julilili42/papers huggingface dataset:
Minimum Quartet Inconsistency is fixed parameter tractable
2009-03-02

We study the parameterized complexity of the problem to reconstruct a binary (evolutionary) tree from a complete set of quartet topologies in the case of a limited number of errors. More precisely, we are given n taxa, exactly one topology for every subset of 4 taxa, and a positive integer k (the parameter). Then, the Minimum Quartet Inconsistency (MQI) problem is the question whether we can nd an evolutionary tree inducing a set of quartet topologies that differs from the given set in only k quartet topologies. The more general version of the problem where we are not necessarily given a topology for every subset of four taxa appears to be fixed parameter intractable. For the MQI problem, however, which is also NP-complete, we can compute the required tree in time
Embryo development, stress protein (Hsp70) responses, and histopathology in zebrafish (Danio rerio) following exposure to nickel chloride, chlorpyrifos, and binary mixtures of them
2009-03-03

Abstract Two different classes of chemicals were tested in a multilevel approach in this study: NiCl 2 as a representative for heavy metals and chlorpyrifos, a pesticide. Both, the single substances and mixtures of them were investigated for their effects on embryonic development, histological alterations, and the stress protein (Hsp70) response in the zebrafish Danio rerio . Fishes were exposed from fertilization of eggs up to a maximum of 168 h post fertilization, depending on the investigated endpoint. NiCl 2 led to effects in all tests which, however, were less severe at the histopathological level than in developmental (hatching success) and stress protein studies. Chlorpyrifos did not lead to developmental alterations but it was found to induce the Hsp70 response as well as histopathological damages. Mixtures of both substances resulted in similar results as the single substances; the results suggest an independent mode of action of these two substances and additivity of their effects. © 2009 Wiley Periodicals, Inc. Environ Toxicol, 2010.
The Inhibitory Effect of Recent Type 2 Diabetes Risk Loci on Insulin Secretion Is Modulated by Insulin Sensitivity
2009-03-03

The negative effects of the risk alleles on ss-cell function appear additive in subjects with low insulin sensitivity but not in subjects with high insulin sensitivity. Effective compensatory mechanisms may exist in subjects with high insulin sensitivity that limit the impact of these genes.
Multiple Focus
2009-03-03

This paper presents the results of an experimental study on multiple focus configurations, that is, structures containing two nested focus-sensitive operators plus two foci supposed to associate with those operators. There has been controversial discussion in the semantic literature regarding whether or not an interpretation is acceptable that corresponds to this association. While the data are unclear, the issue is of considerable theoretical significance, as it distinguishes between the available theories of focus interpretation. Some theories (e.g. Rooth's 1992) predict such a pattern of association with focus to be impossible, while others (such as Wold's 1996) predict it to be acceptable. The results of our study show the data to be unacceptable rather than acceptable, favouring important aspects of the theory of focus interpretation developed by Rooth.
Dewetting of an Organic Semiconductor Thin Film Observed in Real‐time
2009-03-04

We study the growth and the post-growth dewetting process of the organic semiconductor diindenoperylene (DIP) using real-time X-ray reflectivity measurements. We show that a DIP monolayer deposited in UHV onto silicon oxide dewets via the formation of bilayer islands. From the time resolved structural data we estimate the rate constant for interlayer diffusion of DIP molecules. Post-growth AFM measurements confirm the conclusions from the X-ray data and show the morphology of the dewetted film.
Erythropoietin receptor is expressed in meningiomas and lower levels are associated with tumour recurrence
2009-03-04

Aims: The Epo‐EpoR pathway plays a role in tumour growth, metastasis and treatment resistance and is a potential target in oncological treatment. As the EpoR status in human meningiomas is unknown, our aim was to characterize EpoR expression in these tumours. Methods: We examined 131 meningioma samples of all WHO grades from 116 patients by immunohistochemistry for EpoR. Among these, 25 meningiomas showed brain invasion and 29 patients had a further tumour recurrence. A group of 20 patients without tumour recurrence served as controls. In 12 cases we were able to compare both the primary and the following recurrent tumours. The presence of EpoR in meningiomas was confirmed by RT‐PCR and Western blot. Results: EpoR was expressed in all meningiomas. Statistical analysis revealed that the mean expression levels of EpoR were significantly lower in primary tumours with known recurrence compared with a recurrence‐free control group. Additional matched pair analysis in individual cases showed no significant differences between primary and recurrent tumours. No significant correlation between EpoR expression and WHO grade, age, sex or brain invasion was detected. Using specific primer pairs for RT‐PCR, we were able to detect all three known isoforms of EpoR: the full‐length isoform EpoR‐F, the truncated isoform EpoR‐T and the soluble isoform EpoR‐S. Conclusions: Our results demonstrate the expression of EpoR in meningiomas. Lower EpoR mean levels might be a useful marker for a higher recurrence risk, but further studies are needed to clarify the influence of EpoR on recurrences and the role of the different isoforms.
Microsatellite loci for Euglossa annectans (Hymenoptera: Apidae) and their variability in other orchid bees
2009-03-05

Abstract Orchid or euglossine bees are conspicuous Hymenoptera of the Neotropics, where they pollinate numerous plants, including orchids. Allozyme‐based analyses have suggested that their populations suffer from inbreeding, as evidenced by so‐called diploid male production. We have developed nine polymorphic microsatellite loci for the widespread Euglossa annectans , with observed heterozygosities ranging from 0.143 to 0.952 and between 2 and 9 alleles per species. These loci will be useful for analysis of relatedness, population genetic structure and diploid male production in this and related species.
[Sudden death in the presence of systemic mastocytosis and urticaria pigmentosa].
2009-03-05

Systemic mastocytosis is an extremely rare disease characterised by abnormal mast cell production and accumulation of mast cells in the bone marrow or organs, and to some extent also in the skin (urticaria pigmentosa). To date there have been no descriptions of death caused by systemic mastocytosis. The present first description of such a fatality is based upon a case of anaphylactic histamine shock, probably caused by the consumption of peanuts. The affected person suffered from urticaria pigmentosa and developed a fairly typical pruritus prior to death. In the serum sample taken post-mortem the tryptase concentration was markedly elevated. The diagnosis of systemic mastocytosis was established on the basis of two primary and three secondary criteria according to the WHO classification, which underlines the importance of histological investigations in cases where the cause of death is unclear.
Novel multi‐peptide vaccination in Hla‐A2+ hormone sensitive patients with biochemical relapse of prostate cancer
2009-03-06

Abstract BACKGROUND A phase I/II trial was conducted to assess feasibility and tolerability of tumor associated antigen peptide vaccination in hormone sensitive prostate carcinoma (PC) patients with biochemical recurrence after primary surgical treatment. METHODS Nineteen HLA‐A2 positive patients with rising PSA without detectable metastatic disease or local recurrence received 11 HLA‐A*0201‐restricted and two HLA class II synthetic peptides derived from PC tumor antigens subcutaneously for 18 months or until PSA progression. The vaccine was emulgated in montanide ISA51 and combined with imiquimod, GM‐CSF, mucin‐1‐mRNA/protamine complex, local hyperthermia or no adjuvant. PSA was assessed, geometric mean doubling times (DT) calculated and clinical performance monitored. RESULTS PSA DT of 4 out of 19 patients (21%) increased from 4.9 to 25.8 months during vaccination. Out of these, two patients (11%) exhibited PSA stability for 28 and 31 months which were still continuing at data cut‐off. One patient showed no change of PSA DT during vaccination but decline after the therapy. Three patients had an interim PSA decline or DT increase followed by DT decrease compared to baseline PSA DT. Three of the responding patients received imiquimod and one the mucin‐1‐mRNA/protamine complex as adjuvant; both are Toll‐like receptor‐7 agonists. Eleven (58%) patients had progressive PSA values. The vaccine was well tolerated, and no grade III or IV toxicity occurred. CONCLUSION Multi‐peptide vaccination stabilized or slowed down PSA progress in four of 19 cases. The vaccination approach is promising with moderate adverse events. Long‐term stability delayed androgen deprivation up to 31 months. TLR‐7 co‐activation seems to be beneficial. Prostate 69: 917–927, 2009. © 2009 Wiley‐Liss, Inc.
Numerical Values Leave a Semantic Imprint on Associated Signs in Monkeys
2009-03-06

Abstract Animals and humans share an evolutionary ancient quantity representation which is characterized by analog magnitude features: Discriminating magnitudes becomes more difficult with increasing set sizes (size effect) and with decreasing distance between two numerosities (distance effect). Humans show these effects even with number symbols. We wondered whether monkeys would show the same psychophysical effects with numerical signs and addressed this issue by training three monkeys to associate visual shapes with numerosities. We then confronted the monkeys with trials in which they had to match these visual signs with each other. The monkeys' performance in this shape versus shape protocol was positively correlated with the numerical distance and the magnitudes associated with the signs. Additionally, the monkeys responded significantly slower for signs with higher assigned numerical values. These findings suggest that the numerical values imprint their analog magnitudes characteristics onto the associated visual sign in monkeys, an effect that we also found reflected in the discharges of prefrontal neurons. This provides evidence for a precursor of the human number symbol knowledge.
Growth of the MRI in accretion discs - the influence of radiation transport
2009-03-06

In this paper we investigate the influence of radiative transport on the\\ngrowth of the magnetorotational instability (MRI) in accretion discs. The\\nanalysis is performed by use of analytical and numerical means. We provide a\\ngeneral dispersion relation together with the corresponding eigenfunctions\\ndescribing the growth rates of small disturbances on a homogeneous background\\nshear flow. The dispersion relation includes compressibility and radiative\\neffects in the flux-limited diffusion approximation. By introducing an\\neffective speed of sound, all the effects of radiation transport can be\\nsubsumed into one single parameter. It can be shown that the growth rates of\\nthe vertical modes -- which are the fastest growing ones -- are reduced by\\nradiative transport. For the case of non-vertical modes, the growth rates may\\ninstead be enhanced. We quantify the effects of compressibility and radiative\\ndiffusion on the growth rates for the gas-pressure dominated case. The\\nanalytical discussion is supplemented by numerical simulations, which are also\\nused for a first investigation of the non-linear stage of the MRI in\\ngas-pressure dominated accretion discs with radiation transport included.\\n
Increase of BDNF Serum Concentration in Lithium Treated Patients with Early Alzheimer's Disease
2009-03-09

Preclinical and clinical studies gave evidence that lithium could be useful in the treatment of Alzheimer's disease (AD). In experimental investigations, lithium induces brain-derived neurotrophic factor (BDNF). Recent studies have found a decrease of BDNF in the serum and brains of AD patients with potentially consecutive lack of neurotrophic support. We assessed the influence of a lithium treatment on BDNF serum concentration in a subset of a greater sample recruited for a randomized, single-blinded, placebo-controlled, parallel-group multicenter 10-week study, investigating the efficacy of lithium treatment in AD patients. In AD patients treated with lithium, a significant increase of BDNF serum levels, and additionally a significant decrease of ADAS-Cog sum scores in comparison to placebo-treated patients, were found. Diminution of cognitive impairment was inversely correlated with lithium serum concentration. Upregulation of BDNF might be part of a neuroprotective effect of lithium in AD patients. The results of the present investigation encourage performing studies with longer treatment phases to observe potential positive long-term effects of lithium in AD patients.
PUVA-bath photochemotherapy and isotretinoin in sclerodermatous graft-versus-host disease.
2009-03-09

Chronic graft-versus-host disease (GVHD) is almost always associated with skin diseases appearing either as lichenoid GVHD, sclerodermatous GVHD (sGVHD) or as eosinophilic fasciitis-like disease. The two latter frequently result in severe and deep sclerosis. Immunosuppressive therapy is of little help in sclerodermatous or eosinophilic fasciitis-like types of GVHD. Based on data showing that PUVA-bath photochemotherapy is effective in the treatment of severe localized sclerosis of the skin, we investigated the efficacy of PUVA-bath photochemotherapy and isotretinoin in sGVHD. In a retrospective study we analyzed fourteen consecutive patients with sGVHD who received PUVA-bath photochemotherapy, five in combination with oral isotretinoin. Seven patients improved and four showed complete remission. Surprisingly, the therapy was complicated by the development of ulcers within the sclerotic plaques during the early periods of treatment. These ulcers cleared in most patients when PUVA-bath photochemotherapy was continued. Thus, PUVA-bath photochemotherapy alone or in combination with isotretinoin may resolve or improve GVHD associated sclerosis in selected patients.
Intended and unintended consequences of internal motivation to behave nonprejudiced: The case of benevolent discrimination
2009-03-09

Abstract Internal motivation to behave nonprejudiced reduces prejudice. The present research looks at the impact of internal motivation in a special case of prejudiced behavior, namely benevolent discrimination. It was hypothesized that internal motivation does not reduce, but rather increases benevolent discrimination as long as individuals are not aware of its negative consequences. This is because of the positive intention required to show benevolent discrimination. Once the negative consequences have been made salient, internal motivation will facilitate self‐criticism of one's own benevolently discriminating behavior, which will be reflected in a more critical reappraisal of previous benevolently discriminating behavior. The predictions were supported in three studies. Study 1 analyzed the impact of internal motivation on benevolent discrimination. Study 2 and 3 analyzed the effect of internal motivation on the critical reappraisal of one's own benevolently discriminating behavior. The implications for the regulation of benevolent discrimination in the broader context of social discrimination are discussed. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Early Effects of Intravitreal Triamcinolone Acetonide on Inflammation and Proliferation in Human Choroidal Neovascularization
2009-03-09

Triamcinolone acetonide has no inhibitory effect on macrophage infiltration or ICAM-1, Thy-1, or VEGF expression in CNV membranes in the early term. The clinical benefits of TA are probably not based on pure antiinflammatory or VEGF-suppressing mechanisms.
In Vivo and In Vitro Patterns of the Activity of Simocyclinone D8, an Angucyclinone Antibiotic from Streptomyces antibioticus
2009-03-10

ABSTRACT Simocyclinone D8 (SD8) exhibits antibiotic activity against gram-positive bacteria but not against gram-negative bacteria. The molecular basis of the cytotoxicity of SD8 is not fully understood, although SD8 has been shown to inhibit the supercoiling activity of Escherichia coli gyrase. To understand the mechanism of SD8, we have employed biochemical assays to directly measure the sensitivities of E . coli and Staphylococcus aureus type II topoisomerases to SD8 and microarray analysis to monitor the cellular responses to SD8 treatment. SD8 is a potent inhibitor of either E . coli or S . aureus gyrase. In contrast, SD8 exhibits only a moderate inhibitory effect on S . aureus topoisomerase IV, and E . coli topoisomerase IV is virtually insensitive to SD8. The antimicrobial effect of SD8 against E . coli has become evident in the absence of the AcrB multidrug efflux pump. As expected, SD8 treatment exhibits the signature responses to the loss of supercoiling activity in E . coli : upregulation of gyrase genes and downregulation of the topoisomerase I gene. Unlike quinolone treatment, however, SD8 treatment does not induce the SOS response. These results suggest that DNA gyrase is the target of SD8 in both gram-positive and gram-negative bacteria and that the lack of the antibacterial effect against gram-negative bacteria is due, in part, to the activity of the AcrB efflux pump.
The Minute Hand Phenomenon in the Clock Test of Patients With Early Alzheimer Disease
2009-03-10

Common scoring systems for the Clock Test do not sufficiently emphasize the correct time representation by the clock hands. We compared Clock Drawing, Clock Setting, and Clock Reading in healthy control persons, patients with mild cognitive impairment, early Alzheimer disease and progressed Alzheimer disease particularly analyzing clock time representation. We found that healthy control persons and participants with mild cognitive impairment did not show any impairment in Clock Test performance. Patients with early Alzheimer disease could be discriminated from healthy control persons and participants with mild cognitive impairment solely by misplacement of the minute hand in Clock Drawing and Clock Setting. The progressed Alzheimer disease group showed significantly more impairments in all Clock Test variants. It is assumed that early stage Alzheimer disease patient deficits in Clock Tests are mainly determined by a reduced access to semantic memory about the appearance and functionality of a clock.
Cellulose Pads (Hydrotin‐C): A New Solid Coupling Agent
2009-03-10

Objectives: Hydrotin‐C is a bacterial cellulose consisting of 90% of physiological solution. The cellulose pad is smooth and elastic and cannot be torn, and is therefore suitable for use on any local skin condition. The aim of this study was to evaluate the image quality (IQ) and transducer pressure of Hydrotin‐C‐Pads as a solid coupling agent compared with standard coupling gel. Methods: To date, transthoracic echocardiography has been performed in 51 patients (ongoing study) using standard coupling gel and Hydrotin‐C‐Pads. The IQ was categorized as follows: 1 = excellent, 2 = good, 3 = poor, 4 = inadequate. All patients were questioned about the transducer pressure, which was categorized as: 0 = less, 1 = equal, 2 = more. The body mass index (BMI) was documented for all patients. Results: The IQ was very good with Hydrotin‐C‐Pads. The IQ was better in 84% of all patients. In patients with a BMI of over 25 and in patients with a BMI of over 30, Hydrotin‐C‐Pads was also better compared with standard gel. The transducer pressure was lower in 33 patients. Conclusions: Hydrotin‐C‐Pads can be used as a solid ultrasonic coupling agent. Because of the consistent thickness of the coupling zone, the IQ seems to be better for Hydrotin‐C‐Pads compared with standard coupling gel. The transducer presser is lower, and these pads are easy to apply and are reusable and reduce the burden of clean‐up after treatment.
The story of O – is oxytocin the mediator of the placebo response?
2009-03-11

Abstract While the placebo responses in various medical conditions have been shown to follow a few basic principles such as expectancies, reward learning and Pavlovian conditioning, the underlying neurobiology and the mediating hormonal and/or neuromodulating processing have remained obscure. We here report the collected evidence that oxytocin (OXT), a 389‐amino acid polypeptide located on chromosome 3p25 that is released in the brain (hypothalamus) and in peripheral tissue, is the central mediator of the placebo response: we hypothesize that exogenous OXT via an OXT agonist will enhance the placebo response, while exogenous OXT blockade by an antagonist will reduce the placebo response in placebo analgesia and other placebo models. It is furthermore proposed that the placebo response in trials may be predicted by circulating plasma OXT levels, the OXT receptor density in the brain and/or the presence of one or more of the single nucleotide polymorphisms of the OXT promoter gene.
Borazine and Benzene Homo- and Heterodimers
2009-03-12

The homodimers of benzene and borazine as well as a heterodimer consisting of one benzene (bz) and one borazine (bor) molecule are investigated using MP2, SCS-MP2, and CCSD(T) theories in conjunction with basis sets of up to quadruple-zeta quality. Dimer geometries were completely optimized using the resolution of the identity approximation of MP2 with a QZVPP basis set and characterized by computation of harmonic vibrational frequencies using triple-zeta basis sets. While significant higher order correlation effects beyond MP2 are important for the benzene dimer, these are very small for the borazine dimer and intermediate for the heterodimer. The spin-component scaling (SCS) correction of MP2 produces binding energies for the borazine dimer that are too low but yields very good agreement with CCSD(T) for the heterodimer. The decrease in the intermolecular distance in the sandwich (S) configurations from bz(2) via bz-bor to bor(2) is accompanied by an increased binding energy and a change from second-order stationary points to a minimum for bor(2). The T isomer is less stable than the S configuration for bor(2), but it is preferred over the S and a parallel-displaced (PD) arrangement in the heterodimer. The following order of stability is obtained for the minima at the extrapolated CCSD(T) level: T(bz-bor) > S(bor(2)) > PD(bz-bor) > PD(bor(2)) > T(bor(2)) > PD(bz(2)). The most stable isomer at all levels of theory, T(bz-bor), features a NH...pi interaction.
Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation
2009-03-12

Abstract For evolutionary studies of polyploid species estimates of the genetic identity between species with different degrees of ploidy are particularly required because gene counting in samples of polyploid individuals often cannot be done, e.g., in triploids the phenotype AB can be genotypically either ABB or AAB. We recently suggested a genetic distance measure that is based on phenotype counting and made available the computer program POPDIST . The program provides maximum‐likelihood estimates of the genetic identities and distances between polyploid populations, but this approach is not informative for populations within species that only differ in their allele frequencies. We now close this gap by applying the frequencies of shared ‘bands’ in both populations to Nei's identity measure. Our simulation study demonstrates the close correlation between the band‐sharing identity and the genetic identity calculated on the basis of gene frequencies for any degree of ploidy. The new extended version of POPDIST (version 1.2.0) provides the option of choosing either the maximum‐likelihood estimator or the band‐sharing measure.