julilili42/papers huggingface dataset:
Methionine Biosynthesis in Staphylococcus aureus Is Tightly Controlled by a Hierarchical Network Involving an Initiator tRNA-Specific T-box Riboswitch
2013-09-12

In line with the key role of methionine in protein biosynthesis initiation and many cellular processes most microorganisms have evolved mechanisms to synthesize methionine de novo. Here we demonstrate that, in the bacterial pathogen Staphylococcus aureus, a rare combination of stringent response-controlled CodY activity, T-box riboswitch and mRNA decay mechanisms regulate the synthesis and stability of methionine biosynthesis metICFE-mdh mRNA. In contrast to other Bacillales which employ S-box riboswitches to control methionine biosynthesis, the S. aureus metICFE-mdh mRNA is preceded by a 5'-untranslated met leader RNA harboring a T-box riboswitch. Interestingly, this T-box riboswitch is revealed to specifically interact with uncharged initiator formylmethionyl-tRNA (tRNAi(fMet)) while binding of elongator tRNA(Met) proved to be weak, suggesting a putative additional function of the system in translation initiation control. met leader RNA/metICFE-mdh operon expression is under the control of the repressor CodY which binds upstream of the met leader RNA promoter. As part of the metabolic emergency circuit of the stringent response, methionine depletion activates RelA-dependent (p)ppGpp alarmone synthesis, releasing CodY from its binding site and thereby activating the met leader promoter. Our data further suggest that subsequent steps in metICFE-mdh transcription are tightly controlled by the 5' met leader-associated T-box riboswitch which mediates premature transcription termination when methionine is present. If methionine supply is limited, and hence tRNAi(fMet) becomes uncharged, full-length met leader/metICFE-mdh mRNA is transcribed which is rapidly degraded by nucleases involving RNase J2. Together, the data demonstrate that staphylococci have evolved special mechanisms to prevent the accumulation of excess methionine. We hypothesize that this strict control might reflect the limited metabolic capacities of staphylococci to reuse methionine as, other than Bacillus, staphylococci lack both the methionine salvage and polyamine synthesis pathways. Thus, methionine metabolism might represent a metabolic Achilles' heel making the pathway an interesting target for future anti-staphylococcal drug development.
From the Stability Pact to ESM - What Next?
2013-09-12

Europe is struggling with the resolution of the severe debt crisis and is in the process of overhauling its institutional set up.One element of the reform agenda is the European Stability Mechanism (ESM) which is intended to provide liquidity assistance to countries in case financial stability in the Euro Area is at stake.The ESM shall enter into force in July 2012, following ratification of the member states.It will have five instruments at its disposal: direct loans to countries, purchases of assets on the primary or secondary market, contingent credit lines, and funds for bank recapitalization.In this contribution, it is argued that establishing an explicit crisis resolution mechanism is in principle useful.However, the ESM is defined too broadly, and its scope should be limited to the provision of emergency liquidity assistance only under narrowly defined circumstances.Using the option to recapitalize banks might help addressing a potential debt overhang problem.Yet, the current framework has deficiencies in this regard and lacks the necessary backing by complementary institutional reforms, notably a regime for cross-border bank resolution.
IspC as Target for Antiinfective Drug Discovery: Synthesis, Enantiomeric Separation, and Structural Biology of Fosmidomycin Thia Isosters
2013-09-13

The emergence and spread of multidrug-resistant pathogens are widely believed to endanger human health. New drug targets and lead compounds exempt from cross-resistance with existing drugs are urgently needed. We report on the synthesis and properties of "reverse" thia analogs of fosmidomycin, which inhibit the first committed enzyme of a metabolic pathway that is essential for the causative agents of tuberculosis and malaria but is absent in the human host. Notably, IspC displays a high level of enantioselectivity for an α-substituted fosmidomycin derivative.
Fragmentation of Slow Wave Sleep after Onset of Complete Locked-In State
2013-09-13

Locked-in syndrome (LIS) as a result of brainstem lesions or progressive neurodegenerative disorders, such as amyotrophic lateral sclerosis (ALS), is a severe medical condition in which a person is fully conscious but unable to move or talk. LIS can transition into complete locked-in syndrome (CLIS) in which residual abilities to communicate through muscle twitches are entirely lost. It is unknown how CLIS affects circadian rhythm and sleep/wake patterns. Here we report a 39-year-old ALS patient who transitioned from LIS to CLIS while brain activity was continuously recorded using electrocorticography (ECoG) over one month. While we found no circadian rhythm in heart rate and body temperature, transition into CLIS was associated with increased fragmentation of slow wave sleep (SWS) across the day. Total time in SWS did not change. SWS fragmentation might reflect progressive circadian system impairment and should be considered as a factor further limiting communication capabilities in these patients.
Temporal hyperspectral monitoring of chlorophyll, LAI, and water content of barley during a growing season
2013-09-13

We describe a study using the ASIA-Eagle hyperspectral sensor to measure the spectral response of spring barley over an entire climate-controlled growing season and correlate those results with the results of 25 biophysical and biochemical parameters. The spectrum of each hyperspectral image was used to calculate a range of vegetation indices (VIs) that have been recorded in the literature. Furthermore, all combinations of the 252 spectral bands were tested to calculate a range of difference vegetation indices (VIs(xy)) and reflectance value indices (R(x)) at the central wavelength (x nm) of each band (R(x)). For all three index types we examined the relationship with the vegetation variables measured on the ground by using a cross-validation procedure. The relationship between the estimated and the measured canopy chlorophyll content (CCC) was (CV, covariance of variation). An was obtained when modelling leaf area index (LAI), chlorophyll content (Chl-SPAD) as well as leaf gravimetric water content (GWC). The prediction of Chl-SPAD with reflectance VIs leads to greater prediction accuracy compared with published VIs as well as difference VIs. Based on the literature, we used the DI1 vegetation index for extracting vegetation variables such as LAI and GWC. However, because of overlap effects, an explicit assignment of the spectral response to a particular vegetation parameter was not possible. The ascertained subtraction VIy = (565–779) nm also shows very good prediction accuracy compared with LAI. The investigated overlap effects for the published VIs did not result in an explicit responsiveness of the spectral response to the measured vegetation parameters. No index shows an explicit spectral signal for a single vegetation parameter. The optimisation tests show that when compared with univariate techniques, multivariate regressions improved the prediction accuracy of LAI, Chl, and CCC.
Impact of molecular tilt angle on the absorption spectra of pentacene:perfluoropentacene blends
2013-09-13

Abstract We investigate the relation between the optical properties and the average molecular tilt angle for blends of pentacene and perfluoropentacene, which can be considered as a prototypical donor–acceptor complex. Combining near‐edge X‐ray absorption fine‐structure spectroscopy and optical spectroscopy we study thin films of these compounds prepared at three different substrate temperatures T sub . For T sub =180 K we observe a larger average tilt angle than for blends prepared at higher substrate temperatures. This orientational change has significant impact on the uniaxial anisotropic optical properties of the mixed films which we measure post growth as well as in real‐time during growth. (© 2013 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Inductively coupled superconducting half wavelength resonators as persistent current traps for ultracold atoms
2013-09-13

A crucial point in the experimental implementation of hybrid quantum systems\\nconsisting of superconducting circuits and atomic ensembles is bringing the two\\npartners close enough to each other that a strong quantum coherent coupling can\\nbe established. Here, we propose to use the metallization structures of a half\\nwavelength superconducting coplanar waveguide resonator as a persistent current\\ntrap for ultracold paramagnetic atoms. Trapping atoms with the resonator\\nstructure itself is provided by using short-ended and inductively coupled\\nresonators instead of capacitively coupled ones as customary in circuit quantum\\nelectrodynamics.We analyze the external quality factor of short-ended coplanar\\nwaveguide resonators and show that it can be easily designed for the desired\\nregime of quantum circuits. The magnetic field configuration at the resonator\\nis calculated by means of numerical three-dimensional simulations of the London\\nequations. We present a way to transport an atomic ensemble into the coplanar\\nresonator gap where the magnetic field of the cavity mode is maximum. The\\nconfiguration allows stable trapping by persistent currents and paves the route\\ntowards strong coupling between atomic clouds and the cavity mode which is\\nrequired for cooperative effects and gives the interface between atoms and\\ncircuit quantum electrodynamics.\\n
Correction: What Do I Want and When Do I Want It: Brain Correlates of Decisions Made for Self and Other
2013-09-13

A number of recent functional Magnetic Resonance Imaging (fMRI) studies on intertemporal choice behavior have demonstrated that so-called emotion-and reward-related brain areas are preferentially activated by decisions involving immediately available (but smaller) rewards as compared to (larger) delayed rewards.This pattern of activation was not seen, however, when intertemporal choices were made for another (unknown) individual, which speaks to that activation having been triggered by self-relatedness.In the present fMRI study, we investigated the brain correlates of individuals who passively observed intertemporal choices being made either for themselves or for an unknown person.We found higher activation within the ventral striatum, medial prefrontal and orbitofrontal cortex, pregenual anterior cingulate cortex, and posterior cingulate cortex when an immediate reward was possible for the observer herself, which is in line with findings from studies in which individuals actively chose immediately available rewards.Additionally, activation in the dorsal anterior cingulate cortex, posterior cingulate cortex, and precuneus was higher for choices that included immediate options than for choices that offered only delayed options, irrespective of who was to be the beneficiary.These results indicate that (1) the activations found in active intertemporal decision making are also present when the same decisions are merely observed, thus supporting the assumption that a robust brain network is engaged in immediate gratification; and (2) with immediate rewards, certain brain areas are activated irrespective of whether the observer or another person is the beneficiary of a decision, suggesting that immediacy plays a more general role for neural activation.An explorative analysis of participants' brain activation corresponding to chosen rewards, further indicates that activation in the aforementioned brain areas depends on the mere presence, availability, or actual reception of immediate rewards.
An Introduction to International Relations Theory
2013-09-13

This long-awaited new edition has been fully updated and revised by the original authors as well as two new members of the author team. Based on many years of active research and teaching it takes the discipline's most difficult aspects and makes them accessible and interesting. Each chapter builds up an understanding of the different ways of looking at the world. The clarity of presentation allows students to rapidly develop a theoretical framework and to apply this knowledge widely as a way of understanding both more advanced theoretical texts and events in world politics.Suitable for first and second year undergraduates studying international relations and international relations theory.
Cloth-Fluid Contact
2013-09-13

We present a robust and efficient method for the two-way coupling between particle-based fluid simulations and infinitesimally thin solids represented by triangular meshes. Our approach is based on a hybrid method that combines a repulsion force approach with a continuous intersection handling to guarantee that no penetration occurs. Moreover, boundary conditions for the tangential component of the fluids velocity are implemented to model the no-slip boundary condition. The proposed method is particularly useful for dynamic surfaces, like cloth and thin shells. In addition, we demonstrate how standard fluid surface reconstruction algorithms can be modified to prevent the calculated surface from intersecting close objects. We have implemented our approach for the bidirectional interaction between liquid simulations based on Smoothed Particle Hydrodynamics (SPH) and standard mesh-based cloth simulation systems.
The double torus as a 2D cosmos: Groups, geometry, and closed geodesics.
2013-09-13

The double torus provides a relativistic model for a closed 2D cosmos with topology of genus 2 and constant negative curvature. Its unfolding into an octagon extends to an octagonal tessellation of its universal covering, the hyperbolic space H2. The tessellation is analysed with tools from hyperbolic crystallography. Actions on H2 of groups/subgroups are identified for SU(1,1), for a hyperbolic Coxeter group acting also on SU(1,1), and for the homotopy group Φ2 whose extension is normal in the Coxeter group. Closed geodesics arise from links on H2 between octagon centres. The direction and length of the shortest closed geodesics is computed.
Differential Expression of the Tumor Suppressor A-Kinase Anchor Protein 12 in Human Diffuse and Pilocytic Astrocytomas Is Regulated by Promoter Methylation
2013-09-14

The scaffold protein A-kinase anchor protein 12 (AKAP12) exerts tumor suppressor activity and is downregulated in several tumor entities. We characterized AKAP12 expression and regulation in astrocytomas, including pilocytic and diffusely infiltrating astrocytomas. We examined 194 human gliomas and 23 normal brain white matter samples by immunohistochemistry or immunoblotting for AKAP12 expression. We further performed quantitative methylation analysis of the AKAP12 promoter by MassARRAY® of normal brain, World Health Organization (WHO) grade I to IV astrocytomas, and glioma cell lines. Our results show that AKAP12 is expressed in a perivascular distribution in normal CNS, strongly upregulated in tumor cells in pilocytic astrocytomas, and weakly expressed in diffuse astrocytomas of WHO grade II to IV. Methylation analyses revealed specific hypermethylation of AKAP12α promoter in WHO grade II to IV astrocytomas. Restoration experiments using 5-aza-2'-deoxycytidine in primary glioblastoma cells decreased AKAP12α promoter methylation and markedly increased AKAP12α mRNA levels. In summary, we demonstrate that AKAP12 is differentially expressed in human astrocytomas showing high expression in pilocytic but low expression in diffuse astrocytomas of all WHO-grades. Our results further indicate that epigenetic mechanisms are involved in silencing AKAP12 in diffuse astrocytomas; however, a tumor suppressive role of AKAP12 in distinct astrocytoma subtypes remains to be determined.
SU(3) SYMMETRY BREAKING AND OCTET BARYON POLARIZABILITIES ∗
2013-09-14

Static polarizabilities of the low–lying 1+ baryons are studied within the 2 collective coordinate approach to the three flavor generalization of the Skyrme model; in particular, magnetic polarizabilities are considered. Predicted polarizabilities, which result from different treatments of the strange degrees of freedom in this model, are critically compared. Their deviations from the flavor symmetric formulations are discussed. PACS: 12.39.Dc, 14.20.Jn
Hidden Structure in a Lagrangian for Hyperfine Splitting of the Heavy Baryons
2013-09-14

We investigate the hyperfine splitting of the heavy baryons in the bound-state approach. We start with an ordinary relativistic Lagrangian which has been extensively used to discuss finite mass corrections to the heavy limit predictions. It turns out that the dominant contribution arises from terms which do not manifestly break the heavy spin symmetry. The actual heavy spin violating terms are uncovered by carefully performing a 1/M expansion of this Lagrangian.
Gait ataxia—specific cerebellar influences and their rehabilitation
2013-09-15

ABSTRACT It is well known that the cerebellum is important for movement control and plays a critical role in balance and locomotion. As such, one of the most characteristic and sensitive signs of cerebellar damage is gait ataxia. However, characterizing ataxic gait is no easy task, because gait patterns are highly variable. This variability seems to result from the interaction of different factors, namely, (1) the primary motor deficits in balance control and multi‐joint coordination and oculomotor dysfunction, (2) the safety strategies used, and (3) inaccurate adjustments in patients with loss of balance . In this report, we review different approaches to analyzing ataxic gait and studies to identify and quantify the different factors contributing to this movement disorder. We also discuss the influence of the cerebellum in adaptive locomotor control, the interaction between cognitive load and gait in dual‐task paradigms, and the recent advances in rehabilitation of gait and posture for patients with cerebellar degeneration. In the second part, we discuss open questions concerning cerebellar mechanisms in multi‐joint coordination during different walking conditions. Furthermore, we point out potential future directions in motor rehabilitation, with the objective of identifying predictors of rehabilitation outcome and the development of individualized training programs that potentially involve rehabilitation technology. © 2013 International Parkinson and Movement Disorder Society
Emerging therapies for gait disability and balance impairment: Promises and pitfalls
2013-09-15

ABSTRACT Therapeutic management of gait and balance impairment during aging and neurodegeneration has long been a neglected topic. This has changed considerably during recent years, for several reasons: (1) an increasing recognition that gait and balance deficits are among the most relevant determinants of an impaired quality of life and increased mortality for affected individuals; (2) the arrival of new technology, which has allowed for new insights into the anatomy and functional (dis)integrity of gait and balance circuits; and (3) based in part on these improved insights, the development of new, more specific treatment strategies in the field of pharmacotherapy, deep brain surgery, and physiotherapy. The initial experience with these emerging treatments is encouraging, although much work remains to be done. The objective of this narrative review is to discuss several promising developments in the field of gait and balance treatment. We also address several pitfalls that can potentially hinder a fast and efficient continuation of this vital progress. Important issues that should be considered in future research include a clear differentiation between gait and balance as two distinctive targets for treatment and recognition of compensatory mechanisms as a separate target for therapeutic intervention. © 2013 International Parkinson and Movement Disorder Society
The management of breakthrough cancer pain - educational needs a European nursing survey
2013-09-15

Poorly managed cancer pain is well known to profoundly impact the patient's daily life and interfere with quality of life. Nurses who cared for patients with cancer from 12 European countries participated in a survey of breakthrough cancer pain practice. The purpose was to investigate how nurses assess breakthrough cancer pain, use of standardised tools, confidence in supporting patients and awareness of medications. Responses from 1241 participants showed country variations. The majority of the sample was female, Germany had the highest proportion of male nurses (21.0%), followed by Greece (15.8%). A significantly larger proportion of nurses with longer experience and more education (78.8%) used a comprehensive definition of breakthrough cancer pain. Significant variations in training were found; 71% of Finnish nurses had received training compared with 6% of Greek nurses. Training and using a standardised assessment tool was associated with a significant increase in the nurses' perceived ability to distinguish between breakthrough and background pain. Nurses in countries with the highest proportion of training were most confident in supporting patients. In conclusion, there still exists problems with effective management of patients' breakthrough cancer pain, continuing inability to define the difference between background and breakthrough cancer pain leads to poor treatment.
The hooked element in the pes of turtles (Testudines): a global approach to exploring primary and secondary homology
2013-09-15

Abstract The hooked element in the pes of turtles was historically identified by most palaeontologists and embryologists as a modified fifth metatarsal, and often used as evidence to unite turtles with other reptiles with a hooked element. Some recent embryological studies, however, revealed that this element might represent an enlarged fifth distal tarsal. We herein provide extensive new myological and developmental observations on the hooked element of turtles, and re‐evaluate its primary and secondary homology using all available lines of evidence. Digital count and timing of development are uninformative. However, extensive myological, embryological and topological data are consistent with the hypothesis that the hooked element of turtles represents a fusion of the fifth distal tarsal with the fifth metatarsal, but that the fifth distal tarsal dominates the hooked element in pleurodiran turtles, whereas the fifth metatarsal dominates the hooked element of cryptodiran turtles. The term ‘ansulate bone’ is proposed to refer to hooked elements that result from the fusion of these two bones. The available phylogenetic and fossil data are currently insufficient to clarify the secondary homology of hooked elements within R eptilia.