julilili42/papers huggingface dataset:
Staphylococcal Peptidoglycan Co-Localizes with Nod2 and TLR2 and Activates Innate Immune Response via Both Receptors in Primary Murine Keratinocytes
2010-10-07

In mammalian host cells staphylococcal peptidoglycan (PGN) is recognized by Nod2. Whether PGN is also recognized by TLR2 is disputed. Here we carried out PGN co-localization and stimulation studies with TLR2 and Nod2 in wild type and mutant host cells. To exclude contamination with lipoproteins, polymeric staphylococcal PGN (PGN(pol)) was isolated from Staphylococcus aureus Δlgt (lacking lipidated prelipoproteins). PGN(pol) was biotinylated (PGN-Bio) for fluorescence monitoring with specific antibodies. Keratinocytes from murine oral epithelium (MK) readily internalized PGN-Bio in an endocytosis-like process. In wt MK, PGN(pol) induced intracellular accumulation of Nod2 and TLR2 and co-localized with Nod2 and TLR2, but not with TLR4. In TLR2-deficient MK Nod2 and in Nod2-deficient MK TLR2 was induced, indicating that PGN(pol) recognition by Nod2 is independent of TLR2 and vice versa. In both mutants IL-6 and IL-1B release was decreased by approximately 50% compared to wt MK, suggesting that the immune responses induced by Nod2 and TLR2 are comparable and that the two receptors act additively in MK. In TLR2-transfected HEK293 cells PGN(pol) induced NFkB-promoter fused luciferase expression. To support the data, co-localization and signaling studies were carried out with SHL-PGN, a lipase protein covalently tethered to PGN-fragments of varying sizes at its C-terminus. SHL-PGN also co-localized with Nod2 or TLR2 and induced their accumulation, while SHL without PGN did not. The results show that staphylococcal PGN not only co-localizes with Nod2 but also with TLR2. PGN is able to stimulate the immune system via both receptors.
Inhibition of voltage-gated K+ channels in dendritic cells by rapamycin
2010-10-07

Rapamycin, an inhibitor of the serine/threonine kinase mammalian target of rapamycin (mTOR), is a widely used immunosuppressive drug. Rapamycin affects the function of dendritic cells (DCs), antigen-presenting cells participating in the initiation of primary immune responses and the establishment of immunological memory. Voltage-gated K + (Kv) channels are expressed in and impact on the function of DCs. The present study explored whether rapamycin influences Kv channels in DCs. To this end, DCs were isolated from murine bone marrow and ion channel activity was determined by whole cell patch clamp. To more directly analyze an effect of mTOR on Kv channel activity, Kv1.3 and Kv1.5 were expressed in Xenopus oocytes with or without the additional expression of mTOR and voltage-gated currents were determined by dual-electrode voltage clamp. As a result, preincubation with rapamycin (0–50 nM) led to a gradual decline of Kv currents in DCs, reaching statistical significance within 6 h and 50 nM of rapamycin. Rapamycin accelerated Kv channel inactivation. Coexpression of mTOR upregulated Kv1.3 and Kv1.5 currents in Xenopus oocytes. Furthermore, mTOR accelerated Kv1.3 channel activation and slowed down Kv1.3 channel inactivation. In conclusion, mTOR stimulates Kv channels, an effect contributing to the immunomodulating properties of rapamycin in DCs.
The use of positron emission tomography/CT in the diagnosis of tuberculosis-associated uveitis
2010-10-08

In QuantiFERON-positive patients with severe uveitis forms, such as serpiginous choroiditis and occlusive retinal vasculitis, (18)F-FDG-PET/CT is useful to identify lesions appropriate for biopsy and helps to establish the diagnosis and appropriate therapy for presumed tuberculosis-induced intraocular inflammation.
Prognostic significance of p53-expression in colorectal carcinoma as measured by a luminometric immunoassay
2010-10-08

Background: Mutations of the TP53 gene induce the production of abnormal p53-protein with a prolonged half-life allowing its detection by monoclonal antibodies. In the following study we examined if elevated levels of p53 correlate with worse prognosis in colorectal cancer. Methods: We have quantified the protein, using an immunoluminometric assay, in 144 cytosols of primary sporadic colorectal cancer tissues and in 96 specimen of normal mucosa. Results: In 112 samples (77.8%) the p53-expression was higher than the cut-off-value of 0.15 ng p53 per mg total protein. Luminometric immunoassay did not correlate with various clinicopathological parameters. Follow-up ranged from 2.4 to 54.3 (mean 25.3) months. During this period, 61 patients developed recurrences of whom 39 died of the underlying disease. Neither univariate nor multivariate analysis showed any statistically significant differences in prognosis between high and low p53 expression. Conclusion: Our investigation revealed that p53-overexpression as measured by a luminometric immunoassay, is not a useful predictor of prognosis in patients with colorectal adenocarcinoma. Overcoming the limit of semiquantitative immunohistochemistry for p53-protein quantitative immunoluminometry may be useful elucidating the relation between serum p53-antibodies and p53 in cytosols.
Colored Simultaneous Geometric Embeddings and Universal Pointsets
2010-10-09

Universal pointsets can be used for visualizing multiple relationships on the same set of objects or for visualizing dynamic graph processes. In simultaneous geometric embeddings, the same point in the plane is used to represent the same object as a way to preserve the viewer’s mental map. In colored simultaneous embeddings this restriction is relaxed, by allowing a given object
Empathy and Dyspathy with Androids:Philosophical, Fictional, and (Neuro)Psychological Perspectives
2010-10-11

The fact that we develop feelings towards androids, i.e., objects with a humanlike appearance, has fascinated people since ancient times. However, as a short survey of the topic in history, science fiction literature and film shows, our emotional reactions towards them are ambivalent. On the one hand, we can develop feelings of empathy almost as we do with real human beings; on the other hand, we feel repulsion or dyspathy when those creatures show a very high degree of human likeness. Recently, Japanese roboticist Masahiro Mori coined the term “uncanny valley” to refer to this effect. The aim of this essay is, first, to give an explanation as to why we feel empathy towards androids although we know that they do not have feelings themselves. This presupposes a perception-based concept of empathy which is going to be developed on the basis of some of Theodor Lipps’ ideas. The second question to be answered is why empathy with androids turns into dyspathy when they become very humanlike. As I will argue, this is due to a particular kind of interference between perception and the imagination when confronted with very humanlike objects. This makes androids quite special objects right at the divide between humans and non-humans. They are non-human, but we feel ill at ease when treating them as mere objects.
Propagation of elastic waves in granular solid hydrodynamics
2010-10-12

The anisotropic stress-dependent velocity of elastic waves in glass beads--as observed by Khidas and Jia [Phys. Rev. E 81, 021303 (2010)]--is shown to be well accounted for by "granular solid hydrodynamics," a broad-range macroscopic theory of granular behavior. As the theory makes no reference to fabric anisotropy, the influence of which on sound is in doubt.
JSBML
2010-10-12

Abstract The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML's clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use library.LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is a wrapper around the C/C++ core. The real-world experiences of many software developers has been that the deployment of portable libSBML-based Java applications is difficult. Further, the libSBML API and type hierarchy are not sufficiently intuitive from a Java programmer's perspective simply because they were not designed directly for Java.For these reasons, several groups in the SBML community have mounted an open-source effort to develop a pure Java library for SBML. Here we present the JSBML project, whose products are freely available at the website "http://jsbml.sourceforge.net/":http://jsbml.sourceforge.net/. The JSBML project's aim is to provide an SBML parser and programming library that maps all SBML elements to a flexible and extended type hierarchy. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other for those who desire it.Currently, JSBML supports all constructs for SBML up to the latest Level 3 Version 1 release candidate specification, including an API to add SBML extensions. There are no plans to re-implement some of the more complex functions of libSBML, since separate community efforts are expected to make them available to JSBML via web services. These more complex functions include model consistency checking, SBML validation, and the conversion between different SBML Levels and Versions.In summary, JSBML is a young, ongoing software project that provides comprehensive and entirely Java-based data structures to read, write, and manipulate SBML files. Its layered architecture allows for the creation of Java web start applications and CellDesigner plug-ins based on stand-alone programs with very little effort. One program, SBMLsqueezer 1.3, has already been re-implemented and released using JSBML, and many others are planned.
Colistin‐Tobramycin Combinations Are Superior to Monotherapy Concerning the Killing of BiofilmPseudomonas aeruginosa
2010-10-13

Colistin-tobramycin combinations are more efficient than respective single antibiotics for killing P. aeruginosa in biofilms in vitro, and they significantly reduced P. aeruginosa cell counts in a rat lung infection model and in patients with cystic fibrosis.
OpenMS and TOPP: Open Source Software for LC-MS Data Analysis
2010-10-13

Proteomics experiments based on state-of-the-art mass spectrometry produce vast amounts of data, which cannot be analyzed manually. Hence, software is needed which is able to analyze the data in an automated fashion. The need for robust and reusable software tools triggered the development of libraries implementing different algorithms for the various analysis steps. OpenMS is such a software library and provides a wealth of data structures and algorithms for the analysis of mass spectrometric data. For users unfamiliar with programming, TOPP ("The OpenMS Proteomics Pipeline") offers a wide range of already implemented tools sharing the same interface and designed for a specific analysis task each. TOPP thus makes the sophisticated algorithms of OpenMS accessible to nonprogrammers. The individual TOPP tools can be strung together into pipelines for analyzing mass spectrometry-based experiments starting from the raw output of the mass spectrometer. These analysis pipelines can be constructed using a graphical editor. Even complex analytical workflows can thus be analyzed with ease.
Lipidomics Analysis Reveals Efficient Storage of Hepatic Triacylglycerides Enriched in Unsaturated Fatty Acids after One Bout of Exercise in Mice
2010-10-13

These data indicate that high availability of FFA induced by endurance exercise or fasting resulted in a transient hepatic TG accumulation, while muscle TG content was decreased during exercise presumably due to increased muscle fatty acid oxidation.
Ecosystem functioning from a geomicrobiological perspective – a conceptual framework for biogeochemical iron cycling
2010-10-13

Environmental context. Microbial ecosystems are characterised by the interplay of various microorganisms with their biotic and abiotic environment. Biogeochemical niches host adapted microbial communities that are in constant competition for substrates and nutrients. Their natural distribution, interactions and responses to fluctuating environmental conditions are often impossible to simulate in laboratory studies. Using biogeochemical iron redox cycling as an example, we suggest the application of a conceptual framework to improve our understanding of the principal functioning of (geo)microbial ecosystems. Abstract. Our knowledge on how microbial ecosystems function profits from the support of biogeochemical concepts which describe the cycling of elements through various geochemical gradients. Using the example of the iron cycle in freshwater sediments, we propose a theoretical framework that describes the dynamic interactions between chemical and microbial FeII oxidation and FeIII reduction, their spatial location and how they are affected by changing environmental conditions. This contribution emphasises the complexity ecological research faces when dealing with heterogeneous and dynamic natural systems. Our concept aims to provide further insights into how flows of energy and matter are controlled during microbial and chemical Fe redox transformations and how various key variables, such as substrate availability and competition as well as thermodynamic and kinetic parameters, affect flow directions.
Central oscillators in a patient with neuropathic tremor: Evidence from intraoperative local field potential recordings
2010-10-13

Abstract Present pathophysiological concepts of neuropathic tremor assume mistimed and defective afferent input resulting in deregulation of cerebello‐thalamo‐cortical motor networks. Here, we provide direct evidence of central tremor processing in a 76‐year‐old female who underwent bilateral deep brain stimulation of the ventral intermedial nucleus of the thalamus (Vim‐DBS) because of neuropathic tremor associated with IgM paraproteinemia. Electrophysiological recordings of EEG and EMG were performed in three perioperative sessions: (1) preoperatively, (2) intraoperatively, and (3) 4 days after surgery in both rest and postural tremor conditions. Tremor‐related synchronization (coherence) between motor cortex (M1) and muscles (M. extensor digitorum, M. flexor digitorum) was assessed, and additional intraoperative local field potential (LFP) recordings from Vim allowed comprehensive coherence mapping in thalamo‐cortico‐muscular networks. Directionality of information flow was determined by directed transfer function (DTF) and phase analyses. Stimulation effects on tremor and corticomuscular coherence were assessed and the patient was followed for 12 months on clinical outcome measures (Tremor Rating Scale, CADET‐Score). Vim‐DBS reduced tremor (59%) and improved motor functionality in daily activities (31%, CADET‐A) after 12 months. Intraoperative recordings demonstrated significant coherence in the tremor frequency (4 Hz) between M1 and contralateral muscle, Vim and ipsilateral M1, Vim and contralateral muscle, but not between Vim and contralateral M1. Information flow was directed from M1 to Vim and bidirectional between M1 and muscle and between Vim and muscle, respectively. Corticomuscular coherence at tremor frequency was completely suppressed by Vim‐DBS. Our case study demonstrates central oscillators underlying neuropathic tremor and implies a strong pathophysiological rationale for Vim‐DBS. © 2010 Movement Disorder Society
Mesencephalic Corticospinal Atrophy Predicts Baseline Deficit but Not Response to Unilateral or Bilateral Arm Training in Chronic Stroke
2010-10-13

Objective. Stroke survivors with motor deficits often have pyramidal tract atrophy caused by degeneration of corticospinal fibers. The authors hypothesized that the degree of atrophy correlates with severity of motor impairment in patients with chronic stroke and predicts the response to rehabilitation training. Methods. They performed a post hoc analysis of 42 hemiparetic patients (&gt;6 months) who had been randomized to either 6 weeks of bilateral arm training with rhythmic auditory cueing (BATRAC) or dose-matched therapeutic exercise (DMTE). Arm function was measured using the Fugl-Meyer (FM) and modified Wolf Motor Function Test (WMFT). Structural MRI and diffusion tensor imaging (DTI) on the pontine level measured corticospinal tract (CST) atrophy by planimetric measurement of the mesencephalon (mesencephalic atrophy ratio) and fractional anisotropy (FA), respectively. Voxel-based lesion symptom mapping (VLSM) was used to determine the lesions associated with highest degrees of atrophy. The predictive value of CST atrophy for impairment and training response was analyzed. Results. CST atrophy predicted baseline motor arm function measured by the FM and WMFT. The authors found only a trend for the correlation with FA. No measure of atrophy predicted response to either BATRAC or DMTE. CST atrophy was higher with larger lesions and those that affected the CST. VLSM identified internal capsule lesions as being associated with highest CST atrophy. Conclusion. Larger lesions, internal capsule lesions, and those overlapping the pyramidal tract are associated with greater CST atrophy. CST atrophy explains in part the variability of baseline deficits but does not seem to predict the response to BATRAC or unilateral arm training on upper-extremity function.
Association study in eating disorders: TPH2 associates with anorexia nervosa and self-induced vomiting
2010-10-14

Twin studies suggest that genetic factors play a substantial role in anorexia nervosa (AN) and self-induced vomiting (SV), a key symptom that is shared among different types of eating disorders (EDs). We investigated the association of 25 single nucleotide polymorphisms (SNPs), capturing 71-91% of the common variance in candidate genes, stathmin (STMN1), serotonin receptor 1D (HTR1D), tryptophan hydroxylase 2 (TPH2) and brain-derived neurotrophic factor (BDNF), with AN and EDs characterized by regular SV. The first allele frequencies of all the SNPs were compared between a Dutch case group (182 AN, 149 EDs characterized by SV) and 607 controls. Associations rendering P-values &lt; 0.05 from this initial study were then tested for replication in a meta-analysis with two additional independent ED case-control samples, together providing 887 AN cases, 306 cases with an ED characterized by SV and 1914 controls. A significant effect for the minor C-allele of tryptophan hydroxylase 2 rs1473473 was observed for both AN [odds ratio (OR) = 1.30, 95% CI 1.08-1.57, P &lt; 0.003] and EDs characterized by SV (OR = 1.52, 95% CI 1.28-2.04, P &lt; 0.006). In the combined case group, a dominant effect was observed for rs1473473 (OR = 1.38, 95% CI 1.16-1.64, P &lt; 0.0003). The meta-analysis revealed that the tryptophan hydroxylase 2 polymorphism rs1473473 was associated with a higher risk for AN, EDs characterized by SV and for the combined group.
FURTHER RECORDS OF MURINA TIENSA FROM VIETNAM WITH FIRST INFORMATION ON ITS ECHOLOCATION CALLS
2010-10-14

The fairy tube-nosed bat, Murina tiensa, is considered to be endemic to Vietnam. It is known only from the original description, when it was found at two localities in limestone karst areas. In 2008, we conducted a series of intensive field surveys through- out the country and obtained additional records of this species from various habitats, in- cluding degraded to nearly pristine forests and an offshore island. Our results indicate that M. tiensa is a sexually dimorphic species, females being considerably larger than males in all external and craniodental measurements. The species emits broadband, downward fre- quency-modulated echolocation calls with a dominant first harmonic. When handheld or when flying in a flight tent, signals had a similar structure and were emitted in groups of 2- 4 signals. On average, signals swept from 150 to 49 kHz in 2.2 ms for handheld bats, and, from 145 to 50 kHz in 1.9 ms for flying bats. M. tiensa often occurred in sympatry with M. cyclotis and several rhinolophids.
Differences in the perception of seven behaviour‐modifying techniques in paediatric dentistry by undergraduate students using lecturing and video sequences for teaching
2010-10-14

Abstract Whilst preparing undergraduate students for a clinical course in paediatric dentistry, four consecutive classes ( n = 107) were divided into two groups. Seven behaviour‐modifying techniques were introduced: systematic desensitization, operant conditioning, modelling, Tell, Show, Do‐principle, substitution, change of roles and the active involvement of the patient. The behaviour‐modifying techniques that had been taught to group one ( n = 57) through lecturing were taught to group two ( n = 50) through video sequences and vice versa in the following semester. Immediately after the presentations, students were asked by means of a questionnaire about their perceptions of ease of using the different techniques and their intention for clinical application of each technique. After completion of the clinical course, they were asked about which behaviour‐modifying techniques they had actually used when dealing with patients. Concerning the perception of ease of using the different techniques, there were considerable differences for six of the seven techniques ( P &lt; 0.05). Whilst some techniques seemed more difficult to apply clinically after lecturing, others seemed more difficult after video‐based teaching. Concerning the intention for clinical application and the actual clinical application, there were higher percentages for all techniques taught after video‐based teaching. However, the differences were significant only for two techniques in each case ( P &lt; 0.05). It is concluded that the use of video based teaching enhances the intention for application and the actual clinical application only for a limited number of behaviour‐modifying techniques.
Clinical, neuroradiological and genetic findings in pontocerebellar hypoplasia
2010-10-15

Abstract Pontocerebellar hypoplasia is a group of autosomal recessive neurodegenerative disorders with prenatal onset. The common characteristics are cerebellar hypoplasia with variable atrophy of the cerebellum and the ventral pons. Supratentorial involvement is reflected by variable neocortical atrophy, ventriculomegaly and microcephaly. Mutations in the transfer RNA splicing endonuclease subunit genes (TSEN54, TSEN2, TSEN34) were found to be associated with pontocerebellar hypoplasia types 2 and 4. Mutations in the mitochondrial transfer RNA arginyl synthetase gene (RARS2) were associated with pontocerebellar hypoplasia type 6. We studied a cohort of 169 patients from 141 families for mutations in these genes, of whom 106 patients tested positive for mutations in one of the TSEN genes or the RARS2 gene. In order to delineate the neuroradiological and clinical phenotype of patients with mutations in these genes, we compared this group with 63 patients suspected of pontocerebellar hypoplasia who were negative on mutation analysis. We found a strong correlation (P &amp;lt; 0.0005) between TSEN54 mutations and a dragonfly-like cerebellar pattern on magnetic resonance imaging, in which the cerebellar hemispheres are flat and severely reduced in size and the vermis is relatively spared. Mutations in TSEN54 are clinically associated with dyskinesia and/or dystonia and variable degrees of spasticity, in some cases with pure generalized spasticity. Nonsense or splice site mutations in TSEN54 are associated with a more severe phenotype of more perinatal symptoms, ventilator dependency and early death. In addition, we present ten new mutations in TSEN54, TSEN2 and RARS2. Furthermore, we show that pontocerebellar hypoplasia type 1 together with elevated cerebrospinal fluid lactate may be caused by RARS2 mutations.