nils-herrmann/clean_scirepeval huggingface dataset:
Relationship between cytokine levels in serum and gingival crevicular fluid (GCF) in pregnant women.

Periodontal disease has been linked to systemic diseases/disorders and a low-grade systemic inflammatory status originated from periodontitis has been proposed as a possible explanation for this association. This study evaluates the relationship, early in pregnancy, between gingival crevicular fluid (GCF) and serum levels of a panel of cytokines that have been implicated in PTB and periodontal disease.



One hundred pregnant women aged 18-35 years old with a gestational age up to 20 weeks were included (mean±SD gestational age:16.1±3.5 weeks). Four periodontal sites per subject were randomly selected for GCF collection. Serum and GCF levels of IL-1β, IL-6, IL-8, IL-10, IL-12p70 and TNF-α were analyzed using a cytometric bead array. Regression and correlation analyses were used to assess the relationship between serum and GCF cytokine levels.



Participants had widespread periodontal inflammation but limited periodontal destruction. Cytokine levels were significantly higher in GCF than serum for all cytokines but IL-10. GCF levels had small but significant effect on serum levels for IL-10 (β=0.34±0.09, p<0.01), IL-12p70 (β=0.48±0.08, p<0.01) and TNF-α (β=0.29±0.09, p<0.01). Periodontal probing depth and bleeding on probing were significantly associated with GCF levels for IL-1β, IL-6 and IL-8; however, they had negligible effect on serum cytokine levels. Correlation between GCF and serum levels was non-significant, except for IL-12p70, which showed a significant but small correlation between the two sources (r=0.32, p=0.001).



GCF cytokine levels were not strongly associated with serum cytokine levels in pregnant women with widespread periodontal inflammation but limited periodontal destruction.

Field of study: Medicine
WEED DETECTION USING COLOR MACHINE VISION

Many weed species have reddish stems, but stems of wheat and soybean are green. These color features were 
used in this study to establish a simple weed-detection method using a color machine-vision system. This method is more 
practical than texture- or shape-based methods because of its low sensitivity to canopy overlap, leaf orientation, camera 
focusing, and wind effect. Four types of relative color indices formed by RGB gray levels were designed. The most 
effective combinations of these color indices were selected using a statistical method. These combinations were used as 
the input variables for a statistical classifier based on discriminant analysis (DA) and two artificial neural-network (NN) 
classifiers. These classifiers were trained and tested using three weed species (Johnsongrass, redroot pigweed, and yellow 
foxtail) with soybean and three weed species (wild buckwheat, cheat, and field bindweed) with wheat. Preprocessing and 
postprocessing algorithms were developed to shorten the processing time and to reduce noise. The results showed that the 
statistical DA classifier was more accurate than the NN classifiers in classification accuracy. The least-square means of 
the classification rates using the DA classifiers for soybean and wheat were 54.9% and 62.2%, respectively. The 
misclassification rates for most weed species were below 3%. Because the reddish colors on the stems of some weed 
species vary as the plants grow, an in-field calibration procedure will be needed to make the classifiers more adaptive to 
different circumstances.

Field of study: Agricultural and Food sciences
Regulation of Redox Properties of 6-Azaflavin by Hydrogen Bonding with a Receptor in Chloroform-Acetonitrile

A melamine derivative bearing two guanidinium ions binds 6-azaflavin via hydrogen bonds at N(1), C(2)=O, N(3)–H, C(4)=O, N(5), and N(6) positions, and affects considerably the redox properties in CHCl3 containing 20% (v/v) CH3CN.

Field of study: Chemistry
An “Apology” for Philosophy

T HE time was, and that in the not so far distant past, when philosophy was generally known and accepted as "the queen of the sciences." Even that, however, was a real comedown for philosophy from the position she once occupied; namely, that of being the synonym for all ordered and reliable knowledge of any kind. It is, of course, a well-known fact that for the Greeks there existed no science or sciences aside from philosophy, since philosophy, being the love of wisdom, was the all-inclusive term used for the serious study of anything, from mathematics and astronomy to ethics, political science, rhetoric, and poetry. It is necessary, therefore, at the outset of our discussion to make it perfectly clear that philosophy, as at present understood, makes no claims to any such pretentious or all-inclusive program. In fact, there are those who claim that philosophy itself has ceased to have any unusual or even worth-while function to fulfill in the modern world. It has been asserted that, together with religion and mythology, philosophy belongs to the limbo of a bygone day, a day when people who had not yet learned how to "know" the universe in which we live had to depend upon more or less shrewd and more or less adequate speculation. The day of empirical science spelled the doom of philosophy as surely as it spelled the doom of religion and mythology, so we have been told. If this is true, the answer to our discussion becomes easy enough: there is no room for philosophy in the liberal-arts curriculum of an empirically scientific age. One might, of course, proceed simply to pass up all such voices with the Nazarene's first prayer from his cross: "Father, forgive them, for they know not." Such procedure, however, becomes questionable when one

Field of study: Education
Aerobic treatment of swine manure to enhance anaerobic digestion and microalgal cultivation

Aerobic treatment of swine manure was coupled with anaerobic digestion and microalgal cultivation. A 14-day aerobic treatment reduced the total solid content of swine manure by >15%. Ammonia and carbon dioxide were stripped by the air supplied, and this off-gas was further used to aerate the culture of Chlorella vulgaris. The microalgal growth rates in Bristol medium and the wastewater with the off-gas increased from 0.08 to 0.22 g/L/d and from 0.15 to 0.24 g/L/d, respectively. Meanwhile, the aerobically treated swine manure showed a higher methane yield during anaerobic digestion. The experimental results were used to establish a demonstration unit consisting of a 100 L composter, a 200 L anaerobic digester, a 60 L tubular photobioreactor, and a 300 L micro-open raceway pond.

Field of study: Agricultural and Food sciences
Comments on "A variational approach to the extraction of in-phase and quadrature components" [with reply]

For original paper by Gordon see  (1998 May). With a variational method, Gordon defined the quadratures and carrier frequency different from the analytic signal (AS). This approach ignores, however, that quadratures must be bandlimited. Restriction of bandlimiting results in another solution and leads to the AS model. Gordon replies to this comment.

Field of study: Engineering
Conodont Sr/Ca and δ18O record seawater changes at the Frasnian–Famennian boundary

The oxygen isotopic composition (δ 18 O p ) and strontium/calcium (Sr/Ca p ) ratios have been measured in Late Devonian conodonts ( Palmatolepis sp.) from contemporaneous sections at Coumiac (France) and M'rirt (Morocco). The sequences encompass two anoxic horizons, the Lower Kellwasser (LKW) and Upper Kellwasser (UKW) events with the top of the UKW coinciding with the mass-extinction at the Frasnian–Famennian boundary. The genus Palmatolepis survived the faunal crisis but exhibited plastic responses to the environmental changes, which are recorded in the evolution of shape during the anoxic events. The present study demonstrates that shape, δ 18 O p and Sr/Ca p values of conodonts are correlated in both localities excluding diagenesis as the driving process for the measured δ 18 O p and Sr/Ca p values. The conodonts δ 18 O p and Sr/Ca p values are correlated in both localities and distributed into either a “pre-crisis” and “crisis” group. Using the relationships between the δ 18 O p and Sr/Ca p values, we estimate that the variation of the seawater Sr/Ca ratio during the Frasnian–Famennian mass extinction was of about 20% its initial value. This drastic decrease of the seawater Sr/Ca ratio is discussed in the light of the reef demise that occurred during the faunal crisis.

Field of study: Environmental science, Geography
Fatigue Analysis on Stainless Steel 430F Based on Findley, Matake and Normal Stress Models

The fatigue analysis of circular specimen stainless steel 430F was studied based on established Findley,Matake and normal stress fatigue analysis models under conditions of normal load and shear load.By comparing with the analytical values according to fatigue analytical expressions,it is found that Findley,Matake and normal stress fatigue analysis model can accurately predict the fatigue usage factor for circular specimen stainless steel 430F,which can provide guidance and reference for the fatigue prediction of circular specimen.

Field of study: Materials science
Structure of the southwest margin of the Laramie Basin, Wyoming

The Laramie Basin is, in general, a northward-plunging syncline between the Laramie Range on the east and the Medicine Bow Range on the west. The dominant structural elements in the south end of the basin, near the junction of the ranges, are five northward-trending anticlines and the intervening synclines. The east flanks of three anticlines are cut by westward-dipping thrusts; northward, each thrust passes into a tear, which cuts westward across the axis of the anticline near the north end of the pre-Cambrian crystalline core. The thrust and tear constitute a scoop-shaped fault surface along which the block above the fault moved relatively upward to the northeast. The west flank of a fourth anticline is cut by an eastward-dipping thrust, which passes southward and eastward into a tear against which the pre-Cambrian core of the anticline terminates. It is believed that the folds, thrusts, and tears were formed under east-west compressive stress applied to a laterally uniform sheet of sediments overlying pre-Cambrian igneous and metamorphic rocks of varying competence. Two en echelon synclines immediately east of the Medicine Bow Range are cut by westward-dipping thrusts. The west flank of the syncline has moved relatively east‐ward onto the east flank. Along the thrusts at the surface there are drag blocks younger than either of the two formations in contact along the fault.

Field of study: Geology
Superconducting Anisotropies of F-Substituted LaOBiSe 2 Single Crystals

We report the growth and superconducting anisotropy measurement of F-substituted LaOBiSe2 single crystals. The superconducting critical temperature of the single crystal was approximately 3.5 K. The resistivity of the single crystals showed an anomaly at approximately 50 K. The superconducting anisotropies were estimated to be 49 and 24 using the upper critical field and the effective mass model, respectively. The obtained superconducting anisotropies were different between these two approaches.

Field of study: Physics
Glass-ceramics for high precision reflective-optic applications.

Titania- and zirconia-nucleated glasses in the basic Li(2)Al(2)O(4)-SiO(2) system were found suitable for casting relatively large mirror blanks. Upon heat treatment, these glasses crystallized uniformly to yield transparent, very low expansion beta quartz solid solution glass-ceramics. Special care was required in processing large diameter blanks, owing to localized temperature increases resulting from the exothermic heat of crystallization. Glass-ceramics with a wide range of beta quartz solid solution stability resulted in a uniform product. Transparent glass-ceramic mirror blanks were obtained with average expansion coefficients from 5 degrees C to 50 degrees C of 0 +/- 0.3 x 10(-7)/ degrees C. Ware up to 15 cm thick was processed to less than 10 micro/cm strain, with no change in expansion or transparency through the blank. Work with thick ware provided additional insight into the problems that might be encountered in the fabrication of very large castings.

Field of study: Physics
Effect of interfacial property on electrochromic response speed of Ta2O5/NiO and Ta2O5/Ni(OH)2

Ta2O5 layers were deposited on NiO/indium tin oxide (ITO) and Ni(OH)2/ITO, respectively, by means of an RF magnetron sputtering system, and their electrochromic properties were then compared by means of in situ transmittance measurements during continuous potential cycling and pulse potential cycling. The electrochromic response speed of the Ta2O5/Ni(OH)2/ITO was much more rapid than that of the Ta2O5/NiO/ITO. This can be attributed to the interfacial property between the Ta2O5 and the electrochromic layer. The NiO layer of Ta2O5/NiO/ITO was irreversibly transformed into an electrochromic active form, Ni(OH)2, during the first potential cycling, leading to an increase in the interfacial reaction resistance and, as a result, a slow response speed.

Field of study: Materials science
Configuration and performance analysis of magnetic refrigerators

The commercialization of magnetic refrigerators depends upon the ability to meet performance targets while having acceptable equipment costs. This paper links device design parameters and performance of magnetic refrigerators to the cost of cooling delivered. A device configuration parameter, D, is defined that links the field volume to the volume of magnetocaloric material. Combined with the magnet performance parameter, efficiency, and specific exergetic cooling, the cost structure of a magnetic refrigerator is determined. Some magnetic refrigerators reported in the literature are classified using their configuration parameters, and are then compared in terms of demonstrated performance using results available in the literature. The required improvement in performance is calculated such that the cost of a magnetic refrigerator would be equivalent to a conventional compressor-based device. Finally, some of the reasons for different performance are discussed with a focus on opportunities for improvements.

Field of study: Engineering
The relation of feeding and activity following septal lesions in rats.

The patterns of intake of liquid diet and water were recorded in diet-deprived rats with septal lesions and neurologically intact controls during the first hour of diet access. The occurrences of grooming, resting/sleeping, and exploring were also recorded. Both groups of rats consumed similar amounts of diet in one meal during the 1-hr diet access period. Control rats consumed the meal in one prolonged bout of eating, whereas rats with septal lesions consumed the meal in numerous small bouts of eating. Rats with septal lesions were active for longer periods, exhibiting continuous alternation of brief bouts of eating, drinking, exploring, and resting throughout the meal. In tests in which water was not available during the diet access period, both groups of rats increased their intrameal bout size, but rats with septal lesions still showed much smaller bouts of ingestion than did controls. These data suggest that the small-bout pattern of ingestion may reflect a general disruption in the control of behavioral sequences, rather than processes uniquely related to the regulation of eating or drinking.

Field of study: Biology, Psychology
Development of proton-exchange polymer nanocomposite membranes for fuel cell applications

The design and development of proton conducting polymer electrolyte membranes from a linear constituent, sulfonated poly (ether ether ketone) (SPEEK), and inorganic additive, niobium oxide (NBO), have been achieved. The degree of sulfonation of SPEEK was measured by back titration method and found to be 57%. The physicochemical properties such as water uptake ability, ion-exchange capacity, swelling ratio, proton conductivity, and thermal stability of the prepared polymer nanocomposite membranes were studied in detail. The distribution of NBO throughout the polymer matrix has been examined by scanning electron microscopic and X-ray diffraction analyses and found to be uniform. The SP-NBO-10 composite membrane shows 38.4% of water uptake, whereas the pristine membrane limits to 27.1%. The prepared electrolyte membranes exhibit good proton conductivity at temperature varying from 30°C to 90°C and possess less activation energy for the transportation of proton by the incorporation of NBO filler. The thermal studies demonstrated that the stability of the composite membranes was significantly enhanced by the impregnation of NBO. The filler NBO shows excellent improvements on the polymer nanocomposite, making it a very promising additive for other polymers and offers new roads for energy applications.

Field of study: Materials science
Kernel Method for Detecting Higher Order Interactions in multi-view Data: An Application to Imaging, Genetics, and Epigenetics

In this study, we tested the interaction effect of multimodal datasets using a novel method called the kernel method for detecting higher order interactions among biologically relevant mulit-view data. Using a semiparametric method on a reproducing kernel Hilbert space (RKHS), we used a standard mixed-effects linear model and derived a score-based variance component statistic that tests for higher order interactions between multi-view data. The proposed method offers an intangible framework for the identification of higher order interaction effects (e.g., three way interaction) between genetics, brain imaging, and epigenetic data. Extensive numerical simulation studies were first conducted to evaluate the performance of this method. Finally, this method was evaluated using data from the Mind Clinical Imaging Consortium (MCIC) including single nucleotide polymorphism (SNP) data, functional magnetic resonance imaging (fMRI) scans, and deoxyribonucleic acid (DNA) methylation data, respectfully, in schizophrenia patients and healthy controls. We treated each gene-derived SNPs, region of interest (ROI) and gene-derived DNA methylation as a single testing unit, which are combined into triplets for evaluation. In addition, cardiovascular disease risk factors such as age, gender, and body mass index were assessed as covariates on hippocampal volume and compared between triplets. Our method identified $13$-triplets ($p$-values $\leq 0.001$) that included $6$ gene-derived SNPs, $10$ ROIs, and $6$ gene-derived DNA methylations that correlated with changes in hippocampal volume, suggesting that these triplets may be important in explaining schizophrenia-related neurodegeneration. With strong evidence ($p$-values $\leq 0.000001$), the triplet ({\bf MAGI2, CRBLCrus1.L, FBXO28}) has the potential to distinguish schizophrenia patients from the healthy control variations.

Field of study: Computer science
Latent likelihood ratio tests for assessing spatial kernels in epidemic models

One of the most important issues in the critical assessment of spatio-temporal stochastic models for epidemics is the selection of the transmission kernel used to represent the relationship between infectious challenge and spatial separation of infected and susceptible hosts. As the design of control strategies is often based on an assessment of the distance over which transmission can realistically occur and estimation of this distance is very sensitive to the choice of kernel function, it is important that models used to inform control strategies can be scrutinised in the light of observation in order to elicit possible evidence against the selected kernel function. While a range of approaches to model criticism is in existence, the field remains one in which the need for further research is recognised. In this paper, building on earlier contributions by the authors, we introduce a new approach to assessing the validity of spatial kernels—the latent likelihood ratio tests—which use likelihood-based discrepancy variables that can be used to compare the fit of competing models, and compare the capacity of this approach to detect model mis-specification with that of tests based on the use of infection-link residuals. We demonstrate that the new approach can be used to formulate tests with greater power than infection-link residuals to detect kernel mis-specification particularly when the degree of mis-specification is modest. This new tests avoid the use of a fully Bayesian approach which may introduce undesirable complications related to computational complexity and prior sensitivity. Electronic supplementary material The online version of this article (10.1007/s00285-020-01529-3) contains supplementary material, which is available to authorized users.

Field of study: Biology, Mathematics
Multi-gene gateway clone design for expression of multiple heterologous genes in living cells: conditional gene expression at near physiological levels.

Using Multisite Gateway five-DNA-fragment constructs vectors that enable expression of two tandemly situated cDNAs on a single plasmid were developed. Heterologous protein production in cells was achieved by modulating respective cDNA expression to pre-determined and different levels. Optimization of cDNA expression at near physiological protein levels was achieved using promoters from four cell cycle-dependent genes. In comparison with conventionally available promoters, EF-1alpha or CMV, the promoters used in this study were able to modulate cDNA expression levels over a magnitude of approximately 10 or 100-fold, respectively. In transiently transfected cells, two different proteins (CPalpha1 and CPbeta2), which form a heterodimer, each labeled with a different-colored fluorescent protein, were successfully synthesized at pre-determined levels from their respective cDNAs. The above vectors were designed to contain an FRT/Flp recombination site for integration onto chromosomes and for establishment of stable clones in HeLa cells by site-specific recombination. In the stable transformant cells produced only about 4% of the protein production levels measured in the transiently transformed cells. The biological significance of these observations is discussed.

Field of study: Biology, Engineering
Low dose LPS does not increase TLR4 expression on monocytes in a human in vivo model.

Toll like receptor 4 (TLR4) is the major recognition receptor for lipopolysaccharides and plays a major role in the inflammatory response. CD11b is expressed on the surface of many leukocytes including monocytes. The CD11b/CD18 complex is involved in the inflammatory response by mediating migration and adhesion of leukocytes. The aim of this human in vivo study was to investigate the expression of TLR4 and CD11b on the surface of human monocytes after in vivo low-dose LPS stimulation.



We performed a double-blind, randomized crossover study with 16 healthy males who received a bolus injection of bacterial lipopolysaccharide (LPS; 0.4ng/kg) or normal saline. Vital parameters, blood counts, serum cytokine levels, the expression of TLR4, and CD11b on CD14 positive cells were analyzed.



The experimentally induced inflammatory response was reflected by transient increases in body temperature, circulating leukocyte numbers, and plasma levels of pro- (TNF-α, IL-6) and anti-inflammatory cytokines (IL-10, IL-1ra). In contrast to a significant increase in CD11b expression, no changes in TLR4 expression on circulating monocytes were detectable.



Early changes in TLR4 expression on circulating monocytes are not necessarily part of the inflammatory response to low dose LPS in humans whereas the detected increase of CD11b expression might already be sufficient for optimized recognition and signalling.

Field of study: Medicine