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Adaptive threshold estimation procedures sample close to a subject’s perceptual threshold by dynamically adapting the stimulation based on the subject’s performance. Yet, perceptual thresholds not only depend on the observers’ sensory capabilities but also on any bias in terms of their expectations and response preferences, thus distorting the precision of the threshold estimates. Using the framework of signal detection theory (SDT), independent estimates of both, an observer’s sensitivity and internal processing bias can be delineated from threshold estimates. While this approach is commonly available for estimation procedures engaging the method of constant stimuli (MCS), correction procedures for adaptive methods (AM) are only scarcely applied. In this article, we introduce a new AM that takes individual biases into account, and that allows for a bias-corrected assessment of subjects’ sensitivity. This novel AM is validated with simulations and compared to a typical MCS-procedure, for which the implementation of bias correction has been previously demonstrated.
Comparing AM and MCS demonstrates the viability of the presented AM. Besides its feasibility, the results of the simulation reveal both, advantages, and limitations of the proposed AM. The procedure has considerable practical implications, in particular for the design of shaping procedures in sensory training experiments, in which task difficulty has to be constantly adapted to an observer’s performance, to improve training efficiency.
NAD is a coenzyme central to metabolism that was also found to serve as a 5’-terminal cap of bacterial and eukaryotic RNA species. The presence and functionality of NAD-capped RNAs (NAD-RNAs) in the archaeal domain remain to be characterized in detail. Here, by combining LC-MS and NAD captureSeq methodology, we quantified the total levels of NAD-RNAs and determined the identity of NAD-RNAs in the two model archaea, Sulfolobus acidocaldarius and Haloferax volcanii. A complementary differential RNA-Seq (dRNA-Seq) analysis revealed that NAD transcription start sites (NAD-TSS) correlate with well-defined promoter regions and often overlap with primary transcription start sites (pTSS). The population of NAD-RNAs in the two archaeal organisms shows clear differences, with S. acidocaldarius possessing more capped small non-coding RNAs (sncRNAs) and leader sequences. The NAD-cap did not prevent 5’→3’ exonucleolytic activity by the RNase Saci-aCPSF2. To investigate enzymes that facilitate the removal of the NAD-cap, four Nudix proteins of S. acidocaldarius were screened. None of the recombinant proteins showed NAD decapping activity. Instead, the Nudix protein Saci_NudT5 showed activity after incubating NAD-RNAs at elevated temperatures. Hyperthermophilic environments promote the thermal degradation of NAD into the toxic product ADPR. Incorporating NAD into RNAs and the regulation of ADPR-RNA decapping by Saci_NudT5 is proposed to provide additional layers of maintaining stable NAD levels in archaeal cells.
Importance: This study reports the first characterization of 5’-terminally modified RNA molecules in Archaea and establishes that NAD-RNA modifications, previously only identified in the other two domains of life, are also prevalent in the archaeal model organisms Sulfolobus acidocaldarius and Haloferax volcanii. We screened for NUDIX hydrolases that could remove the NAD-RNA cap and showed that none of these enzymes removed NAD modifications, but we discovered an enzyme that hydrolyzes ADPR-RNA. We propose that these activities influence the stabilization of NAD and its thermal degradation to potentially toxic ADPR products at elevated growth temperatures.
The Yacoraite Formation (Salta rift, Argentina) consists of Maastrichtian–Danian lacustrine carbonate and siliciclastic deposits with interbedded volcanic ash layers, organized in four third-order stratigraphic sequences. It offers the exceptional opportunity to jointly apply in situ zircon and carbonate U-Pb geochronology that resulted in two distinct depositional age depth models. Ages of the youngest zircon population from ash layers were linearly interpolated to derive a zircon depositional age depth model. A carbonate depositional age depth model was instead obtained from dated carbonate phases including microbialites, ooids, oncoids of calcitic and dolomitic mineralogy as well as early lacustrine calcite cements. Mean ages were defined from different carbonate phases belonging to the same layer and then linearly interpolated. Sedimentation rates were calculated from both depth models between pairs of dated samples and used to estimate the age of sequence boundaries, as well as the duration of the four stratigraphic sequences. The zircon and carbonate depositional age depth models agree with biostratigraphic constraints and exhibit excellent consistency. The onset and end of sedimentation were estimated at 68.2 ± 0.9 Ma and 62.3 ± 0.6 Ma (duration ca 5.7 Ma) via zircon geochronology and at 67.9 ± 1.7 Ma and 61.9 ± 1.3 Ma (duration ca 6.0 Ma) via carbonate geochronology. Results from this study show that with suitable samples and a newly implemented working strategy, in situ U-Pb dating of depositional and early diagenetic carbonates represent a valuable chronostratigraphic tool for estimating sedimentation rate and duration in poorly time-framed depositional systems.
Influence of the emission site on the photoelectron circular dichroism in trifluoromethyloxirane
(2022)
We report a joint experimental and theoretical study of the differential photoelectron circular dichroism (PECD) in inner-shell photoionization of uniaxially oriented trifluoromethyloxirane. By adjusting the photon energy of the circularly polarized synchrotron radiation, we address 1s-photoionization of the oxygen, different carbon, and all fluorine atoms. The photon energies were chosen such that in all cases electrons with a similar kinetic energy of about 11 eV are emitted. Employing coincident detection of electrons and fragment ions, we concentrate on identical molecular fragmentation channels for all of the electron-emitter scenarios. Thereby, we systematically examine the influence of the emission site of the photoelectron wave on the differential PECD. We observe large differences in the PECD signals. The present experimental results are supported by corresponding relaxed-core Hartree–Fock calculations.
Targeted delivery of nucleic acids is gaining momentum due to improved efficacy, selectivity, increased circulation time and enhanced tissue retention in target cells. Using nucleic acid-based therapies previously undruggable targets have proven now to be amenable for treatment. Currently, several methods for preparing targeted or labelled delivery vehicles for nucleic acids are based on liposomal formulations. Lipid nanoparticles (LNPs) are structurally different from liposomes and these methods should therefore be evaluated before being translated to siRNA LNPs preparation protocols. Here, we describe a robust and facile method for the preparation of targeted or fluorescently labelled siRNA LNPs. Using a copper free strain-promoted azide-alkyne cycloaddition (SPAAC) we demonstrate that post-insertion of ligand-lipid conjugates into preformed LNPs is superior to direct-surface modification because it preserves the physicochemical parameters of the LNPs. We found that the time point of solvent removal by dialysis is critical and affects the hydrodynamic diameter of the LNPs; post-insertion after dialysis shows the smallest increase in hydrodynamic diameter and polydispersity index (PDI). The post-insertion of ligand-lipid conjugates also proceeded with rapid kinetics and high efficacy over a wide temperature range. Using this optimised protocol, we generated siRNA LNPs containing both targeting and fluorescent tracking ligands allowing us to monitor siRNA LNP uptake kinetics in dependence of the targeting ligand. In aggregate, we describe a robust approach for the generation of targeted and labelled siRNA LNPs that allows their controlled and facile decoration with ligand combinations.
Sphingolipids are not only structural components of cell membranes but can also act as signalling molecules in different pathways. Sphingolipid precursors, Ceramides (Cer), are synthesized de novo by six different synthases (CerS1-6) which generate Cer of different chain lengths. Cer can be further synthesized to glycosphingolipids and sphingomyelin. Cell membrane parts that are enriched in glycosphingolipids are so-called lipid rafts and can function as signalling platforms for different receptors, such like the T cell receptor (TCR). CD4+ T cells play a crucial role in the development of ulcerative colitis, a chronic inflammatory disease of the colon. As CerS3 expression was increased in the white blood cells of human colitis patients, the role of CerS3 in the TCR signalling and colitis was investigated in this dissertation. By lenti-viral transduction of a CerS3-shRNA into a CD4+ Jurkat cell line, it was shown that CerS3 has an impact on activated T cells. A decrease of different sphingolipids after T cell activation via CD2/3/28 activation beads and IL2 treatment was observed that was accompanied by an inhibition of Zap70 phosphorylation, an important protein of the TCR signalling. The impaired TCR signalling led to a diminished NFAT1 translocation into the nucleus which subsequently led to a reduced NFAT1- dependent TNFα release. Downregulation of CerS3 in primary CD4+ T cells, obtained from the blood of healthy volunteers, also showed a reduced release of pro-inflammatory cytokines after activation. This dissertation demonstrates a pivotal role for CerS3 in T cell function and highlights CerS3 as potential new target for T cell driven colitis.
The relationship between achievement of a pathologic complete response (pCR) and favorable long-term outcome varies among breast cancer subtypes. We aimed to highlight which neoadjuvant treatment strategy could be most successful in each breast cancer subtype. A recent FDA meta-analysis on randomized neoadjuvant breast cancer trials suggests that the survival differences of patients with or without a pCR were less pronounced in luminal A-like tumors, despite the overall favorable prognosis of these patients. Moreover, even though the strong prognostic effect of pCR in HER2 positive and TNBC, the NOAH study was the only trial which showed a trend in surrogacy of pCR for long-term outcome in HER2-positive subtype. Results from GeparTrio study suggest that patients with hormone-positive tumors might need a response-guided approach, with either an intensification of treatment in case of an early response or a change to other chemotherapy in case of no early response. Furthermore, data from German neoadjuvant trials confirm that an increasing number of chemotherapy cycles is associated with a higher pCR rate, especially in patients with HER2-positive/hormone-positive tumors. In line with these suggestions, Tryphaena study showed a pCR rate that exceeding the 60% threshold, the highest pCR results presented in a large multicenter study. In TNBC, the highest pCR rate in the German neoadjuvant studies was obtained with the simultaneous application of docetaxel, doxorubicin and cyclophosphamide for 6 cycles. However, as shown in GaparQuinto and NSABP 40 trials, treatment effect in TNBC might be further maximized by adding bevacizumab, and two randomized neoadjuvant trials are expected this year to report data on the efficacy of carboplatin.
Effects of a phase transition on HBT correlations in an integrated Boltzmann+hydrodynamics approach
(2009)
A systematic study of HBT radii of pions, produced in heavy ion collisions in the intermediate energy regime (SPS), from an integrated (3+1)d Boltzmann+hydrodynamics approach is presented. The calculations in this hybrid approach, incorporating an hydrodynamic stage into the Ultra-relativistic Quantum Molecular Dynamics transport model, allow for a comparison of different equations of state retaining the same initial conditions and final freeze-out. The results are also compared to the pure cascade transport model calculations in the context of the available data. Furthermore, the effect of different treatments of the hydrodynamic freeze-out procedure on the HBT radii are investigated. It is found that the HBT radii are essentially insensitive to the details of the freeze-out prescription as long as the final hadronic interactions in the cascade are taken into account. The HBT radii RL and RO and the RO/RS ratio are sensitive to the EoS that is employed during the hydrodynamic evolution. We conclude that the increased lifetime in case of a phase transition to a QGP (via a Bag Model equation of state) is not supported by the available data.