nils-herrmann/clean_scirepeval huggingface dataset:
Effect of coenzymes on the quaternary structure conformation of glyceraldehyde-3-phosphate dehydrogenases of mung beans and rabbit muscle.

Kinetics of thermal inactivation of glyceraldehyde-3-phosphate dehydrogenases of mung beans and rabbit muscle have been studied under different pH conditions in the absence and presence of various concentrations of NAD+ and NADH. The data have been discussed with respect to the effect of the coenzymes on the quaternary structure symmetry of the two enzymes and their binding isotherms. Both the (homo-tetrameric) apo-enzymes exhibit biphasic kinetics of thermal inactivation, characteristic of C2 symmetry, at lower pH values and a single exponential decay of enzyme activity, characteristic of D2 symmetry, at higher pHs. In each case, NAD+ has no effect on the biphasic kinetic pattern of thermal inactivation at lower pH values, but NADH brings about a change to single exponential decay. At higher pH values, NADH does not affect the kinetic pattern (single exponential decay) of any enzyme, but NAD+ alters it to biphasic kinetics in each case. The data suggest that NAD+ and NADH have higher affinity for the C2 and D2 symmetry conformation, respectively. With mung beans enzyme, the effect of NAD+ on the two rate constants of biphasic inactivation at pH 7.3 is consistent with a Kdiss equal to 110 microM. The NAD(+)-dependent changes in the kinetic pattern of thermal inactivation of this enzyme at pH 8.6 suggest a positive cooperativity in the coenzyme binding (nH = 3.0). In the binding of NADH to the mung beans enzyme, a weak positive cooperativity is observed at pH 7.3.(ABSTRACT TRUNCATED AT 250 WORDS)

Field of study: Biology, Chemistry, Physics
Optimal control strategies for dividend payments and capital injections in compound Markov binomial risk model with penalties for deficits

We consider the compound Markov binomial risk model. The company controls the amount of dividends paid to the shareholders as well as the capital injections in order to maximize the cumulative expected discounted dividends minus the discounted capital injections and the discounted penalties for deficits prior to ruin. We show that the optimal value function is the unique solution of an HJB equation, and the optimal control strategy is a two-barriers strategy given the current state of the Markov chain. We obtain some properties of the optimal strategy and the optimal condition for ruining the company. We offer a high-efficiency algorithm for obtaining the optimal strategy and the optimal value function. In addition, we also discuss the optimal control problem under a restriction of bounded dividend rates. Numerical results are provided to illustrate the algorithm and the impact of the penalties.

Field of study: Mathematics
A cloud algorithm based on the O 2 -O 2 477 nm absorption band featuring an advanced spectral fitting method and the use of surface geometry-dependent Lambertian-equivalent reflectivity

We discuss a new cloud algorithm that retrieves an effective cloud pressure,
also known as cloud optical centroid pressure (OCP), from oxygen dimer
( O2 - O2 ) absorption at 477 nm after determining an effective
cloud fraction (ECF) at 466 nm, a wavelength not significantly affected by
trace-gas absorption and rotational Raman scattering. The retrieved cloud
products are intended for use as inputs to the operational nitrogen dioxide
( NO2 ) retrieval algorithm for the Ozone Monitoring Instrument (OMI)
flying on the Aura satellite. The cloud algorithm uses temperature-dependent
 O2 - O2 cross sections and incorporates flexible spectral
fitting techniques that account for specifics of the surface reflectivity.
The fitting procedure derives O2 - O2 slant column densities
(SCDs) from radiances after O3 , NO2 , and H2O 
absorption features have been removed based on estimates of the amounts of
these species from independent OMI algorithms. The cloud algorithm is based
on the frequently used mixed Lambertian-equivalent reflectivity (MLER) concept. A geometry-dependent
Lambertian-equivalent reflectivity (GLER), which is a proxy of surface
bidirectional reflectance, is used for the ground reflectivity in our
implementation of the MLER approach. The OCP is derived from a match of the
measured O2 - O2 SCD to that calculated with the MLER method.
Temperature profiles needed for computation of vertical column densities are
taken from the Global Modeling Initiative (GMI) model. We investigate the
effect of using GLER instead of climatological LER on the retrieved ECF and
OCP. For evaluation purposes, the retrieved ECFs and OCPs are compared with
those from the operational OMI cloud product, which is also based on the same
 O2 - O2 absorption band. Impacts of the application of the
newly developed cloud algorithm to the OMI NO2 retrieval are
discussed.

Field of study: Environmental science
Oxymatrine attenuates diabetes-associated cognitive deficits in rats

Oxymatrine (OMT) is the major quinolizidine alkaloid extracted from the root of Sophora flavescens Ait (the Chinese herb Kushen) and exhibits diverse pharmacological actions. In this work we investigated the effects of OMT on diabetes-associated cognitive decline (DACD) in a rat model of diabetes and explored the mechanisms of action.Male Wistar rats were injected with streptozotocin (65 mg/kg, ip) once to induce diabetes. The rats were then treated with vehicle or OMT (60 or 120 mg/kg per day, ip) for 7 weeks. Memory function was assessed using Morris water maze test. The levels of malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), NF-κB p65 unit, TNF-α, IL-1β and caspase-3 in the cerebral cortex and hippocampus were quantified.The diabetic rats exhibited markedly reduced body weight and increased plasma glucose level. The memory function of the rats assessed using Morris water maze test showed significant reduction in the percentage of time spent in the target quadrant and the number of times crossing the platform, coupled with markedly prolongation of escape latency and mean path length. Moreover, the rats showed oxidative stress (significantly increased MDA, decreased SOD and reduced GSH levels), as well as significant increases of NF-κB p65 unit, TNF-α, IL-1β and caspase-3 levels in the cerebral cortex and hippocampus. Chronic treatment with OMT dose-dependently reversed these behavioral, biochemical and molecular changes in the diabetic rats. However, the swimming speed had no significant difference among the control, diabetic and OMT-treated diabetic rats.Chronic treatment with OMT alleviates diabetes-associated cognitive decline in rats, which is associated with oxidative stress, inflammation and apoptotic cascades.

Field of study: Biology, Chemistry, Medicine
Forage type and fish oil cause shifts in rumen bacterial diversity.

Despite evidence supporting improved incorporation of beneficial polyunsaturated fatty acids (PUFA) into ruminant products, such as meat and milk, following red clover and fish oil (FO) inclusion in the ruminant diet, little is known regarding the concomitant bacterial diversity. We evaluated the effects of feeding grass vs. red clover silage with incremental FO inclusion on known lipolytic, biohydrogenating, cellulolytic and proteolytic rumen bacterial communities of steers. Following 14 days of dietary adaptation, liquid-associated (LAB) and solid-associated (SAB) bacterial communities were harvested, DNA extracted and bacterial denaturing gradient gel electrophoresis (DGGE) and specific-bacterial quantitative PCR (QPCR) were undertaken. DGGE-derived dendrograms showed that diet caused the greatest change in LAB and SAB bacterial diversity, with FO inclusion at the 2% and 3% dry matter intake also causing some changes. QPCR revealed that diet resulted in changes in the DNA concentration of Anaerovibrio lipolytica, the Butyrivibrio proteoclasticus group, Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FO inclusion caused changes in A. lipolytica, F. succinogenes and R. flavefaciens DNA concentration only. In the B. proteoclasticus group, which are the only known bacteria with the capacity to biohydrogenate PUFA to 18:0, DNA concentration did not correlate to 18:0 flow to the duodenum, however, suggesting that other bacteria may play a role in biohydrogenation. A greater understanding of microbial changes that accompany beneficial dietary changes will lead to novel strategies to improve ruminant product quality.

Field of study: Biology, Environmental science
Auditory successive conditional discrimination and auditory stimulus equivalence classes.

This paper describes an experimental demonstration of stimulus equivalence classes consisting entirely of auditory stimuli. Stimuli were digitized arbitrary syllables (e.g., "cug," "vek") presented via microcomputer. Training and testing were conducted with a two-choice auditory successive conditional discrimination procedure. On each trial, auditory samples and comparisons were presented successively. As each comparison was presented, a response location (a rectangle) appeared on the computer screen. After all stimuli for a trial were presented, subjects selected one of the response locations. Six subjects acquired the conditional discrimination baseline, 4 subjects demonstrated the formation of three-member auditory equivalence classes resulting from sample-S+ relations, and 1 subject demonstrated equivalence classes resulting from sample-S- relations. Four subjects received additional training and subsequently demonstrated expansion of the three-member classes to four members each.

Field of study: Biology, Psychology
Bayesian Information Sharing Between Noise And Regression Models Improves Prediction of Weak Effects

We consider the prediction of weak effects in a multiple-output regression setup, when covariates are expected to explain a small amount, less than $\approx 1%$, of the variance of the target variables. To facilitate the prediction of the weak effects, we constrain our model structure by introducing a novel Bayesian approach of sharing information between the regression model and the noise model. Further reduction of the effective number of parameters is achieved by introducing an infinite shrinkage prior and group sparsity in the context of the Bayesian reduced rank regression, and using the Bayesian infinite factor model as a flexible low-rank noise model. In our experiments the model incorporating the novelties outperformed alternatives in genomic prediction of rich phenotype data. In particular, the information sharing between the noise and regression models led to significant improvement in prediction accuracy.

Field of study: Computer science
Linear compressor discharge valve behavior using a rigid body valve model and a FSI valve model

The discharge valve of a linear compressor commonly uses a circular plate valve and research on such valves is lacking. Thus, in this study, the rigid body model and the FSI model, widely used for the reed valve, were used to examine the behavior of the discharge valve. Also, a comparison with experimental results was conducted to determine the characteristics of each valve model. According to the results, only the valve lift of the FSI model was in agreement with the experimental result. Moreover, the 3D rigid body valve model could not predict the additional displacement fluctuations of the valve that cause backflow during the expansion process of the compressor whereas the 3D FSI valve model was able to predict the additional displacement fluctuations. Therefore, the FSI model was found to be advantageous in calculating the cooling capacity or EER of the linear compressor with the circular plate discharge valve.

Field of study: Engineering
The Scavenger Receptor CD68 Regulates Platelet Mediated Oxidized Low-Density Lipoprotein (oxLDL) Deposition in Atherosclerotic Vessels at an Early Stage of Atherosclerosis in LDLR-/-/ApoBec-/- Mice.

Oxidative modifications of low-density lipoprotein (ox-LDL) play a key role in initial steps of atheroprogression possibly via specific scavenger receptors on inflammatory and endothelial cells. Amongst others, CD68 might play a crucial role in this leading to fatty streak formation.



Different CD68-Fc fusion proteins were cloned, expressed and tested in vitro for their oxLDL binding properties as a decoy for endogenous oxLDL. Physiological functions were tested in foam cell assays with human monocytes in culture and by binding oxLDL from human blood. The best suited candidate FcIgG2-FL-CD68 was injected twice weekly in LDL receptor and ApoBec deficient mice (LDLR-/-/Apobec-/-), and the oxLDL content was measured in peripheral blood, in different cell types of the spleen and aortic wall by specific oxLDL antibodies using flow cytometry.



Different variants of the CD68-Fc bound to copper-oxided LDL (oxLDL), LDL and to a lesser extent HDL with different efficacy in an ELISA based binding assay in vitro. Native oxLDL content in human blood derived from patients with extended atherosclerosis was reduced after passage through a specific protein G column conjugated with the different CD68-Fc fusion proteins. Foam cell formation from human peripheral blood monocyte-platelet co-culture was reduced by the most effective CD68-Fc fusion proteins. oxLDL was not increased in the blood but markedly increased in the vessel wall from LDLR-/-/Apobec-/- mice at an early stage of atherosclerosis. Platelet-like cells in the vessel well contributed most to the increase in tissue oxLDL. FcIgG2-FL-CD68, reduced oxLDL content of aortic vessel wall cells from LDLR-/-/Apobec-/- mice. However a tissue specific reduction on the oxLDL content in peripheral blood, the spleen or cells from the aortic vessel by FcIgG2-FL-CD68 could not be shown.



Platelets contribute to increased tissue oxLDL in the aortic wall but not in peripheral blood. CD68 seems to play a role in the oxLDL metabolism in the vessel wall at early stages of atherosclerosis. FcIgG2-FL-CD68 could serve as a novel therapeutic option to modify the oxLDL content in the vessel wall.

Field of study: Biology, Chemistry
Heterocyclic structures applied as efficient molecular probes for the investigation of chemically important interactions in the liquid phase

Heterocyclic molecular probes were applied for the investigation chemically significant effects of the liquid phase to solute materials. A brief historic overview of the estimation of solvent effects is reported as well as most recent developments. The familiar three-dimensional concepts of solvent–solute interactions were upgraded to two-dimensional effects similar to surfaces where heterocyclic structures with compensating dipoles give basic insights in processes on the molecular level.

Field of study: Chemistry
Preparation and characterization of monoclonal antibodies against a polysaccharide from Flammulina velutipes mycelium.

Antigen was synthesized for the preparation of monoclonal antibodies (MAbs) against FVP2, a polysaccharide from Flammulina velutipes. FVP2 was coupled to bovine serum albumin (BSA) by 1-cyano-4-dimethyl-aminopyridinium tetrafluoroborate (CDAP) to produce a neoglycoprotein with the degree of substitution (DS; approximately 2.5:1 mol of FVP2 hapten/mol of BSA carrier), whose immunogenicity was enhanced in mice. The neoglycoprotein induced vigorous primary IgM and booster IgG responses to FVP2. IgG1 was elicited as the dominant isotype antibody in BALB/c mice. Then, the MAbs to FVP2 were prepared using hybridoma technology. Resulting hybridomas producing anti-FVP2 antibodies were screened by indirect enzyme-linked immunosorbent assay (ELISA). As a result, three hybridoma cell lines named B11D, C8G, and I6D were acquired, and the immunological characteristics of the MAbs were determined.

Field of study: Biology
The search for the definition, etiology, and effective diagnosis of upper urinary tract obstruction: the Whitaker test then and now.

Robert Whitaker, inspired by Dr William W Scott at the Brady Institute at Johns Hopkins and by Sir David Innes Williams at Great Ormond Street Hospital for Children in the late 1960s, spent much of his career exploring the meaning of persistent dilatation of the upper urinary tract, in an attempt to define obstruction and to find a means of diagnosing it accurately.



This is a historical review of Bob Whitaker's journey from his definition of obstruction to the inception of his eponymous test.



In 1975, he proposed a theory to explain the pathophysiology behind obstructive hydronephrosis and megaureter. He was among the first pediatric urologists to observe that 'it is wrong… to assume that dilatation necessarily indicates obstruction', a statement that was widely stated and even appeared in the textbooks at the time. He defined obstruction as 'an increased pressure in the pelvicalyceal system of the kidney at normal physiological flow rates such that the renal function is adversely affected'. This realization led to the development of a percutaneous pressure-measuring technique at controlled flows, later referred to as the Whitaker test. It predated and later assisted in the interpretation of diuretic renograms.



Whitaker questioned the etiology of 'hydronephrosis' and challenged other hypotheses proposed at the time, which often included causes of mechanical occlusion at the ureteropelvic junction (UPJ) or ureterovesical junction (UVJ). Whitaker's hypothesis is that 'obstruction' at UPJ and UVJ levels is not mechanical but the result of a failure of normal peristalsis to form and propagate a bolus. This, in turn, depends on the potentially abnormal distensibility of the renal pelvic and ureteric wall whether it be congenital or acquired. The aim of this review is to recall the history of the development of a technique to evaluate dilated upper urinary tracts and to re-evaluate various theories that might explain the etiology of the dilatation in the light of more recent evidence. Robert (or Bob, to his colleagues) Whitaker was among the founder members of the British Association of Paediatric Urologists, which now has more than 50 members, in 1992. Together with his colleagues Philip Ransley and David Thomas, Whitaker established the annual pediatric urology course for pediatric surgery and urology trainees in Cambridge, U.K., which still runs to this day. He retired from his surgical practice in 1990 and up until the present time has taught clinical anatomy in the Cambridge University School of Medicine.

Field of study: Medicine
Hospital response to a global budget program under universal health insurance in Taiwan.

Global budget programs are utilized in many countries to control soaring healthcare expenditures. The present study was designed to evaluate the responses of Taiwanese hospitals to a new global budget program implemented in 2002.



Using data obtained from the Bureau of National Health Insurance (NHI) and two nationwide surveys conducted before and after the global budget program, changes in the length of stay, treatment intensity, insurance claims, and out-of-pocket fees were compared in 2002 and 2004. The analysis was conducted using the Generalized Estimating Equations (GEEs) method.



Regression models revealed that implementation of the global budget was followed by a 7% increase in length of stay and a 15% increase in the number of prescribed procedures and medications per admission. The claim expenses increased by 14%, and out-of-pocket fees per admission increased by 6%. Among the hospitals, no coalition action was found during the study period.



In the present study, it appears that hospitals attempted to increase per-case expense claims to protect their reimbursement from possible discounts under a global budget cap.

Field of study: Medicine, Political science
Signals from the Wadden sea: Population declines dominate among waterbirds depending on intertidal mudflats

The Wadden Sea, shared by Denmark, Germany and the Netherlands, is one of the world's largest intertidal wetlands. Waterbirds are an important element of the Wadden Sea ecosystem. By their migratory behaviour they connect the Wadden Sea with other sites, ranging from the arctic to the western seaboards of Europe and Africa, forming the East-Atlantic Flyway. The Joint Monitoring of Migratory Birds (JMMB) project of the Trilateral Monitoring and Assessment Program (TMAP) follows the changes in population size within the Wadden Sea. In this paper we describe and analyse population trends over the years 1991–2009 for 22 waterbird species using the Wadden Sea in internationally important numbers and depending on intertidal mudflats. Population declines predominated in this 18-year period. More populations decreased in Schleswig-Holstein and Niedersachsen than in The Netherlands and Denmark. This is the case particularly for species feeding on polychaetes. In contrast, waterbirds feeding on bivalves are in decline in all regions except Denmark. On the finer spatial scale of tidal basins, these patterns in trends are still apparent, although much variation in trend directions exists within the Dutch Wadden Sea, especially in bivalve specialists. For those species for which we could compare the trend in the Wadden Sea with the trend of their entire flyway population, we found that the former were more negative. This finding and the contrasting trends between regions and tidal basins within the Wadden Sea suggest that causes of the population changes are to be sought within the Wadden Sea itself. These causes, which may act in combination, could be related to factors operating within the Wadden Sea only or with factors operating on a larger scale but having an intensified or differentiated effect within the Wadden Sea. Interestingly, the Wadden Sea regions where negative trends of benthivorous waterbirds predominate are characterized by a large tidal amplitude, whereas areas where bird numbers have generally increased are characterized by a small tidal amplitude. An inventory of possible causes indicated climate change, eutrophication, shellfish fisheries, invasive species and increasing numbers of avian predators as the most important candidates to be investigated further to explain the observed trends.

Field of study: Environmental science
A Reading Instruction Intervention Program for English-Language Learners Who Are Struggling Readers

We used a multiple baseline across students design to evaluate the effects of an intervention program consisting of vocabulary instruction, error correction, and fluency building on oral reading rate and comprehension of five English-language learners who were struggling readers in a primary school. During the first intervention condition (new passage each session), the first author (a) explained the meanings of new vocabulary words from the session's passage, used each vocabulary word in a sentence, and asked the learner to use each word in a sentence; (b) corrected oral reading errors during the learner's initial oral reading of the passage; (c) asked the learner to read the passage as fast as she or he could for three consecutive trials; and (d) asked five literal comprehension questions about the passage. The same procedures were used during the second intervention condition (same passage to criterion), except the same passage was used across sessions until the learner reached a predetermined number of words read correctly per minute. During the new passage each session condition, the oral reading rate of all five learners showed marked improvements over their performance during baseline. During the same passage to criterion condition, four of five learners reached the predetermined fluency criterion of 100 correct words per minute. The mean number of comprehension questions answered correctly per session was notably higher during both intervention conditions than during baseline.

Field of study: Education