. To gain insights into the signalling networks, foliar application of plant hormones was conducted in a native emitter, Ficus septica. Spraying of 50 μM jasmonic acid (JA) gradually decreased isoprene emission by 88% compared with initial levels within 5 days, and emission increased after relief from JA application. We further explored the molecular regulatory mechanism of isoprene emission by analysing photosynthetic rate, gene expression of 2-C-methyl-D-erythrytol 4-phosphate (MEP) pathway, hormone signalling and circadian rhythm processes, and metabolite pool sizes of MEP pathway. Results show that isoprene emission strongly correlated with isoprene synthase (IspS) gene expression and IspS protein levels over the period of JA treatment, indicating transcriptional and possible translational modulation of IspS by JA. Application of JA coordinately modulated genes in the auxin, cytokinin (CK), and circadian rhythm signal transduction pathways. Among the transcriptional factors analysed, MYC2 (JA) and LHY (circadian clock) negatively correlated with isoprene emission. Putative cis-elements predicted on IspS promoter (G-box for MYC2 and circadian for LHY) supports our proposal that isoprene emission is regulated by coordinated transcriptional modulation of IspS gene by phytohormone and circadian rhythm signalling.

Field of study: Environmental science
Sequential Monte Carlo Methods for State and Parameter Estimation in Abruptly Changing Environments

This paper develops a novel sequential Monte Carlo (SMC) approach for joint state and parameter estimation that can deal efficiently with abruptly changing parameters which is a common case when tracking maneuvering targets. The approach combines Bayesian methods for dealing with change-points with methods for estimating static parameters within the SMC framework. The result is an approach that adaptively estimates the model parameters in accordance with changes to the target's trajectory. The developed approach is compared against the Interacting Multiple Model (IMM) filter for tracking a maneuvering target over a complex maneuvering scenario with nonlinear observations. In the IMM filter a large combination of models is required to account for unknown parameters. In contrast, the proposed approach circumvents the combinatorial complexity of applying multiple models in the IMM filter through Bayesian parameter estimation techniques. The developed approach is validated over complex maneuvering scenarios where both the system parameters and measurement noise parameters are unknown. Accurate estimation results are presented.

Field of study: Engineering
A Europe of Courts, a Europe of Factions: Political Groups at Early Modern Centres of Power (1550–1700). Rubén González Cuerva and Alexander Koller, eds. Rulers and Elites 12. Leiden: Brill, 2017. x + 264 pp. $137.

the conquering monarch (like Gustaph Adolphus’s entry into Riga in 1621), they were carefully balanced and often-peculiar events in which the previously established language of festivals appropriated profoundly novel significations. One peculiar case was presented in the text devoted to the city of Valladolid as a “theater of peace” in 1605, when this venerable center of erudition was chosen for the ratification of Anglo-Spanish peace. These ceremonies in peace glorifying Valladolid were, as was often the case, an enactment of political realities, being often a truer mirror than the reality itself. Each of the chapters in this book is an important piece of research in its own right, shedding a new light on the power of festivals in early modern Europe. They greatly differ in their approaches and methodologies, but viewed together, they offer a priceless addition to the understanding of festival culture and the mechanisms of displaying and negotiating power.

Field of study: History
[Detection of Yersinia Enterocolitica Bacteriophage PhiYe-F10 Lysis Spectrum and Analysis of the Relationship between Lysis Ability and Virulence Gene of Yersinia Enterocolitica].

To determine the lysis spectrum of Yersinia enterocolitica bacteriophage phiYe-F10 and to analyze the relationship between the lysis ability of phiYe-F10 and the virulence gene of Yersinia enterocolitica. To observe the lysis ability of the phage phiYe-F10 to the different Yersinia strains with the double-layer technique. The strains used in this study including 213 of Yersinia enterocolitica and 36 of Yersinia pseudotuberculosis and 1 of Yersinia pestis. The virulence genes of these Yersinia enterocolitica (attachment invasion locus (ail) and enterotoxin (ystA, ystB) and yersinia adhesin A (yadA), virulence factor (virF), specific gene for lipopolysaccharide O-side chain of serotype O : 3 (rfbc) were all detected. Among the 213 Yersinia enterocolitica, 84 strains were O : 3 serotype (78 strains with rfbc gene), 10 were serotype O : 5, 13 were serotype O : 8, 34 were serotype O : 9 and 72 were other serotypes. Of these, 77 were typical pathogenic Yersinia enterocolitica harboring with virulence plasmid (ail+, ystA+, ystB-, yadA+, virF+), and 15 were pathogenic bacterial strains deficiency virulence plasmid (ail+, ystA+, ystB-, yadA-, virF-) and the rest 121 were non pathogenic genotype strains. PhiYe-F10 lysed the 71 serotype O : 3 Yersinia enterocolitica strains which were all carried with rfbc+, including 52 pathogenic Yersinia enterocolitica, 19 nonpathogenic Y. enterocolitica. The phiYe-F10 can not lysed serotype O : 5, O : 9 and other serotype Y. enterocolitica, the lysis rate of serotype O : 3 was as high as 84.5%. The phiYe-F10 can not lysed Yersinia pseudotuberculosis and Yersinia pestis. Yersinia phage phiYe-F10 is highly specific for serotype O : 3 Yersinia enterocolitic at 25 degrees C, which showed a typical narrow lysis spectrum. Phage phiYe-F10 can lysed much more pathogenic Y. enterocolitica than nonpathogenic Y. enterocolitica.

Field of study: Biology
Shift of C3 deposition from localization in the glomerulus into the tubulo‐interstitial compartment in the absence of secreted IgM in immune complex glomerulonephritis

The role of secretory IgM in protecting kidney tissue from immune complex glomerulonephritis induced by 4 mg horse spleen apoferritin and 0·05 mg lipopolysaccharide has been investigated in mutant mice in which B cells do not secrete IgM, but are capable of expressing surface IgM and IgD and secreting other Ig isotypes. Glomerular size, number of glomeruli per cross‐section, glomerular cellularity and urine content of protein and creatinine was comparable in treated secreted IgM (sIgM)‐deficient and wild‐type mice. Assessment of urinary proteins by sodium dodecyl sulphate‐polyacrylamide gel electrophoresis showed a 30 kDa low molecular weight protein in treated sIgM‐deficient animals only, reflecting dysfunction of proximal tubules. A shift of bound C3 from glomeruli to the tubulo‐interstitial compartment in sIgM‐deficient mice also suggests tubulo‐interstitial damage. In contrast, local C3 synthesis within the kidney tissue did not differ between the two treated groups. Apoptosis physiologically present to maintain kidney cell homeostasis was increased slightly in treated wild‐type mice. These results indicate that secretory IgM can protect the tubulo‐interstitial compartment from immune complex‐induced damage without having an effect on the glomerulus.

Field of study: Biology, Medicine
Influence of extracellular polymeric substances (EPS) on Cd adsorption by bacteria.

The role of extracellular polymeric substances (EPS) in Cd adsorption by Bacillus subtilis and Pseudomonas putida was investigated using a combination of batch adsorption experiments, potentiometric titrations, Fourier transform infrared spectroscopy (FTIR). An increased adsorption capacity of Cd was observed for untreated bacteria relative to that for EPS-free bacteria. Surface complexation modeling of titration data showed the similar pKa values of functional groups (carboxyl, phosphate and hydroxyl) between untreated and EPS-free bacteria. However, site concentrations on the untreated bacteria were found to be higher than those on the EPS-free bacteria. FTIR spectra also showed that no significant difference in peak positions was observed between untreated and EPS-free bacteria and carboxyl and phosphate groups were responsible for Cd adsorption on bacterial cells. The information obtained in this study is of fundamental significance for understanding the interaction mechanisms between heavy metals and biofilms in natural environments.

Field of study: Environmental science
A Change Will Do Us Good: Threats Diminish Typical Preferences for Male Leaders

The current research explores role congruity processes from a new vantage point by investigating how the need for change might shift gender-based leadership preferences. According to role congruity theory, favorability toward leaders results from alignment between what is desired in a leadership role and the characteristics stereotypically ascribed to the leader. Generally speaking, these processes lead to baseline preferences for male over female leaders. In this research, the authors propose that a shift in gender-based leadership preferences will emerge under conditions of threat. Because the psychological experience of threat signals a need for change, individuals will favor candidates who represent new directions in leadership rather than consistency with past directions in leadership. Specifically, they find that threat evokes an implicit preference for change over stability (Experiment 1) and gender stereotypes align women with change but men with stability (Experiments 2a and 2b). Consequently, the typical preference for male leaders is diminished, or even reversed, under threat (Experiments 3 and 4). Moreover, the shift away from typical gender-based leadership preferences occurs especially among individuals who highly legitimize the sociopolitical system (Experiment 4), suggesting that these preference shifts might serve to protect the underlying system.

Field of study: Psychology
Multilayer adsorption of nitrogen and alkanes by non-porous carbons and silicas

Multilayer adsorption isotherms of nitrogen (at 77K), isobutane (at 261K) and neopentane (Z,l-dimethylpropane, at 273K) have been determined on a number of non-porous carbons and silicas. The results serve to strengthen the view that the structure of the adsorbent surface has very little effect on the development of the nitrogen multilayer. The adsorbent structure has a greater effect on the course of the isobutane and neopentane isotherms, but when plotted on a reduced basis the corresponding isotherms for carbon and silica do appear to coincide at p/po > 0.6 and 8 > 2. All the isotherms give linear FHH plots over a wide range of multilayer coverage.

Field of study: Chemistry
Protein kinase A linked phosphorylation mediates triiodothyronine induced actin gene expression in developing brain.

In the developing rat cerebra, triiodothyronine (T3) stimulates actin mRNA by acting predominantly at the level of transcription whereas tubulin mRNA is enhanced primarily by post-transcriptional regulation. We report here that in primary cultures of rat cerebra, the T3-induced actin gene expression is mediated by phosphorylation events. Inhibition of protein kinase A (PKA), but not of protein kinase C (PKC) or tyrosine kinase, totally blocked the induction of actin mRNA by T3. Under identical conditions, induction of tubulin mRNA by T3 was virtually unaffected by all the inhibitors. Activators of PKA, but not of PKC, potentiated the T3-induced actin gene expression, both at mRNA and protein level, by about 2-fold. In the absence of T3, neither the inhibitor nor the activator of PKA had any significant effect on this induction. The involvement of PKA in mediating the induction of actin mRNA by T3 was confirmed by transfecting primary cultures of rat cerebra with an expression vector encoding the protein kinase A inhibitor which totally abolished the induction. T3 is shown to enhance the phosphorylation of the thyroid hormone receptor, TRalpha, by about 2-fold but the level of phosphorylation of TRbeta remained virtually unaffected.

Field of study: Biology
Spin dynamics of the electron-doped high-T(c) superconducting cuprates.

We show that a basic difference between the electron- and hole-doped cuprates is their proximity to two different quantum critical points in a 2D free fermion system on a square lattice and that the spin dynamics observed recently for the first time in the electron-doped Nd2-xCexCuO4, very different from that in the hole-doped cuprates, can be understood as a consequence of this effect.

Field of study: Physics
Placebo Response as a Latent Characteristic: Application to Analysis of Sequential Parallel Comparison Design Studies

In clinical trials, placebo response can affect the inference about efficacy of the studied treatment. It is important to have a robust way to classify trial subjects with respect to their response to placebo. Simple, criterion-based classification may lead to classification error and bias the inference. The uncertainty about placebo response characteristic has to be factored into the treatment effect estimation. We propose a novel approach that views the placebo response as a latent characteristic and the study sample as an unlabeled mixture of “placebo responders” and “placebo nonresponders.” The likelihood-based methodology is used to estimate the treatment effect corrected for placebo response as defined within sequential parallel comparison design.

Field of study: Mathematics
Subacromial Balloon Interpositional Arthroplasty for the Management of Irreparable Rotator Cuff Tears: Five-year Results

Management of massive irreparable rotator cuff tears can be a source of significant dilemma for the treating surgeon. This is especially true when dealing with patients with poor physiological reserves where options of tendon transfer, superior capsular repair or arthroplasty might be unsuitable. We report the five-year outcomes of 26 patients who underwent balloon interpositional arthoplasty for the management of massive irreparable rotator cuff tears.

Field of study: Medicine
Bond Characteristics of CFRP/Steel Interface End-anchored with G-shaped Clamps

In order to prevent the debonding failure of CFRP laminate/steel plate joints, this study attempted to use a G-shaped clamp anchorage system to eliminate the peeling stress at the end of joints which causes the debonding of interfaces. Bond characteristics of CFRP/steel interface with and without end anchorage were obtained by conducting double strap tensile tests, and the effectiveness of end anchorage was verified as well. By anchoring on the weak points, the bond strength of the composite plates can be increased. However, for completely preventing debonding of the composites, a more advanced anchorage system which could against the intensive shear stress still needs further investigation.

Field of study: Materials science