nils-herrmann/clean_scirepeval huggingface dataset:
Recent developments in the structural organization and regulation of nitrogen fixation genes in Herbaspirillum seropedicae.

Herbaspirillum seropedicae is a nitrogen-fixing bacterium found in association with economically important gramineae. Regulation of nitrogen fixation involves the transcriptional activator NifA protein. The regulation of NifA protein and its truncated mutant proteins is described and compared with that of other nitrogen fixation bacteria. Nitrogen fixation control in H. seropedicae, of the beta-subgroup of Proteobacteria, has regulatory features in common with Klebsiella pneumoniae, of the gamma-subgroup, at the level of nifA expression and with rhizobia and Azospirillum brasilense, of the alpha-subgroup, at the level of control of NifA by oxygen.

Field of study: Biology, Engineering
Crystallization of CcdB in complex with a GyrA fragment.

Plasmid addiction systems consist of a plasmid-encoded toxin-antidote pair that serves to stabilize low-copy-number plasmids in bacterial populations. CcdB, the toxin from the ccd system on the Escherichia coli F plasmid, acts as a gyrase poison. A 14 kDa fragment of gyrase, GyrA14, was found to bind to the toxin CcdB with an affinity of 1.75 x 10(-8) M. Crystals of the (GyrA14)(2) dimer in its free state belong to space group P4(3)2(1)2, with unit-cell parameters a = 86.4, c = 89.4 angstroms, and diffract to 2.4 angstroms. Crystals of the (GyrA14)(2)-(CcdB)(2) complex belong to space group P2(1)2(1)2(1), with a = 52.1, b = 83.3, c = 110.9 angstroms, and diffract to 2.8 angstroms resolution.

Field of study: Chemistry
Exposure to heavy metals and infectious disease mortality in harbour porpoises from England and Wales.

We investigate whether long-term exposure to heavy metals, including immunosuppressive metals like mercury (Hg), is associated with infectious disease in a wild cetacean. Post-mortem investigations on 86 harbour porpoises, Phocoena phocoena, found dead along the coasts of England and Wales revealed that 49 of the porpoises were healthy when they died as a consequence of physical trauma (most frequently entrapment in fishing gear). In contrast, 37 porpoises died of infectious diseases caused by parasitic, bacterial, fungal and viral pathogens (most frequently pneumonia caused by lungworm and bacterial infections). We found that mean liver concentrations of Hg, selenium (Se), the Hg:Se molar ratio, and zinc (Zn) were significantly higher in the propoises that died of infectious disease compared to healthy porpoises that died from physical trauma. Liver concentrations of lead (Pb), cadmium (Cd), copper (Cu) and chromium (Cr) did not differ between the two groups. Hg, Se, and the Hg:Se molar ratio were also positively correlated with age. The association between Zn concentration and disease status may result from Zn redistribution in response to infection. Further work is required to evaluate whether chronic exposure to Hg may have presented a toxic challenge to the porpoises that succumbed to infectious disease.

Field of study: Environmental science
Cognitive constraints, contraction consistency, and the satisficing criterion

A theory of decision making is proposed that offers an axiomatic basis for the notion of "satisficing" postulated by Herbert Simon. The theory relaxes the standard assumption that the decision maker always fully perceives his preferences among the available alternatives, requiring instead that his ability to perceive any given preference be decreasing with respect to the complexity of the choice problem at hand. When complexity is aligned with set inclusion, this exercise is shown to be equivalent to abandoning the contraction consistency axiom of classical choice theory.

Field of study: Economics
Numerical Simulation on Temperature-field of Magnesium Alloy Pulsed Laser Welding

Using finite element analysis software,the thickness in 1.2 mm of AZ31 magnesium pulsed laser welding was simulated.By changing the laser pulse,frequency and welding speed,which compared the effect of parameters'change on the shape molten pool,which can confirm ideal standard parameters of the thickness specification parameters of AZ31 alloy sheet.Finally,the research results indicate that: as the laser pulse width and frequency reduces,the joint penetration reduces;as welding speed reduces,the joint penetration increases.Laser parameters'change has little effect on the width of molten pool.

Field of study: Materials science
Mechanistic and evolutionary aspects of vitamin B12 biosynthesis

For the past 20 years our laboratory has been engaged in the elucidation of the vitamin B12 biosynthetic pathway and a previous Account1 described progress made in the first ten years of this endeavor. By that time (1977), it had been established that 5-aminolevulinic acid (ALA), porphobilinogen (PBG) uro’gen III and three intermediates, Factors I–III, now known to be transformed as the precorrins 1–3, were sequentially formed on the way to the corrin nucleus as summarized in Scheme 1. The ensuing decade has witnessed an exponential increase in the rate of the acquisition of pure enzymes using recombinant DNA techniques and these methods together with the exploration of new NMR pulse sequences have not only cast light on the mechanisms of the B12 synthetic enzymes but have given us considerable optimism with regard to the discovery of the remaining intermediates and of the enzymes which produce them.

Field of study: Chemistry
Discussion on High Hardness and Toughness of the Lining Boards of ZG42CrMnSi2MoRE Cast Steel During Production

The test block is cut from the casting and inspected to acquire the experimental data so as to monitor the quality of products.The mechanical properties of the casting by quenching and tempering two times is higher than those of once quench and temper because the grain size and microstructure of abrasion resisting steel is refined after multi-times phase transformation.The high hardness and toughness in the abrasion resisting steel after quenching and tempering two times is due to bainite formation in the location where cooling rate can meet the formation of bainite The.

Field of study: Materials science
Organophosphate pesticide exposure and neurodevelopment in young Shanghai children.

A large amount of organophosphate pesticides (OPs) is used throughout China. Animal studies have suggested that even moderate doses are toxic to neurodevelopment, but there are a few studies in humans. We investigated both the urinary levels of OP metabolites in children and their relationship with child neurodevelopment. Participating 301 young children (23-25 months of age) were recruited from two community hospitals in Shanghai between February and October 2008. We measured five nonspecific dialkyl phosphate (DAP) metabolite levels of OPs in the children's urine and examined their association with the children's developmental quotients (DQs) based on the Gesell Developmental Schedules (GDS). The creatinine-adjusted geometric means (GMs) of OP metabolites in urine samples were 11.27 μg/g for DMP; 6.99 μg/g for DMTP; 7.96 μg/g for DEP; 14.19 μg/g for DETP; and 4.55 μg/g for DEDTP. The children had relatively higher levels of OP urinary metabolites compared with those reported in developed countries, no association was found between child urinary levels of OP metabolites and any of the DQ scores. However, our results should be interpreted with caution, and more studies of children living in China are warranted given the relatively high levels of child OP urinary metabolites in Shanghai.

Field of study: Environmental science
Button vesicostomy: 13 years of experience.

Over recent years the button vesicostomy has become an alternative management option in children with poor bladder emptying, when clean intermittent catheterisation (CIC) cannot be initiated for reasons of age, sensation, or urethral anatomy. This study reviews recent experience of this technique and evaluates its use.



Retrospective review of patients who had a button vesicostomy to permit bladder drainage between 1998 and 2011.



Thirty children underwent button vesicostomy insertion aged between 4 days and 16 years. Indications were neuropathic bladders (n = 15), congenital hypotonic bladders (n = 6), functional bladder disorders (n = 5), and post-obstruction bladders (n = 4). The median length of use was 11 months; however, 7 patients still have the button in situ. Minor complications (n = 12) included transient leakage, wound infection, and overgranulation. Major complications included 2 UTIs, 1 device failure, and 2 significant leaks, requiring revision of the tract and removal of the button.



The button vesicostomy is a suitable and safe technique for use in the short- and medium-term. The procedure has minimal morbidity and therefore is acceptable to families. It has a wide scope, including patients with a neuropathic bladder as an alternative to CIC and where temporary drainage is required until bladder function can recover.

Field of study: Medicine
Mega-events and their legacy: Image and tourism in Genoa, Turin and Milan

Hosting, or organising, a mega-event is a form of destination branding; it is a way to generate the leveraging process of the event itself and promote the image of a location. Besides, these events allow a destination to attract the attention of the public and the media, enhancing its awareness nationally and internationally. Mega-events promote greater flows of tourists and visitors, especially in the short term. Nevertheless they produce long-lasting effects, such as the attraction and stimulation of investments, urban regeneration, advanced facilities and equipment, in addition to the improvement of accommodation, services and infrastructures. Thanks to those investments and to the growth in tourist arrivals, the mega-events could have a positive impact on the local economy, also over years, but some of their most important outcomes deal with the so-called intangible legacy, or rather social, cultural and political effects, more difficult to identify and measure. They can modify local identity and image, supporting the repositioning of the hosting place at an international level. The above considerations are discussed in this study; most attention is paid to three Italian cities, involved in top events: Genoa, appointed as European Capital of Culture in 2004; Turin, that hosted the XX Olympic Winter Games in 2006; Milan, that is now organising the Universal Expo 2015.

Field of study: Sociology
An embedding technique based upon block prediction

This paper presents a novel data hiding scheme for VQ compression images. This scheme first uses SMVQ prediction to classify encoding blocks into different types, then uses different codebooks and encoding strategies to perform encoding and data hiding simultaneously. In using SMVQ prediction, no extra data is required to identify the combination of encoding strategies and codebook, which helps improve compression performance. Furthermore, the proposed scheme adaptively combines VQ and SMVQ encoding characteristics to provide higher image quality of stego-images while size of the hidden payload remains the same. Experimental results show that the proposed scheme indeed outperforms other previously proposed schemes in image quality of the stego-images and compression performance.

Field of study: Computer science, Engineering
An Industrial Classification for Reports from Individuals

IN A recent article in this JOURNAL, Dr. Gladys L. Palmer discussed the preparation and content of the Convertibility List of Occupations.' Among other things, she pointed out that the Committee on Occupational Classification found it impossible to obtain an adequate grouping of workers from an occupational standpoint without subdividing by industry the occupational titles of "Proprietors, managers, and officials, n.e.c.," "Foremen, n.e.c.," "Inspectors, n.e.c.," "Operatives and kindred workers, n.e.c.," and "Laborers, n.e.c." Some of the problems arising in connection with the determination of these subdivisions showed clearly the need of a thorough examination of an industrial classification system from the point of view of its use in connection with information secured under conditions like those of a house-to-house canvass. Such industry returns are used commonly to classify workers, and occasionally to classify their dependents as well. If the goal is to show the industrial distribution of such items as pay rolls, gross income, or value added by manufacture or by services rendered, the information is almost invariably obtained from employing units, in which case problems of an entirely different kind are encountered. It is the result of the Committee's study of an industrial classification of workers which is presented  In considering the specific industrial groups into which the abovementioned occupations should be subdivided, the starting point was the Standard Industrial Classification, described elsewhere in this JOURNAL by Vladimir S. Kolesnikoff.3 Two reasons for this are obvious -the Standard Industrial Classification provides a carefully thoughtout system covering the entire realm of industry, and is being adopted generally by agencies gathering industrial statistics. In fact, its advantages are so great that deviations from its various levels of principal divisions, major groups, industry groups and industries may be anticipated rarely, unless made necessary by shortcomings in the in-

Field of study: Mathematics
Renaissance Splendor: Catherine de’ Medici's Valois Tapestries. Elizabeth Cleland and Marjorie E. Wieseman. Exh. Cat. Cleveland, OH: Cleveland Museum of Art; New Haven, CT: Yale University Press, 2018. 96 pp. $40.

by the forcefulness of her argumentation. Her careful analysis of what other scholars have written about the works provides yet another valuable contribution of these volumes. But Markham Schulz does much more than clarify or propose new attributions. By deftly combining documentation from archival sources; careful analysis of artistic, social, and religious practices; iconographical analysis; and biographical information on patrons and artists with extensive, careful visual analysis, Markham Schulz reminds the reader of the extraordinary value of connoisseurship. Once the raison d’être of our field, it is now highly unusual, and young scholars are rarely trained in it. Markham Schulz’s volumes model how important—especially in areas of the history of sculpture, which have not been so extensively studied or documented by photography—such an approach can be.

Field of study: History
Seeking for a void top level concept - a wrong way to the exploration of the nature of sport and physical education in China.

The author analyzed the confusions brought by "sport and physical education" as a top level concept,and by analyzing similar concepts used in the United States,the author pointed out that in the United States there is not a top level concept corresponding to sport and physical education,thus considering that localizing such a concept would make it more confusing logically.Seeking for a void top level concept is a wrong way to the study of the nature of sport and physical education in China.

Field of study: Education
Heterozygous PGM3 Variants Are Associated With Idiopathic Focal Epilepsy With Incomplete Penetrance

Idiopathic focal epilepsy (IFE) is a group of self-limited epilepsies. The etiology for the majority of the patients with IFE remains elusive. We thus screened disease-causing variants in the patients with IFE.  Whole-exome sequencing was performed in a cohort of 323 patients with IFE. Protein modeling was performed to predict the effects of missense variants. The genotype–phenotype correlation of the newly defined causative gene was analyzed.  Four novel heterozygous variants in PGM3, including two de novo variants, were identified in four unrelated individuals with IFE. The variants included one truncating variant (c.1432C > T/p.Q478X) and three missense variants (c.478C > T/p.P160S, c.1239C > G/p.N413K, and c.1659T > A/p.N553K), which had no allele frequency in the gnomAD database. The missense variants were predicted to be damaging and affect hydrogen bonds with surrounding amino acids. Mutations Q478X, P160S, and N413K were associated with benign childhood epilepsy with centrotemporal electroencephalograph (EEG) spikes. P160S and N413K were located in the inner side of the enzyme active center. Mutation N553K was associated with benign occipital epilepsy with incomplete penetrance, located in the C-terminal of Domain 4. Further analysis demonstrated that previously reported biallelic PGM3 mutations were associated with severe immunodeficiency and/or congenital disorder of glycosylation, commonly accompanied by neurodevelopmental abnormalities, while monoallelic mutations were associated with milder symptoms like IFE.  The genetic and molecular evidence from the present study implies that the PGM3 variants identified in IFE patients lead to defects of the PGM3 gene, suggesting that the PGM3 gene is potentially associated with epilepsy. The genotype–phenotype relationship of PGM3 mutations suggested a quantitative correlation between genetic impairment and phenotypic severity, which helps explain the mild symptoms and incomplete penetrance in individuals with IFE.

Field of study: Biology
DPPH radical scavenging activity and contents of H2O2, malondialdehyde and proline in determining salinity tolerance in chickpea seedlings.

The involvement of 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity and contents of H2O2, malondialdehyde (MDA) and proline was investigated in determining salinity tolerance among seedlings of thirty chickpea (Cicer arietinum L.) genotypes having different pedigrees. Chickpea genotypes, including cultivars and advanced lines were grown for 7 days under control and salt stress (50 mM NaCl) conditions. The genotypes showed differential response to salt stress in terms of growth, DPPH radical scavenging activity and contents of H2O2, MDA and proline in seedlings. On the basis of seedling growth, the genotypes having better performance under stress conditions had reduced levels of H2O2 and MDA contents, but increased levels of proline and DPPH radical scavenging activity. Stress tolerance index for these parameters was also determined. Agglomerative hierarchal clustering by Pearson correlation coefficient grouped the genotypes into two major clusters--MC I and MC II. MC II and Al-1 sub-cluster of MC-I comprised mainly of genotypes that showed higher stress resistance levels for the respective parameters in comparison to genotypes in other sub-clusters. Thus, it is possible to identify salt-tolerant genotypes on the basis of above parameters without a field trial.

Field of study: Biology, Chemistry, Physics
Mosco: a privacy-aware middleware for mobile social computing

The proliferation of mobile devices coupled with Internet access is generating a tremendous amount of highly personal and sensitive data. Applications such as location-based services and quantified self harness such data to bring meaningful context to users’ behavior. As social applications are becoming prevalent, there is a trend for users to share their mobile data. The nature of online social networking poses new challenges for controlling access to private data, as compared to traditional enterprise systems. First, the user may have a large number of friends, each associated with a unique access policy. Second, the access control policies must be dynamic and fine-grained, i.e. they are content-based, as opposed to all-or-nothing. In this paper, we investigate the challenges in sharing of mobile data in social applications. We design and evaluate a middleware running on Google App Engine, named Mosco, that manages and facilitates sharing of mobile data in a privacy-preserving manner. We use Mosco to develop a location sharing and a health monitoring application. Mosco helps shorten the development process. Finally, we perform benchmarking experiments with Mosco, the results of which indicate small overhead and high scalability.

Field of study: Computer science, Engineering
Continuous ethanol exposure inhibits agonist-stimulated phosphorylation of p70S6 kinase and ribosomal S6 protein in cultured rat astrocytes.

The effects of ethanol exposure on agonist-stimulated phosphorylation of p70S6 kinase and ribosomal S6 protein were determined in confluent astrocyte monolayers. Basal phosphorylation of p70S6 kinase and S6 protein was either unaffected or reduced, respectively, after exposure to 50 mM ethanol for 4 days. The abilities of norepinephrine, carbachol and epidermal growth factor to phosphorylate these proteins were significantly decreased after ethanol exposure. In contrast, ethanol exposure had no effect on the protein expression of either p70S6 kinase or S6 protein. Our data suggest that continuous ethanol exposure results in a generalized decrease in agonist-activation of the p70S6 pathway.

Field of study: Biology
The Intrinsic Self and Defensiveness: Evidence that Activating the Intrinsic Self Reduces Self-Handicapping and Conformity

Two studies were conducted to assess the hypothesis that shifting individuals’ base of self-esteem to more stable, intrinsic self-attributes would reduce psychological defensiveness in the form of self-handicapping attributions and conformity. In Study 1, participants visualized an individual who liked them contingently or noncontingently, or who was neutral toward them, and then made attributions for an impending test performance. Participants who visualized the noncontingently accepting other made fewer self-handicapping attributions. In Study 2, partici pants wrote about an intrinsic self-attribute, an achievement, or a neutral event and then evaluated several abstract art paintings while knowing how other participants purportedly rated the paintings. Participants for whom the intrinsic self was primed conformed less to others’ judgments relative to achievement self-primed and control participants. Discussion focuses on the implications of these findings for understanding the connection between self-esteem and defensiveness.

Field of study: Psychology
Temperature effects on net greenhouse gas production and bacterial communities in arctic thaw ponds.

One consequence of High Arctic permafrost thawing is the formation of small ponds, which release greenhouse gases (GHG) from stored carbon through microbial activity. Under a climate with higher summer air temperatures and longer ice-free seasons, sediments of shallow ponds are likely to become warmer, which could influence enzyme kinetics or select for less cryophilic microbes. There is little data on the direct temperature effects on GHG production and consumption or on microbial communities' composition in Arctic ponds. We investigated GHG production over 16 days at 4°C and 9°C in sediments collected from four thaw ponds. Consistent with an enzymatic response, production rates of CO2 and CH4 were significantly greater at higher temperatures, with Q10 varying from 1.2 to 2.5. The bacterial community composition from one pond was followed through the incubation by targeting the V6-V8 variable regions of the 16S rRNA gene and 16S rRNA. Several rare taxa detected from rRNA accounted for significant community compositional changes. At the higher temperature, the relative community contribution from Bacteroidetes decreased by 15% with compensating increases in Betaproteobacteria, Alphaproteobacteria, Firmicutes, Acidobacteria, Verrucomicrobia and Actinobacteria. The increase in experimental GHG production accompanied by changes in community indicates an additional factor to consider in sediment environments when evaluating future climate scenarios.

Field of study: Biology, Environmental science