julilili42/papers huggingface dataset:
Methods of labeling skin surgical specimens
2009-02-27

Summary Background: Accurate pre‐operative or intra‐operative labeling of the skin is often necessary to mark exactly the surgical excision lines. Pre‐operative “unsterile” permanent skin labeling systems are needed for example for vein and sentinel lymph node surgery; here the dyes must resist two surgical skin disinfection procedures. In contrast, excision borders are labeled during surgery using a “sterile” skin marking system. Methods: Many commercial and non‐commercial pre‐ and intra‐operative skin‐labeling systems are available, such as autologous patient blood, fluorescence triphenylmethane dyes and commercial skin markers. The available skin marking systems have specific advantages and disadvantages. We review the different labeling systems, offering guidelines to help choose a cost‐effective system appropriate for a given surgical procedure. Results: The Edding® permanent markers 400 und 3000 are well suited for preoperative skin labeling and less expensive than commercial skin labeling systems. Autologous patient blood and eosin are well suited for intra‐operative labeling and are most cost effective. Eosin Y is widely used and well suited for labeling of dark skin, bone, cartilage, and muscle tissue and spares the expense of expensive commercial skin markers. Conclusion: Knowledge of the many commercial and non‐commercial pre‐ and intra‐operative skin labeling systems and their advantages and disadvantages helps to reduce the use of relatively expensive commercial skin markers.
CodY in Staphylococcus aureus : a Regulatory Link between Metabolism and Virulence Gene Expression
2009-02-28

ABSTRACT The repressor CodY is reported to inhibit metabolic genes mainly involved in nitrogen metabolism. We analyzed codY mutants from three unrelated Staphylococcus aureus strains (Newman, UAMS-1, and RN1HG). The mutants grew more slowly than their parent strains in a chemically defined medium. However, only codY mutants were able to grow in medium lacking threonine. An excess of isoleucine resulted in growth inhibition in the wild type but not in the codY mutants, indicating that isoleucine plays a role in CodY-dependent repression. Prototypic CodY-repressed genes including the virulence regulator agr are repressed after up-shift with isoleucine. The CodY-dependent repression of agr is consistent with the concomitant influence of CodY on typical agr -regulated genes such as cap , spa , fnbA , and coa . However, some of these virulence genes (e.g., cap , fnbA , and spa ) were also regulated by CodY in an agr- negative background. Microarray analysis revealed that the large majority of CodY-repressed genes were involved in amino acid metabolism; CodY-activated genes were mainly involved in nucleotide metabolism or virulence. In summary, CodY in S. aureus not only acts as a repressor for genes involved in nitrogen metabolism but also contributes to virulence gene regulation by supporting as well as substituting for agr function.
Clinicopathological correlation of 3 patterns of calcification in a hydrophilic acrylic intraocular lens
2009-02-28

We present 3 cases of opacification in the Biocomfold 92S intraocular lens (IOL), with a documented increase in the opacification over time in 1 case. Histopathological analysis revealed the opacification was caused by calcification in the IOL's optic material. The pattern of calcium deposition, however, was different in each IOL. The causative mechanisms for this complication are unclear. Further research is warranted.
A Brain–Computer Interface Controlled Auditory Event‐Related Potential (P300) Spelling System for Locked‐In Patients
2009-03-01

Using brain–computer interfaces (BCI) humans can select letters or other targets on a computer screen without any muscular involvement. An intensively investigated kind of BCI is based on the recording of visual event‐related brain potentials (ERP). However, some severely paralyzed patients who need a BCI for communication have impaired vision or lack control of gaze movement, thus making a BCI depending on visual input no longer feasible. In an effort to render the ERP–BCI usable for this group of patients, the ERP–BCI was adapted to auditory stimulation. Letters of the alphabet were assigned to cells in a 5 × 5 matrix. Rows of the matrix were coded with numbers 1 to 5, and columns with numbers 6 to 10, and the numbers were presented auditorily. To select a letter, users had to first select the row and then the column containing the desired letter. Four severely paralyzed patients in the end‐stage of a neurodegenerative disease were examined. All patients performed above chance level. Spelling accuracy was significantly lower with the auditory system as compared with a similar visual system. Patients reported difficulties in concentrating on the task when presented with the auditory system. In future studies, the auditory ERP–BCI should be adjusted by taking into consideration specific features of severely paralyzed patients, such as reduced attention span. This adjustment in combination with more intensive training will show whether an auditory ERP–BCI can become an option for visually impaired patients.
Myrtucommulone, a natural acylphloroglucinol, inhibits microsomal prostaglandin E2 synthase‐1
2009-03-01

Background and purpose: The selective inhibition of prostaglandin (PG)E 2 formation via interference with microsomal PGE 2 synthase (mPGES)‐1 could have advantages in the treatment of PGE 2 ‐associated diseases, such as inflammation, fever and pain, compared with a general suppression of all PG biosynthesis, provided by inhibition of cyclooxygenase (COX)‐1 and 2. Here, we addressed whether the naturally occurring acylphloroglucinol myrtucommulone (MC) from Myrtus communis L. (myrtle) affected mPGES‐1. Experimental approach: The effect of MC on PGE 2 formation was investigated in a cell‐free assay by using microsomal preparations of interleukin‐1β‐stimulated A549 cells as the source of mPGES‐1, in intact A549 cells, and in lipopolysaccharide‐stimulated human whole blood. Inhibition of COX‐1 and COX‐2 activity in cellular and cell‐free assays was assessed by measuring 12(S)‐hydroxy‐5‐cis‐8,10‐trans‐heptadecatrienoic acid and 6‐oxo PGF 1α formation. Key results: MC concentration‐dependently inhibited cell‐free mPGES‐1‐mediated conversion of PGH 2 to PGE 2 (IC 50 = 1 μmol·L −1 ). PGE 2 formation was also diminished in intact A549 cells as well as in human whole blood at low micromolar concentrations. Neither COX‐2 activity in A549 cells nor isolated human recombinant COX‐2 was significantly affected by MC up to 30 μmol·L −1 , and only moderate inhibition of cellular or cell‐free COX‐1 was evident (IC 50 &gt; 15 μmol·L −1 ). Conclusions and implications: MC is the first natural product to inhibit mPGES‐1 that efficiently suppresses PGE 2 formation without significant inhibition of the COX enzymes. This provides an interesting pharmacological profile suitable for interventions in inflammatory disorders, without the typical side effects of coxibs and non‐steroidal anti‐inflammatory drugs.
Changes in adult olfactory bulb neurogenesis in mice expressing the A30P mutant form of alpha‐synuclein
2009-03-01

Abstract In familial and sporadic forms of Parkinson’s disease (PD), alpha‐synuclein pathology is present in the brain stem nuclei and olfactory bulb (OB) long before Lewy bodies are detected in the substantia nigra. The OB is an active region of adult neurogenesis, where newly generated neurons physiologically integrate. While accumulation of wild‐type alpha‐synuclein is one of the pathogenic hallmarks of non‐genetic forms of PD, the A30P alpha‐synuclein mutation results in an earlier disease onset and a severe clinical phenotype. Here, we study the regulation of adult neurogenesis in the subventricular zone (SVZ)/OB system in a tetracycline‐suppressive (tet‐off) transgenic model of synucleinopathies, expressing human mutant A30P alpha‐synuclein under the control of the calcium/calmodulin‐dependent protein kinase II alpha (CaMK) promoter. In A30P transgenic mice alpha‐synuclein was abundant at the site of integration in the glomerular cell layer of the OB. Without changes in proliferation in the SVZ, significantly fewer newly generated neurons were observed in the OB granule cell and glomerular layers of A30P transgenic mice than in controls, most probably due to increased cell death. By tetracycline‐dependent abrogation of A30P alpha‐synuclein expression, OB neurogenesis and programmed cell death was restored to control levels. Our results indicate that, using A30P conditional (tet‐off) mice, A30P alpha‐synuclein has a negative impact on olfactory neurogenesis and suppression of A30P alpha‐synuclein enhances survival of newly generated neurons. This finding suggests that interfering with alpha‐synuclein pathology can rescue newly generated neurons, possibly leading to new targets for therapeutic interventions in synucleinopathies.
Wireless node localization based on RSSI using a rotating antenna on a mobile robot
2009-03-01

Determining the physical location of radio nodes is crucial in a wireless sensor network in order to geo-reference the sensor information. This paper presents a localization technique using a mobile radio node attached to a robot. Its position is given by a real time kinematic (RTK) GPS. We propose a new method to obtain the relative bearing between the mobile and the static node using commodity radio hardware. The method exploits the anisotropy of the antenna gain and is not only more precise than the mapping of the RSSI to distance only, it also allows to monitor the integrity of the measurement. Experimental results in an outdoor environment show a standard deviation of 5. for the angle of arrival. The applicability of the approach for the localization of static radio nodes is demonstrated by means of a particle filter. The mean error of the position for experimental data is approximately 13 cm.
Proteome wide screening using peptide affinity capture
2009-03-01

Abstract MS‐based strategies are key technologies for identifying proteins in proteomic research. Despite significant improvements in recent years efficient fractionation processes of target analytes remain major bottlenecks in MS‐based protein analysis. Immunoaffinity‐based sample fractionation strategies have shown their potential for the enrichment of analyte peptides of interest, but only small numbers of analytes can be quantified in one experiment. The lack of appropriate capture reagents limits the application of immunoaffinity‐based approaches and only biased biomarker discovery approaches are possible. This perspective discusses the current status of immunoaffinity MS‐based approaches and introduces a novel concept that uses group specific anti‐peptide antibodies – Triple X Proteomics Antibodies – for the enrichment of signature peptides. Classes of peptides with identical termini can be fractionated based on TXP immunoaffinity enrichment steps and can subsequently be identified using established tandem MS procedures. Based on bioinformatic algorithms minimal sets of TXP epitopes can be specified, that cover a wide range of given proteome landscapes of one or even several different species. This opens the possibility to use a minimal number of TXP antibodies as a universal toolbox for general immunoaffinity‐based approaches in proteome analysis.
Microstructural Evolution of Silica on Single‐Crystal Silicon Carbide. Part I: Devitrification and Oxidation Rates
2009-03-01

Dry thermal oxidation of single‐crystal silicon carbide (6H‐SiC) at 1400°C in low‐water oxygen using an alumina tube furnace initially yields a predominantly vitreous oxide scale. After 28 h, approximately one quarter of the oxide scale's surface becomes crystalline, with disk‐like cristobalite aggregates (radialites) statistically distributed within the vitreous matrix. Crystalline areas were found to be thinner than vitreous regions using optical microscopy and atomic force microscopy/hydrofluoric acid (AFM/HF)‐etching analysis, providing evidence for different oxidation rates of SiC covered by vitreous silica and cristobalite. As the bulk oxide scale continues to grow during devitrification, the radialites assume their characteristic morphology with a deepened center. Line profiles of the oxide scale's thickness across radialites obtained from AFM/HF etching were used to determine the oxidation rate of SiC covered by crystalline silica and the crystallisation rate applying a two‐stage parabolic equation. As a result, it was found that the parabolic rate‐constant B vitreous is ≈4.2 times larger than the corresponding rate‐constant in crystalline areas (B cristobalite ), suggesting similar differences in effective oxygen diffusion coefficients. For the crystallization rate ν, we determined a value of 1.5±0.1 μm/h.
Red Devonian Trilobites with Green Eyes from Morocco and the Silicification of the Trilobite Exoskeleton
2009-03-01

Latest Emsian (Early Devonian) sediments at the famous mud−mound− and trilobite−locality Hamar Laghdad (Tafilalt, Morocco) yielded some red−coloured remains of phacopid trilobites. Closer examination revealed that the eyes of these phacopids are often greenish in colour. EDX−analyses showed that the lenses retained their original calcitic composition, possibly greenish due to Fe−impurities, while most of the exoskeleton was silicified. The silicified parts contain elevated concentrations of iron which causes the red colour. This phenomenon is explained by the porosity of the exoskeleton in contrast to the homogeneous and massive construction of the lenses and their Mg−content. These incompletely silicified trilobites enabled a reconstruction of the silicification process in trilobites. Their diagenetic alteration probably occurred as a result of events associated with the Cretaceous transgression.
Cortical Information Processing in Coma
2009-03-01

Results suggest a wide range of cortical information processing in coma, including semantic processing. The question is discussed of whether, and to what extent, these processing operations are related to conscious awareness of stimuli.
Granite formation: Stepwise accumulation of melt or connected networks?
2009-03-01

ABSTRACT Several authors have proposed that granitic melt accumulation and transport from the source region occurs in networks of connected melt-filled veins and dykes. These models envisage the smallest leucosomes as ‘rivulets’ that connect to feed larger dykes that form the ‘rivers’ through which magma ascends through the sub-solidus crust. This paper critically reviews this ‘rivulets-feeding-rivers’ model. It is argued that such melt-filled networks are unlikely to develop in nature, because melt flows and accumulates well before a fully connected network can be established. In the alternative stepwise accumulation model, flow and accumulation is transient in both space and time. Observations on migmatites at Port Navalo, France, that were used to support the existence of melt-filled networks are discussed and reinterpreted. In this interpretation, the structures in these migmatites are consistent with the collapse and draining of individual melt batches, supporting the stepwise accumulation model.
Capillary NMR detection in separation science
2009-03-01

Abstract This review deals with the current status of important separation techniques using capillary NMR detection. The advantages and disadvantages of the different hyphenated methods are discussed referring to a specific application. The use of Capillary‐HPLC‐NMR is demonstrated on an identification method of two bixin stereoisomers. The huge advantages using an HPLC‐SPE‐NMR method for structure determination are explained and discussed. Furthermore, two uncommon coupling techniques such as CE‐NMR and GC‐NMR are described in this review article.
Synthesis of unusual phthalocyanines and naphthalocyanines
2009-03-01

This paper is a summary of the lecture Michael Hanack gave at the 5th ICPP meeting in Moscow. A new method for the preparation of phthalonitriles is reported which makes the syntheses of substituted phthalocyanines much easier. Then the generation of highly reactive dehydrophthalocyanines using different methods is described. The reaction of these intermediates with dienophiles and various solvents is also discussed. In the last section, the syntheses of tetra- and octa- Zn phthalocyanine and -naphthalocyanine carbohydrate conjugates, which will be used for photosensitizers in PDT, is reported.
Revisional studies onThoracophoracarusK. Viets, 1914 (Arachnida, Acari, Hydrachnidia, Arrenuridae)
2009-03-01

Gerecke, Reinhard (2009): Revisional studies on Thoracophoracarus K. Viets, 1914 (Arachnida, Acari, Hydrachnidia, Arrenuridae). Zoosystema 31 (1): 127-145, DOI: 10.5252/z2009n1a7, URL: http://www.bioone.org/doi/abs/10.5252/z2009n1a7
Elimination of a Thiomethyl Substituent from an Anionic 5-Methylenebarbituric Acid Derivative by Oxidation and Substitution
2009-03-01

Triethylammonium 5-[(1,3-dimethyl-2,4,6-trioxo-tetrahydropyrimidin-5(6H)-ylidene)-(methylthio) methyl]-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate (5), obtained from 5-[bis (methylthio)methylene]-1,3-dimethyl-2,4,6(1H,3H,5H)-pyrimidinetrione (2) and 1,3-dimethylbarbituric acid in the presence of triethylamine, is protonated by methanesulfonic acid to give 5,5ʹ-(methylthiomethanediylidene)bis(1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione) (6) in good yield. Compound 6 is oxidized in two steps by m-chloroperbenzoic acid to give 5,5ʹ- (methylsulfinylmethanediylidene)bis(1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione) (7) and 5-[(1,3-dimethyl-2,4,6-trioxo-tetrahydropyrimidin-5(6H)-ylidene)(methylsulfinyl)methyl]-5-hydroxy- 1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione (8), respectively. Excess pyridine eliminates methanesulfinic acid from 8 to give the zwitterionic 5-[(1,3-dimethyl-2,4,6-trioxo-tetrahydropyrimidin- 5(6H)-ylidene(pyridinium-1-yl)methyl]-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydropyrimidin- 4-olate (9). The crystal structures of compounds 6, 8, and 9 are reported.
XQuery Join Graph Isolation: Celebrating 30+ Years of XQuery Processing Technology
2009-03-01

A purely relational account of the true XQuery semantics can turn any relational database system into an XQuery processor. Compiling nested expressions of the fully compositional XQuery language, however, yields odd algebraic plan shapes featuring scattered distributions of join operators that currently overwhelm commercial SQL query optimizers. This work rewrites such plans before submission to the relational database back-end. Once cast into the shape of join graphs, we have found off-the-shelf relational query optimizers - the B-tree indexing subsystem and join tree planner, in particular - to cope and even be autonomously capable of "reinventing" advanced processing strategies that have originally been devised specifically for the XQuery domain, e.g., XPath step reordering, axis reversal, and path stitching. Performance assessments provide evidence that relational query engines are among the most versatile and efficient XQuery processors readily available today.
Sample variability and time stability in scaled silicon nanowires
2009-03-01

We explain variability observed for the resonant tunnelling transport through donors in scaled silicon nanowires by the influence of charge configuration changes at the edges between the channel and the source-drain regions. This charge configuration is remarkably robust with respect to ageing effects, thermal cycling and the associated Id-Vg characteristics at low temperature constitute a real ldquoelectro-fingerprintrdquo for the samples. This stability is prerequisite for applications based on the gate control of single donor orbitals in nanoscale CMOS devices.
Tuning the current-voltage characteristics of Josephson junctions by strong microwave fields
2009-03-01

We observe some unusual resonance-like structures on the current-voltage characteristics (CVC) of thin film ramp-edge Josephson junctions between YBCO and Nb when applying strong microwave fields (MW). The unusual resonances have their voltage position on the CVC dependent on the MW power rather than the MW frequency, while their amplitude is largely unaffected by an increase in the MW power. Such behaviour indicates an intriguing Josephson dynamics associated with the switching from a parametric excitation regime induced by the magnetic field of the MW via oscillations of the Josephson critical current to an ac-current excitation regime triggered by the electric field of the MW. We propose a model, which describes the experimentally observed features on the CVC in terms of MW-induced multiple switching between running and locked solutions of sine-Gordon equation. Such tuning of the CVC via MW could be used to optimize the output of THz emitters.
Towards real-time and memory efficient predictions of valve states in diesel engines
2009-03-01

To reduce production costs of current engines, car manufacturers strive to replace built-in sensors by software solutions. However, the limitations of current micro controllers require time and memory efficient algorithms. In this paper, we propose a real-time framework for the detection of engine valve states based on wavelet analysis of in-cylinder pressure curves. Extracted wavelet features are then filtered out using mutual information such that only the most relevant wavelet coefficients become the input of the chosen support vector regressor. A further speedup is achieved by an approximation of the support vector solution which comprises less support vectors. We show that the combination of relevant feature selection and the regressor model simplification results in a significant decrease of the recall phase complexity while retaining good generalization performance.
Mixing and transport of water in a karst catchment: a case study from precipitation via seepage to the spring
2009-03-02

Abstract. One of the best-known and largest karst areas in Germany, the Blautopf Catchment, offers unique access to waters of the unsaturated zone through a large cave system. It was investigated with stable isotopes (18O/16O and D/H ratios expressed in permille = ‰) in precipitation, seepage- and groundwater as tracers for water flow, mixing, and storage. The precipitation showed a distinct seasonality with δ18O values between −2.9 and −24.6‰ during summer and winter, respectively. However, the isotope signals in seepage water in the caves as well as the discharge were almost completely buffered and ranged around an average δ18O value of −10‰. This value was also close to the long-term average value of local precipitation, −9.3‰. The homogeneous isotopic composition of the Blautopf Spring was unexpected, as its highly variable discharge (0.3 to 32 m3 s−1) is typical for a fast responsive karst system. These isotopic similarities could be explained by nearly complete mixing of the water already in the vadose zone. The data set therefore presents a case study to narrow down zones of mixing in karst catchments. It also confirms the minor role of the fast conduit system in the water balance of the Blautopf Catchment.
Aza-Analogue Dibenzepinone Scaffolds as p38 Mitogen-Activated Protein Kinase Inhibitors: Design, Synthesis, and Biological Data of Inhibitors with Improved Physicochemical Properties
2009-03-02

We recently described a promising novel class of p38 mitogen activated protein (MAP()) kinase inhibitors with dibenzepinone-scaffolds. To optimize their physicochemical properties, characterized by calculated log P values and measured lipophilicity (chromatographic hydrophobicity index = CHI), we synthesized aza-analogue dibenzepinones. Here, we present the synthesis and biological data of compounds with the novel aza-dibenzepinone scaffolds. Although these aza-analogues revealed an improved aqueous solubility, introduction of nitrogen was not effective in the p38 MAPK enzyme assay.