julilili42/papers huggingface dataset:
Effect of Linear Elongation of PDMS-Supported Polyelectrolyte Multilayer Determined by Attenuated Total Reflectance IR Radiation
2013-02-18

Polyelectrolyte multilayers (PEMs) deposited on flexible supports, such as silicone rubber, show interesting properties upon elongation and release, like controlled wrinkling, elongation-based wetting, or dewetting and stimuli responsive nanovalves. To understand the underlying physical effects of PEM experiencing linear elongation, the orientation change of molecular groups within PEM experiencing linear elongation was investigated. The model PEM consists of polystyrenesulphonate and polydimethyldiallyl chloride. The investigation method was infrared attenuated total reflectance. In the study, the orientation change of the benzene and the sulfate groups of polystyrenesulphonate upon elongation of the PEM, prepared at high and low ionic strengths, was tracked. The gained results show that the benzene group shows no sign of orientation change upon elongation, whereas the sulfate group does, whereby the reorientation depends on the ionic strength of the preparation solution. Upon release of elongation, the PEM prepared at low ionic strength shows no orientation change, whereas PEM prepared at high ionic strength does show further orientation change, indicating that the formed wrinkles elongate the PEM on the top of the wrinkles.
Layered pattern receptor signaling via ethylene and endogenous elicitor peptides during Arabidopsis immunity to bacterial infection
2013-02-19

Recognition of molecular patterns characteristic of microbes or altered-self leads to immune activation in multicellular eukaryotes. In Arabidopsis thaliana , the leucine-rich-repeat receptor kinases FLAGELLIN-SENSING2 ( FLS2 ) and EF-TU RECEPTOR ( EFR ) recognize bacterial flagellin and elongation factor EF-Tu (and their elicitor-active epitopes flg22 and elf18), respectively. Likewise, PEP1 RECEPTOR1 ( PEPR1 ) and PEPR2 recognize the elicitor-active Pep epitopes conserved in Arabidopsis ELICITOR PEPTIDE PRECURSOR s ( PROPEP s). Here we reveal that loss of ETHYLENE-INSENSITIVE2 ( EIN2 ), a master signaling regulator of the phytohormone ethylene (ET), lowers sensitivity to both elf18 and flg22 in different defense-related outputs. Remarkably, in contrast to a large decrease in FLS2 expression, EFR expression and receptor accumulation remain unaffected in ein2 plants. Genome-wide transcriptome profiling has uncovered an inventory of EIN2-dependent and EFR-regulated genes. This dataset highlights important aspects of how ET modulates EFR-triggered immunity: the potentiation of salicylate-based immunity and the repression of a jasmonate-related branch. EFR requires ET signaling components for PROPEP2 activation but not for PROPEP3 activation, pointing to both ET-dependent and -independent engagement of the PEPR pathway during EFR-triggered immunity. Moreover, PEPR activation compensates the ein2 defects for a subset of EFR-regulated genes. Accordingly, ein2 pepr1 pepr2 plants exhibit additive defects in EFR-triggered antibacterial immunity, compared with ein2 or pepr1 pepr2 plants. Our findings suggest that the PEPR pathway not only mediates ET signaling but also compensates for its absence in enhancing plant immunity.
Ambient noise induces independent shifts in call frequency and amplitude within the Lombard effect in echolocating bats
2013-02-19

The Lombard effect, an involuntary rise in call amplitude in response to masking ambient noise, represents one of the most efficient mechanisms to optimize signal-to-noise ratio. The Lombard effect occurs in birds and mammals, including humans, and is often associated with several other vocal changes, such as call frequency and duration. Most studies, however, have focused on noise-dependent changes in call amplitude. It is therefore still largely unknown how the adaptive changes in call amplitude relate to associated vocal changes such as frequency shifts, how the underlying mechanisms are linked, and if auditory feedback from the changing vocal output is needed. Here, we examined the Lombard effect and the associated changes in call frequency in a highly vocal mammal, echolocating horseshoe bats. We analyzed how bandpass-filtered noise (BFN; bandwidth 20 kHz) affected their echolocation behavior when BFN was centered on different frequencies within their hearing range. Call amplitudes increased only when BFN was centered on the dominant frequency component of the bats’ calls. In contrast, call frequencies increased for all but one BFN center frequency tested. Both amplitude and frequency rises were extremely fast and occurred in the first call uttered after noise onset, suggesting that no auditory feedback was required. The different effects that varying the BFN center frequency had on amplitude and frequency rises indicate different neural circuits and/or mechanisms underlying these changes.
Artificial vision with wirelessly powered subretinal electronic implant alpha-IMS
2013-02-20

This study aims at substituting the essential functions of photoreceptors in patients who are blind owing to untreatable forms of hereditary retinal degenerations. A microelectronic neuroprosthetic device, powered via transdermal inductive transmission, carrying 1500 independent microphotodiode-amplifier-electrode elements on a 9 mm 2 chip, was subretinally implanted in nine blind patients. Light perception (8/9), light localization (7/9), motion detection (5/9, angular speed up to 35 deg s −1 ), grating acuity measurement (6/9, up to 3.3 cycles per degree) and visual acuity measurement with Landolt C-rings (2/9) up to Snellen visual acuity of 20/546 (corresponding to decimal 0.037 or corresponding to 1.43 logMAR (minimum angle of resolution)) were restored via the subretinal implant. Additionally, the identification, localization and discrimination of objects improved significantly ( n = 8; p &lt; 0.05 for each subtest) in repeated tests over a nine-month period. Three subjects were able to read letters spontaneously and one subject was able to read letters after training in an alternative-force choice test. Five subjects reported implant-mediated visual perceptions in daily life within a field of 15° of visual angle. Control tests were performed each time with the implant's power source switched off. These data show that subretinal implants can restore visual functions that are useful for daily life.
Ultrafast Exciton Self-Trapping upon Geometry Deformation in Perylene-Based Molecular Aggregates
2013-02-20

Femtosecond time-resolved experiments demonstrate that the photoexcited state of perylene tetracarboxylic acid bisimide (PBI) aggregates in solution decays nonradiatively on a time-scale of 215 fs. High-level electronic structure calculations on dimers point toward the importance of an excited state intermolecular geometry distortion along a reaction coordinate that induces energy shifts and couplings between various electronic states. Time-dependent wave packet calculations incorporating a simple dissipation mechanism indicate that the fast energy quenching results from a doorway state with a charge-transfer character that is only transiently populated. The identified relaxation mechanism corresponds to a possible exciton trap in molecular materials.
Prognostic Value of Contrast-enhanced Cardiac Magnetic Resonance Imaging in Patients with Newly Diagnosed Non-Ischemic Cardiomyopathy: Cohort Study
2013-02-20

In consecutive patients presenting with newly diagnosed non-ischemic cardiomyopathy, LGE-positive patients had worse prognosis. However, only traditional risk parameters like left ventricular performance and cardiac biomarkers but not presence of LGE were independent risk predictors.
Synthesis of Rare-Earth-Metal Iminopyrrolyl Complexes from Alkyl Precursors: Ln→Al N-Ancillary Ligand Transfer
2013-02-20

Protonolysis of [YMe3]n with 2-{(N-2,6-dialkylphenyl)iminomethyl)}pyrroles (alkyl = iPr (L1), Me (L2)) gave homoleptic iminopyrrolyl complexes YL13 and YL23 as well as the complex [L2YL2,Me]2 containing a dianionic pyrrolaldiminato ligand, formed via methylation of the imino backbone. Treatment of the half-sandwich complex [(C5Me5)YMe2]3 and yttrocene (C5Me5)2YMe(THF) with either 2 or 1 equiv of HL afforded the monomeric complexes (C5Me5)YL2 and (C5Me5)2YL,respectively. The complex (C5Me5)YL22 readily underwent Ln→Al iminopyrrolyl ligand transfer in the presence of trimethylaluminum, producing the known (C5Me5)Y(AlMe4)2. Salt metatheses of homoleptic Ln(AlMe4)3 (Ln = Y, La) with KL gave complicated reaction mixtures from which the η5/η1:κ1 pyrrolaldiminato-bridged complex [L1,MeLa(AlMe4)]2 and bis(tetramethylaluminate) complex L2Y(AlMe4)2 could be isolated and crystallographically characterized. Moreover, the solid-state structures of YL23, [L2YL2,Me]2, (C5Me5)YL12, (C5Me5)2YL1, and L2AlMe2 are presented.
Stable Respiratory Activity Requires Both P/Q-Type and N-Type Voltage-Gated Calcium Channels
2013-02-20

P/Q-type voltage-gated calcium channels (Ca v 2.1) play critical presynaptic and postsynaptic roles throughout the nervous system and have been implicated in a variety of neurological disorders. Here we report that mice with a genetic ablation of the Ca v 2.1 pore-forming α 1A subunit (α 1A −/− ) encoded by CACNA1a (Jun et al., 1999) suffer during postnatal development from increasing breathing disturbances that lead ultimately to death. Breathing abnormalities include decreased minute ventilation and a specific loss of sighs, which was associated with lung atelectasis. Similar respiratory alterations were preserved in the isolated in vitro brainstem slice preparation containing the pre-Bötzinger complex. The loss of Ca v 2.1 was associated with an alteration in the functional dependency on N-type calcium channels (Ca v 2.2). Blocking N-type calcium channels with conotoxin GVIA had only minor effects on respiratory activity in slices from control (CT) littermates, but abolished respiratory activity in all slices from α 1A −/− mice. The amplitude of evoked EPSPs was smaller in inspiratory neurons from α 1A −/− mice compared with CTs. Conotoxin GVIA abolished all EPSPs in inspiratory neurons from α 1A −/− mice, while the EPSP amplitude was reduced by only 30% in CT mice. Moreover, neuromodulation was significantly altered as muscarine abolished respiratory network activity in α 1A −/− mice but not in CT mice. We conclude that excitatory synaptic transmission dependent on N-type and P/Q-type calcium channels is required for stable breathing and sighing. In the absence of P/Q-type calcium channels, breathing, sighing, and neuromodulation are severely compromised, leading to early mortality.
Simultaneous Occurrence of Three Different Valence Tautomers inmeso-Vinylruthenium-Modified Zinc Porphyrin Radical Cations
2013-02-20

The mixed-valent radical cation of a styrylruthenium-modified meso-tetraarylzinc porphyrin forms a mixture of three different valence tautomers (VTs) in CH2Cl2 or 1,2-C2H4Cl2 solutions. One of these VTs has the charge and spin delocalized over the porphyrin and the styrylruthenium moieties, while the other two display charge and spin localization on just one of the different redox sites. The relative amounts of the three different VTs were determined by EPR and IR spectroscopies at variable temperatures, while delocalization in the ground state was confirmed by DFT calculations.
Vascular Endostapling Systems for Vascular Endografts (T)EVAR—Systematic Review—Current State
2013-02-20

Purpose: Recently, vascular endostapling systems were developed to achieve better sealing at the proximal neck of the aneurysm and to prevent endograft migration. The purpose of this study was to provide a systematic review about the current state and possible options of vascular endostapling systems. Results: No randomized controlled trials were published. The results showed that the use of an endostaple system considerably reduced the rates of endoleaks type 1a and endograft migration. Regarding the use of endostaples in different types of endografts, only a few results were available. Conclusion: The results are not conclusive. With endostaple systems, patients with difficult anatomic features and high risk can potentially be treated. These systems might reduce the high reintervention rates after endovascular aneurysm repair. Controlled randomized trials with larger number of patients are warranted with endostapling use in primary endograft implantation and for use in reintervention for late endoleaks or endograft migrations.
Adhesion of Annexin 7 Deficient Erythrocytes to Endothelial Cells
2013-02-20

Annexin 7 deficiency has previously been shown to foster suicidal death of erythrocytes or eryptosis, which is triggered by increase of intracellular Ca(2+) concentration ([Ca(2+)](i)) and characterized by cell shrinkage and cell membrane scrambling with subsequent phosphatidylserine exposure at the cell surface. Eryptosis following increase of [Ca(2+)](i) by Ca(2+) ionophore ionomycin, osmotic shock or energy depletion was more pronounced in erythrocytes from annexinA7-deficient mice (anxA7(-/-)) than in erythrocytes from wild type mice (anxA7(+/+)). As phosphatidylserine exposure is considered to mediate adhesion of erythrocytes to the vascular wall, the present study explored adhesion of erythrocytes from anx7(-/-) and anx7(+/+)-mice following increase of [Ca(2+)](i) by Ca(2+) ionophore ionomycin (1 μM for 30 min), hyperosmotic shock (addition of 550 mM sucrose for 2 hours) or energy depletion (removal of glucose for 12 hours). Phosphatidylserine exposing erythrocytes were identified by annexin V binding, cell volume estimated from forward scatter in FACS analysis and adhesion to human umbilical vein endothelial cells (HUVEC) utilizing a flow chamber. As a result, ionomycin, sucrose addition and glucose removal all triggered phosphatidylserine-exposure, decreased forward scatter and enhanced adhesion of erythrocytes to human umbilical vein endothelial cells (HUVEC), effects significantly more pronounced in anx7(-/-) than in anx7(+/+)-erythrocytes. Following ischemia, morphological renal injury was significantly higher in anx7(-/-) than in anx7(+/+)-mice. The present observations demonstrate that enhanced eryptosis of annexin7 deficient cells is paralleled by increased adhesion of erythrocytes to the vascular wall, an effect, which may impact on microcirculation during ischemia.
Computational modelling of the BRI1 receptor system
2013-02-20

Abstract Computational models are useful tools to help understand signalling pathways in plant cells. A systems biology approach where models and experimental data are combined can provide experimentally verifiable predictions and novel insights. The brassinosteroid insensitive 1 ( BRI1 ) receptor is one of the best‐understood receptor systems in Arabidopsis with clearly described ligands, mutants and associated phenotypes. Therefore, BRI1 ‐mediated signalling is attractive for mathematical modelling approaches to understand and interpret the spatial and temporal dynamics of signal transduction cascades in planta . To establish such a model, quantitative data sets incorporating local protein concentration, binding affinity and phosphorylation state of the different pathway components are essential. Computational modelling is increasingly employed in studies of plant growth and development. In this section, we have focused on the use of quantitative imaging of fluorescently labelled proteins as an entry point in modelling studies.
Use of preoperative C-reactive protein to improve predictive accuracy in clear cell renal cell carcinoma.
2013-02-20

474 Background: White blood cell count (WBC) and C-reactive protein (CRP) are reliable biomarkers in clear cell renal cell carcinoma (ccRCC). Nevertheless, accepted cut-offs values for risk stratifications are missing. This study re-evaluated the prognostic and predictive significance of preoperatively WBC and CRP that independently predicts patient prognosis and to determine optimal cut-off values for CRP. Methods: 327 patients with surgery for ccRCC were retrospectively evaluated from 1996 to 2005. Cox-proportional hazard models were used, adjusted for the effects of tumor stage, tumor size, Fuhrman grade, and Karnofsky-Index; and to evaluate the prognostic significance of WBC and CRP; and to identify cut-off values. Identified cut-offs were correlated with clinico-pathological parameters and used to estimate cancer-specific survival (CSS). To prove any additional predictive accuracy of the identified cut-off it was compared to a clinico-pathological base model using Harrell c-index. Results: In univariable analyses WBC was a significant prognostic marker at a concentration of 9.5/μl (HR: 1.83) and 11.0/μl (HR: 2.09) and supported a CRP value of 0.25 mg/dL (HR: 6.47, p &lt; 0.001) and 0.5mg/dL (HR: 7.15, p &lt; 0.001) as potential cut-off values. If adjusted by the multivariable models WBC showed no clear breakpoint, but a CRP-value of 0.25mg/dL (HR: 2.80, p = 0.027) proved to be optimal. Reduced CSS was proven for CRP 0.25 mg/dL (median: 69.9 vs. 92.3 months). Median follow-up was 57.5 months with 72 (22%) tumor related deaths. The final model built by the addition of CRP 0.25mg/dL did not improve predictive accuracy (c-index = 0.877) than compared to the clinico-pathological base model (c-index =0.881) which included TNM-stage, grading and Karnofsky-Index. Conclusions: Multivariable analyses revealed an optimal breakpoint of CRP at a value of 0.25mg/dL best to stratify patients at risk of cancer-specific mortality, but CRP 0.25mg/dL added no additional information in the prediction model. Therefore we cannot recommend to measure CRP as the traditional parameters of TNM-stage, grading and Karnofsky-Index were already of high predictive accuracy.
Two-Handed Through-the-Lens-Techniques for Navigation in Virtual Environments
2013-02-20

We present a tool set of techniques for navigation in virtual environments. Based on a through-the-lens concept, the user is enabled to simultaneously view the surrounding virtual world and an arbitrary location of the virtual world as seen through an interactively defined window. For the manipulation and the adjustment of this virtual window we propose three different strategies, loosely based on the well-known eyeball-in-hand, scene-in-hand, and world-in-miniature techniques. Since our technique provides a preview area with controllable size and position, the occluded part of the scene can be flexibly managed, while enabling intuitive and precise work with the proposed tools. The proposed techniques provide powerful tools that are easy to implement and can be applied in any type of virtual environments.
CpG island hypermethylation of corticotropin-releasing hormone-binding protein in kidney cancer and association with clinicopathological parameters.
2013-02-20

414 Background: Significance of Urocortin (Ucn or UcnI), Ucn2, Ucn3, and their receptors, Corticotropin Releasing Factor Receptor 1 and 2 (CRFR1 and CRFR2), and the binding protein, Corticotropin-Releasing Hormone-Binding Protein (CRHBP) in oncology is growing rapidly. Recently we found that the UCN system may also be a relevant structure in renal cell cancer. Here we investigate whether CRHBP CGI methylation occurs in cc-RCC and whether its methylation is associated with clinicopathological parameters of patients. Methods: Tumoral tissues of 109 patients with renal cell cancer and their corresponding normal tissues have been used. Combined bisulfite restriction analysis (COBRA) for detection of relative degree of CpG island (CGI) methylation and pyrosequencing have been performed. Results: We found an approximately five-fold increase in mean methylation of the CRHBP CGI for tumor tissues (p &lt; 0.00005). Higher DNA methylation of the CRHBP CGI showed a positive correlation with advanced disease as well (p = 0.024). Conclusions: To our knowledge we report for the first time the CGI methylation of CRHBP in clear cell renal cell carcinoma indicating a contribution of epigenetic alteration of CRHBP to RCC tumorigenesis. Moreover, our results suggest CRHBP as a potential molecular marker for assessment of progression and aggressiveness of tumors.
Toric Geometry
2013-02-20

Toric Geometry plays a major role where a wide variety of mathematical fields intersect, such as algebraic and symplectic geometry, algebraic groups, and combinatorics. The main feature of this workshop was to bring people from these area together to learn about mutual, possibly up till now unnoticed similarities in their respective research.
A quadratic kernel for computing the hybridization number of multiple trees
2013-02-21

It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter tractable if an instance of the problem consists of precisely two such trees. In this paper, we show that this problem remains fixed-parameter tractable for an arbitrarily large set of rooted binary phylogenetic trees. In particular, we present a quadratic kernel.
Niemann-Pick type C is frequent in adult ataxia with cognitive decline and vertical gaze palsy
2013-02-21

Niemann-Pick type C (NPC) disease is a rare, usually fatal neurodegenerative lysosomal storage disorder. It is inherited in an autosomal-recessive fashion and caused by mutation of either NPC1 (95%) or NPC2 gene.1 Age at onset is broadly variable, ranging from neonatal fatal neurovisceral manifestations to a primarily neurodegenerative disease in adulthood that may be recognized as late as 70 years of age.1 Due to its diverse clinical manifestation, correct diagnosis is challenging, frequencies might be underestimated, and diagnosis may be delayed, in particular in patients with adult-onset disease. This is particularly momentous because a potential therapy for deceleration of disease progression is now available.2
Spinal posture and pelvic position in three hundred forty-five elementary school children: a rasterstereographic pilot study
2013-02-22

Children's posture has been of growing concern due to observations that it seems to be impaired compared to previous generations. So far there is no reference data for spinal posture and pelvic position in healthy children available. Purpose of this pilot study was to determine rasterstereographic posture values in children during their second growth phase. Three hundred and forty-five pupils were measured with a rasterstereographic device in a neutral standing position with hanging arms. To further analyse for changes in spinal posture during growth, the children were divided into 12-month age clusters. A mean kyphotic angle of 47.1°±7.5 and a mean lordotic angle of 42.1°±9.9 were measured. Trunk imbalance in girls (5.85 mm±0.74) and boys (7.48 mm± 0.83) varied only little between the age groups, with boys showing slightly higher values than girls. The trunk inclination did not show any significant differences between the age groups in boys or girls. Girls' inclination was 2.53°±1.96 with a tendency to decreasing angles by age, therefore slightly smaller compared to boys (2.98°±2.18). Lateral deviation (4.8 mm) and pelvic position (tilt: 2.75 mm; torsion: 1.53°; inclination: 19.8°±19.8) were comparable for all age groups and genders. This study provides the first systematic rasterstereographic analysis of spinal posture in children between 6 and 11 years. With the method of rasterstereography a reliable three-dimensional analysis of spinal posture and pelvic position is possible. Spinal posture and pelvic position does not change significantly with increasing age in this collective of children during the second growth phase.