julilili42/papers huggingface dataset:
An engineered promoter driving expression of a microbial avirulence gene confers recognition of TAL effectors and reduces growth of diverse Xanthomonas strains in citrus
2016-06-30

Summary Xanthomonas citri ssp. citri ( X. citri ), causal agent of citrus canker, uses transcription activator‐like effectors (TALEs) as major pathogenicity factors. TALEs, which are delivered into plant cells through the type III secretion system (T3SS), interact with effector binding elements ( EBE s) in host genomes to activate the expression of downstream susceptibility genes to promote disease. Predictably, TALEs bind EBE s in host promoters via known combinations of TALE amino acids to DNA bases, known as the TALE code. We introduced 14 EBE s, matching distinct X. citri TALEs, into the promoter of the pepper Bs3 gene ( ProBs3 1EBE ), and fused this engineered promoter with multiple EBE s ( ProBs3 14EBE ) to either the β‐glucuronidase ( GUS ) reporter gene or the coding sequence (cds) of the pepper gene, Bs3 . TALE‐induced expression of the Bs3 cds in citrus leaves resulted in no visible hypersensitive response (HR). Therefore, we utilized a different approach in which ProBs3 1EBE and ProBs3 14EBE were fused to the Xanthomonas gene, avrGf1 , which encodes a bacterial effector that elicits an HR in grapefruit and sweet orange. We demonstrated, in transient assays, that activation of ProBs3 14EBE by X. citri TALEs is T3SS dependent, and that the expression of AvrGf1 triggers HR and correlates with reduced bacterial growth. We further demonstrated that all tested virulent X. citri strains from diverse geographical locations activate ProBs3 14EBE . TALEs are essential for the virulence of X. citri strains and, because the engineered promoter traps are activated by multiple TALEs, this concept has the potential to confer broad‐spectrum, durable resistance to citrus canker in stably transformed plants.
Dependence of the Startle Response on Temporal and Spectral Characteristics of Acoustic Modulatory Influences in Rats and Gerbils
2016-06-30

The acoustic startle response (ASR) and its modulation by non-startling prepulses, presented shortly before the startle-eliciting stimulus, is a broadly applied test paradigm to determine changes in neural processing related to auditory or psychiatric disorders. Modulation by a gap in background noise as a prepulse is especially used for tinnitus assessment. However, the timing and frequency-related aspects of prepulses are not fully understood. The present study aims to investigate temporal and spectral characteristics of acoustic stimuli that modulate the ASR in rats and gerbils. For noise-burst prepulses, inhibition was frequency-independent in gerbils in the test range between 4 and 18 kHz. Prepulse inhibition (PPI) by noise-bursts in rats was constant in a comparable range (8-22 kHz), but lower outside this range. Purely temporal aspects of prepulse-startle-interactions were investigated for gap-prepulses focusing mainly on gap duration. While very short gaps had no (rats) or slightly facilitatory (gerbils) influence on the ASR, longer gaps always had a strong inhibitory effect. Inhibition increased with durations up to 75 ms and remained at a high level of inhibition for durations up to 1000 ms for both, rats and gerbils. Determining spectral influences on gap-prepulse inhibition (gap-PPI) revealed that gerbils were unaffected in the limited frequency range tested (4-18 kHz). The more detailed analysis in rats revealed a variety of frequency-dependent effects. Gaps in pure-tone background elicited constant and high inhibition (around 75%) over a broad frequency range (4-32 kHz). For gaps in noise-bands, on the other hand, a clear frequency-dependency was found: inhibition was around 50% at lower frequencies (6-14 kHz) and around 70% at high frequencies (16-20 kHz). This pattern of frequency-dependency in rats was specifically resulting from the inhibitory effect by the gaps, as revealed by detailed analysis of the underlying startle amplitudes. An interaction of temporal and spectral influences, finally, resulted in higher inhibition for 500 ms gaps than for 75 ms gaps at all frequencies tested. Improved prepulse paradigms based on these results are well suited to quantify the consequences of central processing disorders.
Allogeneic Blood Product Usage in Coronary Artery Bypass Grafting (CABG) with minimalized Extracorporeal Circulation System (MECC) Versus Standard On-Pump Coronary Artery Bypass Grafting
2016-06-30

Aim: Intraoperative allogeneic blood product transfusion (ABPT) in cardiac surgery is associated with worse overall outcome, including mortality. The objective of this study was to evaluate the ABPTs in minimalized extracorporeal cardiopulmonary (MECC TM ) compared with standard open system on-pump coronary revascularization. Methods: Data of 156 patients undergoing myocardial revascularization between September 2008 and September 2010 were reviewed. 83 patients were operated by the MECC technique and 73 were treated by standard extracorporeal circulation (sECC). ABPT and overall early postoperative complications were analyzed. Results: Operative mortality and morbidity were similar in both groups. ABPT in the MECC group was significantly lower than in the sECC group both intraoperatively (7.2 vs. 60.3% of patients p&lt;0.001) and during the first five postoperative days (19.3 vs. 57.5%; p&lt;0.001). “Skin to skin”- (214 ± 45 vs. 232 ± 45 min; p=0.012), cardiopulmonary bypass (CPB) - (82 ± 25 vs. 95 ± 26 min; p=0.014), and X-clamp- times (50 ± 16 vs. 56 ± 17 min; p=0.024) were significantly lower in the MECC group than in the sECC group. Length of ICU (intensive care unit) - and hospital stay were also significantly lower in the MECC group vs. the sECC group (26.7 ± 20.2 vs. 54.5 ± 68.9 h; p&lt;0.001, and 12.0 ± 4.1 vs. 14.5 ± 4.6 days; p&lt;0.001). Conclusion: Application of MECC as on-pump coronary artery bypass graft (CABG) results in significantly lower ABPT as well as shorter ICU and in-hospital stay. In order to achieve these benefits of MECC autologous retrograde priming, Bispectral index (BIS) monitoring, intraoperative cell salvage, meticulous hemostasis and strict peri- and postoperative volume management are crucial.
Belian categories
2016-06-30

We instal homological algebra, including derived functors, on certain non-additive categories like categories of pointed CW-complexes, modules of monoids or sheaves thereof. We apply this theory to Monoid schemes and sheaves on them, compare the result with the base change and prove several structural theorems.
Product Importance Sampling for Light Transport Path Guiding
2016-07-01

&lt;p&gt;ABSTRACT: The efficiency of Monte Carlo algorithms for light transport simulation is directly related to their ability to importance-sample the product of the illumination and reflectance in the rendering equation. Since the optimal sampling strategy would require knowledge about the transport solution itself, importance sampling most often follows only one of the known factors &ndash; BRDF or an approximation of the incident illumination. To address this issue, we propose to represent the illumination and the reflectance factors by the Gaussian mixture model (GMM), which we fit by using a combination of weighted expectation maximization and non-linear optimization methods. The GMM representation then allows us to obtain the resulting product distribution for importance sampling on-the-fly at each scene point. For its efficient evaluation and sampling we preform an up-front adaptive decimation of both factor mixtures. In comparison to state-of-the-art sampling methods, we show that our product importance sampling can lead to significantly better convergence in scenes with complex illumination and reflectance.&lt;/p&gt;
Jumping mechanisms and performance in beetles. I. Flea beetles (Coleoptera: Chrysomelidae: Alticini)
2016-07-01

ABSTRACT The present study analyses the anatomy, mechanics and functional morphology of the jumping apparatus, the performance and the kinematics of the natural jump of flea beetles (Coleoptera: Chrysomelidae: Galerucinae: Alticini). The kinematic parameters of the initial phase of the jump were calculated for five species from five genera (average values from minimum to maximum): acceleration 0.91–2.25 (×103) m s−2, velocity 1.48–2.80 m s−1, time to take-off 1.35–2.25 ms, kinetic energy 2.43–16.5 μJ, g-force 93–230. The jumping apparatus is localized in the hind legs and formed by the femur, tibia, femoro-tibial joint, modified metafemoral extensor tendon, extensor ligament, tibial flexor sclerite, and extensor and flexor muscles. The primary role of the metafemoral extensor tendon is seen in the formation of an increased attachment site for the extensor muscles. The rubber-like protein resilin was detected in the extensor ligament, i.e. a short, elastic element connecting the extensor tendon with the tibial base. The calculated specific joint power (max. 0.714 W g−1) of the femoro-tibial joint during the jumping movement and the fast full extension of the hind tibia (1–3 ms) suggest that jumping is performed via a catapult mechanism releasing energy that has beforehand been stored in the extensor ligament during its stretching by the extensor muscles. In addition, the morphology of the femoro-tibial joint suggests that the co-contraction of the flexor and the extensor muscles in the femur of the jumping leg is involved in this process.
Comparison of different rate constant expressions for the prediction of charge and energy transport in oligoacenes
2016-07-01

Charge and exciton transport in organic semiconductors is crucial for a variety of optoelectronic applications. The prediction of the material‐dependent exciton diffusion length and the charge carrier mobility is a prerequisite for tailoring new materials for organic electronics. At room temperature often a hopping process can be assumed. In this work, three hopping models based on Fermi's Golden rule but with different levels of approximation—the spectral overlap approach, the Marcus theory, and the Levich–Jortner theory—are compared for the calculation of charge carrier mobilities and exciton diffusion lengths for oligoacenes, using the master equation approach and Monte Carlo simulations. WIREs Comput Mol Sci 2016, 6:694–720. doi: 10.1002/wcms.1273 This article is categorized under: Structure and Mechanism &gt; Computational Materials Science
Intracellular signalling pathways: targets to reverse immunosenescence
2016-07-01

Summary Ageing is a very complex process, the result of the dysregulation of multiple systems interacting in many ways. A prominent change occurring with ageing is related to the architecture and functioning of the immune system, viewed commonly as detrimental and termed ‘immunosenescence’. However, age-associated changes may also lead to increased function in certain respects, which can be viewed as adaptive. None the less, on balance it is well-recognized that immunosenescence is accompanied by the low-grade inflammation observed commonly in elderly people, which has been dubbed ‘inflamm-ageing’. The exact cause and significance of all these changes is not clear, but there is a consensus that they are related to the occurrence of chronic non-infectious age-associated disease, as well as increased susceptibility to infections. Alterations to immune cell signalling may be a prominent cause of malfunctioning immunity. Emerging attempts to reverse immunosenescence have recently targeted the signalling pathways in various different cell types of the immune system. Here, we review and discuss alterations in the signalling pathways of immune cells with ageing and consider current targets and means to modulate altered functions. We discuss the potential dangers as well as the benefits of these interventions, and consider future approaches to this problem.
Seeking advice: A sampling approach to advice taking
2016-07-01

Abstract The present research addresses advice taking from a holistic perspective covering both advice seeking and weighting. We build on previous theorizing that assumes that underweighting of advice results from biased samples of information. That is, decision makers have more knowledge supporting their own judgment than that of another person and thus weight the former stronger than the latter. In the present approach, we assume that participants reduce this informational asymmetry by the sampling of advice and that sampling frequency depends on the information ecology. Advice that is distant from the decision maker’s initial estimate should lead to a higher frequency of advice sampling than close advice. Moreover, we assume that advice distant from the decision maker’s initial estimate and advice that is supported by larger samples of advisory estimates are weighted more strongly in the final judgment. We expand the classical research paradigm with a sampling phase that allows participants to sample any number of advisory estimates before revising their judgments. Three experiments strongly support these hypotheses, thereby advancing our understanding of advice taking as an adaptive process.
Safety of Topical Corticosteroids in Pregnancy
2016-07-01

The available evidence found no associations of maternal use of topical corticosteroids of any potency with mode of delivery, birth defects, preterm delivery, fetal death, and low Apgar score. However, maternal use of potent to very potent topical corticosteroids, especially when the cumulative dosage of topical corticosteroids throughout the pregnancy is very large, is associated with low birth weight.
Evolution of organogenesis and the origin of altriciality in mammals
2016-07-01

SUMMARY Mammals feature not only great phenotypic disparity, but also diverse growth and life history patterns, especially in maturity level at birth, ranging from altriciality to precocity. Gestation length, morphology at birth, and other markers of life history are fundamental to our understanding of mammalian evolution. Based on the first synthesis of embryological data and the study of new ontogenetic series, we reconstructed estimates of the ancestral chronology of organogenesis and life‐history modes in placental mammals. We found that the ancestor of marsupial and placental mammals was placental‐like at birth but had a long, marsupial‐like infancy. We hypothesize that mammalian viviparity might have evolved in association with the extension of growth after birth, enabled through lactation, and that mammalian altriciality is inherited from the earliest amniotes. The precocial lifestyle of extant sauropsids and that of many placental mammals were acquired secondarily. We base our conclusions on the best estimates and provide a comprehensive discussion on the methods used and the limitations of our dataset. We provide the most comprehensive embryological dataset ever published, “rescue” old literature sources, and apply available methods and illustrate thus an approach on how to investigate comparatively organogenesis in macroevolution.
A fully actuated quadrotor UAV with a propeller tilting mechanism: Modeling and control
2016-07-01

Equipped with four actuators, quadrotor Unmanned Aerial Vehicles belong to the family of underactuated systems. The lateral motion of such platforms is strongly coupled with their orientation and consequently it is not possible to track an arbitrary 6D trajectory in space. In this paper, we propose a novel quadrotor design in which the tilt angles of the propellers with respect to the quadrotor body are being simultaneously controlled with two additional actuators by employing the parallelogram principle. Since the velocity of the controlled tilt angles of the propellers does not appear directly in the derived dynamic model, the system cannot be static feedback linearized. Nevertheless, the system is linearizable at a higher differential order, leading to a dynamic feedback linearization controller. Simulations confirm the theoretical findings, highlighting the improved motion capabilities with respect to standard quadrotors.
More than 70 Years of Pyrogen Detection: Current State and Future Perspectives
2016-07-01

In the quality assurance of medical products, tests for sterility are essential. For parenteral pharmaceuticals, avoiding the presence of pyrogens is crucial. These fever-inducing substances (endotoxins and non-endotoxins) are not eliminated by standard sterilisation processes, and are biologically active once in the bloodstream, causing risks to human health, ranging from mild reactions (e.g. fever) to septic shock and death. Therefore, for injectable formulations, pyrogen testing is mandatory. Over the years, various pyrogen testing methods have been introduced, namely: in the 1940s, the rabbit pyrogen test, which is an in vivo test that measures the fever reaction as an endpoint; in the 1970s, the Limulus Amoebocyte Lysate (LAL) test, which is an in vitro test (with the haemolymph of the horseshoe crab) that specifically detects endotoxin; and in 2010, the Monocyte-Activation Test (MAT), which is a non-animal based in vitro pyrogen test that represents a full replacement of the rabbit test. Due to the ubiquity and biological significance of pyrogens, we are currently further developing the MAT so that it can be used for other applications. More specifically, our focus is on the detection of pyrogenic contamination on medical devices, as well as on the measurement of air quality. In addition, further improvements to permit the use of cryopreserved blood in the MAT, to overcome the limitations in the availability of freshly-drawn blood from human donors, are ongoing.
SCISSOR—Spinal Cord Injury Study on Small molecule-derived Rho inhibition: a clinical study protocol
2016-07-01

Introduction The approved analgesic and anti-inflammatory drugs ibuprofen and indometacin block the small GTPase RhoA, a key enzyme that impedes axonal sprouting after axonal damage. Inhibition of the Rho pathway in a central nervous system-effective manner requires higher dosages compared with orthodox cyclooxygenase-blocking effects. Preclinical studies on spinal cord injury (SCI) imply improved motor recovery after ibuprofen/indometacin-mediated Rho inhibition. This has been reassessed by a meta-analysis of the underlying experimental evidence, which indicates an overall effect size of 20.2% regarding motor outcome achieved after ibuprofen/indometacin treatment compared with vehicle controls. In addition, ibuprofen/indometacin may also limit sickness behaviour, non-neurogenic systemic inflammatory response syndrome (SIRS), neuropathic pain and heterotopic ossifications after SCI. Consequently, ‘small molecule’-mediated Rho inhibition after acute SCI warrants clinical investigation. Methods and analysis Protocol of an investigator-initiated clinical open-label pilot trial on high-dose ibuprofen treatment after acute traumatic, motor-complete SCI. A sample of n=12 patients will be enrolled in two cohorts treated with 2400 mg/day ibuprofen for 4 or 12 weeks, respectively. The primary safety end point is an occurrence of serious adverse events, primarily gastroduodenal bleedings. Secondary end points are pharmacokinetics, feasibility and preliminary effects on neurological recovery, neuropathic pain and heterotopic ossifications. The primary safety analysis is based on the incidence of severe gastrointestinal bleedings. Additional analyses will be mainly descriptive and casuistic. Ethics and dissemination The clinical trial protocol was approved by the responsible German state Ethics Board, and the Federal Institute for Drugs and Medical Devices. The study complies with the Declaration of Helsinki, the principles of Good Clinical Practice and all further applicable regulations. This safety and pharmacokinetics trial informs the planning of a subsequent randomised controlled trial. Regardless of the result of the primary and secondary outcome assessments, the clinical trial will be reported as a publication in a peer-reviewed journal. Trial registration number NCT02096913; Pre-results.
Better understanding of phosphoinositide 3-kinase (PI3K) pathways in vasculature: Towards precision therapy targeting angiogenesis and tumor blood supply
2016-07-01

The intracellular PI3K-AKT-mTOR pathway is involved in regulation of numerous important cell processes including cell growth, differentiation, and metabolism. The PI3Kα isoform has received particular attention as a novel molecular target in gene therapy, since this isoform plays critical roles in tumor progression and tumor blood flow and angiogenesis. However, the role of PI3Kα and other class I isoforms, i.e. PI3Kβ, γ, δ, in the regulation of vascular tone and regional blood flow are largely unknown. We used novel isoform-specific PI3K inhibitors and mice deficient in both PI3Kγ and PI3Kδ (Pik3cg(-/-)/Pik3cd(-/-)) to define the putative contribution of PI3K isoform(s) to arterial vasoconstriction. Wire myography was used to measure isometric contractions of isolated murine mesenteric arterial rings. Phenylephrine-dependent contractions were inhibited by the pan PI3K inhibitors wortmannin (100 nM) and LY294002 (10 μM). These vasoconstrictions were also inhibited by the PI3Kα isoform inhibitors A66 (10 μM) and PI-103 (1 μM), but not by the PI3Kβ isoform inhibitor TGX 221 (100 nM). Pik3cg(-/-)/Pik3cd(-/-)-arteries showed normal vasoconstriction. We conclude that PI3Kα is an important downstream element in vasoconstrictor GPCR signaling, which contributes to arterial vasocontraction via α1-adrenergic receptors. Our results highlight a regulatory role of PI3Kα in the cardiovascular system, which widens the spectrum of gene therapy approaches targeting PI3Kα in cancer cells and tumor angiogenesis and regional blood flow.
High Frequency of Pathogenic Rearrangements in SPG11 and Extensive Contribution of Mutational Hotspots and Founder Alleles.
2016-07-01

Biallelic loss-of-function mutations in SPG11 cause a wide spectrum of recessively inherited, neurodegenerative disorders including hereditary spastic paraplegia (HSP), amyotrophic lateral sclerosis, and Charcot-Marie-Tooth disease. By comprehensive screening of three large cohorts of HSP index patients, we identified 83 alleles with "small" mutations and 13 alleles that carry large genomic rearrangements. Including relevant data from previous studies, we estimate that copy number variants (CNVs) account for ∼19% of pathogenic SPG11 alleles. The breakpoints for all novel and some previously reported CNVs were determined by long-range PCR and sequencing. This revealed several Alu-associated recombination hotspots. We also found evidence for additional mutational mechanisms, including for a two-step event in which an Alu retrotransposition preceded the actual rearrangement. Apparently independent samples with identical breakpoints were analyzed by microsatellite PCRs. The resulting haplotypes suggested the existence of two rearrangement founder alleles. Our findings widen the spectra of mutations and mutational mechanisms in SPG11, underscore the pivotal role played by Alus, and are of high diagnostic relevance for a wide spectrum of clinical phenotypes including the most frequent form of recessive HSP.
Electroweakino pair production at the LHC: NLO SUSY-QCD corrections and parton-shower effects
2016-07-01

We present a set of NLO SUSY-QCD calculations for the pair production of\\nneutralinos and charginos at the LHC, and their matching to parton-shower\\nprograms in the framework of the POWHEG-BOX program package. The code we have\\ndeveloped provides a SUSY Les Houches Accord interface for setting\\nsupersymmetric input parameters. Decays of the neutralinos and charginos and\\nparton-shower effects can be simulated with PYTHIA. To illustrate the\\ncapabilities of our program, we present phenomenological results for a\\nrepresentative SUSY parameter point. We find that NLO-QCD corrections increase\\nthe production rates for neutralinos and charginos significantly. The impact of\\nparton-shower effects on distributions of the weakinos is small, but\\nnon-negligible for jet distributions.\\n