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We present a scanning tunneling microscope operating in a 3He cryostat at a base temperature of 0.4 K, suitable for electron spin resonance (ESR) [S. Baumann, W. Paul, T. Choi, C. P. Lutz, A. Ardavan, and A. J. Heinrich, Science 350, 417 (2015)], quantum stochastic resonance (QSR) [M. Hänze, G. McMurtrie, S. Baumann, L. Malavolti, S. N. Coppersmith, and S. Loth, Sci. Adv. 7, eabg2616 (2021)], and electric pump–probe experiments. We achieve excellent signal transmission of −2 to −3 dB between 100 kHz and 100 MHz, −23 dB at 10 GHz, −35 to −40 dB between 25 and 35 GHz, and −45 dB at 40 GHz, using a combination of normal conducting and superconducting semi-rigid, as well as flexible RF cables. SMK type 2.92 mm and mini-SMP connectors are used to minimize reflections and losses over the entire frequency range. The ESR capability of our instrument is demonstrated on possibly hydrogenated titanium atoms adsorbed on two and three monolayers of MgO on Ag(100) at 0.4 and at 4.2 K. We further show QSR measurements for Fe/MgO/Ag(100) and compare the driven relaxation time with the intrinsic energy relaxation time T1 reported for that system [W. Paul, K. Yang, S. Baumann, N. Romming, T. Choi, C. P. Lutz, and A. J. Heinrich, Nat. Phys. 13, 403 (2017)] as a function of magnetic field and tunnel current. [ABSTRACT FROM AUTHOR]

To fully exploit ultra-short X-ray pulse durations routinely available at X-ray free-electron lasers to follow out-of-equilibrium dynamics, inherent arrival time fluctuations of the X-ray pulse with an external perturbing laser pulse need to be measured. In this work, two methods of arrival time measurement were compared to measure the arrival time jitter of hard X-ray pulses. The methods were photoelectron streaking by a THz field and a transient refractive index change of a semiconductor. The methods were validated by shot-to-shot correction of a pump-probe transient reflectivity measurement. An ultimate shot-to-shot full width at half-maximum error between the devices of 19.2 ± 0.1 fs was measured. [ABSTRACT FROM AUTHOR]

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In the last 20 years, the technique of resonant inelastic X‐ray scattering (RIXS) has been progressing at a high pace thanks to the concomitant development of instrumentation, synchrotron technology, and the theoretical description of the related fundamental process. In this article, we describe some recent aspects related to the fast progress of the RIXS technique and dedicate this article to the memory of Prof. Jean‐Claude Dousse, from the University of Fribourg (Switzerland). We conclude this article by describing early experiments using time‐resolved RIXS at X‐ray free electron lasers and give perspectives on high‐resolution and spatially‐resolved RIXS. [ABSTRACT FROM AUTHOR]

Gas attenuators are important devices providing accurate variation of photon intensity for soft X-ray beamlines. In the SwissFEL ATHOS beamline front-end the space is very limited and an innovative approach has been taken to provide attenuation of three orders of magnitude up to an energy of 1200 eV. Additive manufacturing of a differential pumping system vacuum manifold allowed a triple pumping stage to be realized in a space of less than half a meter. Measurements have shown that the response of the device is as expected from theoretical calculations. [ABSTRACT FROM AUTHOR]

The evolutionary origin of vertebrates included innovations in sensory processing associated with the acquisition of a predatory lifestyle1. Vertebrates perceive external stimuli through sensory systems serviced by cranial sensory ganglia, whose neurons arise predominantly from cranial placodes; however, the understanding of the evolutionary origin of placodes and cranial sensory ganglia is hampered by the anatomical differences between living lineages and the difficulty in assigning homology between cell types and structures. Here we show that the homeobox transcription factor Hmx is a constitutive component of vertebrate sensory ganglion development and that in the tunicate Ciona intestinalis, Hmx is necessary and sufficient to drive the differentiation programme of bipolar tail neurons, cells previously thought to be homologues of neural crest2,3. Using Ciona and lamprey transgenesis, we demonstrate that a unique, tandemly duplicated enhancer pair regulated Hmx expression in the stem-vertebrate lineage. We also show notably robust vertebrate Hmx enhancer function in Ciona, demonstrating that deep conservation of the upstream regulatory network spans the evolutionary origin of vertebrates. These experiments demonstrate regulatory and functional conservation between Ciona and vertebrate Hmx, and point to bipolar tail neurons as homologues of cranial sensory ganglia.In the tunicate Ciona intestinalis, the homeobox transcription factor Hmx drives differentiation of bipolar tail neurons, indicating conserved regulation and function, and homology with cranial sensory ganglia in higher vertebrates. [ABSTRACT FROM AUTHOR]

The performance and parameters of the online photon single‐shot spectrometer (PSSS) at the Aramis beamline of the SwissFEL free‐electron laser are presented. The device operates between the photon energies 4 and 13 keV and uses diamond transmission gratings and bent Si crystals for spectral measurements on the first diffraction order of the beam. The device has an energy window of 0.7% of the median photon energy of the free‐electron laser pulses and a spectral resolution (full width at half‐maximum) ΔE/E on the order of 10−5. The device was characterized by comparing its performance with reference data from synchrotron sources, and a parametric study investigated other effects that could affect the reliability of the spectral information. [ABSTRACT FROM AUTHOR]

Employing X‐ray magnetic circular dichroism (XMCD), angle‐resolved photoemission spectroscopy (ARPES), and momentum‐resolved density fluctuation (MRDF) theory, the magnetic and electronic properties of ultrathin NdNiO3 (NNO) film in proximity to ferromagnetic (FM) La0.67Sr0.33MnO3 (LSMO) layer are investigated. The experimental data shows the direct magnetic coupling between the nickelate film and the manganite layer which causes an unusual ferromagnetic (FM) phase in NNO. Moreover, it is shown the metal–insulator transition in the NNO layer, identified by an abrupt suppression of ARPES spectral weight near the Fermi level (EF), is absent. This observation suggests that the insulating AFM ground state is quenched in proximity to the FM layer. Combining the experimental data (XMCD and AREPS) with the momentum‐resolved density fluctuation calculation (MRDF) reveals a direct link between the MIT and the magnetic orders in NNO systems. This work demonstrates that the proximity layer order can be broadly used to modify physical properties and enrich the phase diagram of RENiO3 (RE = rare‐earth element). [ABSTRACT FROM AUTHOR]

Endometrioid endometrial carcinoma is a cancer type with generally excellent prognosis when diagnosed at an early stage, but there is a subset of patients with relapsing disease in spite of early diagnosis and surgical treatment. There is a need to find prognostic markers to identify these patients with increased risk of relapse. Depth of myometrial invasion, histological grade, and presence of lymphovascular invasion are known risk factors. DNA content (ploidy) and proliferation measured as S-phase fraction (SPF) have been discussed as prognostic markers but need additional evaluation. We evaluated relapse-free survival (RFS) with respect to ploidy and SPF, which was analyzed by flow cytometry on fresh tumor tissue, in a cohort of 1001 women treated for stage I endometrioid endometrial carcinoma in northern Sweden during the period of 1993–2010, with a median follow up time of 12.0 years. Data were obtained from historical records. In simple analysis, both aneuploidy and high SPF were associated to increased risk of relapse with hazard ratios (HR) 2.37 (95% CI 1.52–3.70) and 1.94 (95% CI 1.24–3.02), respectively. Our data also confirmed stage, tumor grade, and ploidy as independent prognostic markers in an age adjusted cox regression multivariable analysis but we did not find SPF to contribute to prognosis. However, the combination of aneuploidy and high SPF identified a group of patients with increased risk of relapse, HR 2.02 (95% CI 1.19–3.44). In this study, which is the largest study of ploidy and SPF in stage I endometrioid endometrial carcinoma using fresh frozen tissue, aneuploidy was shown to be an independent prognostic marker. Furthermore, the combination of aneuploidy and high SPF could be used to identify patients with increased risk of relapse. [ABSTRACT FROM AUTHOR]

Understanding the vulnerability of trees to drought-induced mortality is key to predicting the fate of forests in a future climate with more frequent and intense droughts, although the underlying mechanisms are difficult to study in adult trees. Here, we explored the dynamic changes of water relations and limits of hydraulic function in dying adults of Norway spruce (Picea abies L.) during the progression of the record-breaking 2018 Central European drought. In trees on the trajectory to drought-induced mortality, we observed rapid, nonlinear declines of xylem pressure that commenced at the early onset of xylem cavitation and caused a complete loss of xylem hydraulic conductance within a very short time. We also observed severe depletions of nonstructural carbohydrates, though carbon starvation could be ruled out as the cause of the observed tree death, as both dying and surviving trees showed these metabolic limitations. Our observations provide striking field-based evidence for fast dehydration and hydraulic collapse as the cause of drought-induced mortality in adult Norway spruce. The nonlinear decline of tree water relations suggests that considering the temporal dynamics of dehydration is critical for predicting tree death. The collapse of the hydraulic system within a short time demonstrates that trees can rapidly be pushed out of the zone of hydraulic safety during the progression of a severe drought. In summary, our findings point toward a higher mortality risk for Norway spruce than previously assumed, which is in line with current reports of unprecedented levels of droughtinduced mortality in this major European tree species. [ABSTRACT FROM AUTHOR]

One of the main challenges in ultrafast material science is to trigger phase transitions with short pulses of light. Here we show how strain waves, launched by electronic and structural precursor phenomena, determine a coherent macroscopic transformation pathway for the semiconducting-to-metal transition in bistable Ti3O5 nanocrystals. Employing femtosecond powder X-ray diffraction, we measure the lattice deformation in the phase transition as a function of time. We monitor the early intra-cell distortion around the light absorbing metal dimer and the long range deformations governed by acoustic waves propagating from the laser-exposed Ti3O5 surface. We developed a simplified elastic model demonstrating that picosecond switching in nanocrystals happens concomitantly with the propagating acoustic wavefront, several decades faster than thermal processes governed by heat diffusion. Ultrafast control of materials draws interest. Here, the authors extend X-ray powder diffraction to the femtosecond timescale to follow the photo-induced semiconductor to metal transition in titanium pentaoxide, observing a phase front that moves at the speed of sound and proposing a little explored mechanism. [ABSTRACT FROM AUTHOR]

Disease recurrence in surgically treated lung adenocarcinoma (AC) remains high. New approaches for risk stratification beyond tumor stage are needed. Gene expression‐based AC subtypes such as the Cancer Genome Atlas Network (TCGA) terminal‐respiratory unit (TRU), proximal‐inflammatory (PI) and proximal‐proliferative (PP) subtypes have been associated with prognosis, but show methodological limitations for robust clinical use. We aimed to derive a platform independent single sample predictor (SSP) for molecular subtype assignment and risk stratification that could function in a clinical setting. Two‐class (TRU/nonTRU=SSP2) and three‐class (TRU/PP/PI=SSP3) SSPs using the AIMS algorithm were trained in 1655 ACs (n = 9659 genes) from public repositories vs TCGA centroid subtypes. Validation and survival analysis were performed in 977 patients using overall survival (OS) and distant metastasis‐free survival (DMFS) as endpoints. In the validation cohort, SSP2 and SSP3 showed accuracies of 0.85 and 0.81, respectively. SSPs captured relevant biology previously associated with the TCGA subtypes and were associated with prognosis. In survival analysis, OS and DMFS for cases discordantly classified between TCGA and SSP2 favored the SSP2 classification. In resected Stage I patients, SSP2 identified TRU‐cases with better OS (hazard ratio [HR] = 0.30; 95% confidence interval [CI] = 0.18‐0.49) and DMFS (TRU HR = 0.52; 95% CI = 0.33‐0.83) independent of age, Stage IA/IB and gender. SSP2 was transformed into a NanoString nCounter assay and tested in 44 Stage I patients using RNA from formalin‐fixed tissue, providing prognostic stratification (relapse‐free interval, HR = 3.2; 95% CI = 1.2‐8.8). In conclusion, gene expression‐based SSPs can provide molecular subtype and independent prognostic information in early‐stage lung ACs. SSPs may overcome critical limitations in the applicability of gene signatures in lung cancer. What's new? New tools are needed in order to improve risk stratification and therapy selection in early‐stage lung adenocarcinoma. Inherent differences in gene expression between adenocarcinoma subtypes could facilitate the development of such tools. The authors of this study derived platform‐independent, single‐sample predictors (SSP) of adenocarcinoma subtypes, based on gene expression. Derived SSPs successfully provided prognostic information in surgically treated stage I lung adenocarcinoma patients. The single‐sample classifier was readily translated into assays applicable to archival tissue, indicating clinical utility. The findings highlight the clinical relevance of transcriptional signatures and gene expression predictors in lung adenocarcinoma, warranting their further investigation and development. [ABSTRACT FROM AUTHOR]

Resonant core spectroscopies are applied to a study of the excited electron transfer dynamics on a low-femtosecond time scale in systems of aromatic molecules (isonicotinic acid and bi-isonicotinic acid) adsorbed on a rutile TiO[sub 2](110) semiconductor surface. Depending on which adsorbate state is excited, the electron is either localized on the adsorbate in an excitonic effect, or delocalizes rapidly into the substrate in less than 5 fs (3 fs) for isonicotinic acid (bi-isonicotinic acid). The results are obtained by the application of a variant of resonant photoemission spectroscopy. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The transmission of the optical components of the Bernina branch of the Aramis beamline at SwissFEL has been measured with an X‐ray gas monitor from DESY and compared with a PSI gas detector upstream of the optical components. The transmission efficiencies of the Mo, Si and SiC mirror coatings of the Aramis beamline and the various other in‐beam components were evaluated and compared with theoretical calculations, showing an agreement of 6% or better in all cases. The experiment has also shown the efficacy of the high‐harmonic rejection mirrors at the Bernina branch of the Aramis beamline at SwissFEL, and characterized the transmission efficiency of the on‐line spectrometer in the Aramis beamline. The theoretical transmission of the mirror coatings match the experimental data to within 7%. The accuracy of these measurements was checked against a radiative bolometer from a Japanese collaboration and found to agree to a level of 4% or better. Further comparisons with a diamond detector from a US‐based inter‐institute collaboration demonstrated a good agreement for the attenuator settings of the beamline. [ABSTRACT FROM AUTHOR]

Here a direct comparison is made between various X‐ray wavefront sensing methods with application to optics alignment and focus characterization at X‐ray free‐electron lasers (XFELs). Focus optimization at XFEL beamlines presents unique challenges due to high peak powers as well as beam pointing instability, meaning that techniques capable of single‐shot measurement and that probe the wavefront at an out‐of‐focus location are desirable. The techniques chosen for the comparison include single‐phase‐grating Talbot interferometry (shearing interferometry), dual‐grating Talbot interferometry (moiré deflectometry) and speckle tracking. All three methods were implemented during a single beam time at the Linac Coherent Light Source, at the X‐ray Pump Probe beamline, in order to make a direct comparison. Each method was used to characterize the wavefront resulting from a stack of beryllium compound refractive lenses followed by a corrective phase plate. In addition, difference wavefront measurements with and without the phase plate agreed with its design to within λ/20, which enabled a direct quantitative comparison between methods. Finally, a path toward automated alignment at XFEL beamlines using a wavefront sensor to close the loop is presented. [ABSTRACT FROM AUTHOR]

Several studies have documented the importance of optimal work situation and the general well-being of early-career researchers (ECRs) for enhancing the academic performance of universities. Yet, most studies focused on specific categories of ECRs, or on specific academic disciplines as well as on specific outcomes. With this study, we recognize the need for a broader sample encompassing different categories of ECRs across academic disciplines. In a national survey of Swedish universities, the National Junior Faculty of Sweden (NJF) collected data from ECRs in order to study the influence of work situation and well-being on perceived scientific environment. We observed that work situation and well-being are interdependent and jointly influence each other in shaping the conditions for ideal scientific environment. Importantly, we employ structural equation model (SEM) analysis to account for the endogenous relationship between work situation and personal well-being in predicting perceived scientific environment. Results from SEM indicate that support from the university, work time management, job clarity, contract length and quality of life satisfaction were related to the perceived possibility of conducting the best science. Our research also highlighted individual differences across demographic factors and contract length in the perceived work situation and the possibility of conducting the best science. [ABSTRACT FROM AUTHOR]

The Bernina instrument at the SwissFEL Aramis hard X‐ray free‐electron laser is designed for studying ultrafast phenomena in condensed matter and material science. Ultrashort pulses from an optical laser system covering a large wavelength range can be used to generate specific non‐equilibrium states, whose subsequent temporal evolution can be probed by selective X‐ray scattering techniques in the range 2–12 keV. For that purpose, the X‐ray beamline is equipped with optical elements which tailor the X‐ray beam size and energy, as well as with pulse‐to‐pulse diagnostics that monitor the X‐ray pulse intensity, position, as well as its spectral and temporal properties. The experiments can be performed using multiple interchangeable endstations differing in specialization, diffractometer and X‐ray analyser configuration and load capacity for specialized sample environment. After testing the instrument in a series of pilot experiments in 2018, regular user operation begins in 2019. [ABSTRACT FROM AUTHOR]

Presents information from an experiment which studied the texture control of PbTiO3 and Pb(Zr,Ti)O3 thin films with TiO2 seeding. Information on the standard substrate ; Details on the experiment; Results from the experiment.

Studies the adsorption of bi-isonicotinic acid on rutile TiO[sub 2](110). Atomic scale understanding of the bonding of the ligand to rutile TiO[sub 2](110); Results of high resolution x-ray photoelectron spectroscopy and near edge x-ray absorption fine structure.

Electron spin resonance with a scanning tunneling microscope (ESR-STM) combines the high energy resolution of spin resonance spectroscopy with the atomic scale control and spatial resolution of STM. Here we describe the upgrade of a helium-3 STM with a 2D vector-field magnet (Bz = 8.0 T, Bx = 0.8 T) to an ESR-STM. The system is capable of delivering radio frequency (RF) power to the tunnel junction at frequencies up to 30 GHz. We demonstrate magnetic field-sweep ESR for the model system TiH/MgO/Ag(100) and find a magnetic moment of (1.004 ± 0.001) μB. Our upgrade enables to toggle between a DC mode, where the STM is operated with the regular control electronics, and an ultrafast-pulsed mode that uses an arbitrary waveform generator for pump-probe spectroscopy or reading of spin-states. Both modes allow for simultaneous radiofrequency excitation, which we add via a resistive pick-off tee to the bias voltage path. The RF cabling from room temperature to the 350 mK stage has an average attenuation of 18 dB between 5 and 25 GHz. The cable segment between the 350 mK stage and the STM tip presently attenuates an additional 3 4 − 3 + 5 dB from 10 to 26 GHz and 3 8 − 2 + 3 dB between 20 and 30 GHz. We discuss our transmission losses and indicate ways to reduce this attenuation. We finally demonstrate how to synchronize the arrival times of RF and DC pulses coming from different paths to the STM junction, a prerequisite for future pulsed ESR experiments. [ABSTRACT FROM AUTHOR]

Spin-polarized scanning tunneling microscopy (SP-STM) measures magnetoresistance with atomic resolution. While various methods for achieving SP probes have been developed, each is limited with respect to fabrication, performance, and operating conditions. In this study, we present the fabrication and use of SP-STM tips made from commercially available antiferromagnetic Mn88Ni12 foils. The tips are intrinsically SP, which is attractive for exploring magnetic phenomena in the zero field limit. The tip material is relatively ductile, is straightforward to etch, and has a Néel temperature exceeding 300 K. We benchmark the topographic and spectroscopic performance of our tips and demonstrate their spin sensitivity by measuring the two-state switching of holmium single atom magnets on MgO/Ag(100). [ABSTRACT FROM AUTHOR]

The SwissFEL Aramis beamline, covering the photon energies between 1.77 keV and 12.7 keV, features a suite of online photon diagnostics tools to help both users and FEL operators in analysing data and optimizing experimental and beamline performance. Scientists will be able to obtain information about the flux, spectrum, position, pulse length, and arrival time jitter versus the experimental laser for every photon pulse, with further information about beam shape and size available through the use of destructive screens. This manuscript is an overview of the diagnostics tools available at SwissFEL and presents their design, working principles and capabilities. It also features new developments like the first implementation of a THz‐streaking based temporal diagnostics for a hard X‐ray FEL, capable of measuring pulse lengths to 5 fs r.m.s. or better. [ABSTRACT FROM AUTHOR]

The transcription factor Sox2 is necessary to maintain pluripotency of embryonic stem cells, and to regulate neural development. Neurogenesis in the vertebrate olfactory epithelium persists from embryonic stages through adulthood. The role Sox2 plays for the development of the olfactory epithelium and neurogenesis within has, however, not been determined. Here, by analysing Sox2 conditional knockout mouse embryos and chick embryos deprived of Sox2 in the olfactory epithelium using CRISPR-Cas9, we show that Sox2 activity is crucial for the induction of the neural progenitor gene Hes5 and for subsequent differentiation of the neuronal lineage. Our results also suggest that Sox2 activity promotes the neurogenic domain in the nasal epithelium by restricting Bmp4 expression. The Sox2-deficient olfactory epithelium displays diminished cell cycle progression and proliferation, a dramatic increase in apoptosis and finally olfactory pit atrophy. Moreover, chromatin immunoprecipitation data show that Sox2 directly binds to the Hes5 promoter in both the PNS and CNS. Taken together, our results indicate that Sox2 is essential to establish, maintain and expand the neuronal progenitor pool by suppressing Bmp4 and upregulating Hes5 expression. [ABSTRACT FROM AUTHOR]

One of the remaining challenges for accurate photon diagnostics at X-ray freeelectron lasers (FELs) is the shot-to-shot, non-destructive, high-resolution characterization of the FEL pulse spectrum at photon energies between 2 keV and 4 keV, the so-called tender X-ray range. Here, a spectrometer setup is reported, based on the von Hamos geometry and using elastic scattering as a fingerprint of the FEL-generated spectrum. It is capable of pulse-to-pulse measurement of the spectrum with an energy resolution (ΔE/E) of 10-4, within a bandwidth of 2%. The Tender X-ray Single-Shot Spectrometer (TXS) will grant to experimental scientists the freedom to measure the spectrum in a singleshot measurement, keeping the transmitted beam undisturbed. It will enable single-shot reconstructions for easier and faster data analysis. [ABSTRACT FROM AUTHOR]

We present the main specifications of the newly constructed Swiss Free Electron Laser, SwissFEL, and explore its potential impact on ultrafast science. In light of recent achievements at current X-ray free electron lasers, we discuss the potential territory for new scientific breakthroughs offered by SwissFEL in Chemistry, Biology, and Materials Science, as well as nonlinear X-ray science. [ABSTRACT FROM AUTHOR]

COE genes encode transcription factors that have been found in all metazoans examined to date. They possess a distinctive domain structure that includes a DNA-binding domain (DBD), an IPT/TIG domain and a helix-loop-helix (HLH) domain. An intriguing feature of the COE HLH domain is that in jawed vertebrates it is composed of three helices, compared to two in invertebrates. We report the isolation and expression of two COE genes from the brook lamprey Lampetra planeri and compare these to COE genes from the lampreys Lethenteron japonicum and Petromyzon marinus. Molecular phylogenetic analyses do not resolve the relationship of lamprey COE genes to jawed vertebrate paralogues, though synteny mapping shows that they all derive from duplication of a common ancestral genomic region. All lamprey genes encode conserved DBD, IPT/TIG and HLH domains; however, the HLH domain of lamprey COE-A genes encodes only two helices while COE-B encodes three helices. We also identified COE-B splice variants encoding either two or three helices in the HLH domain, along with other COE-A and COE-B splice variants affecting the DBD and C-terminal transactivation regions. In situ hybridisation revealed expression in the lamprey nervous system including the brain, spinal cord and cranial sensory ganglia. We also detected expression of both genes in mesenchyme in the pharyngeal arches and underlying the notochord. This allows us to establish the primitive vertebrate expression pattern for COE genes and compare this to that of invertebrate chordates and other animals to develop a model for COE gene evolution in chordates. [ABSTRACT FROM AUTHOR]

For the investigation of processes happening on the time scale of the motion of bound electrons, well-controlled X-ray pulses with durations in the few-femtosecond and even sub-femtosecond range are a necessary prerequisite. Novel free-electron lasers sources provide these ultrashort, high-brightness X-ray pulses, but their unique aspects open up concomitant challenges for their characterization on a suitable time scale. In this review paper we describe progress and results of recent work on ultrafast pulse characterization at soft and hard X-ray free-electron lasers. We report on different approaches to laser-assisted time-domain measurements, with specific focus on single-shot characterization of ultrashort X-ray pulses from self-amplified spontaneous emission-based and seeded free-electron lasers. The method relying on the sideband measurement of X-ray electron ionization in the presence of a dressing optical laser field is described first. When the X-ray pulse duration is shorter than half the oscillation period of the streaking field, few-femtosecond characterization becomes feasible via linear streaking spectroscopy. Finally, using terahertz fields alleviates the issue of arrival time jitter between streaking laser and X-ray pulse, but compromises the achievable temporal resolution. Possible solutions to these remaining challenges for single-shot, full time-energy characterization of X-ray free-electron laser pulses are proposed in the outlook at the end of the review. [ABSTRACT FROM AUTHOR]

The Photo-Emission and Atomic Resolution Laboratory (PEARL) is a new soft X-ray beamline and surface science laboratory at the Swiss Light Source. PEARL is dedicated to the structural characterization of local bonding geometry at surfaces and interfaces of novel materials, in particular of molecular adsorbates, nanostructured surfaces, and surfaces of complex materials. The main experimental techniques are soft X-ray photoelectron spectroscopy, photoelectron diffraction, and scanning tunneling microscopy (STM). Photoelectron diffraction in angle-scanned mode measures bonding angles of atoms near the emitter atom, and thus allows the orientation of small molecules on a substrate to be determined. In energy scanned mode it measures the distance between the emitter and neighboring atoms; for example, between adsorbate and substrate. STM provides complementary, real-space information, and is particularly useful for comparing the sample quality with reference measurements. In this article, the key features and measured performance data of the beamline and the experimental station are presented. As scientific examples, the adsorbate-substrate distance in hexagonal boron nitride on Ni(111), surface quantum well states in a metal-organic network of dicyano-anthracene on Cu(111), and circular dichroism in the photoelectron diffraction of Cu(111) are discussed. [ABSTRACT FROM AUTHOR]

In many cultural landscapes, the abandonment of traditional grazing leads to encroachment of pastures by woody plants, which reduces habitat heterogeneity and impacts biodiversity typical of semi-open habitats. We developed a framework of mutually interacting spatial models to locate areas where shrub encroachment in Alpine treeline ecosystems deteriorates vulnerable species’ habitat, using black grouse Tetrao tetrix (L.) in the Swiss Alps as a study model. Combining field observations and remote-sensing information we 1) identified and located the six predominant treeline vegetation types; 2) modelled current black grouse breeding habitat as a function thereof so as to derive optimal habitat profiles; 3) simulated from these profiles the theoretical spatial extension of breeding habitat when assuming optimal vegetation conditions throughout; and used the discrepancy between (2) and (3) to 4) locate major aggregations of homogeneous shrub vegetation in otherwise suitable breeding habitat as priority sites for habitat restoration. All six vegetation types (alpine pasture, coniferous forest, Alnus viridis (Chaix), Rhododendron-dominated, Juniperus-dominated and mixed heathland) were predicted with high accuracy (AUC >0.9). Breeding black grouse preferred a heterogeneous mosaic of vegetation types, with none exceeding 50% cover. While 15% of the timberline belt currently offered suitable breeding habitat, twice that fraction (29%) would potentially be suitable when assuming optimal shrub and ground vegetation conditions throughout the study area. Yet, only 10% of this difference was attributed to habitat deterioration by shrub-encroachment of dense heathland (all types 5.2%) and Alnus viridis (4.8%). The presented method provides both a general, large-scale assessment of areas covered by dense shrub vegetation as well as specific target values and priority areas for habitat restoration related to a selected target organism. This facilitates optimizing the spatial allocation of management resources in geographic regions where shrub encroachment represents a major biodiversity conservation issue. [ABSTRACT FROM AUTHOR]

Background: The cranial sensory ganglia represent populations of neurons with distinct functions, or sensory modalities. The production of individual ganglia from distinct neurogenic placodes with different developmental pathways provides a powerful model to investigate the acquisition of specific sensory modalities. To date there is a limited range of gene markers available to examine the molecular pathways underlying this process. Results: Transcriptional profiles were generated for populations of differentiated neurons purified from distinct cranial sensory ganglia using microdissection in embryonic chicken followed by FAC-sorting and RNAseq. Whole transcriptome analysis confirmed the division into somato- versus viscerosensory neurons, with additional evidence for subdivision of the somatic class into general and special somatosensory neurons. Cross-comparison of distinct ganglia transcriptomes identified a total of 134 markers, 113 of which are novel, which can be used to distinguish trigeminal, vestibulo-acoustic and epibranchial neuronal populations. In situ hybridisation analysis provided validation for 20/26 tested markers, and showed related expression in the target region of the hindbrain in many cases. Conclusions: One hundred thirty-four high-confidence markers have been identified for placode-derived cranial sensory ganglia which can now be used to address the acquisition of specific cranial sensory modalities. [ABSTRACT FROM AUTHOR]

Weight regain after caloric restriction results in accelerated fat storage in adipose tissue. This catch-up fat phenomenon is postulated to result partly from suppressed skeletal muscle thermogenesis, but the underlying mechanisms are elusive. We investigated whether the reduced rate of skeletal muscle contraction-relaxation cycle that occurs after caloric restriction persists during weight recovery and could contribute to catch-up fat. Using a rat model of semistarvation-refeeding, in which fat recovery is driven by suppressed thermogenesis, we show that contraction and relaxation of leg muscles are slower after both semistarvation and refeeding. These effects are associated with (i) higher expression of muscle deiodinase type 3 (DIO3), which inactivates tri-iodothyronine (T3), and lower expression of T3-activating enzyme, deiodinase type 2 (DIO2), (ii) slower net formation of T3 from its T4 precursor in muscles, and (iii) accumulation of slow fibers at the expense of fast fibers. These semistarvation-induced changes persisted during recovery and correlated with impaired expression of transcription factors involved in slow-twitch muscle development. We conclude that diminished muscle thermogenesis following caloric restriction results from reduced muscle T3 levels, alteration in muscle-specific transcription factors, and fast-to-slow fiber shift causing slower contractility. These energy-sparing effects persist during weight recovery and contribute to catch-up fat. [ABSTRACT FROM AUTHOR]

Conclusions: Neurogenins are required for the specification of neuronal precursors and regulate the expression of basic Helix-Loop-Helix genes involved in neuronal differentiation. Jawed vertebrates possess three Neurogenin paralogy groups and their combined expression covers the entire nervous system, apart from the autonomic nervous system. Results: Here we report the isolation of two Neurogenin genes, LpNgnA and LpNgnB, from the lamprey Lampetra planeri. Phylogenetic analyses show both genes have orthologues in other lamprey species and in a hagfish. Neither gene shows evidence of orthology to specific jawed vertebrate Neurogenin paralogues. LpNgnA is expressed in the ventricular zone of regions of the brain and spinal cord, with expression in the brain demarcating brain sub-compartments including the pallium, tegmentum, tectum, and dorsal thalamus. In the peripheral nervous system, LpNgnA is expressed in cranial sensory placodes and their derivatives, and in the dorsal root ganglia. LpNgnB is expressed transiently in placodal head ectoderm and throughout the central nervous system in early development, and in a small population cells that form part of the macula. Conclusions: Combined, LpNgnA and LpNgnB were detected in most cell populations marked by Neurogenin gene expression in jawed vertebrates, with the exception of the cerebellum, retina and the non-neural expression sites. Developmental Dynamics 244:1096-1108, 2015. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Weight regain after caloric restriction results in accelerated fat storage in adipose tissue. This catch-up fat phenomenon is postulated to result partly from suppressed skeletal muscle thermogenesis, but the underlying mechanisms are elusive. We investigated whether the reduced rate of skeletal muscle contraction-relaxation cycle that occurs after caloric restriction persists during weight recovery and could contribute to catch-up fat. Using a rat model of semistarvation-refeeding, in which fat recovery is driven by suppressed thermogenesis, we show that contraction and relaxation of leg muscles are slower after both semistarvation and refeeding. These effects are associated with (i) higher expression of muscle deiodinase type 3 (DIO3) which inactivates tri-iodothyronine (T3), and lower expression of T3-activating enzyme, deiodinase type 2 (DIO2), (ii) slower net formation of T3 from its T4 precursor in muscles, and (iii) accumulation of slow fibers at the expense of fast fibers. These semistarvation-induced changes persisted during recovery and correlated with impaired expression of transcription factors involved in slow-twitch muscle development. We conclude that diminished muscle thermogenesis following caloric restriction results from reduced muscle T3 levels, alteration in muscle-specific transcription factors, and fast-to-slow fiber shift causing slower contractility. Energy-sparing effects persist during weight recovery and likely contribute to catch-up fat. [ABSTRACT FROM AUTHOR]

Anthropogenic disturbance of wildlife is of growing conservation concern, but we lack comprehensive approaches of its multiple negative effects. We investigated several effects of disturbance by winter outdoor sports on free-ranging alpine Black Grouse by simultaneously measuring their physiological and behavioral responses. We experimentally flushed radio-tagged Black Grouse from their snow burrows, once a day, during several successive days, and quantified their stress hormone levels (corticosterone metabolites in feces [FCM] collected from individual snow burrows). We also measured feeding time allocation (activity budgets reconstructed from radio-emitted signals) in response to anthropogenic disturbance. Finally, we estimated the related extra energy expenditure that may be incurred: based on activity budgets, energy expenditure was modeled from measures of metabolism obtained from captive birds subjected to different ambient temperatures. The pattern of FCM excretion indicated the existence of a funneling effect as predicted by the allostatic theory of stress: initial stress hormone concentrations showed a wide inter-individual variation, which decreased during experimental flushing. Individuals with low initial pre-flushing FCM values augmented their concentration, while individuals with high initial FCM values lowered it. Experimental disturbance resulted in an extension of feeding duration during the following evening foraging bout, confirming the prediction that Black Grouse must compensate for the extra energy expenditure elicited by human disturbance. Birds with low initial baseline FCM concentrations were those that spent more time foraging. These FCM excretion and foraging patterns suggest that birds with high initial FCM concentrations might have been experiencing a situation of allostatic overload. The energetic model provides quantitative estimates of extra energy expenditure. A longer exposure to ambient temperatures outside the shelter of snow burrows, following disturbance, could increase the daily energy expenditure by .10%, depending principally on ambient temperature and duration of exposure. This study confirms the predictions of allostatic theory and, to the best of our knowledge, constitutes the first demonstration of a funneling effect. It further establishes that winter recreation activities incur costly allostatic behavioral and energetic adjustments, which call for the creation of winter refuge areas together with the implementation of visitor-steering measures for sensitive wildlife. [ABSTRACT FROM AUTHOR]

The eye has served as a classical model to study cell specification and tissue induction for over a century. Nevertheless, the molecular mechanisms that regulate the induction and maintenance of eye-field cells, and the specification of neural retina cells are poorly understood. Moreover, within the developing anterior forebrain, how prospective eye and telencephalic cells are differentially specified is not well defined. In the present study, we have analyzed these issues by manipulating signaling pathways in intact chick embryo and explant assays. Our results provide evidence that at blastula stages, BMP signals inhibit the acquisition of eye-field character, but from neural tube/optic vesicle stages, BMP signals from the lens are crucial for the maintenance of eye-field character, inhibition of dorsal telencephalic cell identity and specification of neural retina cells. Subsequently, our results provide evidence that a Rax2-positive eyefield state is not sufficient for the progress to a neural retina identity, but requires BMP signals. In addition, our results argue against any essential role of Wnt or FGF signals during the specification of neural retina cells, but provide evidence that Wnt signals together with BMP activity are sufficient to induce cells of retinal pigment epithelial character. We conclude that BMP activity emanating from the lens ectoderm maintains eye-field identity, inhibits telencephalic character and induces neural retina cells. Our findings link the requirement of the lens ectoderm for neural retina specification with the molecular mechanism by which cells in the forebrain become specified as neural retina by BMP activity. [ABSTRACT FROM AUTHOR]

Soft-X-ray angle-resolved photoelectron spectroscopy (ARPES) with photon energies around 1 keV combines the momentum space resolution with increasing probing depth. The concepts and technical realisation of the new soft-X-ray ARPES endstation at the ADRESS beamline of SLS are described. The experimental geometry of the endstation is characterized by grazing X-ray incidence on the sample to increase the photoyield and vertical orientation of the measurement plane. The vacuum chambers adopt a radial layout allowing most efficient sample transfer. High accuracy of the angular resolution is ensured by alignment strategies focused on precise matching of the X-ray beam and optical axis of the analyzer. The high photon flux of up to 1013 photons s-1 (0.01% bandwidth)-1 delivered by the beamline combined with the optimized experimental geometry break through the dramatic loss of the valence band photoexcitation cross section at soft-X-ray energies. ARPES images with energy resolution up to a few tens of meV are typically acquired on the time scale of minutes. A few application examples illustrate the power of our advanced soft-X-ray ARPES instrumentation to explore the electronic structure of bulk crystals with resolution in three-dimensional momentum, access buried heterostructures and study elemental composition of the valence states using resonant excitation. [ABSTRACT FROM AUTHOR]

In the wake of accreditation cycles stressing student outcomes, we believed the reflective and practitioner-centered philosophy of action research a perfect fit for effecting institutional improvements for a four-year grant-funded effort in our urban–suburban community colleges in California. We learned that things were both worse and better than we had imagined. While we had anticipated what we will call ‘the Bad’, the classic budgetary and institutional forces buffeting us, our project, and our institutions, we had not anticipated what we will call ‘the Ugly’. And perhaps because of our grasp of ‘the Bad’, we also had not anticipated what we will call ‘the Good’. We found ourselves challenged to rethink how to encourage colleagues to become reflective practitioners, yet able to appreciate the power of action research to lead to genuine transformation. [ABSTRACT FROM PUBLISHER]

We report angle-resolved photoemission spectroscopy (ARPES) on a GaAs thin film protected by an amorphous As layer with thickness exceeding the typical probing depths of vacuum-ultraviolet rays up to ∼100 eV. Increasing the probing depth by increasing photon energy into the soft x-ray (SX) region of several hundred eV clearly exposes the bulk band dispersion of the GaAs underlayer without any surface treatment. Our results demonstrate that the use of SX-ARPES enables access to the three-dimensional band dispersion of buried underlayer through an amorphous overlayer. This opens frontiers in diagnostics of authentic momentum-resolved electronic structure of protected thin-film heterostructures. [ABSTRACT FROM AUTHOR]

When viewed as an elementary particle, the electron has spin and charge. When binding to the atomic nucleus, it also acquires an angular momentum quantum number corresponding to the quantized atomic orbital it occupies. Even if electrons in solids form bands and delocalize from the nuclei, in Mott insulators they retain their three fundamental quantum numbers: spin, charge and orbital. The hallmark of one-dimensional physics is a breaking up of the elementary electron into its separate degrees of freedom. The separation of the electron into independent quasi-particles that carry either spin (spinons) or charge (holons) was first observed fifteen years ago. Here we report observation of the separation of the orbital degree of freedom (orbiton) using resonant inelastic X-ray scattering on the one-dimensional Mott insulator Sr2CuO3. We resolve an orbiton separating itself from spinons and propagating through the lattice as a distinct quasi-particle with a substantial dispersion in energy over momentum, of about 0.2 electronvolts, over nearly one Brillouin zone. [ABSTRACT FROM AUTHOR]

European Alpine landscapes are facing marked land-use changes. On the one hand, outdoor winter recreation is spreading, with ski infrastructure degrading fragile mountain habitats, and snowsports causing disturbance and stress to wildlife. On the other hand, the abandonment of traditional grazing practices on timberline grasslands is leading to their encroachment by shrubs and forest, which decreases habitat heterogeneity and negatively affects biodiversity. We used the black grouse, a declining key indicator species of the Alpine timberline ecosystem, to assess optimal breeding habitat characteristics, with the goal of providing guidelines for appropriate restoration. Using Mixed Effects Logistic Regression analyses, we compared habitat features both at visited and at pseudoabsence locations within individual home ranges in order to determine the optimal habitat for males and females. Horizontal and vertical structural heterogeneity within all vegetation layers was the best predictor of occurrence for both sexes. In contrast, vegetation composition affected the presence of females, but not that of males. Females preferred a diverse, complex mosaic consisting of isolated mature coniferous trees and scattered small regenerating trees, associated with shrub cover (Ericacea) and Alpine meadows (Nardion). Chick-rearing females furthermore avoided roads, forest tracks and walking paths. The optimal predicted proportions of habitat types obtained from the model provide guidelines for the restoration of timberline ecosystems through corrective forestry measures and/or adapted grazing practices. These measures are likely to also benefit other Alpine timberline biodiversity. [ABSTRACT FROM AUTHOR]