nils-herrmann/clean_scirepeval huggingface dataset:
A Formal Semantics for Ciset and Ciset Relation Operators

In this paper we present a formal model of semantics for newly introduced operators of cisets, ciset relations. The notion of alternate worlds is used to formalize the information content of a ciset and ciset relations. A ciset represents a collection of (regular) sets. Similarly, a ciset relation represents a collection of (regular) relations. Once this collection has been identified, any ciset relational operator can be applied on the collection of (regular) relations represented by ciset relations involved. This approach is computationally inefficient and is introduced solely to fully explain in a formal way, the semantics of newly introduced operators.

Field of study: Computer science
Community health centers employ diverse staffing patterns, which can provide productivity lessons for medical practices.

Community health centers are at the forefront of ambulatory care practices in their use of nonphysician clinicians and team-based primary care. We examined medical staffing patterns, the contributions of different types of staff to productivity, and the factors associated with staffing at community health centers across the United States. We identified four different staffing patterns: typical, high advanced-practice staff, high nursing staff, and high other medical staff. Overall, productivity per staff person was similar across the four staffing patterns. We found that physicians make the greatest contributions to productivity, but advanced-practice staff, nurses, and other medical staff also contribute. Patterns of community health center staffing are driven by numerous factors, including the concentration of clinicians in communities, nurse practitioner scope-of-practice laws, and patient characteristics such as insurance status. Our findings suggest that other group medical practices could incorporate more nonphysician staff without sacrificing productivity and thus profitability. However, the new staffing patterns that evolve may be affected by characteristics of the practice location or the types of patients served.

Field of study: Medicine
Medicaid: lessons from a decade.

Drawing on a decade of analysis and examination of the Medicaid program, this paper assesses what we have learned about Medicaid--its role, its successes, and its setbacks. In the absence of universal coverage for health and long-term care, Medicaid is a critical component of our social safety net, taking on the highest-risk, sickest, and often most expensive populations from private insurance and Medicare. Yet the substantial costs to federal and state governments incurred in filling this role, especially in lean economic times, remain its greatest challenge.

Field of study: Economics, Medicine
A comparison of the hemagglutination-inhibition, neutralization and complement fixation tests in the assay of antibody to measles.

The CF, HI and neutralization tests have been used to assay the antibody content of sera from animals and man following vaccination with killed measles virus and/or natural infection with the live virus. The CF test was demonstrated to be the least sensitive method of assay. The HI test was found to be as sensitive to measles antibody as the neutralization test and the titers obtained by the two methods closely parallel one another. The utilization of the HI test for large scale measles serology should result in considerable saving in time and reagents with no loss of reliability.

Field of study: Biology, Medicine
Concentration of mRNA for the natriuretic peptide receptor-C in hypertrophic chondrocytes of the fetal mouse tibia.

The roles of natriuretic peptides in cardiovascular homeostasis have been well characterized. A recent study revealed that mice lacking natriuretic peptide receptor-C (NPR-C) exhibit skeletal-overgrowth. We therefore, performed in situ hybridization with riboprobes to determine the localization of mRNAs for receptors for natriuretic peptides in the growth plate of the fetal mouse tibia The amount of mRNA for NPR-A was below the detectable level in the growth plate. The mRNA for NPR-B was detected predominantly in proliferating chondrocytes. By contrast, high levels of mRNA for NPR-C were found in hypertrophic chondrocytes. In other regions of the growth plate, the levels of mRNA for NPR-C were very low. The patterns of expression of mRNAs for NPR-B and NPR-C, namely, subtype switching during differentiation from proliferating chondrocytes to hypertrophic chondrocytes, suggest that these receptors might be involved in the growth and differentiation of the growth plate during fetal development in the mouse.

Field of study: Biology
Multiphoton multifocal microscopy exploiting a diffractive optical element.

Multiphoton multifocal microscopy (MMM) usually has been achieved through a combination of galvo scanners with microlens arrays, with rotating disks of microlens arrays, and cascaded beam splitters with asynchronous rastering of scanning mirrors. Here we describe the achievement of a neat and compact MMM by use of a high-diffraction-efficiency diffractive-optic element that generates a multiple-spot grid of uniform intensity to achieve higher fidelity in imaging of live cells at adequate speeds.

Field of study: Biology, Physics
Feature Extraction of Handwritten Symbols Using Fuzzy Logic

Feature extraction is a process whereby the input data is transformed into a set of features which characterise the input, and which can therefore be used to classify the input. This paper presents a new technique for feature extraction from handwritten symbols. We present a two-phase process. Firstly a pre-processing phase generates a chord vector for each handwritten stroke, thereby eliminating noise and greatly reducing the number of sections of the input which need to be assessed as potential features. Secondly fuzzy rules are used to determine membership values of chord sequences in fuzzy sets corresponding to feature types: Line, C-shape and O-shape. According to these membership values the most likely set of features is determined. Proper selection of the properties required for each feature type, and appropriate timing of application of the fuzzy rules, leads to an effective and efficient feature extraction algorithm.

Field of study: Computer science
Cognitive functioning and GABAA/benzodiazepine receptor binding in schizophrenia: A 1231-iomazenil SPET study

The role of the inhibitory neurotransmitter gamma aminobutyric acid (GABA) in schizophrenia has previously been investigated using postmortem material. Recently, using single photon emission tomography (SPET) with the selective benzodiazepine antagonist 123I-Iomazenil as the radioligand, we have demonstrated an in vivo relationship between reduced GABAA/benzodiazepine receptor binding and the severity of positive symptomatology in schizophrenia. The present study aimed to build on this using the same in vivo scanning techniques, and relating findings to cognitive functioning.



Ten nonpsychiatric control subjects and 15 schizophrenic patients, matched for age and handedness, were scanned. A battery of neuropsychologic tests was also administered.



Correlational analysis revealed a pattern of increased correlations between GABAA/benzodiazepine receptor binding and task performance, in the schizophrenic group compared to the control group.



Findings are preliminary but suggest a relationship between reduced GABAA/benzodiazepine receptor binding and poorer cognitive functioning, involving memory and visual attention processes, in the schizophrenic group but not in the control group. A role for GABA in the pathophysiology of schizophrenia is suggested. Limitations of the present study and suggestions for future research are discussed.

Field of study: Biology, Medicine, Psychology
Molecular Properties of Oep21, an ATP-regulated Anion-selective Solute Channel from the Outer Chloroplast Membrane*

The flux of phosphorylated carbohydrates, the major export products of chloroplasts, is regulated at the level of the inner and presumably also at the level of the outer membrane. This is achieved through modulation of the outer membrane Oep21 channel currents and tuning of its ion selectivity. Refined analysis of the Oep21 channel properties by biochemical and electrophysiological methods revealed a channel formed by eight β-strands with a wider pore vestibule of dvest ∼2.4 nm at the intermembrane site and a narrower filter pore of drestr ∼1 nm. The Oep21 pore contains two high affinity sites for ATP, one located at a relative transmembrane electrical distance δ = 0.56 and the second close to the vestibule at the intermembrane site. The ATP-dependent current block and reduction in anion selectivity of the Oep21 channel is relieved by the competitive binding of phosphorylated metabolic intermediates like 3-phosphoglycerate and glycerinaldehyde 3-phosphate. Deletion of a C-terminal putative FX4K binding motif in Oep21 decreased the capability of the channel to tune its ion selectivity by about 50%, whereas current block remained unchanged.

Field of study: Biology
The rate-distortion dimension of sets and measures

Data compression of independent samples drawn from a fractal set is considered. The asymptotic ratio of rate to magnitude log distortion characterizes the effective dimension occupied by the underlying distribution. This quantity is shown to be identical to Renyi's (1959) information dimension. For self-similar fractal sets this dimension is distribution dependent-in sharp contrast with the behavior of absolutely continuous measures. The rate-distortion dimension of a set is defined as the maximal rate-distortion dimension for distributions supported on this set. Kolmogorov's metric dimension is an upper bound on the rate-distortion dimension, while the Hausdorff dimension is a lower bound. Examples of sets for which the rate-distortion dimension differs from these bounds are provided.

Field of study: Computer science, Mathematics
A circadian rhythm of calcium intake in the domestic fowl.

Synopsis Observations on the food and calcium intake of six laying hens indicate that when the opportunity is provided, the fowl can control these parameters independently. The results suggest that calcium intake is regulated on an hour‐to‐hour basis by the needs of egg formation and anticipates maximal calcium requirement. Detailed records obtained from a single bird in a Skinner box suggest that calcium intake is controlled by a response to ovulation. This could be either a hormonal or a neural response.

Field of study: Biology
Dose- and Exposure-Response to Ketamine in Depression

W e read with interest the recent report on the repeateddose use of ketamine as a rapidly acting antidepressant in patients with treatment-resistant depression (1). Despite the promising antidepressant responses to this intervention in this and other studies (2– 4), several important technical questions about administration of ketamine have not yet been explored (5). These include route of administration, dose– exposure relationship, and exposure– and dose–response information. In this letter, we present a simulation on projected exposures between intramuscular and intravenous (IV) ketamine to establish comparable doses and report preliminary dose–response data in patients with treatment-refractory bipolar II depression.

Field of study: Medicine, Psychology
Sustained remission in a patient with myelodysplastic syndrome and a complex karyotype after erythropoiesis-stimulating therapy followed by colonic T-cell lymphoblastic lymphoma

1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA, 2 Division of Hematology and Medical Oncology, Weill-Cornell Medical College, New York, NY, USA, 3 Department of Pathology, Rochester General Hospital, Rochester, NY, USA, 4 Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA and 5 Department of Medicine, Rochester General Hospital, Rochester, NY, USA

Field of study: Medicine
Evidence of excretion of chlorinated hydrocarbon pesticides by the human liver

Conclusions1.The liver excretes DDT and dieldrin into the bile.2.The dieldrin content of bile from a worker having very high tissue stores is much greater than it is in persons with no occupational exposure. This suggests the existence of substrate-responsive excretory mechanisms.3.We have tentatively identified the aldehyde degradation product of dieldrin in adipose fat, bile,and gall stone. The ketone product has not been found in fat, bile, or gall stone.

Field of study: Biology
The anatomy and fine structure of the eye in teleost. II. The vascular connections of the lentiform body in Fundulus grandis.

The lentiform body is found in association with the choroid body in the back of teleost eyes. It probably helps to maintain the elevated oxygen tension which has already been produced by the choroid body-choriocapillaris complex. The body contains interdigitating afferent and efferent capillary beds (rete mirabile) which, by counter-current exchange, could have such a conservation effect. It has been reported that lentiform bodies are found only in connection with falciform processes. However, in Fundulus there is no falciform process and the body connects to the hyaloid vessels which in turn supply blood to the retractor lentis muscle and to the vitreous humor at the retinal surface. The lentiform body delivers no blood to the choriocapillaris, but, oddly enough, its venous counter-current blood is supplied by the choriocapillaris.

Field of study: Medicine
SCROTAL HERNIA IN A WHITE-TAILED DEER*

A mature male white-tailed deer (Odocoilerts r ir~ir~irrr~rts oclrr?~ro.rrs) in prime condition was found dead November 20, 1971, near Stites, Idaho. The animal had an enlargement approxinlately 28 x 18 x 18 cm in the scrotal area . At necropsy, the testicles and a significant portion of the small and large intestines were in the enlarged scrotum. N o adhesions were found and the inguinal canal was not constricting the intestines. The apparent lack of complications in this scrotal hernia and the large size and well developed wall of the scrotum suggest the herniated intestines were functional for some time. The prime condition of the carcass supports this. The cause of death was not determined.

Field of study: Medicine
Enhanced hexose fermentation by Saccharomyces cerevisiae through integration of stoichiometric modeling and genetic screening.

In order to determine beneficial gene deletions for ethanol production by the yeast Saccharomyces cerevisiae, we performed an in silico gene deletion experiment based on a genome-scale metabolic model. Genes coding for two oxidative phosphorylation reactions (cytochrome c oxidase and ubiquinol cytochrome c reductase) were identified by the model-based simulation as potential deletion targets for enhancing ethanol production and maintaining acceptable overall growth rate in oxygen-limited conditions. Since the two target enzymes are composed of multiple subunits, we conducted a genetic screening study to evaluate the in silico results and compare the effect of deleting various portions of the respiratory enzyme complexes. Over two-thirds of the knockout mutants identified by the in silico study did exhibit experimental behavior in qualitative agreement with model predictions, but the exceptions illustrate the limitation of using a purely stoichiometric model-based approach. Furthermore, there was a substantial quantitative variation in phenotype among the various respiration-deficient mutants that were screened in this study, and three genes encoding respiratory enzyme subunits were identified as the best knockout targets for improving hexose fermentation in microaerobic conditions. Specifically, deletion of either COX9 or QCR9 resulted in higher ethanol production rates than the parental strain by 37% and 27%, respectively, with slight growth disadvantages. Also, deletion of QCR6 led to improved ethanol production rate by 24% with no growth disadvantage. The beneficial effects of these gene deletions were consistently demonstrated in different strain backgrounds and with four common hexoses. The combination of stoichiometric modeling and genetic screening using a systematic knockout collection was useful for narrowing a large set of gene targets and identifying targets of interest.

Field of study: Biology
Sphingomyelin synthase 1 suppresses ceramide production and apoptosis post-photodamage.

The role of sphingomyelin synthase 1 (SMS1), the Golgi membrane isoform of the enzyme, in ceramide metabolism and apoptosis after photodamage with the photosensitizer Pc 4 (PDT) is unclear. In the present study, using electrospray ionization/double mass spectrometry, we show that in Jurkat cells overexpressing SMS1, increases in ceramides were lower than in empty-vector transfectants post-PDT. Similarly, the responses of dihydroceramides and dihydrosphingosine, precursors of ceramide in the de novo synthetic pathway, were attenuated in SMS1-overexpressor after photodamage, suggesting the involvement of the de novo pathway. Overexpression of SMS1 was associated with differential regulation of sphingomyelin levels, as well as with the reduced inhibition of the enzyme post-treatment. Concomitant with the suppressed ceramide response, PDT-induced DEVDase activation was substantially reduced in SMS1-overexpressors. The data show that overexpression of SMS1 is associated with suppressed ceramide response and apoptotic resistance after photodamage.

Field of study: Biology, Chemistry
Undertreatment of asthma in Dutch general practice.

The relationships between the medication prescribed and four measures of morbidity were assessed in 150 Dutch patients with asthma in general practice. Undertreatment was operationalized as a discrepancy between medication and morbidity severity. Of the patients, 11.3% were undertreated as measured by the number of days during which activities were interrupted by asthmatic symptoms. Additional measures such as the number of nights interrupted by asthma, number of attacks and episodes of wheezing, indicated that 28.0%, 24.0% and 34.5% of the patients respectively were undertreated. It is concluded that asthma seems to be undertreated in general practice in The Netherlands, a finding which is consistent with research on this subject in the UK and other countries. Possible reasons for the persistence of undertreatment of asthma are discussed, and suggestions for overcoming it are offered.

Field of study: Medicine
Relationship between activity of hepatic 3-hydroxy-3-methylglutaryl-coenzyme A reductase and secretion of very-low-density-lipoprotein cholesterol by the isolated perfused liver and in the intact rat.

The hepatic output of triacylglycerol and cholesterol from very-low-density lipoprotein (VLD lipoprotein), and the activity of 3-hydroxy-3-methylglutaryl-coenzyme A reductase were compared in the isolated perfused rat-liver preparation and in the intact rat. The output of triacylglycerol and cholesterol from VLD lipoprotein by the perfused liver was stimulated by oleate concomitant with stimulation of hepatic microsomal hydroxymethylglutaryl-coenzyme A reductase activity. In the intact animal treated with Triton WR-1339, the magnitude of secretion of triacylglycerol and cholesterol from VLD lipoprotein coincided with the diurnal rhythm of hepatic hydroxymethylglutaryl-coenzyme A reductase activity, which was maximal at 24:00 h and minimal at 12:00 h. These observations suggest that the stimulation of the reductase and of the secretion of cholesterol from VLD lipoprotein by non-esterified fatty acids, as observed with the isolated perfused rat liver preparation in vitro, may also be an important physiological mechanism in vivo. Hepatic cholesterogenesis may be stimulated under conditions conductive to the secretion of the VLD lipoprotein, the primary transport form for triacylglycerol in the postabsorptive state.

Field of study: Biology
The effect of fibronectin on the migration of keratinocytes.

Basal cell migration appears to be a crucial factor in the development of acquired cholesteatoma. We studied the effect of fibronectin (FN) on the migration of basal cells. Keratinocytes were prepared from epidermis of newborn rats and fractionated using Percoll gradients. The lightest cells were maturing keratinocytes and the heaviest, basal cells. The effect of various concentrations of FN on keratinocyte migration was studied using Boyden's chamber assay and the spreading assay methods. FN had little effect on mature keratinocytes, but FN markedly stimulated the migration of keratinocyte basal cells. FN appears to play an important role in stimulating basal cell keratinocyte migration.

Field of study: Biology
Involvement of the P Cluster in Intramolecular Electron Transfer within the Nitrogenase MoFe Protein (*)

Nitrogenase is the catalytic component of biological nitrogen fixation, and it is comprised of two component proteins called the Fe protein and MoFe protein. The Fe protein contains a single Fe4S4 cluster, and the MoFe protein contains two metallocluster types called the P cluster (Fe8S8) and FeMo-cofactor (Fe7S9Mo-homocitrate). During turnover, electrons are delivered one at a time from the Fe protein to the MoFe protein in a reaction coupled to component-protein association-dissociation and MgATP hydrolysis. Under conditions of optimum activity, the rate of component-protein dissociation is rate-limiting. The Fe protein's Fe4S4 cluster is the redox entity responsible for intermolecular electron delivery to the MoFe protein, and FeMo-cofactor provides the substrate reduction site. In contrast, the role of the P cluster in catalysis is not well understood although it is believed to be involved in accumulating electrons delivered from the Fe protein and brokering their intramolecular delivery to the substrate reduction site. A nitrogenase component-protein docking model, which is based on the crystallographic structures of the component proteins and which pairs the 2-fold symmetric surface of the Fe protein with the exposed surface of the MoFe protein's pseudosymmetric αβ interface, is now available. During component-protein interaction, this model places the P cluster between the Fe protein's Fe4S4 cluster and FeMo-cofactor, which implies that the P cluster is involved in mediating intramolecular electron transfer between the clusters. In the present study, evidence supporting this idea was obtained by demonstrating that it is possible to alter the rate of substrate reduction by perturbing the polypeptide environment between the P cluster and FeMo-cofactor without necessarily disrupting the metallocluster polypeptide environments or altering component-protein interaction.

Field of study: Biology
Low-density lipoprotein hemoperfusion using a modified polyacrylate adsorber: in vitro, ex vivo, and first clinical results.

Current lipid apheresis techniques can remove low-density lipoprotein (LDL) cholesterol only from plasma, i.e., a primary cell-plasma separation step is mandatory. This article describes in vitro, ex vivo, and clinical results using a new LDL adsorber compatible with human whole blood. It consists of modified polyacrylate, the negative charges of which can interact with the positively charged protein B moiety of LDL, thus retaining these particles on the surface of the adsorber. After the efficacy and selectivity of LDL removal had been demonstrated in vitro and ex vivo, a clinical pilot study corroborated these results. Thus, treating 60 ml of blood per kilogram of body weight in a single session, LDL hemoperfusion reduced LDL cholesterol by 50%, lipoprotein (a) by 17%, and triglycerides by 19% in 6 hypercholesterolemic patients. High-density lipoprotein cholesterol recovery amounted to 97%. In conclusion, LDL hemoperfusion holds great promise for the future.

Field of study: Biology, Medicine