julilili42/papers huggingface dataset:
Inheritance of DNA methylation differences in the mangrove Rhizophora mangle
2020-10-25

Abstract The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and non-genetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the non-genetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions, and is potentially threatened by climate change. Several studies have documented landscape level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of non-genetic variation. To assess one type of non-genetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing or epiGBS) to address the following questions: a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle ? b) How are genetic and epigenetic variation structured within and among populations? c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field and that a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.
A New Method for Detecting Leaks in MEMS Accelerometers at Wafer-Level
2020-10-25

This paper presents a novel method for detecting leaks in wafer-level packages. The hardware setup relies on fully electrical stimuli and measurement, which enables a precise estimation of the device's damping and therefore cavity pressure. This is achieved by measuring the real time movement of the seismic mass via the C-V-curve of the device, which provides distinct advantages over determining the cavity pressure by resonance frequency measurements. While there is no feasible method of determining the transfer function for highly damped devices without significant loss of precision and speed, with this new approach presented here the precision is unaffected by higher damping values. Additionally a test time reduction of 6 to 13 times compared to the current method is achieved. This will help lowering the costs associated with MEMS testing by a significant amount.
Targeting Glutaminolysis: New Perspectives to Understand Cancer Development and Novel Strategies for Potential Target Therapies
2020-10-26

Metabolism rewiring is an important hallmark of cancers. Being one of the most abundant free amino acids in the human blood, glutamine supports bioenergetics and biosynthesis, tumor growth, and the production of antioxidants through glutaminolysis in cancers. In glutamine dependent cancer cells, more than half of the tricarboxylic/critic acid (TCA) metabolites are derived from glutamine. Glutaminolysis controls the process of converting glutamine into TCA cycle metabolites through the regulation of multiple enzymes, among which the glutaminase shows the importance as the very first step in this process. Targeting glutaminolysis <i>via</i> glutaminase inhibition emerges as a promising strategy to disrupt cancer metabolism and tumor progression. Here, we review the regulation of glutaminase and the role of glutaminase in cancer metabolism and metastasis. Furthermore, we highlight the glutaminase inhibitor based metabolic therapy strategy and their potential applications in clinical scenarios.
From metacognitive beliefs to strategy selection: does fake performance feedback influence cognitive offloading?
2020-10-26

Abstract The ubiquitous availability of technological aids requires individuals to constantly decide between either externalizing cognitive processes into these aids (i.e. cognitive offloading) or relying on their own internal cognitive resources. With the present research, we investigated the influence of metacognitive beliefs on individuals’ offloading behavior in an experimental setup ( N = 159). We manipulated participants’ metacognitive beliefs about their memory abilities by providing fake performance feedback: below-average feedback, above-average feedback, or no feedback (control-group). We then measured offloading behavior, using a pattern copying task in which participants copied a color pattern from a model window into a workspace window. While solving this task, participants could rely either more on an internal memory strategy or more on an offloading strategy. Fake performance feedback affected the participants’ metacognitive evaluations about their memory abilities (below-group &lt; control-group &lt; above-group). Although fake performance feedback did not affect actual offloading behavior, the participants receiving below-average performance feedback reported that they had relied more on an offloading strategy than those participants receiving above-average performance feedback. Furthermore, the participants in the below-group reported lower general memory abilities than the other groups at the end of the experiment. We conclude that while fake performance feedback strongly influenced metacognitive beliefs, this did not transfer into a change of strategy selection, thus not influencing offloading behavior. We propose to consider not only metacognitive beliefs but also metacognitive experiences as potential determinants of cognitive offloading.
Determination of the Geographical Origin of Asparagus officinalis L. by 1H NMR Spectroscopy
2020-10-26

Food authenticity concerning the geographical origin becomes increasingly important for consumers, food industries, and food authorities. In this study, <i>nontargeted</i> <sup>1</sup>H NMR metabolomics combined with machine learning methodologies was applied to successfully distinguish the geographical origin of 237 samples of white asparagus from Germany, Poland, The Netherlands, Spain, Greece, and Peru. Support vector classification of the geographical origin achieved an accuracy of 91.5% for the entire sample set and 87.8% after undersampling the majority class. Important regions of the spectra could be identified and assigned to potential chemical markers. A subset of samples was compared to isotope-ratio mass spectrometry (IRMS), an established method for the determination of origin of white asparagus in Germany. Here, SVM classification led to accuracies of 79.4% for NMR and 70.9% for IRMS. Finally, the classification of asparagus from different German regions was evaluated, and the influence of year and variety was analyzed.
Dual-Energy Computed Tomography of the Lung in COVID-19 Patients: Mismatch of Perfusion Defects and Pulmonary Opacities
2020-10-26

To evaluate contrast-enhanced dual-energy computed tomography (DECT) chest examinations regarding pulmonary perfusion patterns and pulmonary opacities in patients with confirmed COVID-19 disease. Fourteen patients with 24 DECT examinations performed between April and May 2020 were included in this retrospective study. DECT studies were assessed independently by two radiologists regarding pulmonary perfusion defects, using a Likert scale ranging from 1 to 4. Furthermore, in all imaging studies the extent of pulmonary opacities was quantified using the same rating system as for perfusion defects. The main pulmonary findings were ground glass opacities (GGO) in all 24 examinations and pulmonary consolidations in 22 examinations. The total lung scores after the addition of the scores of the single lobes showed significantly higher values of opacities compared to perfusion defects, with a median of 12 (9–18) for perfusion defects and a median of 17 (15–19) for pulmonary opacities (p = 0.002). Furthermore, mosaic perfusion patterns were found in 19 examinations in areas with and without GGO. Further studies will be necessary to investigate the pathophysiological background of GGO with maintained perfusion compared to GGO with reduced perfusion, especially regarding long-term lung damage and prognosis.
Ancestral circuits for vertebrate colour vision emerge at the first retinal synapse
2020-10-26

Summary For colour vision, retinal circuits separate information about intensity and wavelength. This requires comparison of at least two spectrally distinct photoreceptors, as in the case of most mammals. However, many vertebrates use the full complement of four ‘ancestral’ cone-types (‘red’, ‘green’, ‘blue’, ‘UV’), and in those cases the nature and implementation of this computation remains poorly understood. Here, we establish the complete circuit architecture of outer retinal circuits underlying colour processing in larval zebrafish, which involves the full ancestral complement of four cone- and three horizontal cell types. Our findings reveal that the synaptic outputs of red- and green-cones efficiently rotate the encoding of natural daylight in a principal component analysis (PCA)-like manner to yield primary achromatic and spectrally-opponent axes, respectively. Together, these two cones capture 91.3% of the spectral variance in natural light. Next, blue-cones are tuned so as to capture most remaining variance when opposed to green-cones. Finally, UV-cones present a UV-achromatic axis for prey capture. We note that fruit flies – the only other tetrachromat species where comparable circuit-level information is available - use essentially the same strategy to extract spectral information from their relatively blue-shifted terrestrial visual world. Together, our results suggest that rotating colour space into primary achromatic and chromatic axes at the eye’s first synapse may be a fundamental principle of colour vision when using more than two spectrally well-separated photoreceptor types.
Quantitative and simultaneous measurement of oxygen consumption rates in rat brain and skeletal muscle using 17O MRS imaging at 16.4T
2020-10-26

Purpose Oxygen‐17 ( 17 O) MRS imaging, successfully used in the brain, is extended by imaging the oxygen metabolic rate in the resting skeletal muscle and used to determine the total whole‐body oxygen metabolic rate in the rat. Methods During and after inhalations of 17 O 2 gas, dynamic 17 O MRSI was performed in rats ( n = 8) ventilated with N 2 O or N 2 at 16.4 T. Time courses of the H 2 17 O concentration from regions of interest located in brain and muscle tissue were examined and used to fit an animal‐adapted 3‐phase metabolic model of oxygen consumption. CBF was determined with an independent washout method. Finally, body oxygen metabolic rate was calculated using a global steady‐state approach. Results Cerebral metabolic rate of oxygen consumption was 1.97 ± 0.19 μmol/g/min on average. The resting metabolic rate of oxygen consumption in skeletal muscle was 0.32 ± 0.12 μmol/g/min and &gt;6 times lower than cerebral metabolic rate of oxygen consumption. Global oxygen consumed by the body was 24.2 ± 3.6 mL O 2 /kg body weight/min. CBF was estimated to be 0.28 ± 0.02 mL/g/min and 0.34 ± 0.06 mL/g/min for the N 2 and N 2 O ventilation condition, respectively. Conclusion We have evaluated the feasibility of 17 O MRSI for imaging and quantifying the oxygen consumption rate in low metabolizing organs such as the skeletal muscle at rest. Additionally, we have shown that CBF is slightly increased in the case of ventilation with N 2 O. We expect this study to be beneficial to the application of 17 O MRSI to a wider range of organs, although further validation is advised.
Impaired visual acuity caused by uncorrected refractive errors and amblyopia in a German paediatric cohort
2020-10-26

Abstract Purpose This study describes the prevalence of visual impairment caused by uncorrected distance refractive error and the spectacle coverage in a large cohort of German children and adolescents. Furthermore, we determined the prevalence of amblyopia and amblyopia treatment. Methods Optometrists carried out visual acuity (VA) testing, non‐cycloplegic autorefraction, VA retesting with the refractive correction obtained by autorefraction, and if necessary subjective refraction and cover‐test in 1,874 subjects (901 girls/973 boys), aged 3 to 16 years. Additionally, a questionnaire on the history of previous eye care was completed. Results Distance visual impairment (VI) with VA worse than 6/18 Snellen in the better eye was present in 0.5% (95% confidence interval [95% CI]: 0.2% to 0.9%) of children. Logistic regression showed a significant positive association between VI and older age (OR = 1.21, P = 0.03). Gender differences were not found ( P = 0.77). The spectacle coverage of all participants was 74.8% (95% CI: 65.2% to 82.8%). Amblyopia was found in 29 participants (1.5%; 95% CI: 1.0% to 2.2%) with no age or sex differences. The causes of unilateral amblyopia (27 cases, 93.1%) were anisometropia in 55.6% of children, strabismus in 25.9% and the combination of these factors in 18.5%. All children with bilateral amblyopia (2 cases, 6.9%) showed bilateral high ametropia. We observed 15 children with current amblyopia, who had been treated with occlusion therapy in the past (62.2%; 95% CI: 42.7% to 83.6%). Conclusions The prevalence of impaired VA caused by uncorrected refractive error and amblyopia is comparable with previous studies conducted in urban areas worldwide. Adding the measurement of refractive error to existing medical check‐ups, possibly using autorefraction, would be desirable.
No-hair theorems for noncanonical self-gravitating static multiple scalar fields
2020-10-26

We prove under certain assumptions no-hair theorems for non-canonical self-gravitating static multiple scalar fields in spherically symmetric spacetimes. It is shown that the only static, spherically symmetric and asymptotically flat black hole solutions consist of the Schwarzschild metric and a constant multi-scalar map. We also prove that there are no static, horizonless, asymptotically flat, spherically symmetric solutions with static scalar fields and a regular center. The last theorem shows that the static, asymptotically flat, spherically symmetric reflecting compact objects with Neumann boundary conditions can not support a non-trivial self-gravitating non-canonical (and canonical) multi-scalar map in their exterior spacetime regions. In order to prove the no-hair theorems we derive a new divergence identity.
Near-optimal rotation of colour space by zebrafish cones in vivo
2020-10-26

Summary For colour vision, retinal circuits must separate information about intensity and wavelength. This requires circuit-level comparison of at least two spectrally distinct photoreceptors. However, many vertebrates use four or more, and in those cases the nature and implementation of this computation remains poorly understood. Here, we establish the complete circuit architecture and function of outer retinal circuits underlying colour processing in the tetrachromatic larval zebrafish. Our findings reveal that the specific spectral tunings of the four cone types near optimally rotate the encoding of natural daylight in a principal component analysis (PCA)-like manner to yield one primary achromatic axis, two colour-opponent axes as well as a secondary UV-achromatic axis for prey capture. We note that fruit flies – the only other tetrachromat species where comparable circuit-level information is available - use essentially the same strategy to extract spectral information from their relatively blue-shifted terrestrial visual world. Together, our results suggest that rotating colour space into achromatic and chromatic axes at the eye’s first synapse may be a fundamental principle of colour vision when using more than two spectrally well-separated photoreceptor types.
Frontispiz: Singlet Heterofission in Tetracene–Pentacene Thin‐Film Blends
2020-10-26

Photophysik Im Forschungsartikel auf S. 20141 untersuchen M. Maiuri, K. Broch et al. gemischte Filmen aus Pentacen und Tetracen mittels ultraschneller optischer Spektroskopie. Spontane Singulett-Fission eines Singulett-Excitons in Pentacen wird beobachtet.
Frontispiece: Singlet Heterofission in Tetracene–Pentacene Thin‐Film Blends
2020-10-26

Photophysics In their Research Article on page 19966, M. Maiuri, K. Broch et al. study mixed thin films of pentacene and tetracene by using ultrafast optical spectroscopy. Spontaneous fission of a singlet exciton on pentacene is observed.
Prodromal Spinocerebellar Ataxia Type 2 Subjects Have Quantifiable Gait and Postural Sway Deficits
2020-10-27

Abstract Background The search for valid preclinical biomarkers of cerebellar dysfunction is a key research goal for the upcoming era of early interventional approaches in spinocerebellar ataxias. This study aims to describe novel preclinical biomarkers of subtle gait and postural sway abnormalities in prodromal spinocerebellar ataxia type 2 (pre‐SCA2). Methods Thirty pre‐SCA2 patients and their matched healthy controls underwent quantitative assessments of gait and postural sway using a wearable sensor‐based system and semiquantitative evaluation of cerebellar features by SARA (Scale for the Assessment and Rating of Ataxia) score. Results Quantitative analysis of natural gait showed a significantly larger variability of the swing period, toe‐off angle and toe‐out angle in pre‐SCA2, and larger mean coronal and transverse ranges of motion of the trunk at the lumbar location and of the sagittal range of motion of the trunk at the sternum location compared to controls. During tandem gait, pre‐SCA2 subjects showed larger lumbar, trunk, and arm ranges of motion than controls. Postural sway analysis showed excessive body oscillation that was increased in tandem stance. Overall, these abnormalities were detected in pre‐SCA2 patients without clinical evidence of abnormalities in SARA. The toe‐off angle and swing time variability were significantly correlated with the time to ataxia onset, whereas the toe‐off angle and transverse range of motion at trunk position during tandem gait were significantly associated with the SARA score. Conclusions This study demonstrates early alteration of gait and postural sway control in prodromal SCA2 using a wearable sensor‐based system. This offers new pathophysiological hints into this early disease stage and provides novel potential biomarkers for future clinical trials. © 2020 International Parkinson and Movement Disorder Society
A new lepto-hadronic model applied to the first simultaneous multiwavelength data set for Cygnus X–1
2020-10-27

ABSTRACT Cygnus X–1 is the first Galactic source confirmed to host an accreting black hole. It has been detected across the entire electromagnetic spectrum from radio to GeV gamma-rays. The source’s radio through mid-infrared radiation is thought to originate from the relativistic jets. The observed high degree of linear polarization in the MeV X-rays suggests that the relativistic jets dominate in this regime as well, whereas a hot accretion flow dominates the soft X-ray band. The origin of the GeV non-thermal emission is still debated, with both leptonic and hadronic scenarios deemed to be viable. In this work, we present results from a new semi-analytical, multizone jet model applied to the broad-band spectral energy distribution of Cygnus X–1 for both leptonic and hadronic scenarios. We try to break this degeneracy by fitting the first-ever high-quality, simultaneous multiwavelength data set obtained from the CHOCBOX campaign (Cygnus X–1 Hard state Observations of a Complete Binary Orbit in X-rays). Our model parametrizes dynamical properties, such as the jet velocity profile, the magnetic field, and the energy density. Moreover, the model combines these dynamical properties with a self-consistent radiative transfer calculation including secondary cascades, both of leptonic and hadronic origin. We conclude that sensitive TeV gamma-ray telescopes like Cherenkov Telescope Array (CTA) will definitively answer the question of whether hadronic processes occur inside the relativistic jets of Cygnus X–1.
Bayesian inference for biophysical neuron models enables stimulus optimization for retinal neuroprosthetics
2020-10-27

While multicompartment models have long been used to study the biophysics of neurons, it is still challenging to infer the parameters of such models from data including uncertainty estimates. Here, we performed Bayesian inference for the parameters of detailed neuron models of a photoreceptor and an OFF- and an ON-cone bipolar cell from the mouse retina based on two-photon imaging data. We obtained multivariate posterior distributions specifying plausible parameter ranges consistent with the data and allowing to identify parameters poorly constrained by the data. To demonstrate the potential of such mechanistic data-driven neuron models, we created a simulation environment for external electrical stimulation of the retina and optimized stimulus waveforms to target OFF- and ON-cone bipolar cells, a current major problem of retinal neuroprosthetics.
Structure of High-Risk Papillomavirus 31 E6 Oncogenic Protein and Characterization of E6/E6AP/p53 Complex Formation
2020-10-27

Variations of carcinogenicity of human papillomaviruses are related to variations of the E6 and E7 interactome. While different HPV species and genera are known to target distinct host proteins, the fine differences between E6 and E7 of closely related HPVs, supposed to target the same cellular protein pools, remain to be addressed. We compare the oncogenic E6 proteins of the closely related high-risk HPV31 and HPV16 with regard to their structure and their efficiency of ternary complex formation with their cellular targets p53 and E6AP, which results in p53 degradation. We solved the crystal structure of 31 E6 bound to the E6AP LxxLL motif. HPV16 E6 and 31 E6 structures are highly similar, but a few sequence variations lead to different protein contacts within the ternary complex and, as quantified here, an overall lower binding affinity of 31 E6 than 16 E6. These results align with the observed lower p53 degradation potential of 31 E6.