Miracle-dz/UniFAR-FTUs huggingface dataset:
Balanced Context-Free Grammars, Hedge Grammars and Pushdown Caterpillar Automata

The XML community generally takes trees and hedges as the model for XML document instances and element content. In contrast, Berstel and Boasson have discussed XML documents in the framework of extended context-free grammar, modeling XML documents as Dyck strings and schemas as balanced grammars. How can these two models be brought closer together? We examine the close relatioship between Dyck strings and hedges, observing that trees and hedges are higher level abstractions than are Dyck primes and Dyck strings. We then argue that hedge grammars are effecively identical to balanced grammars and that balanced languages are identical to regular hedge languages, modulo encoding. From the close relationship between Dyck strings and hedges, we obtain a two-phase architecture for the parsing of balanced languages. We propose caterpillar automata with an additional pushdown stack as a new computational model for the second phase; that is, for the validation of XML documents. Balanced Context-Free Grammars, Hedge Grammars and Pushdown Caterpillar Automata Table of
O R I G I N a L I N V E S T I G a T I O N Open Access

Effect of empagliflozin monotherapy on postprandial glucose and 24-hour glucose variability in Japanese patients with type 2 diabetes mellitus: a randomized, double-blind, placebo-controlled, 4-week study Abstract Background: This study evaluated the effect of empagliflozin on postprandial glucose (PPG) and 24-hour glucose variability in Japanese patients with type 2 diabetes mellitus (T2DM).
Revenue comparisons for auctions when bidders have arbitrary types

This paper develops a methodology for characterizing expected revenue from auctions when bidders’ types come from an arbitrary distribution. In particular, types may be multidimensional, and there may be mass points in the distribution. One application extends existing revenue equivalence results. Another application shows that first-price auctions yield higher expected revenue than second-price auctions when bidders are risk averse and facefinancial constraints. This revenue ranking extends to risk-averse bidders with general forms of nonexpected utility preferences.
The conserved centrosomal protein FOR20 is required for assembly of the transition zone and basal body docking at the cell surface

Summary Within the FOP family of centrosomal proteins, the conserved FOR20 protein has been implicated in the control of primary cilium assembly in human cells. To ascertain its role in ciliogenesis, we have investigated the function of its ortholog, PtFOR20p, in the multiciliated unicellular organism Paramecium. Using combined functional and cytological analyses, we found that PtFOR20p specifically localises at basal bodies and is required to build the transition zone, a prerequisite to their maturation and docking at the cell surface and hence to ciliogenesis. We also found that PtCen2p (one of the two basal body specific centrins, an ortholog of HsCen2) is required to recruit PtFOR20p at the developing basal body and to control its length. By contrast, the other basal-body-specific centrin PtCen3p is not needed for assembly of the transition zone, but is required downstream, for basal body docking. Comparison of the structural defects induced by depletion of PtFOR20p, PtCen2p or PtCen3p, respectively, illustrates the dual role of the transition zone in the biogenesis of the basal body and in cilium assembly. The multiple potential roles of the transition zone during basal body biogenesis and the evolutionary conserved function of the FOP proteins in microtubule membrane interactions are discussed.
Characteristics Associated With Use of Public and Private Web Sites as Sources of Health Care Information: Results From a National Survey

Objective:We sought to determine the frequency with which Americans access health information from governmental (public sector) and nongovernmental (private sector) web sites and to identify similarities and differences in the characteristics associated with use of each type. Methods:Data derive from 928 individuals who responded to a November 2005 national survey. In addition to forms of health communication, we asked about age, gender, race, income, education, insurance, lifestyle, residence, satisfaction, literacy, and health. We report the extent of web site use stratified by sponsorship type—public and private. We also use χ2 tests to examine bivariate associations. Logistic regression and multiple imputation of missing data were used to examine the correlates of use in a multivariate context. Results:More than twice as many respondents visited private web sites (29.6%) than public web sites (13.2%). However, just 23.6% and 18.9% of private and public web site visitors, respectively, reported doing so once a month or more. Both public and private web site visitors were more likely to be better-educated respondents (odds ratio [OR] = 0.83, OR = 1.57) reporting greater concerns about health care access (OR = 1.28, OR = 1.20) than nonvisitors. Younger individuals (OR = 0.83) living in urban areas (OR = 1.59) with stronger health literacy (OR = 1.24) and reporting greater concerns about health care affordability (OR = 1.59) were more likely to visit privately sponsored web sites but nonpublicly sponsored ones. Conclusion:Relatively low utilization levels necessitate a concerted effort to improve the quality, accessibility, and relevance of Internet health information. Efforts to close the digital divide must recognize differences in user characteristics across governmental and nongovernmental web site providers.
Inflammatory Serum Protein Profiling of Patients with Lumbar Radicular Pain One Year after Disc Herniation

Earlier studies suggest that lumbar radicular pain following disc herniation may be associated with a local or systemic inflammatory process. In the present study, we investigated the serum inflammatory protein profile of such patients. All 45 patients were recruited from Oslo University Hospital, Ullevål, Norway, during the period 2007–2009. The new multiplex proximity extension assay (PEA) technology was used to analyze the levels of 92 proteins. Interestingly, the present data showed that patients with radicular pain 12 months after disc herniation may be different from other patients with regard to many measurable serum cytokines. Given a false discovery rate (FDR) of 0.10 and 0.05, we identified 41 and 13 proteins, respectively, which were significantly upregulated in the patients with severe pain one year after disc herniation. On the top of the list ranked by estimated increase we found C-X-C motif chemokine 5 (CXCM5; 217% increase), epidermal growth factor (EGF; 142% increase), and monocyte chemotactic protein 4 (MCP-4; 70% increase). Moreover, a clear overall difference in the serum cytokine profile between the chronic and the recovered patients was demonstrated. Thus, the present results may be important for future protein serum profiling of lumbar radicular pain patients with regard to prognosis and choice of treatment. We conclude that serum proteins may be measurable molecular markers of persistent pain after disc herniation.
Involvement of the Portal at an Early Step in Herpes Simplex Virus Capsid Assembly

ABSTRACT DNA enters the herpes simplex virus capsid by way of a ring-shaped structure called the portal. Each capsid contains a single portal, located at a unique capsid vertex, that is composed of 12 UL6 protein molecules. The position of the portal requires that capsid formation take place in such a way that a portal is incorporated into one of the 12 capsid vertices and excluded from all other locations, including the remaining 11 vertices. Since initiation or nucleation of capsid formation is a unique step in the overall assembly process, involvement of the portal in initiation has the potential to cause its incorporation into a unique vertex. In such a mode of assembly, the portal would need to be involved in initiation but not able to be inserted in subsequent assembly steps. We have used an in vitro capsid assembly system to test whether the portal is involved selectively in initiation. Portal incorporation was compared in capsids assembled from reactions in which (i) portals were present at the beginning of the assembly process and (ii) portals were added after assembly was under way. The results showed that portal-containing capsids were formed only if portals were present at the outset of assembly. A delay caused formation of capsids lacking portals. The findings indicate that if portals are present in reaction mixtures, a portal is incorporated during initiation or another early step in assembly. If no portals are present, assembly is initiated in another, possibly related, way that does not involve a portal.
Has payment by results affected the way that English hospitals provide care? Difference-in-differences analysis

Objective To examine whether the introduction of payment by results (a fixed tariff case mix based payment system) was associated with changes in key outcome variables measuring volume, cost, and quality of care between 2003/4 and 2005/6. Setting Acute care hospitals in England. Design Difference-in-differences analysis (using a control group created from trusts in England and providers in Scotland not implementing payment by results in the relevant years); retrospective analysis of patient level secondary data with fixed effects models. Data sources English hospital episode statistics and Scottish morbidity records for 2002/3 to 2005/6. Main outcome measures Changes in length of stay and proportion of day case admissions as a proxy for unit cost; growth in number of spells to measure increases in output; and changes in in-hospital mortality, 30 day post-surgical mortality, and emergency readmission after treatment for hip fracture as measures of impact on quality of care. Results Length of stay fell more quickly and the proportion of day cases increased more quickly where payment by results was implemented, suggesting a reduction in the unit costs of care associated with payment by results. Some evidence of an association between the introduction of payment by results and growth in acute hospital activity was found. Little measurable change occurred in the quality of care indicators used in this study that can be attributed to the introduction of payment by results. Conclusion Reductions in unit costs may have been achieved without detrimental impact on the quality of care, at least in as far as these are measured by the proxy variables used in this study.
Accurate Task-Space Tracking for Humanoids with Modeling Errors Using Iterative Learning Control

Precise task-space tracking with manipulator-type systems requires an accurate kinematic model. In contrast to traditional manipulators, sometimes it is difficult to obtain an accurate kinematic model of humanoid robots due to complex structure and link flexibility. Also, prolonged use of the robot will lead to some parts wearing out or being replaced with a slightly different alignment, thus throwing off the initial calibration. Therefore, there is a need to develop a control algorithm that can compensate for the modeling errors and quickly retune itself, if needed, taking into account the controller bandwidth limitations and high dimensionality of the system. In this paper, we develop an iterative learning control algorithm that can work with existing inverse kinematics solvers to refine the joint-level control commands to enable precise tracking in the task space. We demonstrate the efficacy of the algorithm on a theme-park-type humanoid doing a drawing task, serving drink in a glass, and serving a drink placed on a tray without spilling. The iterative learning control algorithm is able to reduce the tracking error by at least two orders of magnitude in less than 20 trials.
Two Polymorphic Variants of ABCC1 Selectively Alter Drug Resistance and Inhibitor Sensitivity of the Multidrug and Organic Anion Transporter Multidrug Resistance Protein 1

In this study we compared the in silico predictions of the effect of ABCC1 nonsynonymous single nucleotide polymorphisms (nsSNPs) with experimental data on MRP1 transport function and response to chemotherapeutics and multidrug resistance protein 1 (MRP1) inhibitors. Vectors encoding seven ABCC1 nsSNPs were stably expressed in human embryonic kidney (HEK) cells, and levels and localization of the mutant MRP1 proteins were determined by confocal microscopy and immunoblotting. The function of five of the mutant proteins was determined using cell-based drug and inhibitor sensitivity and efflux assays, and membrane-based organic anion transport assays. Predicted consequences of the mutations were determined by multiple bioinformatic methods. Mutants C43S and S92F were correctly routed to the HEK cell plasma membrane, but the levels were too low to permit functional characterization. In contrast, levels and membrane trafficking of R633Q, G671V, R723Q, A989T, and C1047S were similar to wild-type MRP1. In cell-based assays, all five mutants were equally effective at effluxing calcein, but only two exhibited reduced resistance to etoposide (C1047S) and vincristine (A989T; C1047S). The GSH-dependent inhibitor LY465803 (LY465803 [N-[3-(9-chloro-3-methyl-4-oxo-4H-isoxazolo-[4,3-c]quinolin-5-yl)-cyclohexylmethyl]-benzamide)] was less effective at blocking calcein efflux by A989T, but in a membrane-based assay, organic anion transport by A989T and C1047S was inhibited by MRP1 modulators as well as wild-type MRP1. GSH accumulation assays suggest cellular GSH efflux by A989T and C1047S may be impaired. In conclusion, although six in silico analyses consistently predict deleterious consequences of ABCC1 nsSNPs G671V, changes in drug resistance and inhibitor sensitivity were only observed for A989T and C1047S, which may relate to GSH transport differences.
Data Mining at CALD-CMU: Tools, Experiences and Research Directions

We describe the data mining problems and solutions that we have encountered in the Center for Automated Learning and Discovery (CALD) at CMU. Speci(cid:12)cally, we describe these settings and their operational characteristics, describe our proposed solutions, list the performance results, and (cid:12)nally outline future research directions
Evaluation of Δ(9) -tetrahydrocannabinol detection using DrugWipe5S(®) screening and oral fluid quantification after Quantisal™ collection for roadside drug detection via a controlled study with chronic cannabis users.

Oral fluid (OF) is potentially useful to detect driving under the influence of drugs because of its ease of sampling. While cannabis is the most prevalent drug in Europe, sensitivity issues for Δ(9) -tetrahydrocannabinol (THC) screening and problems during OF collection are observed. The ability of a recently improved OF screening device - the DrugWipe5S(®) , to detect recent THC use in chronic cannabis smokers, was studied. Ten subjects participated in a double-blind placebo-controlled study. The subjects smoked two subsequent doses of THC; 300 µg/kg and 150 µg/kg with a pause of 75 min using a Volcano vapourizer. DrugWipe5S(®) screening and OF collection using the Quantisal™ device were performed at baseline, 5 min after each administration and 80 min after the last inhalation. Blood samples were drawn simultaneously. The screening devices (n = 80) were evaluated visually after 8 min, while the corresponding OF and serum samples were analyzed respectively with ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) or gas chromatography-mass spectrometry (GC-MS). Neat OF THC concentrations ranged from 12 361 ng/g 5 min after smoking down to 34 ng/g 80 min later. Under placebo conditions, a median THC concentration of 8 ng/g OF (0-746 ng/g) and < 1 ng/ mL serum (0-7.8 ng/mL) was observed. The DrugWipe5S(®) was positive just after smoking (90%); however, sensitivity rapidly decreased within 1.5 h (50%). Sensitivity of DrugWipe5S(®) should be improved. As chronic cannabis users have high residual THC concentrations in their serum and OF, confirmation cut-offs should be set according to the aim of detecting recent drug use or establishing zero tolerance.
The Millennium Galaxy Catalogue: on the natural subdivision of galaxies

The distribution of global photometric, spectroscopic, structural and morphological parame- ters for a well-defined sample of 350 nearby galaxies has been examined. The usual trends were recovered demonstrating that E/S0 galaxies are redder, more quiescent, more centrally concentrated and possess larger Sersic indices than late-type galaxies. Multivariate statistical analyses were performed to examine the distribution of all parameters simultaneously. The main result of these analyses was the existence of only two classes of galaxies, corresponding closely to early and late types. Linear discriminant analysis (LDA) was able to reproduce the classifications of early- and late-type galaxies with high success, but further refinement of galaxy types was not reproduced in the distribution of observed galaxy properties. A principal components analysis (PCA) showed that the major variance of the parameter set corresponded to a distinction between early and late types, highlighting the importance of the distinction. A hierarchical clustering analysis (HCA) revealed only two clear natural classes within the parameter set, closely corresponding to early and late types. Early and late types are clearly distinct and the distinction is of fundamental importance. In contrast, late types from Sa to Irr are smoothly distributed throughout the parameter space. A population of galaxies classified by eye as elliptical/lenticular, and exhibiting concentration indices similar to early types were found to have a significant star formation activity. These galaxies are preferentially faint, suggesting they are low-mass systems. Ke yw ords: galaxies: evolution - galaxies: fundamental parameters.
3-Dimensional Optical Orthogonal Codes With Ideal Autocorrelation-Bounds and Optimal Constructions

Several new constructions of 3-D optical orthogonal codes are presented here. In each case, the codes have ideal OFF-peak autocorrelation <inline-formula> <tex-math notation="LaTeX">$\mathbf { \lambda _{a} = 0} $ </tex-math></inline-formula>, and in all, but one case a cross correlation of <inline-formula> <tex-math notation="LaTeX">$\mathbf { \lambda _{c} = 1} $ </tex-math></inline-formula>. All codes produced are optimal with respect to the applicable Johnson bound either presented or developed here. Thus, on one hand the codes are as large as possible, and on the other, the bound(s) are shown to be tight. All codes are constructed by using a particular automorphism (a singer cycle) of PG(k, q), the finite projective geometry of dimension <inline-formula> <tex-math notation="LaTeX">$k $ </tex-math></inline-formula> over the field of order q, or by using an affine analogue in <inline-formula> <tex-math notation="LaTeX">$AG(k, q) $ </tex-math></inline-formula>.
Autoantibodies to IGF-1 binding sites in thyroid associated ophthalmopathy.

Graves' disease is an autoimmune disorder but the nature of the association between hyperthyroidism and ophthalmopathy is not yet understood. Serum autoantibodies to orbital tissues have previously been identified and the cross-reactivity with orbital and thyroid antigens has been implicated in the development of thyroid-associated ophthalmopathy (TAO). The ophthalmopathy of Graves' disease is remarkable for the hypertrophy of extraocular muscles and proliferation of fibroblasts within the orbit; features which suggest a possible involvement of growth factors. The present study was therefore undertaken to investigate the interaction of IgGs extracted from the sera of patients with Graves' disease, with or without overt ophthalmopathy, with respect to IGF-1 receptor binding sites on fibroblasts from human orbital tissue. IGF-1 binding sites were demonstrated on human orbital fibroblast monolayers grown from eye muscle explants. These cells exhibited a population of high affinity IGF-1 binding sites (Kd, 0.5nM SEM +/- 0.05). IgG prepared from sera taken from patients with Graves' disease (n = 23) significantly inhibited [125I]IGF-1 binding to orbital fibroblasts when compared to IgGs prepared from normal volunteers (n = 13, p < 0.002). It was found that 12 of 23 (52%) patients' IgG samples gave rise to significant levels of inhibition of [125I]IGF-1 binding to orbital fibroblasts. The IgG preparations did not bind directly to IGF-1. This study demonstrates that IgG prepared from patients with Graves' disease with or without overt ophthalmopathy interact with IGF-1 binding sites on orbital fibroblasts whereas IgG from normal subjects had no significant effect. (ABSTRACT TRUNCATED AT 250 WORDS)
Prospective study of the value of ultrasound measurements in the diagnosis of acute rejection following renal transplantation

In this prospective study we have used ultrasonographic measurements of the cross‐sectional area of transplanted kidneys, as an objective assessment of graft size, for diagnosis of acute rejection episodes. Sixty episodes of acute graft dysfunction (serum creatinine rise of ≥ 30 μmol/l) were studied in 40 patients. Tru‐Cut® biopsy under ultrasound control was performed in all cases and 36 episodes of acute cellular rejection were identified. An increase in graft cross‐sectional area of ≥ 10 per cent was defined as a positive scan, indicative of an acute rejection episode. Using these criteria, ultrasound correctly diagnosed rejection in 29 out of 36 cases (sensitivity 81 per cent) and there were four false positive results (specificity 83 per cent). The investigation had a predictive value of 88 per cent when positive and 74 per cent when negative.
The differential view of genotype–phenotype relationships

An integrative view of diversity and singularity in the living world requires a better understanding of the intricate link between genotypes and phenotypes. Here we re-emphasize the old standpoint that the genotype–phenotype (GP) relationship is best viewed as a connection between two differences, one at the genetic level and one at the phenotypic level. As of today, predominant thinking in biology research is that multiple genes interact with multiple environmental variables (such as abiotic factors, culture, or symbionts) to produce the phenotype. Often, the problem of linking genotypes and phenotypes is framed in terms of genotype and phenotype maps, and such graphical representations implicitly bring us away from the differential view of GP relationships. Here we show that the differential view of GP relationships is a useful explanatory framework in the context of pervasive pleiotropy, epistasis, and environmental effects. In such cases, it is relevant to view GP relationships as differences embedded into differences. Thinking in terms of differences clarifies the comparison between environmental and genetic effects on phenotypes and helps to further understand the connection between genotypes and phenotypes.
Pimpinella anisum L. ethanolic extract ameliorates the gentamicin‐ induced nephrotoxicity in rats

Gentamicin (GM) is one of the commonest causes of drug‐induced nephrotoxicity. Moreover, oxidative stress plays an important role in gentamicin‐induced nephrotoxicity. The current study aimed to explore the antioxidant and protective effects of Pimpinella anisum (P. anisum) on the alleviation of GM‐induced damage.