julilili42/papers huggingface dataset:
Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis
2016-11-01

Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here, we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprogramming as reflected by differential expression of ∼20% of all genes and changes in several hundred AS events. For more than 60% of all regulated AS events, light promoted the production of a presumably protein-coding variant at the expense of an mRNA with nonsense-mediated decay-triggering features. Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND1, previously identified as a red light signaling component, was shifted to the functional variant under light. Downstream analyses of candidate AS events pointed at a role of photoreceptor signaling only in monochromatic but not in white light. Furthermore, we demonstrated similar AS changes upon light exposure and exogenous sugar supply, with a critical involvement of kinase signaling. We propose that AS is an integration point of signaling pathways that sense and transmit information regarding the energy availability in plants.
Compression therapy in patients with venous leg ulcers
2016-11-01

Summary Wund‐D.A.CH. is the umbrella organization of the various wound care societies in German‐speaking countries. The present consensus paper on practical aspects pertinent to compression therapy in patients with venous leg ulcers was developed by experts from Germany, Austria, and Switzerland. In Europe, venous leg ulcers rank among the most common causes of chronic wounds. Apart from conservative and interventional wound and vein treatment, compression therapy represents the basis of all other therapeutic strategies. To that end, there are currently a wide variety of materials and systems available. While especially short‐stretch bandages or multicomponent systems should be used in the initial decongestion phase, ulcer stocking systems are recommended for the subsequent maintenance phase. Another – to date, far less common – alternative are adaptive Velcro bandage systems. Medical compression stockings have proven particularly beneficial in the prevention of ulcer recurrence. The large number of treatment options currently available enables therapists to develop therapeutic concepts geared towards their patients’ individual needs and abilities, thus resulting in good acceptance and adherence. Compression therapy plays a crucial role in the treatment of patients with venous leg ulcers. In recent years, a number of different treatment options have become available, their use and application differing among German‐speaking countries. The present expert consensus is therefore meant to outline concrete recommendations for routine implementation of compression therapy in patients with venous leg ulcers.
Down-Regulation of the Alternative Sigma Factor SigJ Confers a Photoprotective Phenotype toAnabaenaPCC 7120
2016-11-01

Alternative sigma factors belonging to Group 3 are thought to play an important role in the adaptation of cyanobacteria to environmental challenges by altering expression of genes needed for coping with such stresses. In this study, the role of an alternative sigma factor, SigJ, was analyzed in the filamentous nitrogen-fixing cyanobacterium, Anabaena sp. PCC 7120 by knocking down the expression of the sigJ gene (alr0277) employing an antisense RNA-mediated approach. In the absence of any stress, the knock-down (KD0277) or the wild-type strain both grew similarly. Upon exposure to high-intensity light, KD0277 showed substantially reduced bleaching of its pigments, higher photosynthetic activity and consequently better survival than the wild type. KD0277 also showed an enhanced accumulation of two carotenoids, which were identified as myxoxanthophyll and keto-myxoxanthophyll. Further, KD0277 was more tolerant to ammonium-triggered photodamage than the wild type. Moreover, PSII was better protected against photodamage in KD0277 than in the wild type. Down-regulation of sigJ in Anabaena PCC 7120, however, reduced its ability to cope with desiccation. This study demonstrates that down-regulation of the sigJ gene in Anabaena PCC 7120 differentially affects its ability to tolerate two environmentally relevant stresses, i.e. high-intensity light and desiccation.
Quasi-periodic oscillations as a tool for testing the Kerr metric: A comparison with gravitational waves and iron line
2016-11-01

QPOs are a common feature in the X-ray power density spectrum of black hole binaries and a potentially powerful tool to probe the spacetime geometry around these objects. Here we discuss their constraining power to test the Kerr black hole hypothesis within the relativistic precession model. We compare our results with the constraints that can be obtained from gravitational waves and iron line. We find that QPOs may provide very precise measurements, but they are strongly affected by parameter degeneracy, and it is difficult to test the Kerr metric with this approach in the absence of independent observations to constrain the mass or the spin.
Propensity Scoring after Multiple Imputation in a Retrospective Study on Adjuvant Radiation Therapy in Lymph-Node Positive Vulvar Cancer
2016-11-01

Propensity scoring (PS) is an established tool to account for measured confounding in non-randomized studies. These methods are sensitive to missing values, which are a common problem in observational data. The combination of multiple imputation of missing values and different propensity scoring techniques is addressed in this work. For a sample of lymph node-positive vulvar cancer patients, we re-analyze associations between the application of radiotherapy and disease-related and non-related survival. Inverse-probability-of-treatment-weighting (IPTW) and PS stratification are applied after multiple imputation by chained equation (MICE). Methodological issues are described in detail. Interpretation of the results and methodological limitations are discussed.
The Mental Timeline in a Crossed-Hands Paradigm
2016-11-01

Abstract. The existence of a lateral mental timeline is well established; in left-to-right writing cultures, past is associated with the left, future with the right. Accordingly, participants respond faster with the left to past, and with the right to future. Recent studies indicate that this association does not reverse when participants respond with their hands crossed. We investigated the role of instruction for this association in a crossed-hands paradigm. Participants classified the temporal reference of words by pressing a key on the left with their right hand, or a key on the right with their left. Half of the participants were instructed to respond with their right or left hand; the other half were instructed to respond with the left or right key. An interaction between time and key showed only for participants instructed to respond with the key, providing support for the role of extracorporal space for the mental timeline.
Halogen-Bearing Minerals From the Tamazeght Complex (Morocco): Constraints On Halogen Distribution and Evolution In Alkaline To Peralkaline Magmatic Systems
2016-11-01

Abstract Halogen abundances in apatite, biotite, amphibole, titanite, and other halogen-rich minerals (sodalite and eudialyte) from ultramafic pyroxenites and glimmerites, shonkinites, and gabbroic, monzonitic, and syenitic rocks of the alkaline to peralkaline Tamazeght complex (Morocco) are presented. Apatite, biotite, and amphibole show the highest F contents in the most evolved rocks, which also contain interstitial fluorite (restricted in syenites). The Cl contents of apatite, biotite, and amphibole are highest in the intermediate rocks. Sodalite (Cl-rich) is equally common in the evolved rocks, although Cl contents of apatite, biotite, and amphibole are low. We suggest that the early magmatic crystallization of sodalite causes a strong depletion of Cl in the remaining melt, resulting in the subsequent crystallization of Cl-poor apatite, biotite, and amphibole. Late-magmatic eudialyte in some of the rocks may indicate a late-stage re-enrichment of Cl. The Br contents of biotite, amphibole, eudialyte, and sodalite reveal that Cl-rich minerals generally contain high Br. The Cl/Br ratios of individual minerals are, however, highly variable. This suggests that besides melt composition, other factors, such as crystal-melt partitioning and fluid mobility, may influence Cl/Br ratios in igneous minerals, resulting in potentially strong fractionation of Cl from Br in minerals. Estimation of F and Cl contents in alkaline melts suggests that primitive ultramafic melts are poorer in Cl than evolved melts, whereas their F contents are relatively similar. The low apparent Cl contents of the syenitic melts, calculated based on apatite compositions, may reflect the halogen abundance during late-magmatic conditions, as the presence of early magmatic sodalite indicates Cl-rich syenitic melt compositions.
Motivation in the Writing Centre: A Peer Tutor’s Experience
2016-11-01

This article provides insight into the role of students' writing motivation in a writing centre setting. Based on my personal experiences as a peer tutor at a writing centre, the article highlights the importance of the Self-Determination Theory (SDT) for the evaluation of students' motivational levels. It thus shows that the distinction between the motivational concepts of intrinsic and extrinsic motivation as well as between 'amotivation' vs. 'demotivation' provides a basis for tutors and instructors who endeavour to foster students' motivation. Furthermore, the evaluation of different motivational strategies indicates that both peer tutors and instructors can make a valuable contribution to the development of students' writing motivation by giving informative feedback, setting clear goals, creating relaxed atmosphere and enhancing students' positive image as writers.
Heavy Quark Production at an Electron-Ion Collider
2016-11-01

An Electron-Ion Collider (EIC) with center-of-mass energies sqrt(s_eN) ~ 20-100 GeV and luminosity L ~ 10&lt;sup&gt;34&lt;/sup&gt; cm&lt;sup&gt;-2&lt;/sup&gt; s&lt;sup&gt;-1&lt;/sup&gt; would offer new opportunities to study heavy quark production in high-energy electron or photon scattering on protons and nuclei. We report about an R&amp;D project exploring the feasibility of direct measurements of nuclear gluon densities at large x (gluonic EMC effect, antishadowing) using open charm production at EIC. We describe the charm production rates and angle-momentum distributions at large x and discuss methods of charm identification using next-generation detector capabilities (pi/K identification, vertex reconstruction). The results can be used also for other physics applications of heavy quark production at EIC (fragmentation functions, jets, heavy quark propagation in nuclei).
High-Resolution Virtual Catchment Simulations of the Subsurface-Land Surface-Atmosphere System
2016-11-01

Abstract. Combining numerical models, which simulate water and energy fluxes in the subsurface-land surface-atmosphere system in a physically consistent way, becomes increasingly important to understand and study fluxes at compartmental boundaries and interdependencies of states across these boundaries. Complete state evolutions generated by such models, when run at highest possible resolutions while incorporating as many processes as attainable, may be regarded as a proxy of the real world – a virtual reality – which can be used to test hypotheses on functioning of the coupled terrestrial system and may serve as source for virtual measurements to develop data-assimilation methods. Such simulation systems, however, face severe problems caused by the vastly different scales of the processes acting in the compartments of the terrestrial system. The present study is motivated by the development of cross-compartmental data-assimilation methods, which face the difficulty of data scarcity in the subsurface when applied to real data. With appropriate and realistic measurement operators, the virtual reality not only allows taking virtual observations in any part of the terrestrial system at any density, thus overcoming data-scarcity problems of real-world applications, but also provides full information about true states and parameters aimed to be reconstructed from the measurements by data assimilation. In the present study, we have used the Terrestrial Systems Modeling Platform TerrSysMP, which couples the meteorological model COSMO, the land-surface model CLM, and the subsurface model ParFlow, to set up the virtual reality for a regional terrestrial system roughly oriented at the Neckar catchment in southwest Germany. We find that the virtual reality is in many aspects quite close to real observations of the catchment concerning, e.g., atmospheric boundary-layer height, precipitation, and runoff. But also discrepancies become apparent both in the ability of such models to correctly simulate some processes – which still need improvement – and the realism of the results of some observation operators like the SMOS and SMAP sensors, when faced with model states. In a succeeding step, we will use the virtual reality to generate observations in all compartments of the system for coupled data assimilation. The data assimilation will rely on a coarsened and simplified version of the model system.
Development and psychometric validation of the ‘Parent Perspective University of Rhode Island Change Assessment-Short’ (PURICA-S) Questionnaire for the application in parents of children with overweight and obesity
2016-11-01

Introduction High prevalence rates of childhood obesity urgently call for improved effectiveness of intervention programmes for affected children and their families. One promising attempt can be seen in tailoring interventions according to the motivational stages of parents as ‘agents of change’ for their children. Evidence from other behavioural contexts (eg, addiction) clearly shows the superiority of motivational-stage dependent tailored (behavioural) interventions. For the time-efficient assessment of motivational stages of change, this study aims to develop and psychometrically validate a ‘Parent Perspective Version’ of the existing University of Rhode Island Change Assessment-Short, an instrument assessing the motivational stages based on the theoretical fundamentals of the Transtheoretical Model of Psychotherapy. Methods and analysis In a multistep Delphi procedure, involving experts from the study context, the original items of the University of Rhode Island Change Assessment-Short Questionnaire will be transformed from the ‘self-perspective’ (‘I am having a problem’) to the parent perspective (‘my child is having a problem’). Following item adaptation, the new version of the questionnaire will be psychometrically validated in a cohort of N=300 parents with overweight or obese children. Parents will be recruited within a multicentre and multisite approach involving private paediatric practices, specialised outpatient clinics as well as inpatient and rehabilitation sites. Analyses will include confirmatory factor analyses, internal consistencies (reliability) as well as convergent and criterion validity. Convergent validity will be analysed using subscales of the HAKEMP-90 Questionnaire, an instrument which has been shown to differentiate between ‘state’ and ‘action’ orientation of individuals. Ethics and dissemination This study has been granted ethics committee approval by the University of Tuebingen (number 644/2014BO2). The results of this study will be released to the participating study centres and will be submitted to peer-reviewed journals and presented at international conferences. Trial registration number VfD_PURICA-S_15_003607 .
1st EMBL/DFG Women in Science Network Conference Heidelberg 2016
2016-11-01

Abstract The 1 st EMBL/DFG Women in Science (WiS) Conference “From Genes, Cells and the Immune System towards Therapies” was held on 19 th – 20 th September 2016 in Heidelberg, Germany. The WiS conference was funded by nine Collaborative Research Centers (CRCs) of the German Research Council (Deutsche Forschungsgemeinschaft, DFG; Table 1) and benefited from an outstanding hosting environment at the Advanced Training Center of the European Molecular Biology Laboratory (EMBL). Scientific talks focused at genetic, cellular and immunologic mechanisms, and immune therapy, and progress from all stages of development covering basic research to clinical developments was described. The presentations were embedded between structured networking sessions and a round table discussion with representatives of the DFG, EMBL, European Molecular Biology Organisation (EMBO), and the German Society of Immunology (DGfI).
A Workshop to Help Students Integrate Sources into Their Writing
2016-11-01

Inexperienced academic writers often have difficulty understanding and implementing academic intertextual practices, i.e. interpreting, extrapolating and integrating primary and secondary sources into their own texts. To address this need, we developed a workshop with learning stations. We identified five key difficulties students face and created seven exercises that address them. In the workshop, participants move from station to station, working on the exercises at their own pace by using pre-prepared materials at the stations. In this paper, we describe how we devised the workshop based on analysis of both the problem and the contexts in which the workshop has been carried out. Detailed descriptions for each exercise as well as a dramaturgy of the workshop are included; sample texts and handouts for each station can be found in the Appendix. Based on anecdotal participant feedback, we discuss advantages and disadvantages of the different exercises and of the workshop set-up. With the information provided, readers should be able to replicate this workshop and adapt the exercises to their own educational settings.
An application case study of state-based power optimization with partial networking
2016-11-01

In this paper we perform an application case study of state-based power optimization strategies, which exploit the AUTOSAR energy saving mechanism partial networking. We performed energy consumption measurements of the Electronic Control Units (ECUs) on a production-class Electric Vehicle (EV). Based on the measurement results, we analyzed both the applicability and energy saving effect of the strategies. Results show up to 15.0% energy saving impact on the ECUs energy consumption on our test drives.
Destruction of Be star disk by large scale magnetic fields
2016-11-01

Abstract Classical Be stars are rapidly rotating stars with circumstellar disks that come and go on time scale of years. Recent observational data strongly suggests that these stars lack the 10% incidence of global magnetic fields observed in other main-sequence B stars. Such an apparent lack of magnetic fields may indicate that Be disks are fundamentally incompatible with a significant large scale magnetic field. In this work, using numerical magnetohydrodynamics (MHD) simulations, we show that a dipole field of only 100G can lead to the quick disruption of a Be disk. Such a limit is in line with the observational upper limits for these objects.
<strong>Bioprospecting of Asteraceae Medicinal Plants of Pakistan for their Associated Bioactive Endophytic Actinomycetes for New Drug Targets</strong>
2016-11-01

Since the beginning of mankind, plants have been used as the source of medicinal agents thereby becoming a major course to discovering new drugs. The practice of using traditional medicine is prevalent in Pakistan that has a rich history of herbal plants being used by Hakims in folk medicine (Unani medicine). The Asteraceae family is the largest plant family in Pakistan, with plants of considerable medicinal importance. Endophytes include all organisms that symptomless colonize the living internal tissues of their hosts during a variable period of their lifetime. There they produce a broad variety of bioactive secondary metabolites with unique structure that are advantageous for the plant. Endophytic actinomycetes also colonize the internal tissues of plants without causing any visible changes or damage. They exploit an unusual habitat and considering this, this may enable them to possess the potential to produce bioactive compounds as similar to their host plant. Our study explores the bioprospecting potential related to endophytic actinomycetes of Asteraceae medicinal plants of Pakistan. After isolation and identification the endophytes were screened for their bioactive metabolites potential for new drug targets. This included extensive biological and chemical screening. The bioactive compounds were purified by column chromatography and final identification was done through HPLC-MS and NMR. The purified compounds were observed to be extremely potent with promising antimicrobial potential against major pathogens including algae and fungal strains as well as posessing antioxidant and cytotoxic potential. &nbsp
Backscattering elimination in fog for advanced driver assistance systems with LED matrix headlights
2016-11-01

Backscattering can be a major problem for drivers and camera-based driver assistance systems when driving in fog. In this paper we describe how LED matrix headlights can be used to cast a pattern into the scene that allows us to separate the scattered light from reflected light with compressed sensing. We use a laboratory setup with a fog machine, projector, and camera to simulate the situation in simplified form. This is a first step towards a glare free driving.
Safety consideration in state-based power optimization with partial networking - A case study
2016-11-01

In this paper we perform a safety analysis while applying state-based power optimization strategies using the AUTOSAR energy saving mechanism partial networking. Based on a case study of a braking system of a production-class Electric Vehicle (EV), we first show which safety issues could be introduced by applying partial networking. Then, based on our energy measurements of the ECU and the pressure measurements of the vacuum container, we show how to apply partial networking by considering all identified safety issues.
Line-Driven Ablation of Circumstellar Disks
2016-11-01

Abstract Mass is a key parameter in understanding the evolution and eventual fate of hot, luminous stars. Mass loss through a wind driven by UV-scattering forces is already known to reduce the mass of such stars by 10 −10 − 10 −4 M ⊙ /yr over the course of their lifetimes. However, high-mass stars already drive such strong winds while they are still in their accretion epoch. Therefore, stellar UV-scattering forces will efficiently ablate material off the surface of their circumstellar disks, perhaps even shutting off the final accretion through the last several stellar radii and onto a massive protostar. By using a three-dimensional UV-scattering prescription, we here quantify the role of radiative ablation in controlling the disk’s accretion rate onto forming high-mass stars. Particular emphasis is given to the potential impact of this process on the stellar upper mass limit.
ChemInform Abstract: Snap‐Shots of a Reduction Pathway: The Reaction of WCl6 with Copper Powder.
2016-11-01

Abstract Reaction of copper powder and WCl 6 between room temperature and 400 °C results in the formation of five new compounds: Cu 0.78 WCl 6 (I) at 60 °C (10 h), Cu 0.78 WCl 6 (II) at 100 °C (48 h), Cu 0.77 WCl 6 (III) at 150 °C (10 h), α‐Cu 2 W 2 Cl 10 (IV) at 200 °C (2 h), and β‐Cu 2 W 2 Cl 10 (V) at 240 °C (24 h).