julilili42/papers huggingface dataset:
The Roles of the Wnt-Antagonists Axin and Lrp4 during Embryogenesis of the Red Flour Beetle Tribolium castaneum
2017-10-15

In both vertebrates and invertebrates, the Wnt-signaling pathway is essential for numerous processes in embryogenesis and during adult life. Wnt activity is fine-tuned at various levels by the interplay of a number of Wnt-agonists (Wnt ligands, Frizzled-receptors, Lrp5/6 coreceptors) and Wnt-antagonists (among them Axin, Secreted frizzled and Lrp4) to define anterior–posterior polarity of the early embryo and specify cell fate in organogenesis. So far, the functional analysis of Wnt-pathway components in insects has concentrated on the roles of Wnt-agonists and on the Wnt-antagonist Axin. We depict here additional features of the Wnt-antagonist Axin in the flour beetle Tribolium castaneum. We show that Tc-axin is dynamically expressed throughout embryogenesis and confirm its essential role in head development. In addition, we describe an as yet undetected, more extreme Tc-axin RNAi-phenotype, the ectopic formation of posterior abdominal segments in reverse polarity and a second hindgut at the anterior. For the first time, we describe here that an lrp4 ortholog is involved in axis formation in an insect. The Tribolium Lrp4 ortholog is ubiquitously expressed throughout embryogenesis. Its downregulation via maternal RNAi results in the reduction of head structures but not in axis polarity reversal. Furthermore, segmentation is impaired and larvae develop with a severe gap-phenotype. We conclude that, as in vertebrates, Tc-lrp4 functions as a Wnt-inhibitor in Tribolium during various stages of embryogenesis. We discuss the role of both components as negative modulators of Wnt signaling in respect to axis formation and segmentation in Tribolium.
Seismic monitoring of small alpine rockfalls – validity, precision and limitations
2017-10-16

Abstract. Rockfall in deglaciated mountain valleys is perhaps the most important post-glacial geomorphic process for determining the rates and patterns of valley wall erosion. Furthermore, rockfall poses a significant hazard to inhabitants and motivates monitoring efforts in populated areas. Traditional rockfall detection methods, such as aerial photography and terrestrial laser scanning (TLS) data evaluation, provide constraints on the location and released volume of rock but have limitations due to significant time lags or integration times between surveys, and deliver limited information on rockfall triggering mechanisms and the dynamics of individual events. Environmental seismology, the study of seismic signals emitted by processes at the Earth's surface, provides a complementary solution to these shortcomings. However, this approach is predominantly limited by the strength of the signals emitted by a source and their transformation and attenuation towards receivers. To test the ability of seismic methods to identify and locate small rockfalls, and to characterise their dynamics, we surveyed a 2.16 km2 large, near-vertical cliff section of the Lauterbrunnen Valley in the Swiss Alps with a TLS device and six broadband seismometers. During 37 days in autumn 2014, 10 TLS-detected rockfalls with volumes ranging from 0.053 ± 0.004 to 2.338 ± 0.085 m3 were independently detected and located by the seismic approach, with a deviation of 81−29+59 m (about 7 % of the average inter-station distance of the seismometer network). Further potential rockfalls were detected outside the TLS-surveyed cliff area. The onset of individual events can be determined within a few milliseconds, and their dynamics can be resolved into distinct phases, such as detachment, free fall, intermittent impact, fragmentation, arrival at the talus slope and subsequent slope activity. The small rockfall volumes in this area require significant supervision during data processing: 2175 initially picked potential events reduced to 511 potential events after applying automatic rejection criteria. The 511 events needed to be inspected manually to reveal 19 short earthquakes and 37 potential rockfalls, including the 10 TLS-detected events. Rockfall volume does not show a relationship with released seismic energy or peak amplitude at this spatial scale due to the dominance of other, process-inherent factors, such as fall height, degree of fragmentation, and subsequent talus slope activity. The combination of TLS and environmental seismology provides, despite the significant amount of manual data processing, a detailed validation of seismic detection of small volume rockfalls, and revealed unprecedented temporal, spatial and geometric details about rockfalls in steep mountainous terrain.
Intergenerational environmental effects: functional signals in offspring transcriptomes and metabolomes after parental jasmonic acid treatment in apomictic dandelion
2017-10-16

Summary Parental environments can influence offspring traits. However, the magnitude of the impact of parental environments on offspring molecular phenotypes is poorly understood. Here, we test the direct effects and intergenerational effects of jasmonic acid ( JA ) treatment, which is involved in herbivory‐induced defense signaling, on transcriptomes and metabolomes in apomictic common dandelion ( Taraxacum officinale ). In a full factorial crossed design with parental and offspring JA and control treatments, we performed leaf RNA ‐seq gene expression analysis, LC ‐ MS metabolomics and total phenolics assays in offspring plants. Expression analysis, leveraged by a de novo assembled transcriptome, revealed an induced response to JA exposure that is consistent with known JA effects. The intergenerational effect of treatment was considerable: 307 of 858 detected JA ‐responsive transcripts were affected by parental JA treatment. In terms of the numbers of metabolites affected, the magnitude of the chemical response to parental JA exposure was c . 10% of the direct JA treatment response. Transcriptome and metabolome analyses both identified the phosphatidylinositol signaling pathway as a target of intergenerational JA effects. Our results highlight that parental environments can have substantial effects in offspring generations. Transcriptome and metabolome assays provide a basis for zooming in on the potential mechanisms of inherited JA effects.
The Immunosuppressant Brasilicardin: Determination of the Biosynthetic Gene Cluster in the Heterologous Host Amycolatopsis japonicum
2017-10-16

Nocardia terpenica IFM 0406 is the producer of the immunosuppressants brasilicardins A‐D. Brasilicardin is a promising compound because of its unique mode of action and its higher potency and reduced toxicity compared to today's standard drugs. However, production of brasilicardin is so far hampered as Nocardia terpenica IFM 0406 synthesizes brasilicardin in only low amounts and represents a human pathogen (biosafety level 2 BSL2). In order to achieve a safe and high yield production of brasilicardin A (BraA), the authors heterologously express the brasilicardin gene cluster in the nocardioform actinomycete Amycolatopsis japonicum ( A. japonicum ::bcaAB01), which is fast growing, genetically accessible and closely related to N. terpenica IFM 0406. In A. japonicum ::bcaAB01, four brasilicardin congeners, intermediates of the BraA biosynthesis, are produced. Investigation of the genes flanking the previously defined brasilicardin biosynthetic gene cluster revealed two novel genes ( bra0 , bra12 ), which are involved in brasilicardin biosynthesis: bra12 encodes a transcriptional activator of the brasilicardin gene cluster. bra0 codes for a dioxygenase involved in methoxylation of brasilicardin. Based on this finding the authors are able to revise the proposed brasilicardin biosynthesis.
In vivo characterization of the downfield part of 1H MR spectra of human brain at 9.4 T: Magnetization exchange with water and relation to conventionally determined metabolite content
2017-10-16

Purpose To perform exchange‐rate measurements on the in vivo human brain downfield spectrum (5–10 ppm) at 9.4 T and to compare the variation in concentrations of the downfield resonances and of known upfield metabolites to determine potential peak labels. Methods Non‐water‐suppressed metabolite cycling was used in combination with an inversion transfer technique in two brain locations in healthy volunteers to measure the exchange rates and T 1 values of exchanging peaks. Spectra were fitted with a heuristic model of a series of 13 or 14 Voigt lines, and a Bloch–McConnell model was used to fit the exchange rate curves. Concentrations from non‐water‐inverted spectra upfield and downfield were compared. Results Mean T 1 values ranged from 0.40 to 0.77 s, and exchange rates from 0.74 to 13.8 s −1 . There were no significant correlations between downfield and upfield concentrations, except for N‐acetylaspartate, with a correlation coefficient of 0.63 and P &lt; 0.01. Conclusions Using ultrahigh field allowed improved separation of peaks in the 8.2 to 8.5 ppm amide proton region, and the exchange rates of multiple downfield resonances including the 5.8‐ppm peak, previously tentatively assigned to urea, were measured in vivo in human brain. Downfield peaks consisted of overlapping components, and largely missing correlations between upfield and downfield resonances—although not conclusive—indicate limited contributions from metabolites present upfield to the downfield spectrum. Magn Reson Med 79:2863–2873, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Bulky Phenyl Modifications of the Silanide Ligand Si(SiMe3)3 – Synthesis and Reactivity
2017-10-16

The synthesis and structural characterization of bulkier variations of the very common organometallic compound M Si(SiMe 3 ) 3 , namely M Si(SiMe 3 )(SiPh 3 ) 2 3 and M Si(SiPh 3 ) 3 [ M = Li ( 1 ), K ( 5 )] are presented, which can be synthesized via a step by step exchange of SiMe 3 groups by bulkier SiPh 3 groups. This synthetic route is high selective and is performed in good yields via the silanes Si(SiMe 3 ) 2 (SiPh 3 ) 2 ( 2 ) and Si(SiMe 3 )(SiPh 3 ) 3 ( 4 ). Additionally, the corresponding silanes HSi(SiMe 3 )(SiPh 3 ) 2 ( 6 H ) and HSi(SiPh 3 ) 3 ( 7 H ) are obtained via the reaction of 3 and 5 with aqueous HCl, respectively. Oxidation of 6 H with CCl 4 gives the chlorsilane Cl‐Si(SiMe 3 )(SiPh 3 ) 2 ( 6 Cl ). The bulkiest chlorsilane Cl–Si(SiPh 3 ) 3 ( 7 ) is obtained by the reaction of 5 with E Cl 2 ( E = Sn, Pb).
Bcl-2 proteins: Unraveling the details of a complex and dynamic network
2017-10-16

Apoptosis regulation by Bcl-2 proteins is pivotal for mammalians, not only because it is key for development but also because aberrant apoptosis is prerequisite to severe diseases, like cancer. Recently, we quantified interactions within the Bcl-2 protein network in solution and membranes, and addressed membrane recruitment, preference of interaction partners and the consequences for Bax activation and inhibition.
Psychosocial stress effects on temporal characteristics of EEG microstates
2017-10-16

Multichannel records of the spontaneous brain electrical activity shows that EEG topography does not change randomly over time, but remains stable for short time periods (ca. 80-120 ms). These periods of quasi-stability are often referred to as "EEG microstates" (Lehmann et al., 1987) and are suggested to be the building blocks of brain dynamics that represent basic brain functions (Khanna et al., 2015). Recent studies show that performing various cognitive activities can affect temporal structure of the microstates. Also, changes in the parameters of microstates are associated with psychiatric disorders (schizophrenia, depression, etc.). In this study, we investigated effect of the psychosocial stress on the temporal characteristics of EEG microstates. We analyzed resting-state, eyes-closed recordings from thirty-nine healthy male volunteers over 3 sessions of simultaneous 3 Tesla fMRI and 64-channel EEG. The experiment started with a resting-state session (RS0) that was followed by two tasks to assess attention and a second resting-state session (RS1). The stress response was induced using the ScanSTRESS (Streit et al., 2014), which uses arithmetic tasks as well as mental rotation tasks. The experiment ended with a final resting session (RS2). We identified four microstate classes using EEGLAB plugin for microstates analysis by Thomas Koenig (University of Bern, Switzerland) and calculated the average duration, frequency, and coverage fraction of these microstates. We found that frequency of occurrence and coverage fraction of the microstate class C, known to correspond to the cognitive control/Saliency networks (Britz et al., 2010) were increased after experience of psychosocial stress (occurrence: RS2 vs RS1: p = 0.02, coverage: RS2 vs RS1: p = 0.04, paired t-test) while performance of non-stressful tasks did not affect these parameters (No significant changes between RS1 vs RS0).
ICA-based approach for ROI detection in rt-fMRI Neurofeedback experiment
2017-10-16

Real-time fMRI Neurofeedback (rtfMRI NF) is the technique in which blood oxygen level dependent (BOLD) response of specific Region of Interest (ROI) is presented in real time to the participant with the goal of enabling the subjects to volitionally regulate their brain signals. Neurofeedback is considered a promising alternative or supplementary treatment (Arns et al., 2012, Alegria et al., 2017). Because many neuropsychiatric disorders, MDD, ADHD, etc. are often associated with pathological changes in dynamic interactions between brain areas (that is, functional brain networks), the ability to modulate neural dynamics on a network level with neurofeedback may be a more effective than neurofeedback involving a single area (Sitaram et.al., 2017). We present an Independent Component Analysis (ICA) - based approach which finds the individualized ROI that can be used as the target of NF regulation within real-time fMRI neurofeedback. First, individual resting-state fMRI data are decomposed into 40 Independent Components (IC) using GIFT toolbox, next the Independent Component (IC) that corresponds to a specific network is identified and, on the last step, voxels that pass a certain intensity threshold within specific brain region are chosen as Region of Interest.The algorithm was validated on resting state 3T fMRI recordings of 37 subjects. It shows highly consistent results across subjects, different software packages used to pre-process the data: SPM (The FIL Methods group), CONN (Whitfield-Gabrieli, and Nieto-Castanon, 2012), Turbo-BrainVoyager (www.brainvoyager.com). We also used a special recording with extremely inclined and rotated head and the algorithm showed high accuracy. The execution time of our algorithm is in the range between 1.5 to 5 minutes, depending on the available computational power, which makes it possible to use this algorithm for the rtfMRI NF experiments.
Motivation after stimulation of the vagus nerve at the ear
2017-10-16

Anhedonia is a core symptom in many mental disorders such as schizophrenia and major depression. It is generally defined as the 'inability to experience pleasure' but recent debates push for a conceptual revision emphasizing an understanding of anhedonia as a motivational deficit to work for reward. In this study we aimed to clarify on the interplay of 'wanting' and 'liking' when physical effort is required in order to gain a reward. We used transcutaneous vagus nerve stimulation (tVNS) at the left ear to manipulate metabolic signaling and the perceived availability of energy in the body. In a randomized crossover design, tVNS/sham stimulation was applied to N=20 healthy subjects. They completed 2 sessions of an adapted version of the effort allocation task and had to press a button until reaching a certain proportion of their maximum frequency in order to gain rewards. Preliminary results in 13 participants indicate that the task tracks important aspects of costs and benefits of action as expected. This is reflected in significant effects of reward levels (F(1,12)=9.67, p = .009) and an interaction of reward level and task diffculty (F(1,12)=8.12, p = .015) on the motivation to expend effort across reward domains (money and food). Moreover, our preliminary results point to improvements in response vigor after tVNS, particularly in session 2, but more data is needed to substantiate the hypothesized effect. The findings confirm the suitability of the effort allocation task to study effort based decision making over time. Motivational vigor and subjective assessment of effort might be increased by tVNS. It therefore may be a promising approach to study motivational deficits related with anhedonia.
Serotonin Decreases the Gain of Visual Responses in Awake Macaque V1
2017-10-17

Serotonin, an important neuromodulator in the brain, is implicated in affective and cognitive functions. However, its role even for basic cortical processes is controversial. For example, in the mammalian primary visual cortex (V1), heterogenous serotonergic modulation has been observed in anesthetized animals. Here, we combined extracellular single-unit recordings with iontophoresis in awake animals. We examined the role of serotonin on well-defined tuning properties (orientation, spatial frequency, contrast, and size) in V1 of two male macaque monkeys. We find that in the awake macaque the modulatory effect of serotonin is surprisingly uniform: it causes a mainly multiplicative decrease of the visual responses and a slight increase in the stimulus-selective response latency. Moreover, serotonin neither systematically changes the selectivity or variability of the response, nor the interneuronal correlation unexplained by the stimulus (“noise-correlation”). The modulation by serotonin has qualitative similarities with that for a decrease in stimulus contrast, but differs quantitatively from decreasing contrast. It can be captured by a simple additive change to a threshold-linear spiking nonlinearity. Together, our results show that serotonin is well suited to control the response gain of neurons in V1 depending on the animal's behavioral or motivational context, complementing other known state-dependent gain-control mechanisms. SIGNIFICANCE STATEMENT Serotonin is an important neuromodulator in the brain and a major target for drugs used to treat psychiatric disorders. Nonetheless, surprisingly little is known about how it shapes information processing in sensory areas. Here we examined the serotonergic modulation of visual processing in the primary visual cortex of awake behaving macaque monkeys. We found that serotonin mainly decreased the gain of the visual responses, without systematically changing their selectivity, variability, or covariability. This identifies a simple computational function of serotonin for state-dependent sensory processing, depending on the animal's affective or motivational state.
Effects of Subthalamic and Nigral Stimulation on Gait Kinematics in Parkinson’s Disease
2017-10-17

Conventional subthalamic deep brain stimulation for Parkinson's disease (PD) presumably modulates the spatial component of gait. However, temporal dysregulation of gait is one of the factors that is tightly associated with freezing of gait (FOG). Temporal locomotor integration may be modulated differentially at distinct levels of the basal ganglia. Owing to its specific descending brainstem projections, stimulation of the substantia nigra pars reticulata (SNr) area might modulate spatial and temporal parameters of gait differentially compared to standard subthalamic nucleus (STN) stimulation. Here, we aimed to characterize the differential effect of STN or SNr stimulation on kinematic gait parameters. We analyzed biomechanical parameters during unconstrained over ground walking in 12 PD patients with subthalamic deep brain stimulation and FOG. Patients performed walking in three therapeutic conditions: (i) Off stimulation, (ii) STN stimulation (alone), and (iii) SNr stimulation (alone). SNr stimulation was achieved by stimulating the most caudal contact of the electrode. We recorded gait using three sensors (each containing a tri-axial accelerometer, gyroscope, and magnetometer) attached on both left and right ankle, and to the lumbar spine. STN stimulation improved both the spatial features (stride length, stride length variability) and the temporal parameters of gait. SNr stimulation improved temporal parameters of gait (swing time asymmetry). Correlation analysis suggested that patients with more medial localization of the SNr contact associated with a stronger regularization of gait. These results suggest that SNr stimulation might support temporal regularization of gait integration.
Comparison of visual receptive fields in the dorsolateral prefrontal cortex and ventral intraparietal area in macaques
2017-10-17

Abstract The concept of receptive field ( RF ) describes the responsiveness of neurons to sensory space. Neurons in the primate association cortices have long been known to be spatially selective but a detailed characterisation and direct comparison of RF s between frontal and parietal association cortices are missing. We sampled the RF s of a large number of neurons from two interconnected areas of the frontal and parietal lobes, the dorsolateral prefrontal cortex (dl PFC ) and ventral intraparietal area ( VIP ), of rhesus monkeys by systematically presenting a moving bar during passive fixation. We found that more than half of neurons in both areas showed spatial selectivity. Single neurons in both areas could be assigned to five classes according to the spatial response patterns: few non‐uniform RF s with multiple discrete response maxima could be dissociated from the vast majority of uniform RF s showing a single maximum; the latter were further classified into full‐field and confined foveal, contralateral and ipsilateral RF s. Neurons in dl PFC showed a preference for the contralateral visual space and collectively encoded the contralateral visual hemi‐field. In contrast, VIP neurons preferred central locations, predominantly covering the foveal visual space. Putative pyramidal cells with broad‐spiking waveforms in PFC had smaller RF s than putative interneurons showing narrow‐spiking waveforms, but distributed similarly across the visual field. In VIP , however, both putative pyramidal cells and interneurons had similar RF s at similar eccentricities. We provide a first, thorough characterisation of visual RF s in two reciprocally connected areas of a fronto‐parietal cortical network.
Enhancing light absorption in organic semiconductor thin films by one-dimensional gold nanowire gratings
2017-10-17

The interaction of metallic plasmonic nanostructures and organic semiconductor thin films plays a crucial role in engineering light harvesting and energy transfer processes, e.g., for optoelectronic applications. Plasmonic resonances of the metal structures can be used to increase the light emission or absorption of organic molecules. Here small molecules are employed since they can form organic layers with a defined crystalline order and orientation of the transition dipole. Extinction measurements combined with numerical simulations of a hybrid system consisting of a gold nanowire grating and a thin film of diindenoperylene (DIP) are reported. The experimental results are compared to the simulations and indicate an enhanced absorption in the wavelength region corresponding to the transition from the highest occupied molecular orbital to the lowest unoccupied molecular orbital of DIP. This enhancement is found to be related to the localized field enhancement near the individual nanostructures as well as to grating-induced effects. Notably, the hybrid system also exhibits parallel lattice resonances, which have recently been discussed for two-dimensional (2D) gold nanostructure arrays. In this study a hybrid plasmonic-organic small molecule system exhibiting these modes is investigated. The results for this model system show a way to modify the optical properties of plasmonic nanostructures by collective effects to achieve stronger light-matter interaction in a wide range of hybrid plasmonic systems.