nils-herrmann/clean_scirepeval huggingface dataset:
Helicobacter pylori--an African perspective.

Helicobacter pylori is ubiquitous in Africa, with acquisition in childhood the rule. Despite the prevalence of a virulent strain (in Soweto, most H. pylori organisms are cagA- and vacAS(1)-positive) H. pylori-associated pathology (duodenal ulcer, gastric ulcer and gastric cancer) has a variable, often low distribution in sub-Saharan Africa that does not parallel H. pylori prevalence in the population, suggesting a different natural history from that seen in developed countries. Progression to atrophic gastritis in Africans does not appear to differ from that reported in other regions, but as yet unidentified factors may play a role in inhibiting progression to gastric cancer. Studies have suggested that the specific IgG subclass response to H. pylori is predominately IgG1 (suggestive of a Th2 response), and the Th2 response may provide a protective effect against development of gastric cancer. Host immune mechanisms may be the key to different responses to H. pylori in the developed and developing worlds.

Field of study: Medicine
Reduction of transpiration and altered nutrient allocation contribute to nutrient decline of crops grown in elevated CO(2) concentrations.

Plants grown in elevated [CO(2) ] have lower protein and mineral concentrations compared with plants grown in ambient [CO(2) ]. Dilution by enhanced production of carbohydrates is a likely cause, but it cannot explain all of the reductions. Two proposed, but untested, hypotheses are that (1) reduced canopy transpiration reduces mass flow of nutrients to the roots thus reducing nutrient uptake and (2) changes in metabolite or enzyme concentrations caused by physiological changes alter requirements for minerals as protein cofactors or in other organic complexes, shifting allocation between tissues and possibly altering uptake. Here, we use the meta-analysis of previous studies in crops to test these hypotheses. Nutrients acquired mostly by mass flow were decreased significantly more by elevated [CO(2) ] than nutrients acquired by diffusion to the roots through the soil, supporting the first hypothesis. Similarly, Mg showed large concentration declines in leaves and wheat stems, but smaller decreases in other tissues. Because chlorophyll requires a large fraction of total plant Mg, and chlorophyll concentration is reduced by growth in elevated [CO(2) ], this supports the second hypothesis. Understanding these mechanisms may guide efforts to improve nutrient content, and allow modeling of nutrient changes and health impacts under future climate change scenarios.

Field of study: Environmental science
A Meta-Analysis Including Pre-selected Sequence Variants Associated With Seven Traits in Three French Dairy Cattle Populations

A within-breed genome-wide association study (GWAS) is useful when identifying the QTL that segregates in a breed. However, an across-breed meta-analysis can be used to increase the power of identification and precise localization of QTL that segregate in multiple breeds. Precise localization will allow including QTL information from other breeds in genomic prediction due to the persistence of the linkage phase between the causal variant and the marker. This study aimed to identify and confirm QTL detected in within-breed GWAS through a meta-analysis in three French dairy cattle breeds. A set of sequence variants selected based on their functional annotations were imputed into 50 k genotypes for 46,732 Holstein, 20,096 Montbeliarde, and 11,944 Normande cows to identify QTL for milk production, the success rate at insemination of cows (fertility) and stature. We conducted within-breed GWAS followed by across-breed meta-analysis using a weighted Z-scores model on the GWAS summary data (i.e., P-values, effect direction, and sample size). After Bonferroni correction, the GWAS result identified 21,956 significantly associated SNP (PFWER < 0.05), while meta-analysis result identified 9,604 significant SNP (PFWER < 0.05) associated with the phenotypes. The meta-analysis identified 36 QTL for milk yield, 48 QTL for fat yield and percentage, 29 QTL for protein yield and percentage, 13 QTL for fertility, and 16 QTL for stature. Some of these QTL were not significant in the within-breed GWAS. Some previously identified causal variants were confirmed, e.g., BTA14:1802265 (fat percentage, P = 1.5 × 10−760; protein percentage, P = 7.61 × 10−348) both mapping the DGAT1-K232A mutation and BTA14:25006125 (P = 8.58 × 10−140) mapping PLAG1 gene was confirmed for stature in Montbeliarde. New QTL lead SNP shared between breeds included the intronic variant rs109205829 (NFIB gene), and the intergenic variant rs41592357 (1.38 Mb upstream of the CNTN6 gene and 0.65 Mb downstream of the CNTN4 gene). Rs110425867 (ZFAT gene) was the top variant associated with fertility, and new QTL lead SNP included rs109483390 (0.1 Mb upstream of the TNFAIP3 gene and 0.07 Mb downstream of PERP gene), and rs42412333 (0.45 Mb downstream of the RPL10L gene). An across-breed meta-analysis had greater power to detect QTL as opposed to a within breed GWAS. The QTL detected here can be incorporated in routine genomic predictions.

Field of study: Biology
Simulation study for measurement of horizontal wind profiles in the polarstratosphere and mesosphere using ground-based observations of ozone andcarbon monoxide lines in the 230–250 GHz region

Meteorological and atmospheric models are being extended up to 80 km altitude but there are very few observing techniques that can measure stratospheric–mesospheric winds at altitudes between 20 and 80 km to verify model datasets. Here we demonstrate the feasibility of horizontal wind profile measurements using ground-based passive millimetre-wave spectroradiometric observations of ozone lines centred at 231.28, 249.79, and 249.96 GHz. Vertical profiles of horizontal winds are retrieved from forward and inverse modelling simulations of the line-of-sight Doppler-shifted atmospheric emission lines above Halley station (75°37′ S, 26°14′ W), Antarctica. For a radiometer with a system temperature of 1400 K and 30 kHz spectral resolution observing the ozone 231.28 GHz line we estimate that 12 h zonal and meridional wind profiles could be determined over the altitude range 25–74 km in winter, and 28–66 km in summer. Height-dependent measurement uncertainties are in the range 3–8 m s−1 and vertical resolution  ∼  8–16 km. Under optimum observing conditions at Halley a temporal resolution of 1.5 h for measuring either zonal or meridional winds is possible, reducing to 0.5 h for a radiometer with a 700 K system temperature. Combining observations of the 231.28 GHz ozone line and the 230.54 GHz carbon monoxide line gives additional altitude coverage at 85 ± 12 km. The effects of clear-sky seasonal mean winter/summer conditions, zenith angle of the received atmospheric emission, and spectrometer frequency resolution on the altitude coverage, measurement uncertainty, and height and time resolution of the retrieved wind profiles have been determined.

Field of study: Environmental science
Seyfert 2 galaxies with unusually wide nebular lines

We report on a set of AGN that match the Seyfert 2 galaxy classification criteria, but display unusually wide "narrow" lines, with the 4959 {\AA} and 5007 {\AA} nebular lines overlapping with each other. This spectral line broadening is in most cases evidence of a complex profile with multiple components. It indicates an unusual narrow line region with diverse gas clouds and a range of velocity systems. We list 14 such objects with these characteristics identified in a set of Sloan Digital Sky Survey spectra. We measure the strengths of all lines visible in the spectrum, and attempt to fit multiple Gaussian profiles to the nebular lines. We quantify the line parameters of all multiple velocity systems discovered. We compare the spectral characteristics of our sample with those of other, 'conventional' type 2 Seyferts and attempt to determine whether other systematic spectral differences exist. We consider whether the investigated sample constitutes a clear sub-class of the Seyfert 2 population. In conclusion we offer possible explanations for the unusual line profiles.

Field of study: Physics
For Better or for Worse: The Marriage of Science and Government in the United States

The development of an American science establishment-today an amalgam of scientists, engineers, universities, industrial laboratories, and federal science agencies-began early in the twentieth century when the federal government began to invest in a national scientific infrastructure. During World War II this investment swelled to colossal proportions. At present, the yearly federal investment in basic science and technology amounts to about thirty-five billion dollars. How did this complex marriage between science and government occur? How will increasing economic pressures affect its future? In this engaging overview of the science establishment and its relationship with the federal government, renowned physicist Alfred K. Mann details the reasons behind the creation of the four nonmilitary federal science agencies that are responsible for the bulk of this budget and are the principal supporters of scientific research and technology in American universities. Looking into each agency, he elucidates the ways in which decisions were made, whose interests were at stake, and the resulting discoveries, mishaps, and bureaucratic mazes that were constructed in the name of research. Mann interweaves fascinating stories that grew out of the scientific enterprise: * the allies' invention during World War II of the proximity fuse and its tremendous battlefield success, * the first use of blood plasma in World War II field hospitals, * the invention of radar, * strategic policies of the Cold War, * the double helix of DNA, * space explorations and the space missions, * modern global positioning systems (GPS), * satellite surveillance, and * recent declassification of covert operations. Charting the origins and operations of a remarkable collaboration, For Better or for Worse encompasses many of the key scientific discoveries of our time and offers a renewed vision of the future direction of the United States science establishment.

Field of study: Physics
Nutrition in Acute Renal Failure: A Reappraisal for the 1990s

To review current concepts regarding the rationale for and choice of nutritional support and nutritional assessment techniques in patients with catabolic acute renal failure (ARF). ■  Published references, conference proceedings, and personal observations.  Providing optimal nutritional support to patients with catabolic ARF requires recognition of the nutritional requirements of patients with catabolic ARF, modification of standard nutritional assessment techniques, and familiarity with the unique characteristics of current forms of renal replacement therapies. Use of these techniques may allow for the improvement of nutritional status in this patient population and ultimately have a positive effect on outcome.

Field of study: Medicine
A humidity-based exposure index representing ozone damage effects on vegetation

Surface ozone (O3) is detrimental to plant health. Traditional exposure indexes, such as accumulated hourly O3 concentrations over a threshold of 40 ppb (AOT40), are easy to be derived and widely used to assess O3 damage effects on vegetation. However, the regulation of environmental stresses on O3 stomatal uptake is ignored. In comparison, the dose-based indexes are much more reasonable but require complex parameterization that hinders further applications. Here, we propose a new humidity-based index (O3RH) representing O3 damage effects on vegetation, which can be simply derived using ground-level O3 and relative humidity (RH). Compared with O3 damages to gross primary productivity (GPPd) derived from a process-based scheme over May to October in 2015–2018, the O3RH index shows spatial correlations of 0.59 in China, 0.62 in U.S., and 0.58 (P< 0.01) in Europe, much higher than the correlations of 0.16, −0.22, and 0.24 (P< 0.01) for AOT40. Meanwhile, the O3RH index shows temporal correlations of 0.73 in China, 0.82 in U.S, and 0.81 (P< 0.01) in Europe with GPPd, again higher than the correlations of 0.50, 0.67, and 0.79 (P< 0.01) for AOT40. Analyses of O3RH reveal relatively stable trend of O3 vegetation damages in eastern U.S. and western Europe, despite the long-term reductions in local O3 pollution levels. Our study suggests the substitution of traditional exposure-based indexes such as AOT40 with O3RH for more reasonable assessments of O3 ecological effects.

Field of study: Environmental science
ARYLAMINATION OF 1,3,7-TRIAZAPYRENE

6‑Aryl(hetaryl)amino-1,3,7-triazapyrenes were prepared by direct oxidative nucleophilic substitution of hydrogen. Nucleophilic ipso substitution of methoxy groups gave 6,8-bis(aryl(hetaryl)amino)-1,3,7-triazapyrenes.

Field of study: Chemistry
Perceived Risk, Perceived Technology, Online Trust for the Online Purchase Intention in Malaysia

The past decades have witnessed the beginning of a major directional change of consumer behaviour, from physical stores purchasing behaviour to online purchasing behaviour in the retailing industry, especially the youngsters in Malaysia. Therefore, the aim of this research is to evaluate and validate the impacts of perceived technology and perceived risk on the online trust and how online trust is related to online purchase intention. This study also investigates the impact of online trust in mediating the relationship between perceived technology and online purchase intention. A total of 250 sets of questionnaire were distributed to the full time undergraduate information technology students in a private university that is located in Kuala Lumpur. The findings revealed that perceived technology and perceived risk are positively related to the online trust; online trust is positively related to online purchase intention and perceived technology is positively related to the online purchase intention. In addition, the finding also concluded that perceived technology is positively related to online purchase intention, mediated by online trust.

Field of study: Business
Balanced Treatment incomplete block (BTIB) designs for comparing treatments with a control: minimal complete sets of generator designs for k = 3, p = 3(1)10

Bechhofer and Tamhane (1981) proposed a new class of incomplete block designs called BTIB designs for comparing p ≥ 2 test treatments with a control treatment in blocks of equal size k < p + 1. All BTIB designs for given (p,k) can be constructed by forming unions of replications of a set of elementary BTIB designs called generator designs for that (p,k). In general, there are many generator designs for given (p,k) but only a small subset (called the minimal complete set) of these suffices to obtain all admissible BTIB designs (except possibly any equivalent ones). Determination of the minimal complete set of generator designs for given (p,k) was stated as an open problem in Bechhofer and Tamhane (1981). In this paper we solve this problem for k = 3. More specifically, we give the minimal complete sets of generator designs for k = 3, p = 3(1)10; the relevant proofs are given only for the cases p = 3(1)6. Some additional combinatorial results concerning BTIB designs are also given.

Field of study: Mathematics
Vergleichende Messungen an Ultra- und γ-Strahlen mit Ionisationskammer und Zählrohr

ZusammenfassungDurch Parallelmessungen der Absorption der Ultrastrahlung mit der Ionisationskammer und dem Zählrohr unter vielfach variierten Bedingungen wurde der Einfluß der Sekundärstrahlung auf die beiden Meßweisen untersucht und konnte teilweise gedeutet werden. Auch mit Ra-γ-Strahlen wurden ähnliche Parallelmessungen angestellt.

Field of study: Physics
SU‐DD‐A2‐05: Linear Energy Transfer of Proton Clusters

In conventional particle acceleratorsprotons are produced in long pulses. Therefore, the radiobiology of conventionally accelerated protons is primarily governed by the interaction of a single proton with the cell. In the laser‐plasma interaction scheme, the accelerated protons come as a single bunch of particles with interparticle distances that can be orders of magnitude shorter compared to those in conventional particle accelerators. As laser‐accelerated protons traverse the medium, they not only interact with it but also with each other, which under certain conditions may lead to a coherent interference effect manifested by the increase in their linear stopping power that may eventually lead to higher relative biological effectiveness (RBE) of the cluster. Understanding the exact conditions under which such an effect becomes significant is the main goal of this work.  The dynamic linear response theory of the medium is used to calculate the stopping power of the proton cluster. The proximity function is introduced that defines the enhancement effect in the energy loss of the cluster. The relation between the RBE and the LET is used to predict the cluster's RBE.  When the average distance between protons in a cluster is smaller than certain threshold, the enhanced LET of the cluster is found. The increased stopping power is due to the interference effect between the induced fields. It is conjectured that the accelerated proton cluster will have larger RBE values compared to those accelerated through conventional methods.  The potential impact of this project lies in the development of a deeper understanding of radiobiology of particle clusters, a question that has not been addressed before. If the main conjecture of this project is experimentally confirmed, this may spawn the development of new proton sources for medical accelerators with increased RBE and thus higher tumor controls.

Field of study: Medicine, Physics
Role of interface chemistry and growing surface stoichiometry on the generation of stacking faults in ZnSe/GaAs

The existence of Zn-As and vacancy-contained Ga-Se interfacial layers are suggested by transmission electron microscopy of Zn-and Se-exposed (or - reacted) ZnSe/GaAs interfaces, respectively. A very low density of faulted defects in the range of ∼104cm2 was obtained in samples with Zn passivation on an Asstabilized GaAs-(2 × 4). However, the density of As precipitates increases as the surface coverage of c(4 × 4) reconstruction increased on the Zn-exposed Asstabilized GaAs-(2 × 4) surface and this is associated with an increase of the density of extrinsic-type stacking faults bound by partial edge dislocations with a core structure terminated on additional cations. On the other hand, densities of extrinsic Shockley-and intrinsic Frank-type stacking faults are of ∼5 × 107/cm2 in samples grown on Se-exposed Ga-rich GaAs-(4 × 6) surfaces. Annealing on this Se-exposed Ga-rich GaAs-(4 × 6) generated a high density of vacancy loops (1 × 109/cm2) and an increase of the densities of both Shockley-and Frank-type stacking faults (>5 × 108/cm2) after the growth of the films. Furthermore, we have studied the dependence of the generation and structure of Shockley-type stacking faults on the beam flux ratios in samples grown on Zn-exposed As-stabilized GaAs-(2 × 4) surfaces. Cation-and anion-terminated extrinsic-type partial edge dislocations were generated in samples grown under Zn-and Se-rich conditions, respectively. However, an asymmetric distribution on defect density under varied beam flux ratios (0.3 ≤ PSe/PZn ≤ 10) is obtained.

Field of study: Materials science
A comparative study of iron and manganese diagenesis in continental slope and deep sea basin sediments off Uruguay (SW Atlantic)

Pore water and solid phase from surface sediments of the continental slope off Uruguay and from the Argentine Basin (southwestern Atlantic) were investigated geochemically to ascribe characteristic early diagenetic reactions of iron and manganese. Solid-phase iron speciation was determined by extractions as well as by Mössbauer spectroscopy. Both methods showed good agreement ( <6% deviation) for total-Fe speciation. The proportion of easy reducible iron oxyhydroxide relative to total-Fe oxides decreased from the continental slope to the deep sea which is attributed to an increase in crystallinity during transport as well as to a general decrease of iron mobilization. The product of iron reoxidation is Fe oxyhydroxide which made up less than 5% of total Fe. In addition to this fraction, a proportion of smectite bound iron was found to be redox reactive. This fraction made up to 10% of total Fe in sediments of the Argentine Basin and was quantitatively extracted by 1 N HCl. The redox reactive Fe(+II) fraction of smectite was almost completely reoxidized within 24 h under air atmosphere and may therefore considerably contribute to iron redox cycling if bioturbation occurs. In the case of the slope sediments we found concurrent iron and manganese release to pore water. It is not clear whether this is caused by dissimilatory iron and manganese reduction at the same depth or dissimilatory iron reduction alone inducing Mn(+IV) reduction by (abiotic) reaction with released Fe2+. The Argentine Basin sediment showed a significant manganese solid-phase enrichment above the denitrification depth despite the absence of a distinct pore-water gradient of Mn. This implies a recent termination of manganese mobilization and thus a non-steady-state situation with respect to sedimentation or to organic carbon burial rate.

Field of study: Environmental science
Timing and seasonality of the United States ‘warming hole’

The United States 'warming hole' is a region in the southeast/central U.S. where observed long-term surface temperature trends are insignificant or negative. We investigate the roles of anthropogenic forcing and internal variability on these trends by systematically examining observed seasonal temperature trends over all time periods of at least 10 years during 1901–2015. Long-term summer cooling in the north central U.S. beginning in the 1930s reflects the recovery from the anomalously warm 'Dust Bowl' of that decade. In the northeast and southern U.S., significant summertime cooling occurs from the early 1950s to the mid 1970s, which we partially attribute to increasing anthropogenic aerosol emissions (median fraction of the observed temperature trends explained is 0.69 and 0.17, respectively). In winter, the northeast and southern U.S. cool significantly from the early 1950s to the early 1990s, but we do not find evidence for a significant aerosol influence. Instead, long-term phase changes in the North Atlantic Oscillation contribute significantly to this cooling in both regions, while the Pacific Decadal Oscillation also contributes significantly to southern U.S. cooling. Rather than stemming from a single cause, the U.S. warming hole reflects both anthropogenic aerosol forcing and internal climate variability, but the dominant drivers vary by season, region, and time period.

Field of study: Environmental science
4-Hydroxy-2-quinolones 131. Bromination of 3-allyl-4-hydroxy-2-oxo-1,2-dihydroquinoline

The bromination of 3-allyl-4-hydroxy-2-oxo-1,2-dihydroquinoline by molecular bromine is accompanied by the closure of a five membered furan ring and gives the corresponding 2-bromomethyl-3,9-dihydro-2H-furo[2,3-b]quinolin-4-one.

Field of study: Chemistry