nils-herrmann/clean_scirepeval huggingface dataset:
Nitrogen fixation activity in biological soil crusts dominated by cyanobacteria in the Subpolar Urals (European North-East Russia).

The nitrogen fixation by biological soil crusts with a dominance of cyanobacteria was studied using the acetylene reduction assay in the territory of the Subpolar Urals (65°11' N, 60°18' E), Russia. The field measurements of nitrogen fixation activity were conducted in situ for two different types of soil crusts dominated by Stigonema (V1 type) and Nostoc with Scytonema (V2 type). The nitrogen fixation process had similar dynamics in both crusts but nitrogen fixation rates were different. The crusts of the V2 type showed a significantly higher acetylene reduction activity, with ethylene production rate of 1.76 ± 0.49 g C2H4 m(-2) h(-1) at 15°C, compared with V1-type soil crusts, with a rate of 0.53 ± 0.21 mg C2H4 m(-2) h(-1) at 15°C. The daily value of acetylene reduction activity in V2-type soil crusts was 32.7 ± 6.2 mg C2H4 m(-2) d(-1) and in V1-type crusts, 12.3 ± 1.8 mg C2H4 m(-2) d(-1) After recalculation for N, the daily values of nitrogen fixation were in the range 3.3-22.3 mg N m(-2) d(-1), which is a few times higher than the values of N input from the precipitation to the soil in the studied regions. The dependence of nitrogen-fixation activity on temperature and light intensity of biological soil crusts was investigated. On the basis of temperature models obtained from the dependence, the nitrogen balance was calculated for the growing season (approximately 120 days). The crusts dominated by Stigonema species were fixing 0.3 g N m(-2) (ethylene production rate, 1.10 g C2H4 m(-2)) and crusts dominated by Nostoc and Scytonema were fixing 1.3 g N m(-2) (4.10 g C2H4 m(-2)).

Field of study: Biology, Environmental science
Intensity interferometry with neutrons from the compound nucleus82Kr

Correlations between neutrons have been studied in the 96 MeV18O +64Ni reaction, yielding the compound nucleus82Kr at 88 MeV excitation energy. The observed anticorrelation at small relative momenta evidences dominance of quantum-statistical interference between identical particles, from which it is possible to deduce an average source lifetimeτ=(1.2±0.1)·10−20 s as an upper limit disregarding possible contributions to the correlation function from the competingnn final-state interaction. Lacking appropriate model calculations at present, it is argued that further refinements in the theoretical treatment of strong interactions in the final state are needed to enable truly quantitative conclusions from small-angle nucleon-nucleon correlations at such large timescales.

Field of study: Physics
Time course of improvement with antipsychotic medication in treatment-resistant schizophrenia.

Improvements are greatest in the earlier weeks of antipsychotic treatment of patients with non-resistant schizophrenia.



To address the early time-line for improvement with antipsychotics in treatment-resistant schizophrenia.



Randomised double-blind trials of antipsychotic medication in adult patients with treatment-resistant schizophrenia were investigated (last search June 2010). A series of metaregression analyses were carried out to examine the effect of time on the average item scores in the Positive and Negative Syndrome Scale (PANSS) or Brief Psychiatric Rating Scale (BPRS) at three or more distinct time points within the first 6 weeks of treatment.



Study duration varied from 4 weeks to 1 year and the definitions of treatment resistance as well as of treatment response were not necessarily consistent across 19 identified studies, resulting in highly variable rates of response (0–76%).The mean standardised baseline item score in the PANSS or BPRS was 3.4 (s.e. = 0.06) in the five studies included in the meta-regression analysis, with the average baseline Clinical Global Impression – Severity score being 5.2 (marked illness). For the pooled population treated with a range of antipsychotics (n = 1019), significant reductions in the mean item scores occurred during the first 4 weeks; improvements observed in later weeks were smaller and non-significant. In contrast, weekly improvement with clozapine was significant throughout (n = 356).



Our findings provide preliminary evidence that the majority of improvement with antipsychotics may occur relatively early.More consistent improvements with clozapine may be associated with a gradual titration. To further elucidate response patterns, future studies are needed to provide data over regular intervals during earlier stages of treatment.

Field of study: Medicine, Psychology
The availabilities of arsenic and cadmium in rice paddy fields from a mining area: The role of soil extractable and plant silicon.

Adequate silicon (Si) can greatly boost rice yield and improve grain quality through alleviating stresses associated with heavy metals and metalloids such as arsenic (As) and cadmium (Cd). The soil plant-available Si is relatively low in South China due to severe desilicification and allitization of the soils in this region. Conversely, pollution of heavy metals and metalloids in the soils of this region occurs widely, especially As and Cd pollution in paddy soil. Therefore, evaluating the plant availability of Si in paddy soil of South China and examining its correlation with the availability of heavy metals and metalloids are of great significance. Accordingly, in our study, 107 pairs of soil and rice plant samples were collected from paddy fields contaminated by As and Cd in South China. Significantly positive correlations between Si in rice plants and Si fractions in soils extracted with citric acid, NaOAc-HOAc buffer, and oxalate-ammonium oxalate buffer suggest that these extractants are more suitable for use in extracting plant-available Si in the soils of our present study. Significantly negative correlations between different Si fractions and As or Cd in rice plant tissues and negative exponential correlations between the molar ratios of Si to As/Cd in rice roots, straws, husks or grains and As/Cd in rice grains indicate that Si can significantly alleviate the accumulation of As/Cd from soils to the rice plants. Finally, a contribution assessment of soil properties to As/Cd accumulation in rice grains based on random forest showed that in addition to Si concentrations in soil or rice plants, other factors such as Fe fractions and total phosphorus also contributed largely to As/Cd accumulation in rice grains. Overall, Si exhibited its unique role in mitigating As or Cd stress in rice, and our study results provide strong field evidence for this role.

Field of study: Environmental science
Photocurable Polymeric Blends for Surgical Application

The preparation of photocrosslinkable bioadhesives synthesized from oligomers of lactic acid and polycaprolactone (PCL), both functionalized with 2-isocyanoethyl acrylate (AOI), were studied. The obtained modified macromers of LA-AOI (mLA) and PCL-AOI (mCL) were chemically characterized by 1H NMR and used to formulate polymeric blends with different mass proportions, 1:1, 1:2 and 2:1, respectively. Subsequently, the produced blends were crosslinked, considering two UV irradiation times: 30 and 120 s. After their production, the thermal and mechanical properties of bioadhesives were assessed, where upon the rheology, gel content, hydrolytic degradation and dynamic contact angles were determined. Furthermore, the cytotoxic profile of bioadhesives was evaluated in contact with human dermal fibroblasts cells, whereas their antibacterial effect was studied monitoring Escherichia coli and S. aureus growth. Overall, flexible and resistant films were obtained, presenting promising features to be used as surgical bioadhesives.

Field of study: Materials science
SEISMIC-REFRACTION STUDIES OF THE PACIFIC OCEAN BASIN

On the Mid-Pacific and Capricorn expeditions seismic-refraction observations were made at 42 stations scattered widely within an area of the Central Equatorial Pacific Ocean extending from latitudes 22° S. to 28° N. and longitudes 162° E. to 112° W. At 29 of these stations velocities of about 8 km/sec, or more were reached at the depth of greatest penetration of the refracted waves. The mean of these velocities was 8.24 km/sec.

The crustal thickness, defined as the depth below the sea floor at which the 8 km/sec, velocity is reached, ranges from 4.8 km to 13.0 km. The distribution of thicknesses is bimodal with seven anomalous stations giving values between 10 and 13 km. The group of 22 stations believed to be typical of the deep Pacific Basin has an average thickness of 6.31 km with a standard deviation of 1.01km.

Field of study: Geology
Pointer Networks

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence  and Neural Turing Machines , because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems - finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem - using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.

Field of study: Computer science
Circadian regulation of iodopsin and clock is altered in the retinal degeneration chicken retina.

We are interested in determining if the visual phototransduction cascade plays a role in light entrainment of photoreceptor circadian oscillators. In this study, we compared mRNA levels of iodopsin and the chicken homolog of Clock (cClock) in the retinas of normal and rd (retinal degeneration) chickens that lack functional rod and cone phototransduction cascades. Iodopsin is a circadian-regulated, photoreceptor-specific gene expressed in chicken retina, and Clock is a transcription factor that has been shown to play a role in the circadian clock mechanism in mouse and Drosophila. The results of our analyses show that cClock and iodopsin transcript levels undergo daily oscillations in retinas of normal animals housed under 12 h light:12 h dark (12L:12D) conditions, and that these oscillations are maintained in the absence of light. Levels of these transcripts in the retinas of rd/rd chickens housed under cyclic light conditions did not change significantly over the course of a 12L:12D cycle; however, there was evidence that the photoreceptor oscillators were entrained in these animals. Comparisons of our normal and rd/rd data suggest that there are at least two light entrainment pathways that impinge on the oscillators found in photoreceptor cells, one of which is effectively disabled by the GC1 null mutation carried by the rd chicken.

Field of study: Biology
Bulk oxide charge and slow states in Si–SiO2 structures generated by RIE-mode plasma ☆

The damage induced in the thin SiO2–Si system after an exposure to O2 and N2 plasma working in reactive ion etching (RIE) mode has been studied. A generation of high density (up to ∼5×1012 cm−2 in the first 15 s plasma exposure) of positive oxide charge in bulk traps as well as in slow states has been established. The RIE damage effects become highly process dependent as the plasma time increases, the fixed oxide charge first increases and then slows down or even turns around depending on discharge conditions. It is suggested that the relative contribution of the two main plasma components (ion bombardment and vacuum UV photons) at different discharge regimes is the reason for the appearance or the absence of the “turn-around” effect. It is established that the combination O2 plasma and low pressure is critical for the degradation of the plasma treated samples. The results reveal a strong linear correlation between the leakage current detected and plasma created positive charge.

Field of study: Engineering
An analytical method for determination of pyraflufen-ethyl residues in the cotton plant and soil.

High performance liquid chromatography(HPLC) was used to analyze pyraflufen-ethyl residues in the cotton plant and soil. Pyraflufen-ethyl residues were extracted from leaves and cottonseeds with acetonitrile and purified using GCB/PSA SPE microcolumn. The residues were determined using HPLC equipped by PDA. Pyraflufen-ethyl residues in the soil were extracted with acetone and purified using C18 SPE microcolumn. The minimum detectable concentration of pyraflufen-ethyl in the cotton leaf, cottonseed, and the soil was 0.02 mg·kg-1. The average recoveries of pyraflufen-ethyl in the cotton leaf, cottonseed, and the soil were 93.94%-101.65%, 84.88%-98.62%, and 85.49%-90.71%, respectively, and their variation coefficients were 3.96%-8.06%, 7.59%-10.37% and 5.59%-8.69%, respectively. The results showed that this method met all criteria for the pesticide residue analysis.

Field of study: Agricultural and Food sciences
Interdecadal modulation of ENSO teleconnections

Seasonal climate anomalies over North America exhibit rather large variability between years characterized by the same ENSO phase. This lack of consistency reduces potential statistically based ENSO-related climate predictability. The authors show that the North Pacific oscillation (NPO) exerts a modulating effect on ENSO teleconnections. Sea level pressure (SLP) data over the North Pacific, North America, and the North Atlantic and daily rainfall records in the contiguous United States are used to demonstrate that typical ENSO signals tend to be stronger and more stable during preferred phases of the NPO. Typical El Nino patterns (e.g., low pressure over the northeastern Pacific, dry northwest, and wet southwest, etc.) are strong and consistent only during the high phase of the NPO, which is associated with an anomalously cold northwestern Pacific. The generally reversed SLP and precipitation patterns during La Nina winters are consistent only during the low NPO phase. Climatic anomalies tend to...

Field of study: Environmental science
Energy balance for viscoelastic bodies in frictionless contact

In this paper it is shown that the change in the energy for a linearly viscoelastic body (with Kelvin–Voigt type viscosity) in frictionless contact with a rigid obstacle can be accounted for by viscous losses and the work done by external forces. Thus there is no change in the energy due to impacts, unlike the case of rigid-body dynamics. The result can be extended to a wide class of dynamic viscoelastic boundary thin obstacle problems of similar type.

Field of study: Mathematics
Detection, delineation, measurement and display of cavities in macromolecular structures.

A computer program, VOIDOO, is described which can be employed in the study of cavities such as they occur in macromolecular structures (in particular, in proteins). The program can be used to detect unknown cavities or to delineate known cavities, either of which may be connected to the outside of the molecule or molecular assembly under study. Optionally, output files can be requested that contain a description of the shape of the cavity which can be displayed by the crystallographic modelling program O. Additionally, VOIDOO can be used to calculate the volume of a molecule and to create a file containing data pertaining to the surface of the molecule which can also be displayed using O. Examples of the use of VOIDOO are given for P2 myelin protein, cellular retinol-binding protein and cellobiohydrolase II. Finally, operational definitions to discern different types of cavity are introduced and guidelines for assessing the accuracy and improving the comparability of cavity calculations are given.

Field of study: Chemistry
Carbon isotope fractionation in tree ring early and late wood in relation to intra‐growing season water balance

We determined the stable carbon isotope composition (δ1.3C) of cellulose extracted from early and late wood in Douglas fir [Pseudotsuga menziexii (Mirb.) Franco] tree rings. Data were obtained for the period 1962 to 1981, at the start of which the trees were 20 years old. A water balance model was used to calculate daily stand transpiration and water deficit. The model incorporates site factors (soil water availability, slope and aspect) and environmental variables (solar radiation, air temperature and rainfall). There was far greater variability in late wood than in early wood δ1.3C. In wet years, late wood δ1.3C was significantly lighter (by as much as 2δ) than early wood δ1.3C but in dry years this difference was reversed. Differences between spring and summer cumulative transpiration accounted for almost 60δ of the variability in differences between early and late wood δ1.3C. We found excellent correspondence between summer cumulative transpiration and late wood δ1.3C, with estimates of transpiration accounting for up to 93% of the variability in δ1.3C. Correlations between early wood δ1.3C and spring transpiration were generally poor (r2<0.4), but we were able to identify those exceptional years in which there had been a very dry spring. Our results indicate that, while tree ring δ1.3C correlates reasonably well with basal area increment, it is a far better indicator of inter- and intra-annual variability in water availability than radial growth.

Field of study: Environmental science
First Principles Calculations of Superconducting Critical Temperature of ThCr$_2$Si$_2$-Type Structure

High critical temperature (T$_c$) superconductor has a great potential in many industrial applications. However, discovering a compound having high T$_c$ is still remaining a big challenge for experimental approach due to time-consuming and high cost. In this paper, we investigated the critical temperature (T$_c$) of several compounds of ThCr$_2$Si$_2$-type structure (space group I4/mmm) since some of them had already been investigated and trusted as the potential candidates for superconductivity. First principle calculation was performed to compute the critical temperature (T$_c$) based on allen-dynes equation modification of McMillian formula. In order to confirm our calculation scheme, we compared our result with compounds which had been experimentally determined obtained from $NIMS$ database. The result showed a very good agreement with experimental data. Based on this scheme, finally, we found ThCu$_2$Si$_2$ and ThAu$_2$Si$_2$ which were most likely to exhibit a superconductivity around 3.88 K and 4.27. 
$keywords$ : superconductivity, ThCr$_2$Si$_2$-type structure, ThCu$_2$Si$_2$, ThAu$_2$Si$_2$, critical temperature

Field of study: Physics
CEVL training to SFU grade pediatric hydronephrosis: a guide for pediatric caregivers.

Traditional resources now used to train healthcare procedures such as SFU grading of pediatric hydronephrosis largely include textbooks, journals, and casual conversations with colleagues. In 2003 the CEVL platform began its development as internet accessed e-learning to promote training for healthcare procedures. Specifically, the platform approaches the promotion of procedure training to grade hydronephrosis by supplementing presentation of static content, such as an ultrasound image, with user interactivity. Herein, we show how we apply this approach to train Grading of SFU pediatric hydronephrosis. CEVL presents samples of SFU grades 0e4 as grayscale images along with interactive colored overlays which denote pyelocalyceal ultrasound anatomy. A self test promotes user confidence in ultrasound grading. Opportunity to upload images for “expert” review is offered.

Field of study: Medicine
Theoretical models describing far-field intensity distributions of laser diode

This paper presents a detailed comparison of several typical theoretical models describing far-field intensity distributions of laser diode with the experimental results in the literature.It is found that the propagation and far-field properties of laser diode have to be described by the non-paraxial theory,and the far-field intensity distributions vary with the output power in general.Different models should be suitably chosen to simulate the far-field behavior in the fast and slow axes of heterostructure laser diode at different power levels.In addition,the Hermite-Gaussian(H-G) model is modified,where the contributions of the odd-order H-G modes are included and the coherent superposition of H-G modes is replaced by the incoherent superposition of H-G modes.The improved model is in better agreement with the experimental data in the slow axis direction of double heterostructure GaAlAs laser diode at 100 mW output power.

Field of study: Physics
Adaptive Parallel Ant Colony Algorithm

An adaptive parallel ant colony algorithm is presented by considering the critical factors influencing the parallelization of the ant colony algorithm.Two different strategies for information exchange between processors are proposed: selecting the partner processor based on the fitness and on the distance.These strategies enable each processor to choose the partner processor to communicate and update the pheromone adaptively.In order to increase the ability of optimization and to avoid early convergence,we also propose a method of adjusting the iteration interval adaptively according to the diversity of the solutions. These techniques are tested on the traveling salesman problem using the massive parallel processors(MPP) Shengteng1800.Experimental results show that our algorithm can converge very quickly and has high speedup.

Field of study: Computer science