julilili42/papers huggingface dataset:
Serum and Glucocorticoid-Inducible Kinase in Pulmonary Tissue of Preterm Fetuses Exposed to Chorioamnionitis
2007-11-21

&lt;i&gt;Objectives:&lt;/i&gt; The interaction between inflammation and transepithelial Na&lt;sup&gt;+&lt;/sup&gt; transport is poorly understood. Chorioamnionitis has been shown to be associated with preterm labor and postnatal pulmonary morbidity of preterm infants. The human isoform of serum and glucocorticoid-inducible kinase (SGK1) is upregulated by proinflammatory cytokines and stimulates epithelial Na&lt;sup&gt;+&lt;/sup&gt; channel ENaC and the Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt;-ATPase activity, an effect presumably participating in the regulation of transepithelial Na&lt;sup&gt;+&lt;/sup&gt; transport. &lt;i&gt;Study Design:&lt;/i&gt; Lung tissue sections from 31 stillborn fetuses (range 21–41 weeks of gestational age) with or without chorioamnionitis were analyzed. Macrophages, neutrophils and lymphocytes were stained immunohistochemically. In addition, in situ hybridization for the detection of SGK1 mRNA was performed in fetal lung tissue. Positively labeled cells were compared by semiquantitative assessment. &lt;i&gt;Results:&lt;/i&gt; A marked influx of macrophages into the pulmonary tissue of fetuses exposed to intrauterine inflammation when compared to fetuses without exposure to chorioamnionitis was observed (p &lt; 0.05). There was also a tendency towards an increased density of neutrophils in fetuses exposed to chorioamnionitis. However, only small numbers of lymphocytes were detected in both groups. In fetuses exposed to chorioamnionitis, 6 of 8 fetuses did not express SGK1; however, in the group of fetuses without exposure to intrauterine inflammation 15 of 23 cases exhibited a profound SGK1 detection rate in lung tissue and airway epithelium, independent of the gestational age of the fetuses (p &lt; 0.05). &lt;i&gt;Conclusions:&lt;/i&gt; Human serine threonine kinase SGK1 mRNA is observed in fetal lung tissue. On the basis of this study, we speculate that exposure to chorioamnionitis is associated with a downregulation of SGK1 in fetal lung tissue. The possible consequences of a decreased rate of SGK1 mRNA could be an impaired ability to clear the lungs from excessive fluid immediately after preterm birth.
First-person visualizations of the special and general theory of relativity
2007-11-22

Visualizations that adopt a first-person point of view allow observation and, in the case of interactive simulations, experimentation with relativistic scenes. This paper gives examples of three types of first-person visualizations: watching objects that move at nearly the speed of light, being a high-speed observer looking at a static environment and having a look-around near a compact object. I illustrate and explain the main aspects of the visual observations, outline their use in teaching relativity and report on teaching experiences. For teaching purposes, our visualization work is available on the website www.spacetimetravel.org and its German counterpart www.tempolimit-lichtgeschwindigkeit.de. This paper assumes some basic knowledge about relativity on the part of the reader. It addresses instructors of physics at the undergraduate and advanced secondary school level as well as their students.
The activity of lipopeptide TLR2 agonists critically depends on the presence of solubilizers
2007-11-22

Abstract Lipoproteins activate cells of the innate immune system via heteromers of Toll‐like receptor (TLR) 2 with either TLR1 or TLR6. In spite of progress in understanding TLR‐dependent signal transduction and the pathophysiological relevance of TLR2, the molecular basis of ligand recognition by this receptor is poorly defined. Here, we show that the bioactivity of lipopeptides (LP) critically depends on the dilution protocol and especially the presence of proteins or detergents acting as solubilizers. Fluorescence correlation spectroscopy of fluorescently labeled analogs of synthetic LP revealed that the LP form aggregates in solution. Dilution into protein‐ and serum‐free buffers led to a complete loss of activity due to formation of large and highly heterogeneous aggregates. When dimethylsulfoxide stock solutions were diluted into BSA or serum‐containing buffers particles of strongly reduced size were obtained. For some LP, an intermediary dilution step either with tert. ‐butyl alcohol/H 2 O (4:1) or with octyl‐β‐D‐glucopyranoside further increased activity. For a panel of LP exhibiting very different activities when diluted directly into protein‐containing solutions, introduction of this dilution step resulted in comparable bioactivities. These results demonstrate the significance of solubilizing agents for the bioactivity of LP and are highly relevant for analyzing structure‐activity relationships of LP‐dependent TLR2 activation.
Time-course of changes in amounts of specific proteins upon exposure to hyper-g, 2-D clinorotation, and 3-D random positioning of Arabidopsis cell cultures
2007-11-26

In previous studies it has been shown that callus cell cultures of Arabidopsis thaliana respond to changes in gravitational field strengths by altered gene expression. In this study an investigation was carried out into how different g conditions affect the proteome of such cells. For this purpose, callus cells were exposed to 8 g (centrifugation) and simulated microgravity (2-D clinorotation: fast rotating clinostat, yielding 0.0016 g at maximum; and 3-D random positioning) for up to 16 h. Extracts containing total soluble protein were subjected to 2-D SDS-PAGE. Image analysis of Sypro Ruby-stained gels showed that approximately 28 spots reproducibly and significantly (P <0.05) changed in amount after 2 h of hypergravity (18 up- and 10 down-regulated). These spots were analysed by electrospray ionization tandem mass spectrometry (ESI-MS/MS). In the case of 2-D clinorotation, 19 proteins changed in a manner similar to hypergravity, while random positioning affected only eight spots. Identified proteins were mainly stress related, and are involved in detoxification of reactive oxygen species, signalling, and calcium binding. Surprisingly, centrifugation and clinorotation showed homologies which were not detected for random positioning. The data indicate that simulation of weightlessness is different between clinorotation and random positioning.
Vertex renormalization of weak interactions and Cooper-pair breaking in cooling compact stars
2007-11-26

At temperatures below the critical temperature of superfluid phase transition baryonic matter emits neutrinos by breaking and recombination of Cooper pairs formed in the condensate. The strong interactions in the nuclear medium modify the weak interaction vertices and the associated neutrino loss rates. We study these modifications non-perturbatively by summing infinite series of particle-hole loops in the S-wave superfluid neutron matter. The pairing and particle-hole interactions in neutron matter are described in the framework of the BCS and Fermi-liquid theories derived from microscopic interactions. Consistent with the f-sum rule, the leading order contribution to the polarization tensor arises at O(q^2) in the small momentum transfer, q, expansion. The associated neutrino emission rate is parametrically suppressed compared to its one-loop counterpart by a factor of the order of 5\\times 10^{-3}, the parameter being the baryon recoil in units of temperature.
Approximation theorems for the propagators of higher order abstract Cauchy problems
2007-11-26

In this paper, we present two quite general approximation theorems for the propagators of higher order (in time) abstract Cauchy problems, which extend largely the classical Trotter-Kato type approximation theorems for strongly continuous operator semigroups and cosine operator functions. Then, we apply the approximation theorems to deal with the second order dynamical boundary value problems.
Dihydroxyacetone Induced Autophagy in African Trypanosomes
2007-11-26

Dihydroxyacetone (DHA) was examined to explore its trypanocidal activity. The compound is easily taken up by trypanosomes via its aquaglyceroporins but is not converted to a glycolytic intermediate due to the lack of a respective kinase. Investigating the DHA-induced cell death it became evident that parasites die by autophagy rather than by necrosis or apoptosis. Since autophagy is not well studied in African trypanosomes our work offers a way to investigate the importance of autophagy for trypanosomes not only for stress coping but also for organelle reconstruction during differentiation.
In Vivo and in Vitro Activity And Mechanism Of Action of the Multidrug Cytarabine-L-Glycerylyl-Fluorodeoxyuridine
2007-11-26

Multidrugs have the potential to bypass resistance. We investigated the in vitro activity and resistance circumvention of the multidrug cytarabine-L-fluorodeoxyuridine (AraC-L-5FdU), linked via a glycerophospholipid linkage. Cytotoxicity was determined using sensitive (A2780, FM3A/0) and resistant (AG6000, AraC resistant, deoxycytidine kinase deficient; FM3A/TK-, 5FdU resistant, thymidine kinase deficient) cell lines. Circumvention of nucleoside transporter and activating enzymes was determined using specific inhibitors, HPLC analysis and standard radioactivity assays. AraC-L-5FdU was active (IC50: 0.03 microM in both A2780 and FM3A/0), had some activity in AG6000 (IC50: 0.28 microM), but no activity in FM3A/TK(-) (IC50: 18.3 microM). AraC-nucleotides were not detected in AG6000. 5FdU-nucleotides were detected in all cell lines. AraC-L-5FdU did not inhibit TS in FM3A/TK(-) (5%). Since phosphatase/nucleotidase-inhibition reduced cytotoxicity 7-70-fold, cleavage seems to be outside the cell, presumably to nucleotides, and then to nucleosides. The multidrug was orally active in the HT-29 colon carcinoma xenografts which are resistant toward the single drugs.
Host–microbe interaction: mechanisms of defensin deficiency in Crohn’s disease
2007-11-26

Defensins are endogenous antibiotics with microbicidal activity against Gram-negative and -positive bacteria, fungi, enveloped viruses and protozoa. A disturbed antimicrobial defense, as provided by Paneth and other epithelial cell defensins, seems to be a critical factor in the pathogenesis of Crohn's disease, an inflammatory disease of the intestinal tract. Different direct and indirect mechanisms leading to a breakdown of antimicrobial barrier function include direct changes in defensin gene numbers (e.g., copy number polymorphism), genetic mutations in pattern-recognition receptors (e.g., nucleotide-binding oligomerization domain 2) and, as described recently, a differentiation problem of epithelial stem cells mediated by the wingless type (Wnt) pathway. Knowledge regarding the regulation and biology of defensins provides an attractive target to open up new therapeutic avenues.
A dynamic global model for planktonic foraminifera
2007-11-26

Abstract. Seasonal changes in the flux of planktonic foraminifera have to be understood to interpret corresponding proxy-based reconstructions. To study the seasonal cycle of planktonic foraminifera species we developed a numerical model of species concentration (PLAFOM). This model is forced with a global hydrographic dataset (e.g. temperature, mixed layer depth) and with biological information taken from an ecosystem model (e.g. "food type", zooplankton abundance) to predict monthly concentrations of the most common planktonic foraminifera species used for proxies: N. pachyderma (sinistral and dextral varieties), G. bulloides, G. ruber (white variety) and G. sacculifer. The sensitivity of each species with respect to temperature (optimal temperature and range of tolerance) is derived from sediment-trap studies. Overall, the spatial distribution patterns of most of the species are comparable to core-top data. N. pachyderma (sin.) is limited to polar regions, N. pachyderma (dex.) and G. bulloides are the most common species in high productivity zones like upwelling areas, while G. ruber and G. sacculifer are more abundant in tropical and subtropical oligotrophic waters. Modeled seasonal variation match well with sediment-trap records in most of the locations for N. pachyderma (sin), N. pachyderma (dex.) and G. bulloides. G. ruber and G. sacculifer show, in general, lower concentrations and less seasonal variability in all sites. The lower variability is reflected in the model output, but the small scale variations are not reproduced by the model in several locations. Due to the fact that the model is forced by climatological data, it can not capture interannual variations. The sensitivity experiments we carried out show that, inside the temperature tolerance range, food availability is the main parameter which controls the abundance of some species. The here presented model represents a powerful tool to explore the response of planktonic foraminifera to different boundary conditions, and to quantify the seasonal bias in foraminifera-based proxy records.
Effectiveness of metrical pacing in the treatment of apraxia of speech
2007-11-27

Background: One class of methods used in the treatment of apraxia of speech is based on rhythmic stimulation. Controlled trials investigating the effectiveness of these methods are still rare. Aims: To examine the effectiveness of a new treatment of apraxia of speech based on a metrical pacing technique (MPT) with acoustic stimulation. Methods & Procedures: MPT was applied to 10 patients with apraxia of speech. Conventional, non‐rhythmic therapeutic techniques were used as a control treatment (cross‐over design). Therapeutic effects were measured by variables describing speech rate, fluency, and segmental accuracy of sentence production. Corrections for spontaneous recovery were based on estimates inferred from a baseline period. Group statistics and multiple single case statistics were performed. Outcomes & Results: The complete intervention (MPT plus control treatment) yielded significant improvements in speech rate, fluency, and segmental accuracy. Regarding rate and fluency, MPT was superior to the control treatment. Regarding segmental accuracy, both treatments yielded comparable benefits. Conclusions: In a sample of 10 patients apraxia of speech could be modulated by behavioural treatment methods. The Metrical Pacing Therapy yielded specific improvements of rate and fluency, but also of segmental accuracy, which exceeded the effects of spontaneous recovery.
Factors influencing the absorbed dose in intraoral radiography
2007-11-27

Instead of increasing the tube voltage or using additional lead foils or metal film holders, a substantial dose reduction is provided by digital radiography or more sensitive films while a low tube potential level is maintained and the milliampere seconds setting is reduced.
A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels
2007-11-27

A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner’s (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions.
Telomere length analysis in monocytes and lymphocytes from patients with systemic lupus erythematosus using multi-color flow-FISH
2007-11-27

In order to analyse telomere length in subsets of human peripheral blood lymphocytes and monocytes, we modified a recently developed multicolor flow- fluorescent in situ hybridization (FISH) methodology that combines flow-FISH and antibody staining for cell surface antigens. We analysed telomere length of peripheral blood mononuclear cells in a group of 22 patients with systemic lupus erythematosus (SLE) and 20 age-matched healthy donors. We found that neither CD4+, CD8+, CD19+ cells nor CD14+ monocytes have significantly shorter telomeres compared with their healthy counterparts. On the basis of these findings, we then used monocyte telomere length as internal reference in order to control for intra-individual variability in telomere length. By using this approach, we could demonstrate significant telomere shortening in all three lymphocyte subsets (in all cases P &lt; 0.05) compared with monocytes. However, these differences did not vary significantly between SLE patients and controls. In summary, telomere lengths in subpopulations of hematopoietic cells can be monitored in patients with SLE using multicolor flow-FISH. While confirming data by other groups on telomere length in lymphocyte subpopulations, our data argue against an increased proliferation rate of peripheral blood monocytes reflected by accelerated telomere shortening in patients with SLE. Lupus (2007) 16, 955—962.
Cep68 and Cep215 (Cdk5rap2) are required for centrosome cohesion
2007-11-28

The centrosome duplicates during the cell cycle but functions as a single microtubule-organising centre until shortly before mitosis. This raises the question of how centrosome cohesion is maintained throughout interphase. One dynamic model proposes that parental centrioles are held together through centriole-associated, entangling filaments. Central to this model are C-Nap1, a putative centriolar docking protein and rootletin, a fibrous component. Here we identify two novel proteins, Cep68 and Cep215, as required for centrosome cohesion. Similar to rootletin, Cep68 decorates fibres emanating from the proximal ends of centrioles and dissociates from centrosomes during mitosis. Furthermore, Cep68 and rootletin depend both on each other and on C-Nap1 for centriole association. Unlike rootletin, overexpression of Cep68 does not induce extensive fibre formation, but Cep68 is readily recruited to ectopic rootletin fibres. These data suggest that Cep68 cooperates with rootletin and C-Nap1 in centrosome cohesion. By contrast, Cep215 associates with centrosomes throughout the cell cycle and does not appear to interact with Cep68, rootletin or C-Nap1. Instead, our data suggest that Cep215 functionally interacts with pericentrin, suggesting that both proteins influence centrosome cohesion through an indirect mechanism related to cytoskeletal dynamics.
Levo- but not dextro-1-methyl tryptophan abrogates the IDO activity of human dendritic cells
2007-11-28

Clinical trials have been started with the aim of inducing tumor immunity by blocking the immunosuppressive action of indoleamine-2,3-dioxygenase (IDO) with the IDO2-inhibitor dextro-1-methyl-tryptophan (D-1MT). Here we show that human dendritic cells (DCs) express both IDO-1 and IDO-2, but that only IDO1 mediates tryptophan catabolism; furthermore, its activity is blocked by levo-1MT, whereas D-1MT is inefficient. Consequently, in humans any possible antitumor effects of D-1MT cannot be attributed to abrogation of IDO activity in DCs as described in this study.
Diversity of Fibroblasts – A Review on Implications for Skin Tissue Engineering
2007-11-28

Enormous advances in the development of skin substitutes have occurred in the past 3 decades. Major obstacles yet to be overcome in the quest for an optimal skin substitute include controlling scar formation, contraction and the loss of adnexal structures. Mesenchyme-derived signals are essential for epithelial proliferation, skin morphogenesis, homeostasis and differentiation. Having previously shown that fibroblasts differentiate along a lineage from highly proliferative progenitor fibroblasts with characteristic spindle-shaped appearance to differentiated postmitotic polygonal fibrocytes, we have now established that the different subsets of fibroblasts exert significantly different patterns of cytokine release and that the highest levels of keratinocyte growth factor and transforming growth factor-β&lt;sub&gt;1&lt;/sub&gt; expression result from differentiated fibroblasts. Coculture studies with keratinocytes reveal that postmitotic fibroblasts stimulate keratinocyte proliferation to a greater extent than progenitor fibroblasts. Acellular and fibroblast-seeded dermal substitutes have been shown to improve scarring and contraction in animal studies, the latter substitutes yielding the most favorable results. Fibroblasts from different body sites display different functional properties which may affect their suitability for dermal substitutes. Future in vivo human studies in tissue-engineered dermal substitutes will likely focus on fibroblast-seeded lattices and the impact of fibroblast subpopulations and bone marrow-derived mesenchymal stem cells on dermal regeneration.
Development of reverse phase protein microarrays for clinical applications and patient-tailored therapy.
2007-11-28

While genomics provide important information about the somatic genetic changes, and RNA transcript profiling can reveal important expression changes that correlate with outcome and response to therapy, it is the proteins that do the work in the cell. At a functional level, derangements within the proteome, driven by post-translational and epigenetic modifications, such as phosphorylation, is the cause of a vast majority of human diseases. Cancer, for instance, is a manifestation of deranged cellular protein molecular networks and cell signaling pathways that are based on genetic changes at the DNA level. Importantly, the protein pathways contain the drug targets in signaling networks that govern overall cellular survival, proliferation, invasion and cell death. Consequently, the promise of proteomics resides in the ability to extend analysis beyond correlation to causality. A critical gap in the information knowledge base of molecular profiling is an understanding of the ongoing activity of protein signaling in human tissue: what is activated and "in use" within the human body at any given point in time. To address this gap, we have invented a new technology, called reverse phase protein microarrays, that can generate a functional read-out of cell signaling networks or pathways for an individual patient obtained directly from a biopsy specimen. This "wiring diagram" can serve as the basis for both, selection of a therapy and patient stratification.
[Visualization of biological traces on evidence by ninhydrin].
2007-11-28

Because of possible contamination of samples with PCR inhibitors and to avoid the typing of mixed profiles the source material for forensic DNA investigations should be collected as directly and securely as possible from the evidence. This approach requires a detectability of the source material which is often not given. The procedure introduced here using selected cases enables visualization of DNA-containing materials on evidence and hence controlled analysis. For this purpose the specimen is treated with ninhydrin. A following dye reaction verifies the presence of biological material, which possibly contains DNA. An impact on subsequent STR-analysis was not observed.