nils-herrmann/clean_scirepeval huggingface dataset:
Design of a compact synchrotron light source for medical applications at NIRS.

A synchrotron light source dedicated to medical applications is required to be compact for installation in limited spaces at hospitals. The NIRS storage ring, with a circumference of 44.8 m, is designed to accelerate electrons up to 1.8 GeV and to store a beam of 400 mA. The ring is composed of superconducting bending magnets for downsizing. A beam of 300 MeV is injected into the ring from a microtron operated at an L-band RF frequency. There are two superconducting multipole wigglers with nine poles and a maximum field of 8 T, which can produce a photon flux of about 1.4 x 10(13) photons s(-1) mrad(-1) (0.1% bandwidth)(-1) at 33 keV used for coronary angiography.

Field of study: Physics
Proximate compositions, bioactive compounds and antioxidant activity from large-leafed mangrove (Bruguiera gymnorrhiza) fruit.

Antioxidants are compounds that can inhibit or prevent the oxidation of the easily oxidized substrate. One of the plants as a potential source of bioactive compounds and antioxidant activity is large-leafed mangrove (Bruguiera gymnorrhiza). This plant was commonly found in the Pacific region of Southeast Asia, Ryukyu Islands, Micronesia and Polynesia (Samoa) to subtropical regions of Australia and has been used by the society. This study aimed to determine the proximate compositions, bioactive compounds and antioxidant activity from large-leafed mangrove fruit which extracted by methanol. It have high carbohydrate content is 29.28%, 66.39% moisture, 2.11% protein, 1.07% fat and 1.15% ash. Old fruit yield greater than young fruit with value 9.94% and 6.83%, respectively. Old fruit has a more effective antioxidant activity (13.47 ppm) compared to young fruit (81.60 ppm) and classified as a very strong antioxidant (IC50 < 50 ppm). Bioactive compounds that act as antioxidants are phenol group. By TLC chromatography technique produces the best eluent, namely methanol and water (4:1) and result 3 fractions. Fraction III had the most effective antioxidant activity with IC50 value of 26.69 ppm.

Field of study: Agricultural and Food sciences
Synergistic Fluorescence Enhancement of Terbium Probe with Sodium Dodecyl Sulfate and Boric Acid and Its Determination of Sarafloxacin

A spectrofluorimetric method for the determination of Sarafloxacin( SARA) based on the fluorescence enhancement of Tb3 +-SARA complex in the presence of sodium dodecyl sulfate( SDS) and boric acid was developed.The effect of various experimental parameters,such as pH value,the type and amount of surfactant,the type and amount of buffer solution and the concentration of Tb3 +,on the fluorescence intensity of the complex was investigated.Under the optimum conditions,the enhanced fluorescence intensity of the system showed a good linear relationship with the concentration of SARA in the range of 0.100-1.80×103μg/L with a correlation coefficient of 0.9994.The detection limit of SARA was found to be 0.02 μg/L,and relative standard deviation( RSD) was 1.8%( c=10.0 μg/L,n=11).The method has been successfully applied to the determination of SARA in milk samples with the recoveries of 95.5%-101%.

Field of study: Chemistry
Microbial sulfide oxidation in the oxic-anoxic transition zone of freshwater sediment: involvement of lithoautotrophic Magnetospirillum strain J10.

The oxic-anoxic transition zone (OATZ) of freshwater sediments, where opposing gradients exist of reduced iron and sulfide with oxygen, creates a suitable environment for microorganisms that derive energy from the oxidation of iron or sulfide. Gradient microcosms incubated with freshwater sediment showed rapid microbial turnover of sulfide and oxygen compared with sterile systems. Microcosms with FeS as a substrate also showed growth at the OATZ and subsequent dilution series resulted in the isolation of three novel strains, of which strain J10 grows chemolithoautotrophically with reduced sulfur compounds under microaerobic conditions. All three strains are motile spirilla with bipolar flagella, related to the genera Magnetospirillum and Dechlorospirillum within the Alphaproteobacteria. Strain J10 is closely related to Magnetospirillum gryphiswaldense and is the first strain in this genus found to be capable of autotrophic growth. Thiosulfate was oxidized completely to sulfate, with a yield of 4 g protein mol(-1) thiosulfate, and autotrophic growth was evidenced by incorporation of (13)C derived from bicarbonate into biomass. A putative gene encoding ribulose 1,5-bisphosphate carboxylase/oxygenase type II was identified in strain J10, suggesting that the Calvin-Benson-Bassham cycle is used for autotrophic growth. Analogous genes are also present in other magnetospirilla, and in the autotrophically growing alphaproteobacterium magnetic vibrio MV-1.

Field of study: Biology, Environmental science
Fuzzy Clustering Algorithm in Medical Image Segmentation and Its New Development

Image segmentation is a important part of medical image processing,and it is the basis of the analysis,comprehension,description and 3D reconstruction.Fuzziness of medical image makes it difficult to find the edge between different individuals.Fuzzy thesis provides a good method for solving this problem,so fuzzy clustering algorithm becomes an effective way of image segmentation.Mainly reviews and discusses fuzzy clustering algorithm,especially focuses on fuzzy C-means and its new development.

Field of study: Computer science
Abnormalities in the expression of the leucocyte-common antigen in chronic lymphocytic leukaemia.

The surface glycoproteins of lymphocytes isolated from patients suffering from B cell chronic lymphocytic leukaemia (B-CLL) have been studied by radioactive labelling with impermeable probes and with MoAb. Several features not found in normal B cells have been observed. The abnormalities found in the expression of polypeptides of the leucocyte common (L-C) antigen, identified by appropriate MoAb, have been examined in detail. It has been shown by both biochemical analysis and MoAb binding that this group of polypeptides can, within a panel of B-CLL patients, range from a typical B cell pattern to the pattern resembling that normally found in T cells. The T lymphocyte profile is correlated with a poor prognosis (MVA C rating) and in the one patient where a change in the glycoprotein profile towards that of the T cell was observed, the change coincided with a clinical deterioration. The biological significance of the molecular diversity is discussed.

Field of study: Biology, Medicine
Analysis of Treatment and Utilization Approaches of Solid Waste from Metal Mines

Abundant solid waste such as waste ore(soil),slag,tailings is produced during mining and mineral processing of metal mines,which will take up many lands and result in environmental pollution and damage.Zijinshan Gold-copper Mine in Fujian province is one of the super huge bases for producing nonferrous metals,chiefly using open pit mining,heap leaching and CIL reclaim processes.The main solid waste generated includes waste ore,heap leaching slag and CIL tailings.As the annual output of solid waste is tremendous and will have profound impact on the ecological environment in mining area if disposed on site,various means and methods have been adopted to deal with the solid waste in Zinjinshan Gold-copper Mine during more than 10 years since its foundation.The paper makes a conclusion and analysis on the treatment and utilization approaches of solid waste in Zijinshan Gold-copper Mine and presents effective recommendations on ecological rehabilitation and reconstruction of abandoned mining lands,which can be as the reference for the solid waste treatment of numerous gold mines in China.

Field of study: Materials science
Joint estimation of time delays and directions of arrival of multiple reflections of a known signal

We present an efficient algorithm for estimating the time delays and the directions-of-arrival (DOAs) of multiple reflections of a known signal. The algorithm is based on an iterative scheme that transforms the multidimensional maximum likelihood criterion into two sets of simple one-dimensional (1-D) maximization problems. Simulation results illustrating the performance of the algorithm in comparison with the Cramer-Rao bound are included.

Field of study: Engineering
The Effectiveness of Direct Learning in Academic Writing Referred to Students Reading Habit in Indonesia

This research was conducted to uncover the effectiveness of Direct Learning in academic writing. The objectives of the research are: (1) to find which method is the most effective among Direct Learning, Inquiry Learning and Problem Based Learning methods in academic writing, (2) to find which is more influencing between high reading habit and low reading habit in academic writing, and (3) to know the interaction between the three methods and the reading habit in academic writing. The research finds that: (1) Direct Learning is the most effective method in academic writing, whereas Inquiry Learning has the same effectiveness with Problem Based Learning (2) high reading habit is more influencing in academic writing, and (3) there is an interaction between Direct Learning, Inquiry Learning and Problem Based Learning methods and students reading habit toward academic writing.  Direct Learning, academic writing, reading habit

Field of study: Education
Use of a chiA probe for detection of chitinase genes in bacteria from the Chesapeake Bay(1).

PCR primers specific for the chiA gene were designed by alignment and selection of highly conserved regions of chiA sequences from Serratia marcescens, Alteromonas sp., Bacillus circulans and Aeromonas caviae. These primers were used to amplify a 225 bp fragment of the chiA gene from Vibrio harveyi to produce a chiA gene probe. The chiA PCR primers and probe were used to detect the presence of the chiA gene in an assemblage of 53 reference strains and gave consistent results. Selected chiA fragments amplified by PCR were cloned and sequenced from nine known strains and from Chesapeake Bay isolates 6d and 11d. This confirmed the specificity and utility of the primers for detection of chiA-positive environmental strains. Over 1000 bacterial isolates from Chesapeake Bay water samples were tested for the presence of the chiA gene which was found to be present in 5-41% (average 21%) of the culturable bacterial community. The approach developed in this study was valuable for isolation and enumeration of chiA-positive bacteria in environmental samples.

Field of study: Biology, Environmental science
Dosimetric characterization of the iBEAM evo carbon fiber couch for radiotherapy.

This study characterizes the dosimetric properties of the iBEAM evo carbon fiber couch manufactured by Medical Intelligence and examines the accuracy of the CMS XiO and Nucletron Oncentra Masterplan (OMP) treatment planning systems for calculating beam attenuation due to the presence of the couch.



To assess the homogeneity of the couch, it was CT scanned at isocentric height and a number of signal intensity profiles were generated and analyzed. To simplify experimental procedures, surface dose and central axis depth dose measurements were performed in a solid water slab phantom using Gafchromic film for 6 and 10 MV photon beams at gantry angles of 0 degree (normal incidence), 30 degrees, and 60 degrees with an inverted iBEAM couch placed on top of the phantom. Attenuation measurements were performed in a cylindrical solid water phantom with an ionization chamber positioned at the isocenter. Measurements were taken for gantry angles from 0 degree to 90 degrees in 10 degrees increments for both 6 and 10 MV photon beams. This setup was replicated in the XiO and OMP treatment planning systems. Dose was calculated using the pencil beam, collapsed cone, convolution, and superposition algorithms.



The CT scan of the couch showed that it was uniformly constructed. Surface dose increased by (510 +/-0)% for a 6 MV beam and (600 +/- 20)% for a 10 MV beam passing through the couch at normal incidence. Obliquely incident beams resulted in a higher surface dose compared to normally incident beams for both open fields and fields with the couch present. Depth dose curves showed that the presence of the couch resulted in an increase in dose in the build up region. For 6 and 10 MV beams incident at 60 degrees, nearly all skin sparing was lost. Attenuation measurements derived using the ionization chamber varied from 2.7% (0 degree) to a maximum of 4.6% (50 degrees) for a 6 MV beam and from 1.9% (0 degree) to a maximum of 4.0% (50 degrees) for a 10 MV beam. The pencil beam and convolution algorithms failed to accurately calculate couch attenuation. The collapsed cone and superposition algorithms calculated attenuation within an absolute error of +/- 1.2% for 6 MV and +/- 0.8% for 10 MV for gantry angles from 0 degree to 40 degrees. Some differences in attenuation were observed dependent on how the couch was contoured.



These results demonstrate that the presence of the iBEAM evo carbon fiber couch increases the surface dose and dose in the build up region. The inclusion of the couch in the planning scan is limited by the field of view employed and the couch height at the time of CT scanning.

Field of study: Medicine, Physics
Trends in Atmospheric Science Journals: A Reader's Perspective

A survey of 22 atmospheric science journals shows that the number of published articles tripled in 30 years during 1965–95, so that it has become increasingly difficult to keep abreast of the literature. A total of 1642 peer-reviewed articles in the journals were categorized numerically in terms of features of the abstracts and the conclusions. Consistent differences were found between journals. Most journals are mediocre in terms of their reader-friendliness, with little or no improvement over recent decades. The abstract and/or the conclusions in many papers have become too long and too discursive, preventing the reader from making a rapid assessment of the papers' usefulness. These trends may retard atmospheric research. Therefore journal editors are urged to insist on some easy improvements.

Field of study: Environmental science
Nonlocal form of quantum off-shell kinetic equation

A new nonlocal form of the off-shell kinetic equation is derived. While being equivalent to the Kadanoff-Baym and Botermans-Malfliet formulations in the range of formal applicability, it has certain advantages beyond this range. It possessesmore accurate conservation laws for Noether quantities than those in the Botermans-Malfliet formulation. At the same time the nonlocal form, similarly to the Botermans-Malfliet one, allows application of the test-particle method for its numerical solution, which makes it practical for simulations of heavy-ion collisions. The physical meaning of the time-space nonlocality is clarified.

Field of study: Physics
Implications of migrating geoid anomalies for the interpretation of high-level fossil coral reefs

Uplift of islands is frequently inferred from high-level fossil coral reefs, and evolutionary chronologies and regional geotectonic models are developed on the assumption that only uplift and glacio-eustatic fluctuations constitute observed shoreline movements. This practice is unsatisfactory, as it omits the effects of geoidal eustasy. The “emergence” of selected islands with high-level fossil coral reefs in the Pacific, Atlantic, and Indian Oceans is reviewed and the likely contribution of geoidal eustasy highlighted, particularly in cases in which geotectonic reasons for island uplift are absent or doubted. A simple model is used to illustrate the similar effect of uplift and of the passage of a positive geoid anomaly on coastal geomorphology. The possibility of island emergence either having been incorrectly calculated or being simply illusory is shown graphically. Uplift of particular islands must be inferred or deduced independently of high-level fossil coral reefs.

Field of study: Geology
Genome-Wide Identification and Analysis of Enhancer-Regulated microRNAs Across 31 Human Cancers

Enhancers are cis-regulatory DNA elements that positively regulate the transcription of target genes in a tissue-specific manner, and dysregulation of target genes could lead to various diseases, such as cancer. Recent studies have shown that enhancers can regulate microRNAs (miRNAs) and participate in their biological synthesis. However, the network of enhancer-regulated miRNAs across multiple cancers is still unclear. Here, a total of 2,418 proximal enhancer–miRNA interactions and 1,280 distal enhancer–miRNA interactions were identified through the integration of genomic distance, co-expression, and 3D genome data in 31 cancers. The results showed that both proximal and distal interactions exhibited a significant cancer type-specific feature trend at the tissue level rather than at the single-cell level, and there was a noteworthy positive correlation between the expression of the miRNA and the number of enhancers regulating the same miRNA in most cancers. Furthermore, we found that there was a high correlation between the formation of enhancer–miRNA pairs and the expression of enhancer RNAs (eRNAs) whether in distal or proximal regulation. The characteristics analysis showed that miRes (enhancers that regulated miRNAs) and non-miRes presented significant differences in sequence conservation, guanine–cytosine (GC) content, and histone modification signatures. Notably, GC content, H3K4me1, and H3K36me3 were present differently between distal and proximal regulation, suggesting that they might participate in chromosome looping of enhancer–miRNA interactions. Finally, we introduced a case study, enhancer: chr1:1186391–1186507 ∼ miR-200a was highly relevant to the survival of thyroid cancer patients and a cis-eQTL SNP on the enhancer affected the expression of the TNFRSF18 gene as a tumor suppressor.

Field of study: Biology
Estimation for the Box-Cox Transformation Model Without Assuming Parametric Error Distribution

Box and Cox proposed a power transformation for the response variable that yields a linear regression model with normal error and constant variance. Inference procedures for the regression coefficients and transformation parameter under this model setting have been studied extensively. In this article we propose a simple semiparametric estimation method for the Box–Cox transformation model with no specific parametric assumption on the distribution of the error term. The resulting estimators are strongly consistent and asymptotically normal. Their covariance matrix can be estimated through a novel resampling method without involving nonparametric function estimates of the underlying unknown density function for the error term. The new proposal is illustrated with a well-known dataset in the literature of transformation, and its efficiency and robustness are closely examined through numerical studies.

Field of study: Mathematics
Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.

A novel method is proposed in which combined restraints derived from linear-scaling semiempirical quantum-mechanical (QM) calculations and X-ray diffraction data are combined to refine crystal structures of proteins. Its performance has been tested on a small protein molecule, bovine pancreatic trypsin inhibitor (BPTI). The refinement involves minimization of the sum of a geometric energy function and an X-ray target function based on either the least-squares residual or the maximum-likelihood formalism. For comparison, similar refinement runs have also been performed using energy restraints derived from the force field available in the Crystallography & NMR System (CNS) program. The QM refinements were carried out with weights that were varied by several orders of magnitude and the optimal weights were identified by observing the trend in the final free R values, QM heats of formation and coordinate root-mean-square deviations (r.m.s.d.s) from the crystal structure. It is found that the QM weights are typically smaller but generally on the same scale as the molecular-mechanics (MM) weights for the respective X-ray target functions. The crystallographic R, free R, real-space R values and correlation coefficients based on the structures refined with the energy restraints derived from our QM calculations and Engh and Huber parameters are comparable, suggesting that the QM restraints are capable of maintaining reasonable stereochemistry to a similar degree as the force-field parameters. A detailed inspection of the structures refined with the QM and MM energy restraints reveals that one of the common differences between them and the crystal structure is that the strained bond angles in the crystal structure are corrected after energetically restrained refinements. Systematic differences in certain bond lengths between the QM-refined structures and the statistical averages of experimental structures have also been observed and discussed.

Field of study: Chemistry
Investigated on the Emulsification Influenced by Emulsifier

The laser particle size analyzer was used to investigate the emulsification of emulsifier, which containing lignin emulsifier, polyether and non-ionic additive, in this paper. Some control experiments have been designed to demonstrate that the polyether and non-ionic additive contributed much more to emulsifiability of emulsifier. With polyether and non-ionic additive as auxiliaries, the modulus particle size and average particle size of emulsifier could reach to 1.65 μm and 1.97 μm. The mechanism indicated that polyether and non-ionic additive could decrease the critical micelle concentration of emulsifier.

Field of study: Engineering