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Barbarossa, Maria Vittoria ; Fuhrmann, Jan ; Meinke, Jan H. ; Krieg, Stefan F. ; Vinod Varma, Hridya ; Castelletti, Noemi ; Lippert, Thomas
The novel coronavirus (SARS-CoV-2), identified in China at the end of December 2019 and causing the disease COVID-19, has meanwhile led to outbreaks all over the globe with about 2.2 million confirmed cases and more than 150,000 deaths as of April 17, 2020 [37]. In view of most recent information on testing activity [32], we present here an update of our initial work [4]. In this work, mathematical models have been developed to study the spread of COVID-19 among the population in Germany and to asses the impact of non-pharmaceutical interventions. Systems of differential equations of SEIR type are extended here to account for undetected infections, as well as for stages of infections and age groups. The models are calibrated on data until April 5, data from April 6 to 14 are used for model validation. We simulate different possible strategies for the mitigation of the current outbreak, slowing down the spread of the virus and thus reducing the peak in daily diagnosed cases, the demand for hospitalization or intensive care units admissions, and eventually the number of fatalities. Our results suggest that a partial (and gradual) lifting of introduced control measures could soon be possible if accompanied by further increased testing activity, strict isolation of detected cases and reduced contact to risk groups.
Ballweg, Stephanie ; Sezgin, Erdinc ; Doktorova, Milka ; Covino, Roberto ; Reinhard, John ; Wunnicke, Dorith ; Hänelt, Inga ; Levental, Ilya ; Hummer, Gerhard ; Ernst, Robert
Cells maintain membrane fluidity by regulating lipid saturation, but the molecular mechanisms of this homeoviscous adaptation remain poorly understood. We have reconstituted the core machinery for regulating lipid saturation in baker’s yeast to study its molecular mechanism. By combining molecular dynamics simulations with experiments, we uncover a remarkable sensitivity of the transcriptional regulator Mga2 to the abundance, position, and configuration of double bonds in lipid acyl chains, and provide insights into the molecular rules of membrane adaptation. Our data challenge the prevailing hypothesis that membrane fluidity serves as the measured variable for regulating lipid saturation. Rather, we show that Mga2 senses the molecular lipid-packing density in a defined region of the membrane. Our findings suggest that membrane property sensors have evolved remarkable sensitivities to highly specific aspects of membrane structure and dynamics, thus paving the way toward the development of genetically encoded reporters for such properties in the future.
In search for practical silvicultural management tools to identify alternative tree species for predicted Central European climate conditions, a cross-species survey with five evergreen, semi-evergreen, and deciduous Quercus taxa with contrasting morphological leaf traits was performed. Fast chlorophyll fluorescence induction of PSII and relative leaf chlorophyll contents were performed to assess the overall plant vitality at any point in time during two complete vegetation periods in consecutive years (2012 and 2013). Maximum photochemical efficiency of PSII and the performance index on absorption base showed a very conservative relationship to each other and a similar intra-annual progress in all deciduous species, but with a different speed of increase and decrease during leaf development and senescence and thus a different length of vegetation period. The intra-annual variability of OJIP and chlorophyll content parameters is considered with respect to the practicability of measurements in the field for management purposes.
Stabilization exercise (SE) is evident for the management of chronic non-specific low back pain (LBP). The optimal dose-response-relationship for the utmost treatment success is, thus, still unknown. The purpose is to systematically review the dose-response-relationship of stabilisation exercises on pain and disability in patients with chronic non-specific LBP. A systematic review with meta-regression was conducted (Pubmed, Web of Knowledge, Cochrane). Eligibility criteria were RCTs on patients with chronic non-specific LBP, written in English/German and adopting a longitudinal core-specific/stabilising/motor control exercise intervention with at least one outcome for pain intensity and/or disability. Meta-regressions (dependent variable = effect sizes (Cohens d) of the interventions (for pain and for disability), independent variable = training characteristics (duration, frequency, time per session)), and controlled for (low) study quality (PEDro) and (low) sample sizes (n) were conducted to reveal the optimal dose required for therapy success. From the 3,415 studies initially selected, 50 studies (n = 2,786 LBP patients) were included. N = 1,239 patients received SE. Training duration was 7.0 ± 3.3 weeks, training frequency was 3.1 ± 1.8 sessions per week with a mean training time of 44.6 ± 18.0 min per session. The meta-regressions’ mean effect size was d = 1.80 (pain) and d = 1.70 (disability). Total R2 was 0.445 and 0.17. Moderate quality evidence (R2 = 0.231) revealed that a training duration of 20 to 30 min elicited the largest effect (both in pain and disability, logarithmic association). Low quality evidence (R2 = 0.125) revealed that training 3 to 5 times per week led to the largest effect of SE in patients with chronic non-specific LBP (inverted U-shaped association). In patients with non-specific chronic LBP, stabilization exercise with a training frequency of 3 to 5 times per week (Grade C) and a training time of 20 to 30 min per session (Grade A) elicited the largest effect on pain and disability.
In this paper we present a new approach to deterministic modelling of COVID-19 epidemic. Our model dynamics is expressed by a single prognostic variable which satisfies an integro-differential equation. All unknown parameters are described with a single, time-dependent variable R(t). We show that our model has similarities to classic compartmental models, such as SIR, and that the variable R(t) can be interpreted as a generalized effective reproduction number. The advantages of our approach are the simplicity of having only one equation, the numerical stability due to an integral formulation and the reliability since the model is formulated in terms of the most trustable statistical data variable: the number of cumulative diagnosed positive cases of COVID-19. Once this dynamic variable is calculated, other non-dynamic variables, such as the number of heavy cases (hospital beds), the number of intensive-care cases (ICUs) and the fatalities, can be derived from it using a similarly stable, integral approach. The formulation with a single equation allows us to calculate from real data the values of the sample effective reproduction number, which can then be fitted. Extrapolated values of R(t) can be used in the model to make reliable forecasts, though under the assumption that measures for reducing infections are maintained. We have applied our model to more than 15 countries and the ongoing results are available on a web-based platform [1]. In this paper, we focus on the data for two exemplary countries, Italy and Germany, and show that the model is capable of reproducing the course of the epidemic in the past and forecasting its course for a period of four to five weeks with a reasonable numerical stability.
Airborne transmission of SARS-CoV-2 through virus-containing aerosol particles has been established as an important pathway for Covid-19 infection. Suitable measures to prevent such infections are imperative, especially in situations when a high number of persons convene in closed rooms. Here we tested the efficiency and practicability of operating four air purifiers equipped with HEPA filters in a high school classroom while regular classes were taking place. We monitored the aerosol number concentration for particles > 3 nm at two locations in the room, the aerosol size distribution in the range from 10 nm to 10 µm, PM10 and CO2 concentration. For comparison, we performed similar measurements in a neighboring classroom without purifiers. In times when classes were conducted with windows and door closed, the aerosol concentration was reduced by more than 90 % within less than 30 minutes when running the purifiers (air exchange rate 5.5 h-1). The reduction was homogeneous throughout the room and for all particle sizes. The measurements are supplemented by a calculation estimating the maximum concentration levels of virus-containing aerosol from a highly contagious person speaking in a closed room with and without air purifiers. Measurements and calculation demonstrate that air purifiers potentially represent a well-suited measure to reduce the risks of airborne transmission of SARS-CoV-2 substantially. Staying for two hours in a closed room with a highly infective person, we estimate that the inhaled dose is reduced by a factor of six when using air purifiers with a total air exchange rate of 5.7 h-1.
Johé, Patrick ; Jaenicke, Elmar ; Neuweiler, Hannes ; Schirmeister, Tanja ; Kersten, Christian ; Hellmich, Ute
Rhodesain is the lysosomal cathepsin L-like cysteine protease of T. brucei rhodesiense, the causative agent of Human African Trypanosomiasis. The enzyme is essential for the proliferation and pathogenicity of the parasite as well as its ability to overcome the blood-brain barrier of the host. Lysosomal cathepsins are expressed as zymogens with an inactivating pro-domain that is cleaved under acidic conditions. A structure of the uncleaved maturation intermediate from a trypanosomal cathepsin L-like protease is currently not available. We thus established the heterologous expression of T. brucei rhodesiense pro-rhodesain in E. coli and determined its crystal structure. The trypanosomal pro-domain differs from non-parasitic pro-cathepsins by a unique, extended α-helix that blocks the active site and whose interactions resemble that of the antiprotozoal inhibitor K11777. Interdomain dynamics between pro- and core protease domain as observed by photoinduced electron transfer fluorescence correlation spectroscopy increase at low pH, where pro-rhodesain also undergoes autocleavage. Using the crystal structure, molecular dynamics simulations and mutagenesis, we identify a conserved interdomain salt bridge that prevents premature intramolecular cleavage at higher pH values and may thus present a control switch for the observed pH-sensitivity of pro-enzyme cleavage in (trypanosomal) CathL-like proteases.
WaterGAP (Water - Global Assessment and Prognosis) is a tool for modeling global water use and water availability. It participates among other models in the ISIMIP initiative (The Inter-Sectoral Impact Model Intercomparison Project). As part of this initiative, the water temperature should be calculated by participating hydrological models because it plays a vital role in many chemical, physical and biological processes. Therefore, the subject of this master thesis is to implement the physically based surface water temperature computation after VAN BEEK ET AL. (2012) and WANDERS ET AL. (2019) into WaterGAP and compare the results to the statistical regression approach by PUNZET ET AL. (2012). The computation is validated with observed water temperature data obtained from the GEMStat water quality database. The results are good for arctic and temperate latitudes. Surface water temperatures for tropical rivers are overestimated, most likely due to the overestimation of precipitation temperatures, incoming radiation and groundwater temperatures. The comparison with the regression model by PUNZET ET AL. (2012) shows matching results. The regression model even matches with WaterGAP results for most of the simulations of the future under climate change conditions, where the regression model should stop working due to changing environmental parameters. Several assumptions had to be made in order to implement the water temperature calculation in Water-GAP. These include, e.g., discharge temperatures for power plant cooling water, precipitation and surface runoff temperatures. For model improvements, perhaps three different values for the different regions of the world should be used to cool down the precipitation and surface runoff. The model could also be improved by refining the ice formation calculation, especially for the conditions when the ice melts, breaks up and is transported downstream. Furthermore, the feedback to the river channel roughness could be implemented if ice has formed. The WaterGAP model upgraded with the water temperature calculation will help the ISIMIP initiative in the future.
The development of binocular vision is an active learning process comprising the development of disparity tuned neurons in visual cortex and the establishment of precise vergence control of the eyes. We present a computational model for the learning and self-calibration of active binocular vision based on the Active Efficient Coding framework, an extension of classic efficient coding ideas to active perception. Under normal rearing conditions, the model develops disparity tuned neurons and precise vergence control, allowing it to correctly interpret random dot stereogramms. Under altered rearing conditions modeled after neurophysiological experiments, the model qualitatively reproduces key experimental findings on changes in binocularity and disparity tuning. Furthermore, the model makes testable predictions regarding how altered rearing conditions impede the learning of precise vergence control. Finally, the model predicts a surprising new effect that impaired vergence control affects the statistics of orientation tuning in visual cortical neurons.
Turoňová, Beata ; Sikora, Mateusz ; Schürmann, Christoph ; Hagen, Wim ; Welsch, Sonja ; Blanc, Florian E. C. ; Bülow, Sören von ; Gecht, Michael ; Bagola, Katrin ; Hörner, Cindy ; Zandbergen, Ger van ; Landry, Jonathan ; Trevisan Doimo de Azevedo, Nayara ; Mosalaganti, Shyamal Narayan ; Schwarz, Andre ; Covino, Roberto ; Mühlebach, Michael D. ; Hummer, Gerhard ; Krijnse-Locker, Jacomine ; Beck, Martin
The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo–electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines.
Turoňová, Beata ; Sikora, Mateusz ; Schürmann, Christoph ; Hagen, Wim ; Welsch, Sonja ; Blanc, Florian E. C. ; Bülow, Sören von ; Gecht, Michael ; Bagola, Katrin ; Hörner, Cindy ; Zandbergen, Ger van ; Mosalaganti, Shyamal Narayan ; Schwarz, Andre ; Covino, Roberto ; Mühlebach, Michael D. ; Hummer, Gerhard ; Krijnse-Locker, Jacomine ; Beck, Martin
The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the major focus for vaccine development. We combine cryo electron tomography, subtomogram averaging and molecular dynamics simulations to structurally analyze S in situ. Compared to recombinant S, the viral S is more heavily glycosylated and occurs predominantly in a closed pre-fusion conformation. We show that the stalk domain of S contains three hinges that give the globular domain unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and the development of safe vaccines. The large scale tomography data set of SARS-CoV-2 used for this study is therefore sufficient to resolve structural features to below 5 Ångstrom, and is publicly available at EMPIAR-10453.
Klevanski, Maja ; Herrmannsdörfer, Frank ; Venkataramani, Varun ; Saß, Steffen ; Heilemann, Mike ; Kuner, Thomas
Understanding the nano-architecture of protein machines in diverse subcellular compartments remains a challenge despite rapid progress in super-resolution microscopy. While single-molecule localization microscopy techniques allow the visualization and identification of cellular structures with near-molecular resolution, multiplex-labeling of tens of target proteins within the same sample has not yet been achieved routinely. However, single sample multiplexing is essential to detect patterns that threaten to get lost in multi-sample averaging. Here, we report maS3TORM (multiplexed automated serial staining stochastic optical reconstruction microscopy), a microscopy approach capable of fully automated 3D direct STORM (dSTORM) imaging and solution exchange employing a re-staining protocol to achieve highly multiplexed protein localization within individual biological samples. We demonstrate 3D super-resolution images of 15 targets in single cultured cells and 16 targets in individual neuronal tissue samples with <10 nm localization precision, allowing us to define distinct nano-architectural features of protein distribution within the presynaptic nerve terminal.
González Palomares, Eugenia ; López Jury, Luciana ; García Rosales, Francisco ; Hechavarria-Cueria, Julio C.
The auditory midbrain (inferior colliculus, IC) plays an important role in sound processing, acting as hub for acoustic information extraction and for the implementation of fast audio-motor behaviors. IC neurons are topographically organized according to their sound frequency preference: dorsal IC regions encode low frequencies while ventral areas respond best to high frequencies, a type of sensory map defined as tonotopy. Tonotopic maps have been studied extensively using artificial stimuli (pure tones) but our knowledge of how these maps represent information about sequences of natural, spectro-temporally rich sounds is sparse. We studied this question by conducting simultaneous extracellular recordings across IC depths in awake bats (Carollia perspicillata) that listened to sequences of natural communication and echolocation sounds. The hypothesis was that information about these two types of sound streams is represented at different IC depths since they exhibit large differences in spectral composition, i.e., echolocation covers the high-frequency portion of the bat soundscape (> 45 kHz), while communication sounds are broadband and carry most power at low frequencies (20–25 kHz). Our results showed that mutual information between neuronal responses and acoustic stimuli, as well as response redundancy in pairs of neurons recorded simultaneously, increase exponentially with IC depth. The latter occurs regardless of the sound type presented to the bats (echolocation or communication). Taken together, our results indicate the existence of mutual information and redundancy maps at the midbrain level whose response cannot be predicted based on the frequency composition of natural sounds and classic neuronal tuning curves.
García Rosales, Francisco ; López Jury, Luciana ; González Palomares, Eugenia ; Cabral-Calderı́n, Yuranny ; Kössl, Manfred ; Hechavarria-Cueria, Julio C.
Neural oscillations are at the core of important computations in the mammalian brain. Interactions between oscillatory activities in different frequency bands, such as delta (1-4 Hz), theta (4-8 Hz), or gamma (>30 Hz), are a powerful mechanism for binding fundamentally distinct spatiotemporal scales of neural processing. Phase-amplitude coupling (PAC) is one such plausible and well-described interaction, but much is yet to be uncovered regarding how PAC dynamics contribute to sensory representations. In particular, although PAC appears to have a major role in audition, the characteristics of coupling profiles in sensory and integration (i.e. frontal) cortical areas remain obscure. Here, we address this question by studying PAC dynamics in the frontal-auditory field (FAF; an auditory area in the bat frontal cortex) and the auditory cortex (AC) of the bat Carollia perspicillata. By means of simultaneous electrophysiological recordings in frontal and auditory cortices examining local-field potentials (LFPs), we show that the amplitude of gamma-band activity couples with the phase of low-frequency LFPs in both structures. Our results demonstrate that the coupling in FAF occurs most prominently in delta/high-gamma frequencies (1-4/75-100 Hz), whereas in the AC the coupling is strongest in the theta/low-gamma (2-8/25-55 Hz) range. We argue that distinct PAC profiles may represent different mechanisms for neuronal processing in frontal and auditory cortices, and might complement oscillatory interactions for sensory processing in the frontal-auditory cortex network.
Animals extract behaviorally relevant signals from “noisy” environments. To investigate signal extraction, echolocating provides a rich system testbed. For orientation, bats broadcast calls and assign each echo to the corresponding call. When orienting in acoustically enriched environments or when approaching targets, bats change their spectro-temporal call design. Thus, to assess call adjustments that are exclusively meant to facilitate signal extraction in “noisy” environments, it is necessary to control for distance-dependent call changes. By swinging bats in a pendulum, we tested the influence of acoustic playback on the echolocation behavior of Carollia perspicillata. This paradigm evokes reproducible orientation behavior and allows a precise definition of the influence of the acoustic context. Our results show that bats dynamically switch between different adaptations to cope with sound-based navigation in acoustically contaminated environments. These dynamics of echolocation behavior may explain the large variety of adaptations that have been reported in the bat literature.
Bojkova, Denisa ; Costa, Rui ; Bechtel, Marco ; Ciesek, Sandra ; Michaelis, Martin ; Cinatl, Jindrich
It becomes more and more obvious that deregulation of host metabolism play an important role in SARS-CoV-2 pathogenesis with implication for increased risk of severe course of COVID-19. Furthermore, it is expected that COVID-19 patients recovered from severe disease may experience long-term metabolic disorders. Thereby understanding the consequences of SARS-CoV-2 infection on host metabolism can facilitate efforts for effective treatment option. We have previously shown that SARS-CoV-2-infected cells undergo a shift towards glycolysis and that 2-deoxy-D-glucose (2DG) inhibits SARS-CoV-2 replication. Here, we show that also pentose phosphate pathway (PPP) is remarkably deregulated. Since PPP supplies ribonucleotides for SARS-CoV-2 replication, this could represent an attractive target for an intervention. On that account, we employed the transketolase inhibitor benfooxythiamine and showed dose-dependent inhibition of SARS-CoV-2 in non-toxic concentrations. Importantly, the antiviral efficacy of benfooxythiamine was further increased in combination with 2DG.
Endogenous clocks enable organisms to adapt their physiology and behavior to daily variation in environmental conditions. Metabolic processes in cyanobacteria to humans are effected by the circadian clock, and its dysregulation causes metabolic disorders. In mouse and Drosophila were shown that the circadian clock directs translation of factors involved in ribosome biogenesis and synchronizes protein synthesis. However, the role of clocks in Drosophila neurogenesis and the potential impact of clock impairment on neural circuit formation and function is less understood. Here we demonstrate that light stimuli or circadian clock causes a defect in neural stem cell growth and proliferation accompanied by reduced nucleolar size. Further, we define that light and clock independently affect the InR/TOR growth regulatory pathway due to the effect on regulators of protein biosynthesis. Altogether, these data suggest that alterations in growth regulatory pathways induced by light and clock are associated with impaired neural development.
Otomo, Kanako ; Perkins, Jessica ; Kulkarni, Anand ; Stojanovic, Strahinja ; Roeper, Jochen ; Paladini, Carlos A.
The firing pattern of ventral midbrain dopamine neurons is controlled by afferent and intrinsic activity to generate prediction error signals that are essential for reward-based learning. Given the absence of intracellular in vivo recordings in the last three decades, the subthreshold membrane potential events that cause changes in dopamine neuron firing patterns remain unknown. By establishing stable in vivo whole-cell recordings of >100 spontaneously active midbrain dopamine neurons in anaesthetized mice, we identified the repertoire of subthreshold membrane potential signatures associated with distinct in vivo firing patterns. We demonstrate that dopamine neuron in vivo activity deviates from a single spike pacemaker pattern by eliciting transient increases in firing rate generated by at least two diametrically opposing biophysical mechanisms: a transient depolarization resulting in high frequency plateau bursts associated with a reactive, depolarizing shift in action potential threshold; and a prolonged hyperpolarization preceding slower rebound bursts characterized by a predictive, hyperpolarizing shift in action potential threshold. Our findings therefore illustrate a framework for the biophysical implementation of prediction error and sensory cue coding in dopamine neurons by tuning action potential threshold dynamics.
Baumgarten, Nina ; Schmidt, Florian ; Wegner, Martin ; Hebel, Marie ; Kaulich, Manuel ; Schulz, Marcel Holger
Genome-wide CRISPR screens are becoming more widespread and allow the simultaneous interrogation of thousands of genomic regions. Although recent progress has been made in the analysis of CRISPR screens, it is still an open problem how to interpret CRISPR mutations in non-coding regions of the genome. Most of the tools concentrate on the interpretation of mutations introduced in gene coding regions. We introduce a computational pipeline that uses epigenomic information about regulatory elements for the interpretation of CRISPR mutations in non-coding regions. We illustrate our approach on the analysis of a genome-wide CRISPR screen in hTERT-RPE-1 cells and reveal novel regulatory elements that mediate chemoresistance against doxorubicin in these cells. We infer links to established and to novel chemoresistance genes. Our approach is general and can be applied on any cell type and with different CRISPR enzymes.
Prost, Stefan ; Petersen, Malte ; Grethlein, Martin ; Hahn, Sarah Joy ; Kuschik-Maczollek, Nina ; Olesiuk, Martyna Ewa ; Reschke, Jan-Olaf ; Schmey, Tamara Elke ; Zimmer, Caroline ; Gupta, Deepak Kumar ; Schell, Tilman ; Coimbra, Raphael T. F. ; Raad, Jordi de ; Lammers, Fritjof ; Winter, Sven ; Janke, Axel
Background: Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university Master’s course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behaviour. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published HiC data.
Findings: The use of nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using previously published HiC data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 95.8% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly.
Conclusion: We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university Master’s course. The use of ~35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.
Entorhinal-retrosplenial circuits for allocentric-egocentric transformation of boundary coding
(2020)
Spatial navigation requires landmark coding from two perspectives, relying on viewpoint-invariant and self-referenced representations. The brain encodes information within each reference frame but their interactions and functional dependency remains unclear. Here we investigate the relationship between neurons in the rat's retrosplenial cortex (RSC) and entorhinal cortex (MEC) that increase firing near boundaries of space. Border cells in RSC specifically encode walls, but not objects, and are sensitive to the animal’s direction to nearby borders. These egocentric representations are generated independent of visual or whisker sensation but are affected by inputs from MEC that contains allocentric spatial cells. Pharmaco- and optogenetic inhibition of MEC led to a disruption of border coding in RSC, but not vice versa, indicating allocentric-to-egocentric transformation. Finally, RSC border cells fire prospective to the animal’s next motion, unlike those in MEC, revealing the MEC-RSC pathway as an extended border coding circuit that implements coordinate transformation to guide navigation behavior.
Sanz Perl, Yonatan ; Pallavicini, Carla ; Pérez Ipiña, Ignacio ; Demertzi, Athena ; Bonhomme, Vincent ; Martial, Charlotte ; Panda, Rajanikant ; Annen, Jitka ; Ibañez, Agustín ; Kringelbach, Morten L. ; Deco, Gustavo ; Laufs, Helmut ; Sitt, Jacobo D. ; Laureys, Steven ; Tagliazucchi, Enzo
Central Europe was affected by a compressional tectonic event in the Late Cretaceous, caused by the convergence of Iberia and Europe. Basement uplifts, inverted graben structures and newly formed marginal troughs are the main expressions of crustal shortening. Although the maximum activity occurred in a short period between 90 and 75 Ma, the exact timing of this event is still unclear. Dating of start and end of basin inversion is very different depending on the applied method. On the basis of borehole data, facies and thickness maps, the timing of basin re-organisation was reconstructed for several basins in Central Europe. The obtained data point to a synchronous start of basin inversion already at 95 Ma (Cenomanian), 5 Million years earlier than commonly assumed. The end of the Late Cretaceous compressional event is more difficult to pinpoint, because regional uplift and salt migration disturb the signal of shifting marginal troughs. Unconformities of Late Campanian to Paleogene age on inverted structures indicate slowly declining uplift rates.
Several studies suggested that transcription factor (TF) binding to DNA may be impaired or enhanced by DNA methylation. We present MeDeMo, a toolbox for TF motif analysis that combines information about DNA methylation with models capturing intra-motif dependencies. In a large-scale study using ChIP-seq data for 335 TFs, we identify novel TFs that are affected by DNA methylation. Overall, we find that CpG methylation decreases the likelihood of binding for the majority of TFs. For a considerable subset of TFs, we show that intra-motif dependencies are pivotal for accurately modelling the impact of DNA methylation on TF binding.
Griesinger, Frank ; Eberhardt, Wilfried E. E. ; Nusch, Arnd ; Reiser, Marcel ; Zahn, Mark-Oliver ; Maintz, Christoph ; Bernhardt, Christiane ; Losem, Christoph ; Stenzinger, Albrecht ; Heukamp, Lukas ; Büttner, Reinhard ; Marschner, Sebastian ; Jänicke, Martina ; Fleitz, Annette ; Spring, Lisa ; Sahlmann, Jörg ; Karatas, Aysun ; Hipper, Annette ; Weichert, Wilko ; Heilmann, Monika ; Sadjadian, Parvis ; Gleiber, Wolfgang ; Grah, Christian ; Waller, Cornelius ; Reck, Martin ; Rittmeyer, Achim ; Christopoulos, Petros ; Sebastian, Martin ; Thomas, Michael
Objectives: An increasing number of treatment-determining biomarkers has been identified in non-small cell lung cancer (NSCLC) and molecular testing is recommended to enable optimal individualized treatment. However, data on implementation of these recommendations in the “real-world” setting are scarce. This study presents comprehensive details on the frequency, methodology and results of biomarker testing of advanced NSCLC in Germany.
Patients and methods: This analysis included 3,717 patients with advanced NSCLC (2,921 non-squamous; 796 squamous), recruited into the CRISP registry at start of systemic therapy by 150 German sites between December 2015 and June 2019. Evaluated were the molecular biomarkers EGFR, ALK, ROS1, BRAF, KRAS, MET, TP53, RET, HER2, as well as expression of PD-L1.
Results: In total, 90.5 % of the patients were tested for biomarkers. Testing rates were 92.2 % (non-squamous), 70.7 % (squamous) and increased from 83.2 % in 2015/16 to 94.2% in 2019. Overall testing rates for EGFR, ALK, ROS1, and BRAF were 72.5 %, 74.5 %, 66.1 %, and 53.0 %, respectively (non-squamous). Testing rates for PD-L1 expression were 64.5 % (non-squamous), and 58.5 % (squamous). The most common testing methods were immunohistochemistry (68.5 % non-squamous, 58.3 % squamous), and next-generation sequencing (38.7 % non-squamous, 14.4 % squamous). Reasons for not testing were insufficient tumor material or lack of guideline recommendations (squamous). No alteration was found in 37.8 % (non-squamous), and 57.9 % (squamous), respectively. Most common alterations in non-squamous tumors (all patients/all patients tested for the respective biomarker): KRAS (17.3 %/39.2 %), TP53 (14.1 %/51.4 %), and EGFR (11.0 %/15.1 %); in squamous tumors: TP53 (7.0 %/69.1 %), MET (1.5 %/11.1 %), and EGFR (1.1 %/4.4 %). Median PFS (non-squamous) was 8.7 months (95 % CI 7.4–10.4) with druggable EGFR mutation, and 8.0 months (95 % CI 3.9–9.2) with druggable ALK alterations.
Conclusion: Testing rates in Germany are high nationwide and acceptable in international comparison, but still leave out a significant portion of patients, who could potentially benefit. Thus, specific measures are needed to increase implementation.
Wurzel, Patrick ; Ackermann, Jörg ; Schäfer, Hendrik ; Scharf, Sonja ; Hansmann, Martin-Leo ; Koch, Ina
Human lymph nodes play a central part of immune defense against infection agents and tumor cells. Lymphoid follicles are compartments of the lymph node which are spherical, mainly filled with B cells. B cells are cellular components of the adaptive immune systems. In the course of a specific immune response, lymphoid follicles pass different morphological differentiation stages. The morphology and the spatial distribution of lymphoid follicles can be sometimes associated to a particular causative agent and development stage of a disease. We report our new approach for the automatic detection of follicular regions in histological whole slide images of tissue sections immuno-stained with actin. The method is divided in two phases: (1) shock filter-based detection of transition points and (2) segmentation of follicular regions. Follicular regions in 10 whole slide images were manually annotated by visual inspection, and sample surveys were conducted by an expert pathologist. The results of our method were validated by comparing with the manual annotation. On average, we could achieve a Zijbendos similarity index of 0.71, with a standard deviation of 0.07.
García Rosales, Francisco ; López Jury, Luciana ; González Palomares, Eugenia ; Cabral-Calderı́n, Yuranny ; Hechavarria-Cueria, Julio C.
Most mammals rely on the extraction of acoustic information from the environment in order to survive. However, the mechanisms that support sound representation in auditory neural networks involving sensory and association brain areas remain underexplored. In this study, we address the functional connectivity between an auditory region in frontal cortex (the frontal auditory field, FAF) and the auditory cortex (AC) in the bat Carollia perspicillata. The AC is a classic sensory area central for the processing of acoustic information. On the other hand, the FAF belongs to the frontal lobe, a brain region involved in the integration of sensory inputs, modulation of cognitive states, and in the coordination of behavioural outputs. The FAF-AC network was examined in terms of oscillatory coherence (local-field potentials, LFPs), and within an information theoretical framework linking FAF and AC spiking activity. We show that in the absence of acoustic stimulation, simultaneously recorded LFPs from FAF and AC are coherent in low frequencies (1-12 Hz). This “default” coupling was strongest in deep AC layers and was unaltered by acoustic stimulation. However, presenting auditory stimuli did trigger the emergence of coherent auditory-evoked gamma-band activity (>25 Hz) between the FAF and AC. In terms of spiking, our results suggest that FAF and AC engage in distinct coding strategies for representing artificial and natural sounds. Taken together, our findings shed light onto the neuronal coding strategies and functional coupling mechanisms that enable sound representation at the network level in the mammalian brain.
Lewis, Christopher Murphy ; Jianguang, Ni ; Wunderle, Thomas ; Jendritza, Patrick ; Lazar, Andreea ; Diester, Ilka ; Fries, Pascal
Synchronization has been implicated in neuronal communication, but causal evidence remains indirect. We used optogenetics to generate depolarizing currents in pyramidal neurons of cat visual cortex, emulating excitatory synaptic inputs under precise temporal control, while measuring spike output. Cortex transformed constant excitation into strong gamma-band synchronization, revealing the well-known cortical resonance. Increasing excitation with ramps increased the strength and frequency of synchronization. Slow, symmetric excitation profiles revealed hysteresis of power and frequency. Crucially, white-noise input sequences enabled causal analysis of network transmission, establishing that cortical resonance selectively transmits coherent input components. Models composed of recurrently coupled excitatory and inhibitory units uncovered a crucial role of feedback inhibition and suggest that hysteresis can arise through spike-frequency adaptation. The presented approach provides a powerful means to investigate the resonance properties of local circuits and probe how these properties transform input and shape transmission.
Lewis, Christopher Murphy ; Jianguang, Ni ; Wunderle, Thomas ; Jendritza, Patrick ; Diester, Ilka ; Fries, Pascal
The gamma rhythm has been implicated in neuronal communication, but causal evidence remains indirect. We measured spike output of local neuronal networks and emulated their synaptic input through optogenetics. Opsins provide currents through somato-dendritic membranes, similar to synapses, yet under experimental control with high temporal precision. We expressed Channelrhodopsin-2 in excitatory neurons of cat visual cortex and recorded neuronal responses to light with different temporal characteristics. Sine waves of different frequencies entrained neuronal responses with a reliability that peaked for input frequencies in the gamma band. Crucially, we also presented white-noise sequences, because their temporal unpredictability enables analysis of causality. Neuronal spike output was caused specifically by the input’s gamma component. This gamma-specific transfer function is likely an emergent property of in-vivo networks with feedback inhibition. The method described here could reveal the transfer function between the input to any one and the output of any other neuronal group.
The plant family Brassicaceae includes some of the most studied hosts of plant microbiomes, targeting microbial diversity, community assembly rules, and effects on host performance. Compared to bacteria, eukaryotes in the brassicaceous microbiome remain understudied, especially under natural settings. Here, we assessed the impact of host identity and age on the assembly of fungal and oomycete root communities, using DNA metabarcoding of roots and associated soil of three annual co-habiting Brassicaceae collected at two time points. Our results showed that fungal communities are more diverse and structured than those of oomycetes. In both cases, plant identity and sampling time had little influence on community variation, whereas root/soil compartment had a strong effect by exerting control on the entry of soil microorganisms into the roots. The enrichment in roots of specific fungi suggests a specialization towards the asymptomatic colonization of plant tissues, which could be relevant to host’s fitness and health.
Heim, Ramona Julia ; Bucharova, Anna ; Brodt, Leya ; Kamp, Johannes ; Rieker, Daniel ; Soromotin, Andrey V. ; Yurtaev, Andrey ; Hölzel, Norbert
Wildfires are relatively rare in subarctic tundra ecosystems, but they can strongly change ecosystem properties. Short-term fire effects on subarctic tundra vegetation are well documented, but long-term vegetation recovery has been studied less. The frequency of tundra fires will increase with climate warming. Understanding the long-term effects of fire is necessary to predict future ecosystem changes.
We used a space-for-time approach to assess vegetation recovery after fire over more than four decades. We studied soil and vegetation patterns on three large fire scars (>44, 28 and 12 years old) in dry, lichen-dominated forest tundra in Western Siberia. On 60 plots, we determined soil temperature and permafrost thaw depth, sampled vegetation and measured plant functional traits. We assessed trends in NDVI to support the field-based results on vegetation recovery.
Soil temperature, permafrost thaw depth and total vegetation cover had recovered to pre-fire levels after >44 years, as well as total vegetation cover. In contrast, after >44 years, functional groups had not recovered to the pre-fire state. Burnt areas had lower lichen and higher bryophyte and shrub cover. The dominating shrub species, Betula nana, exhibited a higher vitality (higher specific leaf area and plant height) on burnt compared with control plots, suggesting a fire legacy effect in shrub growth. Our results confirm patterns of shrub encroachment after fire that were detected before in other parts of the Arctic and Subarctic. In the so far poorly studied Western Siberian forest tundra we demonstrate for the first time, long-term fire-legacies on the functional composition of relatively dry shrub- and lichen-dominated vegetation.
Signal transfer of visual stimuli to V4 occurs in gamma-rhythmic, pulsed information packages
(2020)
Summary Selective visual attention allows the brain to focus on behaviorally relevant information while ignoring irrelevant signals. As a possible mechanism, routing by synchronization was proposed: neural populations sending attended signals align their gamma-rhythmic activities with receiving populations, such that spikes from the senders arrive at excitability peaks of the receivers, enhancing signal transfer. Conversely, the non-attended signals arrive unaligned to the receiver’s oscillation, reducing signal transfer. Therefore, visual signals should be transferred through periodically pulsed information packages, resulting in a modulation of the stimulus content within the receiver’s activity by its gamma phase and amplitude. To test this prediction, we quantified gamma phase-specific stimulus content within neural activity from area V4 of macaques performing a visual attention task. For the attended stimulus we find enhanced stimulus content reaching its maximum near excitability peaks, with effect magnitude increasing with oscillation amplitude, establishing a functional link between selective processing and gamma activity.
Chiu, Wei-Hua ; Kovacheva, Lora ; Musgrove, Ruth E. ; Arien-Zakay, Hadar ; Koprich, James B. ; Brotchie, Jonathan M. ; Yaka, Rami ; Ben-Zvi, Danny ; Hanani, Menachem ; Roeper, Jochen ; Goldberg, Joshua A.
No disease modifying therapy is currently available for Parkinson’s disease (PD), the second most common neurodegenerative disease. The long non-motor prodromal phase of PD is a window of opportunity for early detection and intervention. However, we lack the pathophysiological understanding to develop selective biomarkers and interventions. By developing a mutant α-synuclein selective-overexpression mouse model of prodromal PD, we identified a cell-autonomous selective Kv4 channelopathy in dorsal motor nucleus of the vagus (DMV) neurons. This functional remodeling of intact DMV neurons leads to impaired pacemaker function in vitro and in vivo, which in turn reduces gastrointestinal motility which is a common, very early symptom of prodromal PD. We show for the first time a causal chain of events from α-synuclein via a biophysical dysfunction of specific neuronal populations to a clinically relevant prodromal symptom. These findings can facilitate the rational design of clinical biomarkers to identify people at risk for PD.
Learning in the eyes: specific changes in gaze patterns track explicit and implicit visual learning
(2020)
What is the link between eye movements and sensory learning? Although some theories have argued for a permanent and automatic interaction between what we know and where we look, which continuously modulates human information- gathering behavior during both implicit and explicit learning, there exist surprisingly little evidence supporting such an ongoing interaction. We used a pure form of implicit learning called visual statistical learning and manipulated the explicitness of the task to explore how learning and eye movements interact. During both implicit exploration and explicit visual learning of unknown composite visual scenes, eye movement patterns systematically changed in accordance with the underlying statistical structure of the scenes. Moreover, the degree of change was directly correlated with the amount of knowledge the observers acquired. Our results provide the first evidence for an ongoing and specific interaction between hitherto accumulated knowledge and eye movements during both implicit and explicit learning.
Gagl, Benjamin ; Richlan, Fabio ; Ludersdorfer, Philipp ; Sassenhagen, Jona ; Eisenhauer, Susanne ; Gregorova, Klara ; Fiebach, Christian
To characterize the left-ventral occipito-temporal cortex (lvOT) role during reading in a quantitatively explicit and testable manner, we propose the lexical categorization model (LCM). The LCM assumes that lvOT optimizes linguistic processing by allowing fast meaning access when words are familiar and filter out orthographic strings without meaning. The LCM successfully simulates benchmark results from functional brain imaging. Empirically, using functional magnetic resonance imaging, we demonstrate that quantitative LCM simulations predict lvOT activation across three studies better than alternative models. Besides, we found that word-likeness, which is assumed as input to LCM, is represented posterior to lvOT. In contrast, a dichotomous word/non-word contrast, which is assumed as the LCM’s output, could be localized to upstream frontal brain regions. Finally, we found that training lexical categorization results in more efficient reading. Thus, we propose a ventral-visual-stream processing framework for reading involving word-likeness extraction followed by lexical categorization, before meaning extraction.
Gagl, Benjamin ; Sassenhagen, Jona ; Haan, Sophia ; Gregorova, Klara ; Richlan, Fabio ; Fiebach, Christian
Most current models assume that the perceptual and cognitive processes of visual word recognition and reading operate upon neuronally coded domain-general low-level visual representations – typically oriented line representations. We here demonstrate, consistent with neurophysiological theories of Bayesian-like predictive neural computations, that prior visual knowledge of words may be utilized to ‘explain away’ redundant and highly expected parts of the visual percept. Subsequent processing stages, accordingly, operate upon an optimized representation of the visual input, the orthographic prediction error, highlighting only the visual information relevant for word identification. We show that this optimized representation is related to orthographic word characteristics, accounts for word recognition behavior, and is processed early in the visual processing stream, i.e., in V4 and before 200 ms after word-onset. Based on these findings, we propose that prior visual-orthographic knowledge is used to optimize the representation of visually presented words, which in turn allows for highly efficient reading processes.
Gagl, Benjamin ; Sassenhagen, Jona ; Haan, Sophia ; Gregorova, Klara ; Richlan, Fabio ; Fiebach, Christian
Most current models assume that the perceptual and cognitive processes of visual word recognition and reading operate upon neuronally coded domain-general low-level visual representations – typically oriented line representations. We here demonstrate, consistent with neurophysiological theories of Bayesian-like predictive neural computations, that prior visual knowledge of words may be utilized to ‘explain away’ redundant and highly expected parts of the visual percept. Subsequent processing stages, accordingly, operate upon an optimized representation of the visual input, the orthographic prediction error, highlighting only the visual information relevant for word identification. We show that this optimized representation is related to orthographic word characteristics, accounts for word recognition behavior, and is processed early in the visual processing stream, i.e., in V4 and before 200 ms after word-onset. Based on these findings, we propose that prior visual-orthographic knowledge is used to optimize the representation of visually presented words, which in turn allows for highly efficient reading processes.
Mental imagery provides an essential simulation tool for remembering the past and planning the future, with its strength affecting both cognition and mental health. Research suggests that neural activity spanning prefrontal, parietal, temporal, and visual areas supports the generation of mental images. Exactly how this network controls the strength of visual imagery remains unknown. Here, brain imaging and transcranial magnetic phosphene data show that lower resting activity and excitability levels in early visual cortex (V1-V3) predict stronger sensory imagery. Further, electrically decreasing visual cortex excitability using tDCS increases imagery strength, demonstrating a causative role of visual cortex excitability in controlling visual imagery. Together, these data suggest a neurophysiological mechanism of cortical excitability involved in controlling the strength of mental images.
Background: Nations are imposing unprecedented measures at large-scale to contain the spread of COVID-19 pandemic. Recent studies indicate that measures such as lockdowns may have slowed down the growth of COVID-19. However, in addition to substantial economic and social costs, these measures also limit the exposure to Ultraviolet-B radiation (UVB). Emerging observational evidence indicate the protective role of UVB and vitamin D in reducing the severity and mortality of COVID-19 deaths. In this observational study, we empirically outline the independent protective roles of lockdown and UVB exposure as measured by ultraviolet index (UVI), whilst also examining whether the severity of lockdown is associated with a reduction in the protective role.
Methods: We apply a log-linear fixed-effects model to a panel dataset of 162 countries over a period of 108 days (n=6049). We use the cumulative number of COVID-19 deaths as the dependent variable and isolate the mitigating influence of lockdown severity on the association between UVI and growth-rates of COVID-19 deaths from time-constant country-specific and time-varying country-specific potentially confounding factors.
Findings: After controlling for time-constant and time-varying factors, we find that a unit increase in UVI and lockdown severity are independently associated with 17% [-1.8 percentage points] and 77% [-7.9 percentage points] decline in COVID-19 deaths growth rate, indicating their respective protective roles. However, the widely utilized and least severe lockdown (recommendation to not leave the house) already fully mitigates the protective role of UVI by 95% [1.8 percentage points] indicating its downside.
Interpretation: We find that lockdown severity and UVI are independently associated with a slowdown in the daily growth rates of cumulative COVID-19 deaths. However, we find consistent evidence that increase in lockdown severity is associated with a significant reduction in the protective role of UVI in reducing COVID-19 deaths. Our results suggest that lockdowns in conjunction with adequate exposure to UVB radiation might have provided even more substantial health benefits, than lockdowns alone. For example, we estimate that there would be 21% fewer deaths on average with sufficient UVB exposure while people were recommended not to leave their house. Therefore, our study outlines the importance of considering UVB exposure, especially while implementing lockdowns and may support policy decision making in countries imposing such measures.
Competing Interest Statement: RKM is a PhD researcher at Goethe University, Frankfurt. He also is an employee of a multinational chemical company involved in vitamin D business and holds the shares of the company. This study is intended to contribute to the ongoing COVID-19 crisis and is not sponsored by his company. All other authors declare no competing interests. The views expressed in the paper are those of the authors and do not represent that of any organization. No other relationships or activities that could appear to have influenced the submitted work.
The clinical and economic value of a successful shutdown during the SARS-CoV-2 pandemic in Germany
(2020)
Background and aim A shutdown of businesses enacted during the SARS-CoV-2 pandemic can serve different goals, e.g., preventing the intensive care unit (ICU) capacity from being overwhelmed (‘flattening the curve’) or keeping the reproduction number substantially below one (‘squashing the curve’). The aim of this study was to determine the clinical and economic value of a shutdown that is successful in ‘flattening’ or ‘squashing the curve’ in Germany.
Methods In the base case, the study compared a successful shutdown to a worst-case scenario with no ICU capacity left to treat COVID-19 patients. To this end, a decision model was developed using, e.g., information on age-specific fatality rates, ICU outcomes, and the herd protection threshold. The value of an additional life year was borrowed from new, innovative oncological drugs, as cancer reflects a condition with a similar morbidity and mortality burden in the general population in the short term as COVID-19.
Results A shutdown that is successful in ‘flattening the curve’ is projected to yield an average health gain between 0.02 and 0.08 life years (0.2 to 0.9 months) per capita in the German population. The corresponding economic value ranges between €1543 and €8027 per capita or, extrapolated to the total population, 4% to 19% of the gross domestic product (GDP) in 2019. A shutdown that is successful in ‘squashing the curve’ is expected to yield a minimum health gain of 0.10 life years (1.2 months) per capita, corresponding to 24% of the GDP in 2019. Results are particularly sensitive to mortality data and the prevalence of undetected cases.
Conclusion A successful shutdown is forecasted to yield a considerable gain in life years in the German population. Nevertheless, questions around the affordability and underfunding of other parts of the healthcare system emerge.
Antimicrobial resistance is a major threat to global health and food security today. Scheduling cycling therapies by targeting phenotypic states associated to specific mutations can help us to eradicate pathogenic variants in chronic infections. In this paper, we introduce a logistic switching model in order to abstract mutation networks of collateral resistance. We found particular conditions for which unstable zero-equilibrium of the logistic maps can be stabilized through a switching signal. That is, persistent populations can be eradicated through tailored switching regimens.
Starting from an optimal-control formulation, the switching policies show their potential in the stabilization of the zero-equilibrium for dynamics governed by logistic maps. However, employing such switching strategies, deserve a specific characterization in terms of limit behaviour. Ultimately, we use evolutionary and control algorithms to find either optimal and sub-optimal switching policies. Simulations results show the applicability of Parrondo’s Paradox to design cycling therapies against drug resistance.
COVID-19 pandemic has underlined the impact of emergent pathogens as a major threat for human health. The development of quantitative approaches to advance comprehension of the current outbreak is urgently needed to tackle this severe disease. In this work, several mathematical models are proposed to represent SARS-CoV-2 dynamics in infected patients. Considering different starting times of infection, parameters sets that represent infectivity of SARS-CoV-2 are computed and compared with other viral infections that can also cause pandemics.
Based on the target cell model, SARS-CoV-2 infecting time between susceptible cells (mean of 30 days approximately) is much slower than those reported for Ebola (about 3 times slower) and influenza (60 times slower). The within-host reproductive number for SARS-CoV-2 is consistent to the values of influenza infection (1.7-5.35). The best model to fit the data was including immune responses, which suggest a slow cell response peaking between 5 to 10 days post onset of symptoms. The model with eclipse phase, time in a latent phase before becoming productively infected cells, was not supported. Interestingly, both, the target cell model and the model with immune responses, predict that virus may replicate very slowly in the first days after infection, and it could be below detection levels during the first 4 days post infection. A quantitative comprehension of SARS-CoV-2 dynamics and the estimation of standard parameters of viral infections is the key contribution of this pioneering work.
Tanneberger, Anna Maria ; Maawi, Sarah al- ; Herrera-Vizcaíno, Carlos ; Orlowska, Anna ; Kubesch, Alica ; Sader, Robert Alexander ; Kirkpatrick, Charles James ; Ghanaati, Shahram Michael
Objectives: The aim of the present study was to characterize the cellular reaction to a xenogeneic resorbable collagen membrane of porcine origin using a subcutaneous implantation model in Wistar rats over 30 days.
Materials and methods: Ex vivo, liquid platelet-rich fibrin (PRF), a leukocyte and platelet-rich cell suspension, was used to evaluate the blood cell membrane interaction. The material was implanted subcutaneously in rats. Sham-operated rats without biomaterial displayed physiological wound healing (control group). Histological, immunohistological, and histomorphometric analyses were focused on the inflammatory pattern, vascularization rate, and degradation pattern.
Results: The membrane induced a large number of mononuclear cells over the observation period, including lymphocytes, macrophages, and fibroblasts. After 15 days, multinucleated giant cells (MNGCs) were observed on the biomaterial surface. Their number increased significantly, and they proceeded to the center of the biomaterial on day 30. These cells highly expressed CD-68, calcitonin receptor, and MMP-9, but not TRAP or integrin-ß3. Thus, the membrane lost its integrity and underwent disintegration as a consequence of the induction of MNGCs. The significant increase in MNGC number correlated with a high rate of vascularization, which was significantly higher than the control group. Physiological wound healing in the control group did not induce any MNGCs at any time point. Ex vivo blood cells from liquid-PRF did not penetrate the membrane.
Conclusion: The present study suggests a potential role for MNGCs in biomaterial degradation and questions whether it is beneficial to accept them in clinically approved biomaterials or focus on biomaterials that induce only mononuclear cells. Thus, further studies are necessary to identify the function of biomaterial-induced MNGCs.
Clinical relevance: Understanding the cellular reaction to biomaterials is essential to assess their suitability for specific clinical indications and outline the potential benefit of specific group of biomaterials in the respective clinical indications.
Combining market data with a publicly available monthly snapshot of Deutsche Börse’s index ranking list, I create a model that predicts index changes in the DAX, MDAX, SDAX, and TecDAX from 2010 to 2019 before they are officially announced. Even though I empirically show that index changes are predictable, they still earn sizeable post-announcement 1-day abnormal returns up to 1.42% and − 1.54% for promotions and demotions, respectively. While abnormal returns are larger in smaller stocks, I find no evidence that they are related to funding constraints or additional risk for trading on wrong predictions. A trading strategy that trades according to my model yields an annualized Sharpe ratio of 0.83 while being invested for just 4 days a year.
Sikora, Mateusz ; Bülow, Sören von ; Blanc, Florian E. C. ; Gecht, Michael ; Covino, Roberto ; Hummer, Gerhard
The severity of the COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, calls for the urgent development of a vaccine. The primary immunological target is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface to mediate viral entry into the host cell. To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. We find that the extensive and inherently flexible glycan coat shields a surface area larger than expected from static structures, highlighting the importance of structural dynamics in epitope mapping.
Disordered proteins and nucleic acids can condense into droplets that resemble the membraneless organelles observed in living cells. MD simulations offer a unique tool to characterize the molecular interactions governing the formation of these biomolecular condensates, their physicochemical properties, and the factors controlling their composition and size. However, biopolymer condensation depends sensitively on the balance between different energetic and entropic contributions. Here, we develop a general strategy to fine-tune the potential energy function for molecular dynamics simulations of biopolymer phase separation. We rebalance protein–protein interactions against solvation and entropic contributions to match the excess free energy of transferring proteins between dilute solution and condensate. We illustrate this formalism by simulating liquid droplet formation of the FUS low-complexity domain (LCD) with a rebalanced MARTINI model. By scaling the strength of the nonbonded interactions in the coarse-grained MARTINI potential energy function, we map out a phase diagram in the plane of protein concentration and interaction strength. Above a critical scaling factor of αc ≈ 0.6, FUS-LCD condensation is observed, where α = 1 and 0 correspond to full and repulsive interactions in the MARTINI model. For a scaling factor α = 0.65, we recover experimental densities of the dilute and dense phases, and thus the excess protein transfer free energy into the droplet and the saturation concentration where FUS-LCD condenses. In the region of phase separation, we simulate FUS-LCD droplets of four different sizes in stable equilibrium with the dilute phase and slabs of condensed FUS-LCD for tens of microseconds, and over one millisecond in aggregate. We determine surface tensions in the range of 0.01–0.4 mN/m from the fluctuations of the droplet shape and from the capillary-wave-like broadening of the interface between the two phases. From the dynamics of the protein end-to-end distance, we estimate shear viscosities from 0.001 to 0.02 Pa s for the FUS-LCD droplets with scaling factors α in the range of 0.625–0.75, where we observe liquid droplets. Significant hydration of the interior of the droplets keeps the proteins mobile and the droplets fluid.
Hintergrund: Die Erstversorgung von Wunden und kleinere chirurgische Eingriffe gehören neben der hochspezialisierten Medizin zu den allgemein notwendigen Grundleistungen der Notfallversorgung in den Kliniken. Die Vergütung der ambulanten Notfallleistungen für gesetzlich Versicherte erfolgt derzeit nach dem Einheitlichen Bewertungsmaßstab (EBM), welchem die betriebswirtschaftliche Aufwandserfassung des niedergelassenen Sektors als Kalkulationsgrundlage dient. Krankenhäuser haben im Vergleich zu Arztpraxen wesentlich höhere Vorhaltungskosten.
Ziel der Arbeit: In dieser Arbeit wird das entstehende Kosten-Erlös-Verhältnis der ambulanten Wundversorgung in einer Notaufnahme durch die Vergütung nach EBM analysiert.
Material und Methoden: Die Daten wurden in der Notaufnahme des Universitätsklinikums Frankfurt am Main über 12 Monate erhoben. Eingeschlossen wurden alle Patienten, die in diesem Zeitraum eine Wundversorgung mittels Naht erhielten. Die Kosten wurden der Abrechnung nach EBM 01210 (bzw. 01212) mit der Zusatzpauschale für kleinchirurgische Eingriffe EBM 02301 gegenübergestellt.
Ergebnisse: Im Beobachtungszeitraum wurden 1548 Patienten versorgt; das entspricht 19,52 % aller unfallchirurgischen Fälle. Den Kosten einer Standardwundversorgung in Höhe von 45,40 € steht eine Vergütung von 31,83 € gegenüber. Die Berechnung des Gesamterlöses weist einen Defizitbetrag von 13,57 € pro ambulantem Fall auf; dies entspricht einem Jahresdefizit von 21.006,36 €.
Diskussion: Es konnte gezeigt werden, dass ohne Betrachtung der relevanten Vorhaltekosten in keinem Fall eine Kostendeckung erreicht werden kann.
Die bisherige Vergütung der ambulanten Wundversorgung nach EBM erscheint unzureichend. Eine Anpassung bzw. Zusatzvergütung scheint notwendig, um eine ausreichende Versorgungsqualität in Zukunft sicherstellen zu können.
This paper defends The Transformation of Values into Prices on the Basis of Random Systems, published in EIER, by answering to the Comments made in the same journal by Professors Mori, Morioka and Yamazaki. The clarifications mainly concern the justification of the randomness assumptions, the conditions needed to obtain the equality of total profit with total surplus value in the simplified one-industry system and the invariance of the results to changes in the units of measurement.
Summary We introduce fsbrain, an R package for the visualization of neuroimaging data. The package can be used to visualize vertex-wise and region-wise morphometry data, parcellations, labels and statistical results on brain surfaces in three dimensions (3D). Voxel data can be displayed in lightbox mode. The fsbrain package offers various customization options and produces publication quality plots which can be displayed interactively, saved as bitmap images, or integrated into R notebooks.
Availability and Implementation The software, source code and documentation are available under the MIT license at https://github.com/dfsp-spirit/fsbrain. Releases can be installed directly from the Comprehensive R Archive Network (CRAN).
Visual scene perception is mediated by a set of cortical regions that respond preferentially to images of scenes, including the occipital place area (OPA) and parahippocampal place area (PPA). However, the differential contribution of OPA and PPA to scene perception remains an open research question. In this study, we take a deep neural network (DNN)-based computational approach to investigate the differences in OPA and PPA function. In a first step we search for a computational model that predicts fMRI responses to scenes in OPA and PPA well. We find that DNNs trained to predict scene components (e.g., wall, ceiling, floor) explain higher variance uniquely in OPA and PPA than a DNN trained to predict scene category (e.g., bathroom, kitchen, office). This result is robust across several DNN architectures. On this basis, we then determine whether particular scene components predicted by DNNs differentially account for unique variance in OPA and PPA. We find that variance in OPA responses uniquely explained by the navigation-related floor component is higher compared to the variance explained by the wall and ceiling components. In contrast, PPA responses are better explained by the combination of wall and floor, that is scene components that together contain the structure and texture of the scene. This differential sensitivity to scene components suggests differential functions of OPA and PPA in scene processing. Moreover, our results further highlight the potential of the proposed computational approach as a general tool in the investigation of the neural basis of human scene perception.