XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates.

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

Harmonic radiation contribution and X-ray transmission at the Small Quantum Systems instrument of European XFEL.

Transmission measurements of the soft X-ray beamline to the Small Quantum Systems (SQS) scientific instrument at the SASE3 undulator of European XFEL are presented. Measurements are reported for a wide range of photon energies (650 eV to 2400 eV), using X-ray gas monitors as well as a bolometric radiometer. The results are in good agreement with simulations for the beam transport and show a transmission of up to 80% over the whole photon energy range. The contribution of second- and third-harmonic radiation of the soft X-ray undulator is determined at selected photon energies by performing transmission measurements using a gas absorber to provide variable attenuation of the incoming photon flux. A comparison of the results with semi-analytic calculations for the generation of free-electron laser pulses in the SASE3 undulator reveals an influence of apertures along the beam transport on the exact harmonic content to be accounted for at the experiment. The second-harmonic content is measured to be in the range of 0.1% to 0.3%, while the third-harmonic contributed a few percent to the SASE3 emission. For experiments at the SQS instrument, these numbers can be reduced through specific selections of the mirror reflection angles.

The beam transport system for the Small Quantum Systems instrument at the European XFEL: optical layout and first commissioning results.

The Small Quantum Systems instrument is one of the six operating instruments of the European XFEL, dedicated to the atomic, molecular and cluster physics communities. The instrument started its user operation at the end of 2018 after a commissioning phase. The design and characterization of the beam transport system are described here. The X-ray optical components of the beamline are detailed, and the beamline performances, transmission and focusing capabilities are reported. It is shown that the X-ray beam can be effectively focused as predicted by ray-tracing simulations. The impact of non-ideal X-ray source conditions on the focusing performances is discussed.

Recall bias of students' affective experiences in adolescence: The role of personality and internalizing behavior.

INTRODUCTION: Adolescence is characterized by multiple biopsychosocial changes, associated with a high intraindividual variability of emotional experiences. Previous findings suggest that this intraindividual variability is reflected in a recall bias of adolescents' emotion reports. However, corresponding findings are scarce and inconclusive. Studies on predictors of recall bias in adulthood indicate that personality traits, especially neuroticism and extraversion, as well as specific internalizing disorders might affect recall bias of emotion reports. METHODS: The sample consists of 118 Swiss adolescent students in grade 8 and 9 (Mage = 15.15, SDage = 0.89). The students' momentary affective experience was recorded using smartphones over seven consecutive days in situ at 42 randomly generated occasions (six per day), with a total of 1059 protocols on current events. At the end of the experience-sampling phase, students filled out an online questionnaire, providing information about their personality and typical behavior as well as their retrospective affective experience. In addition, the students' behavior was evaluated by their teachers. We applied two-level structural equation modeling with latent difference variables. RESULTS: Adolescents high in extraversion showed retrospective overestimation of positive affective experiences and underestimation of negative affective experiences. Adolescents with high neuroticism tended to overestimate negative affect retrospectively, showing no significant effects for positive affect. However, internalizing behavior did not predict a negative recall bias in adolescents' affective experience. CONCLUSIONS: Retrospective self-reports about adolescents' affective experience are biased by relatively stable individual factors, whereas less stable individual factors did not seem to have any influence.

Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids.

Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2-5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12-90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids.

High-resolution electron time-of-flight spectrometers for angle-resolved measurements at the SQS Instrument at the European XFEL.

A set of electron time-of-flight spectrometers for high-resolution angle-resolved spectroscopy was developed for the Small Quantum Systems (SQS) instrument at the SASE3 soft X-ray branch of the European XFEL. The resolving power of this spectrometer design is demonstrated to exceed 10 000 (E/ΔE), using the well known Ne 1s-13p resonant Auger spectrum measured at a photon energy of 867.11 eV at a third-generation synchrotron radiation source. At the European XFEL, a width of ∼0.5 eV full width at half-maximum for a kinetic energy of 800 eV was demonstrated. It is expected that this linewidth can be reached over a broad range of kinetic energies. An array of these spectrometers, with different angular orientations, is tailored for the Atomic-like Quantum Systems endstation for high-resolution angle-resolved spectroscopy of gaseous samples.

Borderline We-Space? The Phenomenology of the Background of Safety in Borderline Personality Disorder.

Borderline personality disorder (BPD) is a severe psychiatric condition characterized by instability in identity, relationships, and affect. Individuals, with BPD typically lack a coherent sense of self, are highly sensitive to interpersonal stressors, experience intense fluctuations in mood, and frequently engage in impulsive and self-destructive behaviors. Although both empirical research and development of effective psychotherapy have evidently progressed over the past years, many aspects regarding the structure of experience and the life-world typical for persons with BPD are not yet fully understood. Somewhat surprisingly, phenomenological psychopathology has only recently started to pay more attention to the disorder. A comprehensive elaboration of the phenomenology of BPD is therefore still lacking. This article aimed to contribute to such a phenomenological understanding by focusing on what we think is an essential aspect that has yet not been sufficiently addressed: the background of safety. To clarify what this means, we depart from Sandler's [Int J Psychoan. 1960;41:352-6] psychoanalytic concept and elaborate on it phenomenologically. This leads us to argue that the development of a background of safety requires a particular embodied presence of others, which, in turn, contributes to the constitution of a safe we-space, a shared and familiar environment providing a matrix for the experience of a stable world. However, even when established, the background of safety remains in need of a continuous reconfirmation through corresponding experiences within a sufficiently reliable and controllable environment. The background of safety is vulnerable and open to (interpersonal) disruptions like trauma or neglect. In BPD, we suggest 3 aspects regarding the phenomenology of the background of the safety need to be considered: first, typically, patients with BPD did not develop a robust background of safety in infancy; second, weakening of the background of safety gives rise to symptoms and dynamics typical for BPD; third, these symptoms and dynamics further undermine the possible development of a background of safety in adult life and thus gravitate toward a petrification of the borderline condition, a "stable instability." To conclude, we examine whether this concept should be understood as a trouble générateur and, last, consider its clinical implications.

Timing and X-ray pulse characterization at the Small Quantum Systems instrument of the European X-ray Free Electron Laser.

This contribution presents the initial characterization of the pump-probe performance at the Small Quantum Systems (SQS) instrument of the European X-ray Free Electron Laser. It is demonstrated that time-resolved experiments can be performed by measuring the X-ray/optical cross-correlation exploiting the laser-assisted Auger decay in neon. Applying time-of-arrival corrections based on simultaneous spectral encoding measurements allow us to significantly improve the temporal resolution of this experiment. These results pave the way for ultrafast pump-probe investigations of gaseous media at the SQS instrument combining intense and tunable soft X-rays with versatile optical laser capabilities.

Resonance-Enhanced Multiphoton Ionization in the X-Ray Regime.

Here, we report on the nonlinear ionization of argon atoms in the short wavelength regime using ultraintense x rays from the European XFEL. After sequential multiphoton ionization, high charge states are obtained. For photon energies that are insufficient to directly ionize a 1s electron, a different mechanism is required to obtain ionization to Ar^{17+}. We propose this occurs through a two-color process where the second harmonic of the FEL pulse resonantly excites the system via a 1s→2p transition followed by ionization by the fundamental FEL pulse, which is a type of x-ray resonance-enhanced multiphoton ionization (REMPI). This resonant phenomenon occurs not only for Ar^{16+}, but also through lower charge states, where multiple ionization competes with decay lifetimes, making x-ray REMPI distinctive from conventional REMPI. With the aid of state-of-the-art theoretical calculations, we explain the effects of x-ray REMPI on the relevant ion yields and spectral profile.

Development of the Commercial Manufacturing Process for Ipatasertib.

Ipatasertib is a potent small molecule Akt kinase inhibitor currently being tested in Phase III clinical trials for the treatment of metastatic castration-resistant prostate cancer and triple negative metastatic breast cancer. In this paper an overview of the development achievements towards the commercial manufacturing process is given. The convergent synthesis consists of ten steps with eight isolated intermediates and utilizes a wide range of chemical techniques and technologies to build-up this complex drug. All three stereocenters are introduced using enzyme or metal catalysis.

Double Core-Hole Generation in O_{2} Molecules Using an X-Ray Free-Electron Laser: Molecular-Frame Photoelectron Angular Distributions.

We report on a multiparticle coincidence experiment performed at the European X-ray Free-Electron Laser at the Small Quantum Systems instrument using a COLTRIMS reaction microscope. By measuring two ions and two electrons in coincidence, we investigate double core-hole generation in O_{2} molecules in the gas phase. Single-site and two-site double core holes have been identified and their molecular-frame electron angular distributions have been obtained for a breakup of the oxygen molecule into two doubly charged ions. The measured distributions are compared to results of calculations performed within the frozen- and relaxed-core Hartree-Fock approximations.

Formation of a Thiol-Ene Addition Product of Asthma Medication Montelukast Caused by a Widespread Tin-Based Thermal Stabilizer.

We report the formation and characterization of two diastereomeric thiol-ene addition products of the asthma medication Montelukast within chewing tablets. Widespread tin-based thermal stabilizers dioctyltin bis(2-ethylhexyl thioglycolate) and monooctyltin tris(2-ethylhexyl thioglycolate), used in the manufacturing process of the medication's forming foil, were identified as the source of the thiol reactant, showing that these stabilizers may play a part in the degradation of Montelukast and APIs with functionalities similar to those of Montelukast, which should be considered during development of medication. The isolation and analysis of these impurities was performed by HPLC and UV-vis spectroscopy. HRMS and NMR data were collected to characterize and determine the structures of these compounds.

Electronic Decay of Singly Charged Ground-State Ions by Charge Transfer via van der Waals Bonds.

We report the observation of the radiative decay of singly charged noble gas ground-state ions embedded in heterogeneous van der Waals clusters. Electron-photon coincidence spectroscopy and dispersed photon spectroscopy are applied to identify the radiative charge transfer from Kr atoms to a Ne_{2}^{+} dimer, which forms after single valence photoionization of Ne atoms at the surface of a NeKr cluster. This mechanism might be a fundamental decay process of ionized systems in an environment.

Season-Long Experimental Drought Alters Fungal Community Composition but Not Diversity in a Grassland Soil.

Using terrestrial model ecosystems (TMEs), we investigated how reduced moisture conditions impact soil fungal communities from a temperate grassland over the course of an entire season. Starting at about 65% of the soil's maximum water holding capacity (WHCmax), TME soils were adjusted to three moisture levels for 15 weeks: 70% WHCmax, approximating starting conditions, 50% WHCmax, and 30% WHCmax, representing reduced moisture conditions. Diversity and abundances of soil fungi at the start and at the end of the experiment were characterized using Illumina meta-barcoding. Community diversity at the end of the experiment did not differ between experimental moisture levels and was comparable to diversity measures from the field. However, fungal communities did change compositionally in both abundances and presence/absence of species. Analyzing class-level and individual contributions of fungi to these changes revealed that only a minor portion reacted significantly, indicating that most compositional change was likely driven by many consistent small-scale shifts in presence/absences or abundances. Together, our results show that prolonged reduction in soil moisture conditions will trigger compositional changes in soil fungal communities but not necessarily change overall diversity. We highlight the cumulative contribution of minor but consistent changes among community members, as opposed to significant responses of individual species. We also detected a strong general experimental effect on soil fungi that are moved from the field to experimental TMEs, suggesting the importance of acclimatization effects in these communities under laboratory conditions.

Circular Dichroism in Fluorescence Emission Following the C 1s→π* Excitation and Resonant Auger Decay of Carbon Monoxide.

Dichroism in angle-resolved spectra of circularly polarized fluorescence from freely-rotating CO molecules was studied experimentally and theoretically. For this purpose, carbon monoxide in the gas phase was exposed to circularly polarized soft X-ray synchrotron radiation. The photon energy was tuned across the C 1s→π* resonant excitation, which decayed via the participator Auger transition into the CO⁺ A ²Π state. The dichroic parameter ß1 of the subsequent CO⁺ (A ²Π → X ²Σ⁺) visible fluorescence was measured by photon-induced fluorescence spectroscopy. Present experimental results are explained with the ab initio electronic structure and dynamics calculations performed by the single center method. Our results confirm the possibility to perform partial wave analysis of the emitted photoelectrons in closed-shell molecules.

Activated CD4+ T cells enter the splenic T-cell zone and induce autoantibody-producing germinal centers through bystander activation.

CD4(+) T (helper) cells migrate in huge numbers through lymphoid organs. However, little is known about traffic routes and kinetics of CD4(+) T-cell subsets within different organ compartments. Such information is important because there are indications that CD4(+) T cells may influence the function of microenvironments depending on their developmental stage. Therefore, we investigated the migration of resting (naïve), activated, and recently activated (memory) CD4(+) T cells through the different compartments of the spleen. Resting and recently activated CD4(+) T cells were separated from thoracic duct lymph and activated CD4(+) T cells were generated in vitro by cross-linking the T-cell receptor and CD28. The present study shows that all three CD4(+) T-cell subsets selectively accumulate in the T-cell zone of the spleen. However, only activated T cells induce the formation of germinal centers (GCs) and autoantibodies in rats and mice. Our results suggest that in a two-step process they first activate B cells independent of the T-cell receptor repertoire and CD40 ligand (CD154) expression. The activated B cells then form GCs whereby CD154-dependent T-cell help is needed. Thus, activated T cells may contribute to the development of autoimmune diseases by activating autoreactive B cells in an Ag-independent manner.

Aggregometric assessment of clonidine's impact on the efficacy of dual platelet inhibition.

BACKGROUND: Clonidine is commonly used as a calmative and antihypertensive agent in perioperative care. Due to the drug's alpha-2-agonistic effects, it has recently been hypothesised that clonidine may affect platelet aggregability. The present investigation aimed to study the potential impact of clonidine on the efficacy of dual antiplatelet therapy. METHODS: In this prospective, observational, single-centre study, patients treated with dual antiplatelet therapy were screened for eligibility. The patients were enrolled in the study if ex vivo thrombin-induced (TRAPtest), arachidonic acid-induced (ASPItest) and adenosine diphosphate-induced (ADPtest) platelet aggregation, as measured using multiple electrode aggregometry (MEA; Multiplate, Roche AG, Grenzach, Germany), confirmed efficient dual platelet inhibition. Ex vivo induced platelet aggregation was assessed before (baseline) and 3 minutes after (T1) spiking blood samples with either 1 ng/mL clonidine or sodium chloride 0.9% (control group). RESULTS: In total, 34 patients were finally enrolled in the study. Compared with baseline, platelet aggregation in the ASPItest and ADPtest was significantly increased at T1 in both groups. Platelet aggregation in the TRAPtest remained unchanged between baseline and T1 in both groups. Comparing platelet aggregation at T1, we detected no differences between blood samples that were spiked with clonidine and blood samples that were spiked with sodium chloride 0.9% in the TRAPtest, the ASPItest, or the ADPtest. CONCLUSIONS: The results of this study indicate that clonidine does not affect platelet aggregability in patients treated with dual antiplatelet therapy. The findings of the study also indicate that ex vivo induced platelet aggregation in the ASPItest and ADPtest increases with the duration between blood drawing and MEA analyses.

Ras palmitoylation is necessary for N-Ras activation and signal propagation in growth factor signalling.

Ras GTPases undergo post-translational modifications that govern their subcellular trafficking and localization. In particular, palmitoylation of the Golgi tags N-Ras and H-Ras for exocytotic transport and residency at the PM (plasma membrane). Following depalmitoylation, PM-Ras redistributes to all subcellular membranes causing an accumulation of palmitate-free Ras at endomembranes, including the Golgi and endoplasmic reticulum. Palmitoylation is unanimously regarded as a critical modification at the crossroads of Ras activity and trafficking control, but its precise relevance to native wild-type Ras function in growth factor signalling is unknown. We show in the present study by use of palmitoylation-deficient N-Ras mutants and via the analysis of palmitate content of agonist-activated GTP-loaded N-Ras that only palmitoylated N-Ras becomes activated by agonists. In line with an essential role of palmitoylation in Ras activation, dominant-negative RasS17N loses its blocking potency if rendered devoid of palmitoylation. Live-cell Ras-GTP imaging shows that N-Ras activation proceeds only at the PM, consistent with activated N-Ras-GTP being palmitoylated. Finally, palmitoylation-deficient N-Ras does not sustain EGF (epidermal growth factor) or serum-elicited mitogenic signalling, confirming that palmitoylation is essential for signal transduction by N-Ras. These findings document that N-Ras activation proceeds at the PM and suggest that depalmitoylation, by removing Ras from the PM, may contribute to the shutdown of Ras signalling.

Observation of a single protein by ultrafast X-ray diffraction.

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

Identification of determinants required for agonistic and inverse agonistic ligand properties at the ADP receptor P2Y12.

The ADP receptor P2Y(12) belongs to the superfamily of G protein-coupled receptors (GPCRs), and its activation triggers platelet aggregation. Therefore, potent antagonists, such as clopidogrel, are of high clinical relevance in prophylaxis and treatment of thromboembolic events. P2Y(12) displays an elevated basal activity in vitro, and as such, inverse agonists may be therapeutically beneficial compared with antagonists. Only a few inverse agonists of P2Y(12) have been described. To expand this limited chemical space and improve understanding of structural determinants of inverse agonist-receptor interaction, this study screened a purine compound library for lead structures using wild-type (WT) human P2Y(12) and 28 constitutively active mutants. Results showed that ATP and ATP derivatives are agonists at P2Y(12). The potency at P2Y(12) was 2-(methylthio)-ADP > 2-(methylthio)-ATP > ADP > ATP. Determinants required for agonistic ligand activity were identified. Molecular docking studies revealed a binding pocket for the ATP derivatives that is bordered by transmembrane helices 3, 5, 6, and 7 in human P2Y(12,) with Y(105), E(188), R(256), Y(259), and K(280) playing a particularly important role in ligand interaction. N-Methyl-anthraniloyl modification at the 3'-OH of the 2'-deoxyribose leads to ligands (mant-deoxy-ATP [dATP], mant-deoxy-ADP) with inverse agonist activity. Inverse agonist activity of mant-dATP was found at the WT human P2Y(12) and half of the constitutive active P2Y(12) mutants. This study showed that, in addition to ADP and ATP, other ATP derivatives are not only ligands of P2Y(12) but also agonists. Modification of the ribose within ATP can result in inverse activity of ATP-derived ligands.