julilili42/papers huggingface dataset:
Gravitational Waves from Color-Magnetic “Mountains” in Neutron Stars
2012-08-22

Neutron stars may harbor the true ground state of matter in the form of strange quark matter. If present, this type of matter is expected to be a color superconductor, a consequence of quark pairing with respect to the color and flavor degrees of freedom. The stellar magnetic field threading the quark core becomes a color-magnetic admixture and, in the event that superconductivity is of type II, leads to the formation of color-magnetic vortices. In this Letter, we show that the volume-averaged color-magnetic vortex tension force should naturally lead to a significant degree of nonaxisymmetry in systems such as radio pulsars. We show that gravitational radiation from such color-magnetic "mountains" in young pulsars, such as the Crab and Vela, could be observable by the future Einstein Telescope, thus, becoming a probe of paired quark matter in neutron stars. The detectability threshold can be pushed up toward the sensitivity level of Advanced LIGO if we invoke an interior magnetic field about a factor ten stronger than the surface polar field.
Upper Urinary Tract Laparoendoscopic Single-Site Surgery Based on a Novel Cost-Effective Reusable Platform
2012-08-22

LESS with a completely reusable platform is feasible for different upper urinary tract procedures yielding favorable functional and cosmetic results. A simplified combination of standard straight instruments and a single prebent grasper facilitates handling and shortens the learning curve. Reusable materials significantly reduce cost and may help to further adopt LESS surgery in surgical practice.
Development and construct validation of the angioedema quality of life questionnaire
2012-08-23

Abstract Background Recurrent angioedema is a frequent clinical problem characterized by unpredictably and rapidly occurring cutaneous and mucosal swellings. These swellings may be painful and/or disfiguring. Upper airway involvement can also lead to dyspnea and suffocation. Although the disease burden is high, there is currently no specific instrument to measure health‐related quality of life (QoL) impairment. Objective To develop and validate the first symptom‐specific tool to assess QoL impairment in recurrent angioedema patients, adhering to established methodological recommendations. Methods During the development phase, 29 questions (items) were generated. Subsequently, item reduction was performed by means of impact analysis and factor analysis as well as by checking for content and face validity. As a result, 17 items were selected and included in the final instrument, the Angioedema QoL Questionnaire ( AE ‐QoL). AE ‐QoL was then tested for its validity, reliability, and influence factors. Results One hundred and ten angioedema patients took part in the validation of AE ‐QoL. AE ‐QoL was found to have a four‐dimensional structure as well as a valid total score. All of its four domains (functioning, fatigue/mood, fears/shame, food) showed good levels of internal consistency with Cronbach's alpha &gt; 0.8. Test–retesting revealed a good reliability of the instruments total score and domain scores. Gender as well as the patients' self‐rated disease activity was found to be predictors of the AE ‐QoL total score. Conclusions Angioedema Quality of Life Questionnaire is the first angioedema‐specific QoL questionnaire. It is a short, valid and reliable instrument that may serve as a valuable tool in future clinical studies and in routine patient care.
Induction of slow oscillations by rhythmic acoustic stimulation
2012-08-23

Summary Slow oscillations are electrical potential oscillations with a spectral peak frequency of ∼0.8 Hz, and hallmark the electroencephalogram during slow‐wave sleep. Recent studies have indicated a causal contribution of slow oscillations to the consolidation of memories during slow‐wave sleep, raising the question to what extent such oscillations can be induced by external stimulation. Here, we examined whether slow oscillations can be effectively induced by rhythmic acoustic stimulation. Human subjects were examined in three conditions: (i) with tones presented at a rate of 0.8 Hz (‘0.8‐Hz stimulation’); (ii) with tones presented at a random sequence (‘random stimulation’); and (iii) with no tones presented in a control condition (‘sham’). Stimulation started during wakefulness before sleep and continued for the first ∼90 min of sleep. Compared with the other two conditions, 0.8‐Hz stimulation significantly delayed sleep onset. However, once sleep was established, 0.8‐Hz stimulation significantly increased and entrained endogenous slow oscillation activity. Sleep after the 90‐min period of stimulation did not differ between the conditions. Our data show that rhythmic acoustic stimulation can be used to effectively enhance slow oscillation activity. However, the effect depends on the brain state, requiring the presence of stable non‐rapid eye movement sleep.
ATHB4 and HAT3, two class II HD-ZIP transcription factors, control leaf development in Arabidopsis
2012-08-23

In response to plant proximity or canopy shade, plants can react by altering elongation growth and development. Several members of the class II homeodomain-leucine zipper (HD-ZIPII) transcription factor family have been shown to play an instrumental role in the responses to shade. HD-ZIP members of the class III (HD-ZIPIII), by contrast, are involved in basic patterning processes. We recently showed that REVOLUTA (REV), a member of the HD-ZIPIII family, directly and positively regulates the expression of several genes involved in shade-induced growth, such as those encoding HD-ZIPII factors HAT2, HAT3, ATHB2/HAT4 and ATHB4, and of the components of the auxin biosynthesis pathway YUCCA5 and TAA1. Furthermore, we could demonstrate a novel role for HD-ZIPIII in shade-induced promotion of growth. Here we show that besides responding to shade, ATHB4 and HAT3 have a critical role in establishing the dorso-ventral axis in cotyledons and developing leaves. Loss-of-function mutations in these two HD-ZIPII genes (athb4 hat3) results in severely abaxialized, entirely radialized leaves. Conversely, overexpression of HAT3 results in adaxialized leaf development. Taken together, our findings unravel a so far unappreciated role for an HD-ZIPII/HD-ZIPIII module required for dorso-ventral patterning of leaves. The finding that HD-ZIPII/HD-ZIPIII also function in shade avoidance suggests that this module is at the nexus of patterning and growth promotion.
Release of lysophospholipid ‘find-me’ signals during apoptosis requires the ATP-binding cassette transporter A1
2012-08-23

Efficient engulfment of apoptotic cells is essential in multi-cellular organisms in order to prevent inflammatory responses. Apoptotic cells secure this process by releasing 'find-me' signals for the attraction of phagocytes. A major 'find-me' signal liberated from apoptotic cells is lysophosphatidylcholine (LPC). So far, however, the mechanisms underlying LPC release are poorly understood. In this study, we demonstrate that pharmacological inhibition and RNAi-mediated knock-down of the lipid transporter ABCA1 in apoptotic cells completely abolished phagocyte attraction. Moreover, ectopic expression of ABCA1 significantly enhanced monocyte migration to supernatants of apoptotic cells. Hence, ABCA1 represents a novel regulator of LPC release during apoptosis.
Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes
2012-08-24

Tail-anchored (TA) proteins have a single C-terminal transmembrane domain, making their biogenesis dependent on posttranslational translocation. Despite their importance, no dedicated insertion machinery has been uncovered for mitochondrial outer membrane (MOM) TA proteins. To decipher the molecular mechanisms guiding MOM TA protein insertion, we performed two independent systematic microscopic screens in which we visualized the localization of model MOM TA proteins on the background of mutants in all yeast genes. We could find no mutant in which insertion was completely blocked. However, both screens demonstrated that MOM TA proteins were partially localized to the endoplasmic reticulum (ER) in ∆spf1 cells. Spf1, an ER ATPase with unknown function, is the first protein shown to affect MOM TA protein insertion. We found that ER membranes in ∆spf1 cells become similar in their ergosterol content to mitochondrial membranes. Indeed, when we visualized MOM TA protein distribution in yeast strains with reduced ergosterol content, they phenocopied the loss of Spf1. We therefore suggest that the inherent differences in membrane composition between organelle membranes are sufficient to determine membrane integration specificity in a eukaryotic cell.
Ghost propagator and the Coulomb form factor from the lattice
2012-08-24

We calculate the Coulomb ghost propagator G(|p|) and the static Coulomb\\npotential V_C(|r|) for SU(2) Yang-Mills theory on the lattice. In view of\\npossible scaling violations related to deviations from the Hamiltonian limit we\\nuse anisotropic lattices to improve the temporal resolution. We find that the\\nghost propagator is infrared enhanced with an exponent kappa_gh ~ 0.5 while the\\nCoulomb potential exhibits a string tension larger than the Wilson string\\ntension, sigma_C ~ 2 sigma. This agrees with the Coulomb "scaling" scenario\\nderived from the Gribov-Zwanziger confinement mechanism.\\n
Association of 25‐hydroxyvitamin D with type 2 diabetes among patients undergoing coronary angiography: cross‐sectional findings from the LUdwigshafen Risk and Cardiovascular Health (LURIC) Study
2012-08-24

Summary Objective Evidence suggests that vitamin D may protect against the onset of diabetes. However, the mechanisms underlying the role of vitamin D on glycaemic status are unclear and warrant further investigation. We sought to determine the relationship between serum 25‐hydroxyvitamin D (25[ OH ] D ) and glycaemic status among intermediate‐to‐high‐risk patients scheduled for coronary angiography. Methods Participants were 3316 male and female patients (mean ± SD age, 62·7 ± 10·6 years). Four categories were formed according to serum 25[ OH ] D levels. The association between serum 25[ OH ] D and diabetes was assessed using multivariable logistic regression. Results Fasting and 2 h post‐load glucose, HbA1c and the HOMA ‐ IR indices diminished with increasing serum 25[ OH ] D levels ( P &lt; 0·001). However, no associations were observed between insulin, pro‐insulin or C ‐peptide and serum 25[ OH ] D concentrations. The pro‐inflammatory markers IL ‐6 and hs‐ CRP also decreased considerably with higher vitamin D levels ( P &lt; 0·001). After full adjustment, those with optimal serum 25[ OH ]D levels had a reduced odds for fasting diabetes ( OR = 0·63; 95% CI , 0·46–0·86; P trend = 0·01), 2 h post‐load diabetes ( OR = 0·46; 95% CI , 0·29–0·74; P trend = 0·004), both fasting/2 h post‐load diabetes ( OR = 0·61; 95% CI , 0·42–0·87; P trend = 0·001) and all of the combined hyperglycaemic states ( OR = 0·68; 95% CI , 0·52–0·80; P trend = 0·01). Conclusions Higher serum 25[ OH ]D levels were associated with better glycaemic status and lower inflammation. Should these observations be confirmed in future studies, vitamin D supplementation may prove a useful adjunct in attenuating the onset of diabetes.
Spherical Orbifolds for Cosmic Topology
2012-08-24

Harmonic analysis is a tool to infer cosmic topology from the measured\\nastrophysical cosmic microwave background CMB radiation. For overall positive\\ncurvature, Platonic spherical manifolds are candidates for this analysis. We\\ncombine the specific point symmetry of the Platonic manifolds with their deck\\ntransformations. This analysis in topology leads from manifolds to orbifolds.\\nWe discuss the deck transformations of the orbifolds and give eigenmodes for\\nthe harmonic analysis as linear combinations of Wigner polynomials on the\\n3-sphere. These provide new tools for detecting cosmic topology from the CMB\\nradiation.\\n
Akathisia and Suicidal Ideation in First-Episode Schizophrenia
2012-08-25

Patients with first-episode schizophrenia (FES) are known to be notably sensitive for developing extrapyramidal adverse effects, but the relation of akathisia and suicidal ideation has rarely been studied. The current report is an ongoing analysis of an 8-week double-blind randomized controlled multicenter trial in 289 FES, comparing risperidone and haloperidol. Assessments were conducted weekly and included the Hillside Akathisia Scale and 21-item Hamilton Depression Rating Scale ratings. Suicidal ideation was significantly associated with clinician observed akathisia, depressed mood, younger age, and use of propranolol. The allocated treatment, anxiety, and nervousness had no influence. The present findings suggest a promoting effect of akathisia on suicidal ideation can not be ruled out in patients with FES.
Molecular structure and conformational preferences of 1-bromo-1-silacyclohexane, CH2(CH2CH2)2SiH-Br, as studies by gas-phase electron diffraction and quantum chemistry
2012-08-25

The molecular structure of axial and equatorial conformer of the 1-bromo-1-silacyclohexane molecule, CH2(CH2CH2)2SiH-Br, as well as thermodynamic equilibrium between these species are investigated by means of gas-phase electron diffraction and quantum chemistry on the MP2(full)/SDB-AUG-cc-PVTZ level of theory. It is revealed that according to electron diffraction data, the compound exists in the gasphase as a mixture of conformers possessing the chair conformation of the six-membered ring and C s symmetry and differing in the axial and equatorial position of the Si-Br bond (ax. = 80(5) mol %, eq. = 20(7) mol %) at 352 K, that corresponds to the value of A = (G ax ○ − G eq ○ ) = −0.82(32) kcal/mol. It is found that observed data agree well with theoretical ones. Using Natural Bond Orbital (NBO) analysis it is revealed that axial conformer of 1-bromo-1-silacyclohexane molecule is an example of the stabilization of the form that is unfavorable from the point of view of steric effects and effects of conjugations. It is concluded that stabilization is achieved due to electrostatic interactions.
Phosphoproteome of Pristionchus pacificus Provides Insights into Architecture of Signaling Networks in Nematode Models
2012-08-25

Pristionchus pacificus is a nematode that is increasingly used as a model organism in evolutionary biology. The genome of P. pacificus differs markedly from that of C. elegans, with a high number of orphan genes that are restricted to P. pacificus and have no homologs in other species. To gain insight into the architecture of signal transduction networks in model nematodes, we performed a large-scale qualitative phosphoproteome analysis of P. pacificus. Using two-stage enrichment of phosphopeptides from a digest of P. pacificus proteins and their subsequent analysis via high accuracy MS, we detected and localized 6,809 phosphorylation events on 2,508 proteins. We compared the detected P. pacificus phosphoproteome to the recently published phosphoproteome of C. elegans. The overall numbers and functional classes of phosphoproteins were similar between the two organisms. Interestingly, the products of orphan genes were significantly underrepresented among the detected P. pacificus phosphoproteins. We defined the theoretical kinome of P. pacificus and compared it to that of C. elegans. While tyrosine kinases were slightly underrepresented in the kinome of P. pacificus, all major classes of kinases were present in both organisms. Application of our kinome annotation to a recent transcriptomic study of dauer and mixed stage populations showed that Ser/Thr and Tyr kinases show similar expression levels in P. pacificus but not in C. elegans. This study presents the first systematic comparison of phosphoproteomes and kinomes of two model nematodes and, as such, will be a useful resource for comparative studies of their signal transduction networks.
A truncated lamin A in the Lmna−/−mouse line
2012-08-27

During recent years a number of severe clinical syndromes, collectively termed laminopathies, turned out to be caused by various, distinct mutations in the human LMNA gene. Arising from this, remarkable progress has been made to unravel the molecular pathophysiology underlying these disorders. A great benefit in this context was the generation of an A-type lamin deficient mouse line (Lmna (-/-) ) by Sullivan and others, ( 1) which has become one of the most frequently used models in the field and provided profound insights to many different aspects of A-type lamin function. Here, we report the unexpected finding that these mice express a truncated Lmna gene product on both transcriptional and protein level. Combining different approaches including mass spectrometry, we precisely define this product as a C-terminally truncated lamin A mutant that lacks domains important for protein interactions and post-translational processing. Based on our findings we discuss implications for the interpretation of previous studies using Lmna (-/-) mice and the concept of human laminopathies.
Serum Response Factor (SRF)-cofilin-actin signaling axis modulates mitochondrial dynamics
2012-08-27

Aberrant mitochondrial function, morphology, and transport are main features of neurodegenerative diseases. To date, mitochondrial transport within neurons is thought to rely mainly on microtubules, whereas actin might mediate short-range movements and mitochondrial anchoring. Here, we analyzed the impact of actin on neuronal mitochondrial size and localization. F-actin enhanced mitochondrial size and mitochondrial number in neurites and growth cones. In contrast, raising G-actin resulted in mitochondrial fragmentation and decreased mitochondrial abundance. Cellular F-actin/G-actin levels also regulate serum response factor (SRF)-mediated gene regulation, suggesting a possible link between SRF and mitochondrial dynamics. Indeed, SRF-deficient neurons display neurodegenerative hallmarks of mitochondria, including disrupted morphology, fragmentation, and impaired mitochondrial motility, as well as ATP energy metabolism. Conversely, constitutively active SRF-VP16 induced formation of mitochondrial networks and rescued huntingtin (HTT)-impaired mitochondrial dynamics. Finally, SRF and actin dynamics are connected via the actin severing protein cofilin and its slingshot phosphatase to modulate neuronal mitochondrial dynamics. In summary, our data suggest that the SRF-cofilin-actin signaling axis modulates neuronal mitochondrial function.
Biotic controls on shallow translational landslides
2012-08-27

ABSTRACT In undisturbed tropical montane rainforests massive organic layers accommodate the majority of roots and only a small fraction of roots penetrate the mineral soil. We investigated the contribution of vegetation to slope stability in such environments by modifying a standard model for slope stability to include an organic layer with distinct mechanical properties. The importance of individual model parameters was evaluated using detailed measurements of soil and vegetation properties to reproduce the observed depth of 11 shallow landslides in the Andes of southern Ecuador. By distinguishing mineral soil, organic layer and above‐ground biomass, it is shown that in this environment vegetation provides a destabilizing effect mainly due to its contribution to the mass of the organic layer (up to 973 t ha − 1 under wet conditions). Sensitivity analysis shows that the destabilizing effect of the mass of soil and vegetation can only be effective on slopes steeper than 37.9°. This situation applies to 36% of the study area. Thus, on the steep slopes of this megadiverse ecosystem, the mass of the growing forest promotes landsliding, which in turn promotes a new cycle of succession. This feedback mechanism is worth consideration in further investigations of the impact of landslides on plant diversity in similar environments. Copyright © 2012 John Wiley &amp; Sons, Ltd.
An improved constraint ordering heuristics for compiling configuration problems
2012-08-27

Abstract. This paper is a case study on generating BDDs (binary decision diagrams) for propositional encodings of industrial configuration problems. As a testbed we use product configuration formulas arising in the automotive industry. Our main contribution is the introduction of a new improved constraint ordering heuristics incorporating structure-specific knowledge of the problem at hand. With the help of this constraint ordering, we were able to compile all formulas of our testbed to BDDs which was not possible with an arbitrary constraint order. 1
The Inflammatory Chemokine CXC Motif Ligand 16 Triggers Platelet Activation and Adhesion Via CXC Motif Receptor 6–Dependent Phosphatidylinositide 3-Kinase/Akt Signaling
2012-08-28

Rationale: The recently discovered chemokine CXC motif ligand 16 (CXCL16) is highly expressed in atherosclerotic lesions and is a potential pathogenic mediator in coronary artery disease. Objective: The aim of this study was to test the role of CXCL16 on platelet activation and vascular adhesion, as well as the underlying mechanism and signaling pathway. Methods and Results: Reverse-transcriptase polymerase chain reaction, Western blotting, confocal microscopy, and flow cytometry revealed that CXCL16-specific receptor, CXC motif receptor 6, is highly expressed in platelets. According to flow cytometry and confocal microscopy, stimulation of platelets with CXCL16 induced platelet degranulation, integrin α IIb β 3 activation, and shape change. CXCL16 increased Akt phosphorylation (Thr 308 /Ser 473 ), an effect abrogated by phosphatidylinositide 3-kinase inhibitors wortmannin (100 nmol/L) and LY294002 (25 μmol/L). The phosphatidylinositide 3-kinase inhibitors and Akt inhibitor SH-6 (20 μmol/L) further diminished CXCL16-induced platelet activation. CXCL16-mediated platelet degranulation, integrin α IIb β 3 activation, and Akt phosphorylation were blunted in platelets lacking CXCL16-specific receptor CXC motif receptor 6. CXCL16-induced platelet activation was abrogated in Akt1- or Akt2-deficient platelets. CXCL16 enhanced platelet adhesion to endothelium in vitro after high arterial shear stress (2000 −s ) and to injured vascular wall in vivo after carotid ligation. CXCL16-induced stimulation of platelet adhesion again was prevented by phosphatidylinositide 3-kinase and Akt inhibitors. Apyrase and antagonists of platelet purinergic receptors P 2 Y 1 (MRS2179, 100 μmol/L) and especially P 2 Y 12 (Cangrelor, 10 μmol/L) blunted CXCL16-triggered platelet activation as well as CXCL16-induced platelet adhesion under high arterial shear stress in vitro and after carotid ligation in vivo. Conclusions: The inflammatory chemokine CXCL16 triggers platelet activation and adhesion via CXC motif receptor 6–dependent phosphatidylinositide 3-kinase/Akt signaling and paracrine activation, suggesting a decisive role for CXCL16 in linking vascular inflammation and thrombo-occlusive diseases.
Activity of Gallidermin on Staphylococcus aureus and Staphylococcus epidermidis Biofilms
2012-08-28

ABSTRACT Due to their abilities to form strong biofilms, Staphylococcus aureus and Staphylococcus epidermidis are the most frequently isolated pathogens in persistent and chronic implant-associated infections. As biofilm-embedded bacteria are more resistant to antibiotics and the immune system, they are extremely difficult to treat. Therefore, biofilm-active antibiotics are a major challenge. Here we investigated the effect of the lantibiotic gallidermin on two representative biofilm-forming staphylococcal species. Gallidermin inhibits not only the growth of staphylococci in a dose-dependent manner but also efficiently prevents biofilm formation by both species. The effect on biofilm might be due to repression of biofilm-related targets, such as ica (intercellular adhesin) and atl (major autolysin). However, gallidermin's killing activity on 24-h and 5-day-old biofilms was significantly decreased. A subpopulation of 0.1 to 1.0% of cells survived, comprising “persister” cells of an unknown genetic and physiological state. Like many other antibiotics, gallidermin showed only limited activity on cells within mature biofilms.