julilili42/papers huggingface dataset:
ScbA from Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize γ-butyrolactones
2007-04-26

gamma-Butyrolactones play an important role in the regulation of antibiotic production and differentiation in Streptomyces. However the biosynthetic pathway for these small molecules has not yet been determined, and in vitro synthesis has not been reported. The function of the AfsA family of proteins, originally proposed to catalyse gamma-butyrolactone synthesis, has been in debate. To clarify the function of the AfsA family, and to understand the synthesis of the gamma-butyrolactones, we performed in silico analysis of this protein family. AfsA proteins consist of two divergent domains, each of which has similarity to the fatty acid synthesis enzymes FabA and FabZ. The two predicted active sites in ScbA, which is the AfsA orthologue found in Streptomyces coelicolor, were mutated, and gamma-butyrolactone biosynthesis was abolished in all four constructed mutants, strongly suggesting that ScbA has enzymic activity.
High Circulating Retinol-Binding Protein 4 Is Associated With Elevated Liver Fat but Not With Total, Subcutaneous, Visceral, or Intramyocellular Fat in Humans
2007-04-27

OBJECTIVE—Retinol-binding protein 4 (RBP4) is an adipokine that induced insulin resistance in mice, and high plasma RBP4 levels were associated with insulin-resistant states in humans. To determine which fat compartments are associated with elevated RBP4 levels in humans, we measured circulating RBP4 in 75 healthy subjects and used state-of-the-art measurements of body fat distribution. RESEARCH DESIGN AND METHODS—Total body, visceral, and subcutaneous abdominal fat were determined by magnetic resonance tomography and liver fat and intramyocellular fat by localized proton magnetic resonance spectroscopy. Insulin sensitivity was measured by the euglycemic-hyperinsulinemic clamp and, together with insulin clearance, estimated from the oral glucose tolerance test (OGTT). RESULTS—Adjusted circulating RBP4 correlated negatively with insulin sensitivity (clamp: r = −0.33, P = 0.005; OGTT: r = −0.36, P = 0.002) and positively with parameters in the fasting state as insulin levels (r = 0.35, P = 0.003) and homeostasis model assessment of insulin resistance (r = 0.34, P = 0.004). In addition, circulating RBP4 correlated negatively with hepatic insulin clearance (r = −0.25, P = 0.04). Circulating RBP4 was not associated with total body, visceral, or subcutaneous abdominal fat (all P ≥ 0.29). Plasma RBP4 levels were also not associated with intramyocellular fat or circulating adiponectin or leptin. In contrast, plasma RBP4 levels correlated positively with liver fat in cross-sectional (r = 0.27, P = 0.03) and longitudinal (r = 0.37, P = 0.04) analyses. CONCLUSIONS—Circulating RBP4 is not associated with the amount of fat in the classical depots or in the ectopic depots in muscle. However, it correlates positively with liver fat. Furthermore, metabolic parameters support the close relationship between circulating RBP4 with liver fat and, presumably, hepatic insulin resistance.
Distribution of intracellular and secreted surfactant during postnatal rat lung development
2007-04-27

Abstract Pulmonary surfactant prevents alveolar collapse via reduction of surface tension. In contrast to human neonates, rats are born with saccular lungs. Therefore, rat lungs serve as a model for investigation of the surfactant system during postnatal alveolar formation. We hypothesized that this process is associated with characteristic structural and biochemical surfactant alterations. We aimed to discriminate changes related to alveolarization from those being either invariable or follow continuous patterns of postnatal changes. Secreted active (mainly tubular myelin (tm)) and inactive (unilamellar vesicles (ulv)) surfactant subtypes as well as intracellular surfactant (lamellar bodies (lb)) in type II pneumocytes (PNII) were quantified before (day (d) 1), during (d 7), at the end of alveolarization (d 14), and after completion of lung maturation (d 42) using electron microscopic methods supplemented by biochemical analyses (phospholipid quantification, immunoblotting for SP‐A). Immunoelectron microscopy determined the localization of surfactant protein A (SP‐A). (1) At d 1 secreted surfactant was increased relative to d 7–42 and then decreased significantly. (2) Air spaces of neonatal lungs comprised lower fractions of tm and increased ulv, which correlated with low SP‐A concentrations in lung lavage fluid (LLF) and increased respiratory rates, respectively. (3) Alveolarization (d 7–14) was associated with decreasing PNII size although volume and sizes of Lb continuously increased. (4) The volume fractions of Lb correlated well with the pool sizes of phospholipids in lavaged lungs. Our study emphasizes differential patterns of developmental changes of the surfactant system relative to postnatal alveolarization. Pediatr Pulmonol. 2007; 42:548–562. © 2007 Wiley‐Liss, Inc.
Cortisol–cortisone ratios in small for gestational age (SGA) children without postnatal catch‐up growth
2007-04-29

Summary Objective Low birthweight is a risk factor for metabolic and cardiovascular disorders in later adult life. Changes in the activity of 11β‐hydroxysteroid dehydrogenase type 2 (11β‐HSD2) and the consequent disequilibrium between cortisol (F) and cortisone (E) are thought to be a key mechanism for these effects. We investigated whether prenatal programming leads to alterations in F/E ratios on a systemic level. Design, patients and methods In a cross‐sectional, retrospective study we analysed sera of 132 children born small for gestational age (SGA) (aged 2–13 years) with persistent short stature [&lt; –2 standard deviation score (SDS)] and of 25 children born appropriate for gestational age (AGA) (aged 4–11 years) with normal body height. Thirty‐one per cent of the SGA and 44% of the AGA children were born preterm. Serum E and F concentrations were measured using tandem mass spectrometry. To exclude species‐specific effects, we studied the 11β‐HSD system by measuring the ratio of corticosterone (B) to dehydrocorticosterone (11OH‐B) in rats that were born SGA after protein restriction of the female dams during pregnancy. Results F, E and the F/E ratio in serum did not differ in these children when comparing SGA to children who were born AGA and had normal height. The concentrations were independent of weight and length SDS at birth as well as gestational age. In rats born SGA, the B/11OH‐B ratio was not different to that in normal control animals at 6, 11 and 15 weeks of life. Conclusion We found no alterations in systemic cortisol–cortisone conversion either in short children born SGA or in SGA rats. However, local modifications of the 11β‐HSD system may be possible.
MAGIC or not MAGIC--does the MAGIC (mouth and genital ulcers with inflamed cartilage) syndrome really exist? A case report and review of the literature.
2007-04-30

Relapsing polychondritis is associated with HLA-DRB1*04 suballeles, but not necessarily only with those being associated with RA (DRB1*0401 and 0404). In 2 MAGIC patients these suballeles were found. All patients described in the literature had typical polychondritis, but not all did fulfil the classification criteria for BD. Many features of both diseases overlap and are not specific. As polychondritis is associated with other inflammatory rheumatic conditions such as SLE, spondyloarthropathy, rheumatoid arthritis and systemic vasculitides in 30% of all cases, we suggest that MAGIC syndrome is not a disease entity, but merely the association of BD with polychondritis.
Highly efficient, tunable single photon source based on single molecules
2007-04-30

The authors studied spatially isolated terrylene molecules immobilized in a quasiplanar optical λ∕2-microresonator using confocal microscopy and spectroscopy at variable temperatures. At T=1.8K, they observed individual molecules relaxing into microresonator-allowed vibronic levels of their electronic ground state by emission of single fluorescence photons. Coupling the purely electronic transition of embedded molecules to the longitudinal photonic mode of the microresonator resulted in an ultimate spectral narrowing and an increased collection efficiency of the emitted single photon wave trains.
Her-2 Overexpression Increases the Metastatic Outgrowth of Breast Cancer Cells in the Brain
2007-05-01

Abstract Retrospective studies of breast cancer patients suggest that primary tumor Her-2 overexpression or trastuzumab therapy is associated with a devastating complication: the development of central nervous system (brain) metastases. Herein, we present Her-2 expression trends from resected human brain metastases and data from an experimental brain metastasis assay, both indicative of a functional contribution of Her-2 to brain metastatic colonization. Of 124 archival resected brain metastases from breast cancer patients, 36.2% overexpressed Her-2, indicating an enrichment in the frequency of tumor Her-2 overexpression at this metastatic site. Using quantitative real-time PCR of laser capture microdissected epithelial cells, Her-2 and epidermal growth factor receptor (EGFR) mRNA levels in a cohort of 12 frozen brain metastases were increased up to 5- and 9-fold, respectively, over those of Her-2–amplified primary tumors. Co-overexpression of Her-2 and EGFR was also observed in a subset of brain metastases. We then tested the hypothesis that overexpression of Her-2 increases the colonization of breast cancer cells in the brain in vivo. A subclone of MDA-MB-231 human breast carcinoma cells that selectively metastasizes to brain (231-BR) overexpressed EGFR; 231-BR cells were transfected with low (4- to 8-fold) or high (22- to 28-fold) levels of Her-2. In vivo, in a model of brain metastasis, low or high Her-2–overexpressing 231-BR clones produced comparable numbers of micrometastases in the brain as control transfectants; however, the Her-2 transfectants yielded 3-fold greater large metastases (&amp;gt;50 μm2; P &amp;lt; 0.001). Our data indicate that Her-2 overexpression increases the outgrowth of metastatic tumor cells in the brain in this model system. [Cancer Res 2007;67(9):4190–8]
The tubulin homologue FtsZ contributes to cell elongation by guiding cell wall precursor synthesis in Caulobacter crescentus
2007-05-01

Summary The tubulin homologue FtsZ is well known for its essential function in bacterial cell division. Here, we show that in Caulobacter crescentus , FtsZ also plays a major role in cell elongation by spatially regulating the location of MurG, which produces the essential lipid II peptidoglycan cell wall precursor. The early assembly of FtsZ into a highly mobile ring‐like structure during cell elongation is quickly followed by the recruitment of MurG and a major redirection of peptidoglycan precursor synthesis to the midcell region. These FtsZ‐dependent events occur well before cell constriction and contribute to cell elongation. In the absence of FtsZ, MurG fails to accumulate near midcell and cell elongation proceeds unperturbed in appearance by insertion of peptidoglycan material along the entire sidewalls. Evidence suggests that bacteria use both a FtsZ‐independent and a FtsZ‐dependent mode of peptidoglycan synthesis to elongate, the importance of each mode depending on the timing of FtsZ assembly during elongation.
From Neo-Kantianism to Critical Realism: Space and the Mind-Body Problem in Riehl and Schlick
2007-05-01

This article deals with Moritz Schlick's critical realism and its sources that dominated his philosophy until about 1925. It is shown that his celebrated analysis of Einstein's relativity theory is the result of an earlier philosophical discussion about space perception and its role for the theory of space. In particular, Schlick's "method of coincidences" did not owe anything to "entirely new principles" based on the work of Einstein, Poincaré or Hilbert, as claimed by Michael Friedman, but was already in place before these principles were developed.The first part of the article is devoted to Alois Riehl's critical realism—a neo-Kantian variant which rejects the dominant interpretation of the thing-in-itself as a mere limiting concept and takes empirical theories of space perception into consideration. The second part deals with the central role of "Psychological Parallelism" for Riehl and its integration with Kant's epistemology. In the third part it is shown that Schlick's theory of knowledge is based on Riehl's intricate reworking of Kantian epistemology, physiological psychology, theory of sense perception and philosophy of mathematics. The conclusion stresses the position of the unity of consciousness in Riehl's philosophy which Schlick admittedly cannot cope with.
THE TAXONOMIC AND PHYLOGENETIC POSITION OF THE PLESIOSAUROIDEA FROM THE LOWER JURASSIC POSIDONIA SHALE OF SOUTH‐WEST GERMANY
2007-05-01

Abstract: The two plesiosauroid species from the Posidonia shale of Holzmaden, ‘ Plesiosaurus ’ guilelmiimperatoris and ‘ Plesiosaurus ’ brachypterygius , do not belong to Plesiosaurus but form new monotypic genera. The new genus Hydrorion is erected for ‘ P .’ brachypterygius , and the genus Seeleyosaurus is re‐established for ‘ P .’ guilelmiimperatoris . The recently described species Plesiopterys wildii is regarded as a junior synonym of S. guilelmiimperatoris . A short phylogenetic analysis shows that S. guilelmiimperatoris and Muraenosaurus are basal elasmosaurs. H. brachypterygius , Occitanosaurus tournemirensis from France and Microcleidus homalospondylus from England form a monophyletic clade, which is the sister taxon to the Cretaceous elasmosaurs. A palaeobiogeographical comparison of plesiosaur localities in the Lower Jurassic shows distinct palaeobiogeographical zones for the Toarcian, with different plesiosaur taxa in England, Germany and France.
Integrating 3D Time-of-Flight Camera Data and High Resolution Images for 3DTV Applications
2007-05-01

Applying the machine-learning technique of inference in Markov random fields we build improved 3D models by integrating two different modalities. Visual input from a standard color camera delivers high-resolution texture data but also enables us to enhance the 3D data calculated from the range output of a 3D time-of-flight camera in terms of noise and spatial resolution. The proposed method to increase the visual quality of the 3D data makes this kind of camera a promising device for various upcoming 3DTV applications. With our two-camera setup we believe that the design of low-cost, fast and highly portable 3D scene acquisition systems will be possible in the near future.
Buried interfacial layer of highly oriented molecules in copper phthalocyanine thin films on polycrystalline gold
2007-05-01

The growth of copper phthalocyanine thin films evaporated on polycrystalline gold is examined in detail using near edge x-ray absorption fine structure spectroscopy and surface sensitive x-ray photoemission spectroscopy. The combination of both methods allows distinguishing between the uppermost layers and buried interface layers in films up to ∼3nm thickness. An interfacial layer of approximately 3 ML of molecules with an orientation parallel to the substrate surface was found, whereas the subsequent molecules are perpendicular to the metal surface. It was shown that even if the preferred molecular orientation in thin films is perpendicular, the buried interfacial layer can be oriented differently.
Crossed cortico‐spinal motor control after capsular stroke
2007-05-01

Abstract While it is widely accepted that multiple nonprimary motor areas such as the dorsal premotor cortex contribute to recovery from stroke, the contribution of the ipsilesional and contralesional primary motor cortex (M1) is controversial. It has been suggested that re‐instating ‘near normal’ activation patterns is a good strategy for recovery of function [Baron et al ., (2004) Cerebrovasc. Dis. , 18, 260–267; Ward &amp; Cohen, (2004) Arch. Neurol. , 61, 1844–1848]. The present study addressed this aspect of stroke recovery by combining transcranial magnetic stimulation (TMS) and magnetoencephalography (MEG) in a cross‐sectional design on nine patients with well‐recovered motor function 17.6 ± 5.5 months (mean ± SD) after subcortical stroke. While TMS was applied to probe the integrity of the cortico‐spinal tract (CST) at rest, MEG was used to test for recruitment of CST pathways during a motor challenge [cortico‐muscular coherence (CMC) in a precision grip task]. With both techniques, crossed cortico‐spinal connectivity could be demonstrated. A significant correlation ( r = 0.85) of CMC magnitude and recovered muscle strength underlined the functional relevance of crossed CST integrity for successful recovery. In conclusion, at the descriptive level, crossed CST connectivity is a common finding in well‐recovered patients with capsular stroke. This renders it likely that maintaining or regaining use of crossed CST fibers is one way to achieve effective recovery.
Real-time Analysis of Flow Data for Network Attack Detection
2007-05-01

With the wide deployment of flow monitoring in IP networks, the analysis of the exported flow data has become an important research area. It has been shown that flow data can be used to detect traffic anomalies, DoS attacks, and the propagation of worms. In practice, anomalies and attacks should be detected as fast as possible in order to allow taking appropriate countermeasures. We describe the necessary steps from the raw flow data to the detection result in a systematic way. Furthermore, we present TOPAS, a system and framework for real-time analysis of flow data, that has been developed in order to meet these requirements. Performance measurements and various application examples point out the capabilities and benefits of our approach.
Prepulse inhibition of the startle reflex and its attentional modulation in the human S-ketamine and N,N-dimethyltryptamine (DMT) models of psychosis
2007-05-01

Patients with schizophrenia exhibit diminished prepuLse inhibition (PPI) of the acoustic startle reflex and deficits in the attentional moduLation of PPI. Pharmacological challenges with hallucinogens are used as models for psychosis in both humans and animals. RemarkabLy, in contrast to the findings in schizophrenic patients and in animal hallucinogen modeLs of psychosis, previous studies with healthy volunteers demonstrated increased levels of PPI after administration of low to moderate doses of either the antiglutamatergic hallucinogen ketamine or the serotonergic hallucinogen psilocybin. The aim of the present study was to investigate the influence of moderate and high doses of the serotonergic hallucinogen N,N-dimethyltryptamine (DMT) and the N-methyl-D-aspartate antagonist S-ketamine on PPI and its attentional modulation in humans. Fifteen healthy volunteers were included in a double-blind cross-over study with two doses of DMT and S-ketamine. Effects on PPI and its attentional modulation were investigated. Nine subjects completed both experimental days with the two doses of both drugs. S-ketamine increased PPI in both dosages, whereas DMT had no significant effects on PPI. S-ketamine decreased and DMT tended to decrease startle magnitude. There were no significant effects of either drug on the attentional modulation of PPI. In human experimental hallucinogen psychoses, and even with high, clearly psychotogenic doses of DMT or S-ketamine, healthy subjects failed to exhibit the predicted attenuation of PPI. In contrast, PPI was augmented and the startle magnitude was decreased after S-ketamine. These data point to important differences between human hallucinogen models and both animal hallucinogen models of psychosis and naturally occurring schizophrenia.
The Etiopathogenesis of Parkinson Disease and Suggestions for Future Research. Part II
2007-05-01

We are at a critical juncture in our knowledge of the etiology and pathogenesis of Parkinson disease (PD). It is clear that PD is not a single entity simply resulting from a dopaminergic deficit; rather it is most likely caused by a combination of genetic and environmental factors. Although there is extensive new information on the etiology and pathogenesis of PD, which may advance its treatment, new syntheses of this information are needed. The second part of this two-part, state-of-the-art review by leaders in PD research critically examines the research field to identify areas for which new knowledge and ideas might be helpful for treatment purposes. Topics reviewed in Part II are genetics, animal models, and oxidative stress.
Central Slowing During the Night
2007-05-01

The present study determined whether central information processing is subject to a circadian rhythm and, therefore, contributes to the well-known time-of-day effect on reaction time (RT). To assess the duration of central processing chronometrically, we employed the psychological refractory period (PRP) paradigm. In this task, subjects make fast responses to two successive stimuli. RT to the second stimulus is usually prolonged as the interval between the two stimuli decreases. This PRP effect is commonly attributed to a central-processing bottleneck. Subjects performed the PRP task every 2 hr during 28 hr of constant wakefulness under controlled conditions. The PRP effect was most pronounced in the early morning. We conclude that central processing is subject to a circadian rhythm, exhibiting a slowing during the night and a nadir in the early morning.
AN ALMOST COMPLETE JUVENILE SPECIMEN OF THE CHELONIID TURTLE CTENOCHELYS STENOPORUS (HAY, 1905) FROM THE UPPER CRETACEOUS NIOBRARA FORMATION OF KANSAS, USA
2007-05-01

Abstract: A new, unusually well‐preserved juvenile specimen of Ctenochelys stenoporus from the Niobrara Formation is described. The skull has come apart at its sutures and all bones of the braincase and ear region are preserved three‐dimensionally. This allows a detailed reconstruction of the important brain structures of a basal juvenile cheloniid turtle. It is compared with adult Ctenochelys specimens, and the major ontogenetic changes in the skull and postcranial skeleton are described. Furthermore, the specimen is compared with other fossil and extant cheloniids with well‐known braincases and the differences between basal and advanced cheloniids turtles are specified.
Biosynthesis of the Isoprenoid Moieties of Furanonaphthoquinone I and Endophenazine A in Streptomyces cinnamonensis DSM 1042
2007-05-01

Streptomyces cinnamonensis DSM 1042 produces the polyketide-isoprenoid compound furanonaphthoquinone I (FNQ I) and isoprenylated phenazines, predominantly endophenazine A. However, the recently identified biosynthetic gene cluster for these compounds only contains a single gene for a mevalonate pathway enzyme, that is, a putative mevalonate kinase gene. This is in strong contrast to all Streptomyces strains examined so far, where all six genes encoding the mevalonate pathway enzymes are clustered in a single operon of 6.8 kb and, thus, raised the question about the biosynthetic origin of the isoprenoid moieties of FNQ I and endophenazine A. In this study, we investigated the incorporation of [13C2]acetate and [2-13C]glycerol into FNQ I and endophenazine A. The results unequivocally prove that the isoprenoid building blocks of both compounds are predominantly formed via the mevalonate pathway (approximately 80%) but that the MEP pathway (approximately 20%) contributes to the biosynthesis of these molecules, too. In actinomycetes, this is the first experimentally proven example of the utilization of both biosynthetic routes for the formation of one single secondary metabolite. The incorporation pattern of [2-13C]glycerol was consistent with a "reverse" prenyl transfer, that is, with the formation of a C-C bond from C-3 of GPP to the polyketide nucleus of FNQ I.