julilili42/papers huggingface dataset:
Functional and Structural Connectivity Patterns Associated with Clinical Outcomes in Deep Brain Stimulation of the Globus Pallidus Internus for Generalized Dystonia
2020-02-13

Functional and structural connectivity with multiple nodes of the motor network is associated with motor improvement in patients with generalized dystonia undergoing deep brain stimulation. Results from this study may serve as a basis for future development of clinical markers to guide deep brain stimulation targeting and programming in dystonia.
Rotating tensor-multiscalar solitons
2020-02-13

In the context of a special class of tensor-multi-scalar theories of gravity for which the target-space metric admits an isometry under which the theory is invariant, we present rotating vacuum solutions, namely with no matter fields. These objects behave like nontopological solitons, whose primary stability is due to the conserved charge arising from the global symmetry. We consider theories with two and three scalar fields, different Gauss curvatures and quartic interaction coefficients. As it occurs for boson stars, their angular momentum is quantized.
Uncertainty as a Driving Force for Geoscientific Development
2020-02-13

Geoscientists invest significant effort to cope with uncertainty in Earth system observation and modeling. While general discussions exist about uncertainty and risk communication, judgment and decision-making, and science communication with regard to Earth sciences, in this article, we tackle uncertainty from the perspective of Earth science practitioners. We argue different scientific methodologies must be used to recognize all types of uncertainty inherent to a scientific finding. Following a discovery science methodology results in greater potential for the quantification of uncertainty associated to scientific findings than staying inside hypothesis-driven science methodology, as is common practice. Enabling improved uncertainty quantification could relax debates about risk communication and decision-making since it reduces the room for personality traits when communicating scientific findings.
Phenomenology in Pedagogical Settings. Overview of the current discourse on phenomenological pedagogy
2020-02-13

Phenomenology has been well-received in pedagogy from the very beginning. With direct reference to Husserl, Aloys Fischer calls for a Descriptive Pedagogy. Only on the basis of a close description of educational processes similar to the phenomenological reduction can the educational sciences rediscover their actual subject matter. In this article the author traces the development of phenomenological thought in educational theory with a special focus on the notions of corporeality and negativity. As a necessary condition of perception in general, corporeality constitutes an important factor in the structural being-to-the-world of the human being. Apart from being able to sense its surroundings the body can also be perceived as part of these surroundings. Due to this double role, the subject opens up to foreign influences and negativity. Thus, the other plays an important role in the constitution of the identity of the subject. Through corporeality, a sphere of intersubjectivity is opened up. A recapitulation of Käte Meyer-Drawe’s Pedagogy of Inter-Subjectivity and Wilfried Lippitz’ Theory of Bildung and Alterity shows how these thoughts can be made useful for pedagogical discussion. Hereby, sociality and alterity prove to be foundational categories for educational settings in general. Finally, the author gives an outlook on current developments in phenomenological pedagogy.
Abnormal Regional and Global Connectivity Measures in Subjective Cognitive Decline Depending on Cerebral Amyloid Status
2020-02-13

<title>Abstract</title> <underline>Background</underline>: While cerebral beta-amyloid accumulation was found in many studies to alter precuneus-based functional connectivity (FC) in mild cognitive impairment and demented Alzheimer’s disease (AD) patients, its impact is less well understood in subjective cognitive decline (SCD), which in the presence of underlying AD pathologic change corresponds to a progression to stage 2 of the clinical Alzheimer’s continuum in the 2018 National Institute on Aging and Alzheimer’s Association research framework, and represents the earliest clinical manifestation of AD. <underline>Methods</underline>: From the DELCODE (DZNE – Longitudinal Cognitive Impairment and Dementia Study) cohort, two groups of 24 age- and gender-matched amyloid-positive SCD (SCD<sub>Aβ+</sub>) and amyloid-negative SCD (SCD<sub>Aβ-</sub>) patients were selected according to visual [18F]-Florbetaben PET readings, and studied with resting-state BOLD fMRI. Local (regional homogeneity (ReHo), amplitude of low-frequency fluctuation (ALFF) and fractional ALFF (fALFF)) and global (degree centrality (DC), precuneus seed-based FC maps) measures were calculated and compared between both groups. Furthermore, follow-up correlation analyses probed linear relationships of observed group differences with global as well as precuneal amyloid load measured by Florbetaben standard uptake value ratios (SUVR<sub>FBB</sub>). <underline>Results</underline>: For the local measures, ReHo was significantly higher in the bilateral precuneus for the SCD<sub>Aβ+ </sub>group, whereas ALFF and fALFF measures were not altered between groups. For the global measures, relatively higher precuneus-based FC with occipital areas (but no altered DC) was observed in the SCD<sub>Aβ+ </sub>group. Moreover, the FC differences between precuneus and occipital areas were positively correlated with global (SCD<sub>Aβ+</sub>) and local precuneus SUVR<sub>FBB</sub> (both groups). <underline>Conclusions</underline>: While confounding influences due to a higher ratio of APOE e4 carriers in the SCD<sub>Aβ+</sub> group cannot be excluded, results indicate functional alterations in the precuneus hub region that were linearly related to beta-amyloid load, highlighting incipient pathology and possible compensatory mechanisms in stage 2 of the AD continuum.
Radixin modulates stereocilia function and contributes to cochlear amplification
2020-02-13

Abstract The stereocilia of the sensory cells in the inner ear contain high levels of the actin-binding protein radixin, encoded by the RDX gene. Radixin which is associated with mechanotransduction process such as PIP 2 is known to be important for hearing but its functional role remains obscure. To determine how radixin influences hearing sensitivity, we used a custom rapid imaging technique to directly visualize stereocilia motion while measuring the amplitude of the electrical potentials produced by sensory cells during acoustic stimulation. Experiments were performed in guinea pigs, where upon blocking radixin, a large decrease in sound-evoked electrical potentials occurred. Despite this decrease other important functional measures, such as electrically induced sensory cell motility and the sound-evoked deflections of stereocilia, showed a minor amplitude increase. This unique set of functional properties alterations demonstrate that radixin is necessary to ensure that the inner ear converts sound into electrical signals at acoustic rates. Radixin is therefore a necessary and important component of the cochlear amplifier, the energy-consuming process that boosts hearing sensitivity by up to 60 dB.
Superiority of temozolomide over radiotherapy for elderly patients with RTK II methylation class, MGMT promoter methylated malignant astrocytoma
2020-02-14

Abstract Background O6-methylguanine DNA-methyl transferase (MGMT) promoter methylation status is predictive for alkylating chemotherapy, but there are non-benefiting subgroups. Methods This is the long-term update of NOA-08 (NCT01502241), which compared efficacy and safety of radiotherapy (RT, n = 176) and temozolomide (TMZ, n = 193) at 7/14 days in patients &amp;gt;65 years old with anaplastic astrocytoma or glioblastoma. DNA methylation patterns and copy number variations were assessed in the biomarker cohort of 104 patients and in an independent cohort of 188 patients treated with RT+TMZ-containing regimens in Heidelberg. Results In the full NOA-08 cohort, median overall survival (OS) was 8.2 [7.0–10.0] months for TMZ treatment versus 9.4 [8.1–10.4] months for RT; hazard ratio (HR) = 0.93 (95% CI: 0.76–1.15) of TMZ versus RT. Median event-free survival (EFS) [3.4 (3.2–4.1) months vs 4.6 (4.2–5.0) months] did not differ, with HR = 1.02 (0.83–1.25). Patients with MGMT methylated tumors had markedly longer OS and EFS when treated with TMZ (18.4 [13.9–24.4] mo and 8.5 [6.9–13.3] mo) versus RT (9.6 [6.4–13.7] mo and 4.8 [4.3–6.2] mo, HR 0.44 [0.27–0.70], P &amp;lt; 0.001 for OS and 0.46 [0.29–0.73], P = 0.001 for EFS). Patients with glioblastomas of the methylation classes receptor tyrosine kinase I (RTK I) and mesenchymal subgroups lacked a prognostic impact of MGMT in both cohorts. Conclusion MGMT promoter methylation is a strong predictive biomarker for the choice between RT and TMZ. It indicates favorable long-term outcome with initial TMZ monotherapy in patients with MGMT promoter-methylated tumors primarily in the RTK II subgroup.
Metabolic Labeling of RNAs Uncovers Hidden Features and Dynamics of the Arabidopsis Transcriptome
2020-02-14

Transcriptome analysis by RNA sequencing (RNA-seq) has become an indispensable research tool in modern plant biology. Virtually all RNA-seq studies provide a snapshot of the steady state transcriptome, which contains valuable information about RNA populations at a given time but lacks information about the dynamics of RNA synthesis and degradation. Only a few specialized sequencing techniques, such as global run-on sequencing, have been used to provide information about RNA synthesis rates in plants. Here, we demonstrate that RNA labeling with the modified, nontoxic uridine analog 5-ethynyl uridine (5-EU) in Arabidopsis (<i>Arabidopsis thaliana</i>) seedlings provides insight into plant transcriptome dynamics. Pulse labeling with 5-EU revealed nascent and unstable RNAs, RNA processing intermediates generated by splicing, and chloroplast RNAs. Pulse-chase experiments with 5-EU allowed us to determine RNA stabilities without the need for chemical transcription inhibitors such as actinomycin and cordycepin. Inhibitor-free, genome-wide analysis of polyadenylated RNA stability via 5-EU pulse-chase experiments revealed RNAs with shorter half-lives than those reported after chemical inhibition of transcription. In summary, our results indicate that the Arabidopsis nascent transcriptome contains unstable RNAs and RNA processing intermediates and suggest that polyadenylated RNAs have low stability in plants. Our technique lays the foundation for easy, affordable, nascent transcriptome analysis and inhibitor-free analysis of RNA stability in plants.
Genetic basis of neurodevelopmental disorders in 103 Jordanian families
2020-02-14

Abstract We recruited 103 families from Jordan with neurodevelopmental disorders (NDD) and patterns of inheritance mostly suggestive of autosomal recessive inheritance. In each family, we investigated at least one affected individual using exome sequencing and an in‐house diagnostic variant interpretation pipeline including a search for copy number variation. This approach led us to identify the likely molecular defect in established disease genes in 37 families. We could identify 25 pathogenic nonsense and 11 missense variants as well as 3 pathogenic copy number variants and 1 repeat expansion. Notably, 11 of the disease‐causal variants occurred de novo . In addition, we prioritized a homozygous frameshift variant in PUS3 in two sisters with intellectual disability. To our knowledge, PUS3 has been postulated only recently as a candidate disease gene for intellectual disability in a single family with three affected siblings. Our findings provide additional evidence to establish loss of PUS3 function as a cause of intellectual disability.
Modeling uncertainties in X-ray reflection spectroscopy measurements I: Impact of higher order disk images
2020-02-14

There are many simplifications in current relativistic reflection models and\\nthis introduces systematic uncertainties in the measurement of the properties\\nof the source. In this paper, we study the impact of the radiation crossing the\\nequatorial plane between the black hole and the inner edge of the accretion\\ndisk; that is, the radiation produced by the other side of the disk or circling\\nthe black hole one or more times (higher order disk images). For slow-rotating\\nblack holes with a larger plunging region, the effect is not very sensitive to\\nthe exact inclination angle of the disk. For fast-rotating black holes with a\\nsmaller plunging region, the effect is very weak for low inclination angles and\\nbecomes more important as the angle increases. We simulate some observations\\nwithout and with higher order disk images and fit the data with the reflection\\nmodel RELXILL_NK to check its capability of recovering the correct input\\nparameters. Our results suggest that the effect of higher order disk images can\\nbe safely ignored for observations with present and near future X-ray missions,\\neven for tests of the Kerr hypothesis.\\n
Slow oscillation-spindle coupling predicts sequence-based language learning
2020-02-14

Abstract Sentence comprehension involves the rapid decoding of both semantic and grammatical information, a process fundamental to communication. As with other complex cognitive processes, language comprehension relies, in part, on long-term memory. However, the electrophysiological mechanisms underpinning the initial encoding and generalisation of higher-order linguistic knowledge remain elusive, particularly from a sleep-based consolidation perspective. One candidate mechanism that may support the consolidation of higher-order language is the temporal coordination of slow oscillations (SO) and sleep spindles during non-rapid eye movement sleep (NREM). To examine this hypothesis, we analysed electroencephalographic (EEG) data recorded from 35 participants (M age = 25.4, SD = 7.10; 16 males) during an artificial language learning task, contrasting performance between individuals who were given an 8hr nocturnal sleep period or an equivalent period of wake. We found that sleep relative to wake was associated with superior performance for rules that followed a sequence-based word order. Post-sleep sequence-based word order processing was further associated with less task-related theta desynchronisation, an electrophysiological signature of successful memory consolidation, as well as cognitive control and working memory. Frontal NREM SO-spindle coupling was also positively associated with behavioural sensitivity to sequence-based word order rules, as well as with task-related theta power. As such, theta activity during retrieval of previously learned information correlates with SO-spindle coupling, thus linking neural activity in the sleeping and waking brain. Taken together, this study presents converging behavioral and neurophysiological evidence for a role of NREM SO-spindle coupling and task-related theta activity as signatures of successful memory consolidation and retrieval in the context of higher-order language learning. SIGNIFICANCE STATEMENT The endogenous temporal coordination of neural oscillations supports information processing during both wake and sleep states. Here we demonstrate that slow oscillation-spindle coupling during non-rapid eye movement sleep predicts the consolidation of complex grammatical rules and modulates task-related oscillatory dynamics previously implicated in sentence processing. We show that increases in theta power predict enhanced sensitivity to grammatical violations after a period of sleep and strong slow oscillation-spindle coupling modulates subsequent task-related theta activity to influence behaviour. Our findings reveal a complex interaction between both wake- and sleep-related oscillatory dynamics during the early stages of language learning beyond the single word level.
2D and 3D immunogold localization on (epoxy) ultrathin sections with and without osmium tetroxide
2020-02-14

Abstract For nearly 50 years immunogold labeling on ultrathin sections has been successfully used for protein localization in laboratories worldwide. In theory and in practice, this method has undergone continual improvement over time. In this study, we carefully analyzed circulating protocols for postembedding labeling to find out if they are still valid under modern laboratory conditions, and in addition, we tested unconventional protocols. For this, we investigated immunolabeling of Epon‐embedded cells, immunolabeling of cells treated with osmium, and the binding behavior of differently sized gold particles. Here we show that (in contrast to widespread belief) immunolabeling of Epon‐embedded cells and of cells treated with osmium tetroxide is actually working. Furthermore, we established a “speed protocol” for immunolabeling by reducing antibody incubation times. Finally, we present our results on three‐dimensional immunogold labeling.
A TGF-β– and p63-Responsive Enhancer Regulates IFN-κ Expression in Human Keratinocytes
2020-02-14

Abstract Type I IFNs have antiviral and immune-modulating activities. IFN-α/-β have very low basal expression levels but are strongly induced upon activation of pattern recognition receptors. In contrast, IFN-κ is constitutively expressed in uninfected keratinocytes and responds only weakly to pattern recognition receptor activation. IFN-κ expression has been implicated in the pathogenesis of inflammatory skin diseases and in limiting human papillomavirus replication in human keratinocytes. We have identified an enhancer ∼5 kb upstream of the IFNK gene driving its expression in keratinocytes. The enhancer consists of binding sites for the transcription factors jun-B, SMAD3/4, AP-2α/γ, and p63, of which the latter two are key regulators of keratinocyte biology. The jun-B and SMAD3/4 elements confer activation by the TGF-β pathway. Furthermore, inhibition of ERK1/2 kinases activates IFN-κ expression. Our study provides a framework for the cell type–specific, constitutive expression of IFN-κ and its modulation by signal transduction pathways in human keratinocytes.
Synthesis of (TeI3)2[W6I14] via Iodination of WTe2
2020-02-14

The new compound (TeI 3 ) 2 [W 6 I 14 ] appeared as an unforeseen product from a reaction of WTe 2 with iodine at 250 °C, representing an exceptionally low temperature for the formation of an octahedral tungsten iodide cluster. The crystal structure, as refined by single‐crystal X‐ray diffraction, reveals (TeI 3 ) + ions and the well‐known [W 6 I 14 ] 2– cluster. A chemical analysis confirms the identity of the product. The electronic structure of (TeI 3 ) 2 [W 6 I 14 ] is analyzed in view of the relative position of tellurium states by density functional theory (DFT) calculations. This cluster compound exhibits an indirect band gap as confirmed by the band structure calculation based on the HSE06 hybrid functional theory.
When vision lags, motor prediction follows
2020-02-14

Abstract When we act, our brains register the visual feedback of the outcome of our actions only approximately 150 ms after sending the motor commands to the muscles. By anticipating the sensory consequences of our actions, temporal prediction mechanisms help us to accurately perform time-critical motor actions, such as catching a ball, and to experience the world as temporally coherent. It remains unclear whether these prediction mechanisms can adapt in a general way to changing sensory feedback delays, as they occur, for instance, when neural processing times increase during development. We here used Augmented Reality to train participants for one hour in a range of everyday life tasks with different levels of artificial visual feedback delay: 0 ms (No Delay), 100 ms (Small Delay) and 250 ms (Large Delay). We tested whether temporal aftereffects (increased motor-anticipation) generalize across different perceptual and motor tasks that participants did not practice during training and that involve different aspects of sensorimotor integration (motor planning, feedback control, sensorimotor time perception). Our results show a consistent temporal aftereffect of 33% across tasks and levels of delay. This suggests that the human sensorimotor system can adapt to the presence of visual feedback delays in a that affects sensorimotor prediction in general.
Investigating the flexibility of male Eurasian jays' food-sharing behavior
2020-02-14

Male Eurasian jays were previously reported to alter their food-sharing response in line with the specific satiety of their female partner. Here, we tested the flexibility of the same males’ food-sharing behavior by testing whether they can process information from contextual cues that predict the opposite pattern of food shared to that observed in previous studies. In Experiment 1, we manipulated the amount of food eaten by the females in a choice context before males shared with them. In Experiment 2, we manipulated the identity of the non-chosen food that was available in a choice context before males shared with the females. In both experiments, males showed flexibility in their sharing pattern in a comparison between the experimental and control conditions. In Experiment 1, this observed pattern appears to be based on the males’ response to the amount of food eaten by the female, and in Experiment 2, it appears to be based on the males’ response to the choice context in which the female’s eating took place. Although the experimental conditions in Experiments 1 and 2 were conceptual replications, the predicted pattern of food shared by the males was detected only in the latter. While replications are needed to test the generalizability and robustness of these results, the current study provides a first set of data in line with the hypothesis that the Eurasian jay males may be able to flexibly adjust their food-sharing behavior to contextual cues. Raw data are available at 10.5281/zenodo.3633986, and code and meta-data are available at https://osf.io/n9rcd/.
Reversible Iodine Intercalation into Tungsten Ditelluride
2020-02-14

The new compound WTe2I was prepared by a reaction of WTe2 with iodine in a fused silica vessel at temperatures between 40 and 200 °C. Iodine atoms are intercalated into the van der Waals gap between tungsten ditelluride layers. As a result, the WTe2 layer separation and therefore the c-axis length is significantly increased, and the orthorhombic space group is preserved. Iodine atoms form planar layers between each tungsten ditelluride layer. Due to oxidation by iodine the semi-metallic nature of WTe2 is changed, as shown by comparative band structure calculations for WTe2 and WTe2I based on density functional theory. The calculated phonon band structure of WTe2I suggests a charge density wave instability at low temperature.
Reversible Iodine Intercalation into Tungsten Ditelluride
2020-02-14

The new compound WTe2I was prepared by a reaction of WTe2 with iodine in a fused silica vessel at temperatures between 40 and 200 °C. Iodine atoms are intercalated into the van der Waals gap between tungsten ditelluride layers. As a result, the WTe2 layer separation and therefore the c-axis length is significantly increased, and the orthorhombic space group is preserved. Iodine atoms form planar layers between each tungsten ditelluride layer. Due to oxidation by iodine the semi-metallic nature of WTe2 is changed, as shown by comparative band structure calculations for WTe2 and WTe2I based on density functional theory. The calculated phonon band structure of WTe2I suggests a charge density wave instability at low temperature.&lt;br&gt;