Live Iterative Ptychography.

We demonstrate live-updating ptychographic reconstruction with the extended ptychographical iterative engine, an iterative ptychography method, during ongoing data acquisition. The reconstruction starts with a small subset of the total data, and as the acquisition proceeds the data used for reconstruction are extended. This creates a live-updating view of object and illumination that allows monitoring the ongoing experiment and adjusting parameters with quick turn around. This is particularly advantageous for long-running acquisitions. We show that such a gradual reconstruction yields interpretable results already with a small subset of the data. We show simulated live processing with various scan patterns, parallelized reconstruction, and real-world live processing at the hard X-ray ptychographic nanoanalytical microscope PtyNAMi at the PETRA III beamline.

(Sub-)Picosecond Surface Correlations of Femtosecond Laser Excited Al-Coated Multilayers Observed by Grazing-Incidence X-ray Scattering.

Femtosecond high-intensity laser pulses at intensities surpassing 1014 W/cm2 can generate a diverse range of functional surface nanostructures. Achieving precise control over the production of these functional structures necessitates a thorough understanding of the surface morphology dynamics with nanometer-scale spatial resolution and picosecond-scale temporal resolution. In this study, we show that single XFEL pulses can elucidate structural changes on surfaces induced by laser-generated plasmas using grazing-incidence small-angle X-ray scattering (GISAXS). Using aluminium-coated multilayer samples we distinguish between sub-picosecond (ps) surface morphology dynamics and subsequent multi-ps subsurface density dynamics with nanometer-depth sensitivity. The observed subsurface density dynamics serve to validate advanced simulation models representing matter under extreme conditions. Our findings promise to open new avenues for laser material-nanoprocessing and high-energy-density science.

Ultra-short pulse laser acceleration of protons to 80 MeV from cryogenic hydrogen jets tailored to near-critical density.

Laser plasma-based particle accelerators attract great interest in fields where conventional accelerators reach limits based on size, cost or beam parameters. Despite the fact that particle in cell simulations have predicted several advantageous ion acceleration schemes, laser accelerators have not yet reached their full potential in producing simultaneous high-radiation doses at high particle energies. The most stringent limitation is the lack of a suitable high-repetition rate target that also provides a high degree of control of the plasma conditions required to access these advanced regimes. Here, we demonstrate that the interaction of petawatt-class laser pulses with a pre-formed micrometer-sized cryogenic hydrogen jet plasma overcomes these limitations enabling tailored density scans from the solid to the underdense regime. Our proof-of-concept experiment demonstrates that the near-critical plasma density profile produces proton energies of up to 80 MeV. Based on hydrodynamic and three-dimensional particle in cell simulations, transition between different acceleration schemes are shown, suggesting enhanced proton acceleration at the relativistic transparency front for the optimal case.

Application Experiences on a GPU-Accelerated Arm-based HPC Testbed.

This paper assesses and reports the experience of ten teams working to port, validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HPC Developer Kit systems, each one equipped with a server-class Arm CPU from Ampere Computing and two data center GPUs from NVIDIA Corp. The systems are connected together using InfiniBand interconnect. The selected applications and mini-apps are written using several programming languages and use multiple accelerator-based programming models for GPUs such as CUDA, OpenACC, and OpenMP offloading. Working on application porting requires a robust and easy-to-access programming environment, including a variety of compilers and optimized scientific libraries. The goal of this work is to evaluate platform readiness and assess the effort required from developers to deploy well-established scientific workloads on current and future generation Arm-based GPU-accelerated HPC systems. The reported case studies demonstrate that the current level of maturity and diversity of software and tools is already adequate for large-scale production deployments.

Target specificity of the Candida albicans Efg1 regulator.

Efg1 is a central transcriptional regulator of morphogenesis and metabolism in Candida albicans. In vivo genome-wide ChIP chip and in vitro footprint analyses revealed the Efg1 recognition sequence (EGR-box) TATGCATA in the yeast growth form of this human fungal pathogen. Upstream regions of EFG1 and genes encoding transcriptional regulators of hyphal growth including TCC1, CZF1, TEC1, DEF1 and NRG1 contained EGR- and/or EGR-like boxes. Unexpectedly, after brief hyphal induction the genome-wide Efg1 binding pattern was completely altered and new binding sites of yet unknown specificity had appeared. Hyphal induction abolished Efg1 accumulation on EFG1 and TCC1 promoters and led to rapid decline of both transcripts, although the Efg1 protein persisted in cells. While EFG1 promoter activity in the yeast growth form did not depend on bound Efg1, its downregulation under hyphal induction depended on the presence of Efg1 and the protein kinase A isoform Tpk2. Deletion analyses of the EFG1 upstream region revealed that none of its resident EGR-boxes is uniquely responsible for EFG1 promoter downregulation. These results suggest different binding specificities of Efg1 in yeast growth and in hyphal induction and suggest a brief time window following hyphal induction, in which Efg1 exerts its repressive effect on target promoters.

A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum.

Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory. Measurement(s) Gene Expression Analysis Technology Type(s) Two Color Microarray Factor Type(s) WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain Sample Characteristic - Organism Corynebacterium glutamicum Sample Characteristic - Environment laboratory environment Sample Characteristic - Location Germany.

RosR (Cg1324), a hydrogen peroxide-sensitive MarR-type transcriptional regulator of Corynebacterium glutamicum.

The cg1324 gene (rosR) of Corynebacterium glutamicum encodes a MarR-type transcriptional regulator. By a comparative transcriptome analysis with DNA microarrays of a ΔrosR mutant and the wild type and subsequent EMSAs with purified RosR protein, direct target genes of RosR were identified. The narKGHJI operon, which encodes a nitrate/nitrite transporter and the dissimilatory nitrate reductase complex, was activated by RosR. All other target genes were repressed by RosR. They encode four putative monooxygenases, two putative FMN reductases, a protein of the glutathione S-transferase family, a putative polyisoprenoid-binding protein, and RosR itself. The DNA binding site of RosR was characterized as an 18-bp inverted repeat with the consensus sequence TTGTTGAYRYRTCAACWA. The in vitro DNA binding activity of RosR was reversibly inhibited by the oxidant H(2)O(2). Mutational analysis of the three cysteine residues present in RosR (Cys-64, Cys-92, and Cys-151) showed that these are responsible for the inhibition of DNA binding by H(2)O(2). A deletion mutant (Δcg1322) lacking the putative polyisoprenoid-binding protein showed an increased sensitivity to H(2)O(2), supporting the role of RosR in the oxidative stress response of C. glutamicum.

Do subjectively and objectively impaired oral health parameters influence geriatric assessment results in hospitalized geriatric patients?

BACKGROUND: Impaired oral health affects oral health-related quality of life (OHrQoL) in orthogeriatric hospitalized patients, and both might be associated with potential risk factors for functional impairment, based on the comprehensive geriatric assessment (CGA) and related blood laboratory values. As data on this field are scarce, we investigated possible associations between oral health, items of the geriatric oral health assessment instrument (GOHAI), CGA assessment tools, and relevant laboratory values. METHODS: Explorative cross-sectional pilot study investigating oral and general health, OHrQoL, and functionality based on objective oral health, GOHAI, CGA, and routinely assessed laboratory parameters of orthogeriatric patients. Correlations (Spearman's rho and Pearson's) and regression analysis were performed for the dependent variables functionality, cognition, Mini-Nutritional Assessment, Falls Efficacy Scale (FES), and the 15-item geriatric depression scale (GDS). RESULTS: Among all participants (N = 40), several GOHAI single items (GOHAI 1,4,5,7,10,11) correlated with certain CGA assessment results (fear of falling, Barthel index, handgrip power). Reduced subjective oral health (GOHAI, xerostomia) and objective oral health (oral hygiene index, root caries index, unstimulated salivation rate) correlated with reduced general health and CGA results (polypharmacy, handgrip power, FES, GDS). Anemia was seen in all participants, but no associations between reduced oral health and laboratory blood values were detected. CONCLUSION: Our results demonstrate the association between impaired subjective and objective oral health, OHrQoL, and physical functional impairment among orthogeriatric patients. Impaired GOHAI item results at the dentist, and the association between GOHAI values and CGA results that implies an association between physical and oral health, should encourage a geriatric check based on CGA, and vice versa. Results encourage interdisciplinary cooperation between geriatricians and dentists, but also indicate the need for further research in this field. TRIAL REGISTRATION: DRKS00013230.

Molecular Basis of Growth Inhibition by Acetate of an Adenylate Cyclase-Deficient Mutant of Corynebacterium glutamicum.

In Corynebacterium glutamicum, cyclic adenosine monophosphate (cAMP) serves as an effector of the global transcriptional regulator GlxR. Synthesis of cAMP is catalyzed by the membrane-bound adenylate cyclase CyaB. In this study, we investigated the consequences of decreased intracellular cAMP levels in a ΔcyaB mutant. While no growth defect of the ΔcyaB strain was observed on glucose, fructose, sucrose, or gluconate alone, the addition of acetate to these growth media resulted in a severe growth inhibition, which could be reversed by plasmid-based cyaB expression or by supplementation of the medium with cAMP. The effect was concentration- and pH-dependent, suggesting a link to the uncoupling activity of acetate. In agreement, the ΔcyaB mutant had an increased sensitivity to the protonophore carbonyl cyanide m-chlorophenyl hydrazone (CCCP). The increased uncoupler sensitivity correlated with a lowered membrane potential of acetate-grown ΔcyaB cells compared to wild-type cells. A reduced membrane potential affects major cellular processes, such as ATP synthesis by F1F O -ATP synthase and numerous transport processes. The impaired membrane potential of the ΔcyaB mutant could be due to a decreased expression of the cytochrome bc 1-aa 3 supercomplex, which is the major contributor of proton-motive force in C. glutamicum. Expression of the supercomplex genes was previously reported to be activated by GlxR-cAMP. A suppressor mutant of the ΔcyaB strain with improved growth on acetate was isolated, which carried a single mutation in the genome leading to an Ala131Thr exchange in GlxR. Introduction of this point mutation into the original ΔcyaB mutant restored the growth defect on acetate. This supported the importance of GlxR for the phenotype of the ΔcyaB mutant and, more generally, of the cAMP-GlxR system for the control of energy metabolism in C. glutamicum.

Femtosecond laser produced periodic plasma in a colloidal crystal probed by XFEL radiation.

With the rapid development of short-pulse intense laser sources, studies of matter under extreme irradiation conditions enter further unexplored regimes. In addition, an application of X-ray Free-Electron Lasers (XFELs) delivering intense femtosecond X-ray pulses, allows to investigate sample evolution in IR pump - X-ray probe experiments with an unprecedented time resolution. Here we present a detailed study of the periodic plasma created from the colloidal crystal. Both experimental data and theory modeling show that the periodicity in the sample survives to a large extent the extreme excitation and shock wave propagation inside the colloidal crystal. This feature enables probing the excited crystal, using the powerful Bragg peak analysis, in contrast to the conventional studies of dense plasma created from bulk samples for which probing with Bragg diffraction technique is not possible. X-ray diffraction measurements of excited colloidal crystals may then lead towards a better understanding of matter phase transitions under extreme irradiation conditions.

Xerostomia and hyposalivation in orthogeriatric patients with fall history and impact on oral health-related quality of life.

PURPOSE: Falls are a common cause of morbidity and mortality in older people, and identification of risk indicators and risk factors to prevent falling is essential. Dry mouth (xerostomia and hyposalivation) can exacerbate conditions known to be fall risk indicators, such as nutritional status and sarcopenia. But there is little evidence regarding whether it is an independent risk factor for falling. We explored xerostomia prevalence and intensity and objective salivation rates in hospitalized geriatric patients to determine whether they were associated with an increased risk of falling. PATIENTS AND METHODS: Hospitalized geriatric patients with and without a fall history were compared. We investigated several oral health issues including xerostomia, stimulated and unstimulated salivation rates, total number of teeth and prosthetics, periodontal status, and oral health-related quality of life. RESULTS: Forty patients were included, 28 in the fall history group and 12 in the control group. All patients had oral health issues that impacted on their oral health-related quality of life. However, there were no significant differences between the groups, including xerostomia and hyposalivation, apart from increased dysphagia and less flavor in food in patients with a fall history. CONCLUSION: Dry mouth does not appear to be an independent risk factor for falling in this population, but oral health was impaired. Thus, it is important that dentists and geriatricians are aware of and investigate these conditions in their patients and that appropriate action is taken to reduce the consequences of impaired oral health, including a potential reduction in falls.

Technical Note: Experimental verification of magnetic field-induced beam deflection and Bragg peak displacement for MR-integrated proton therapy.

PURPOSE: Given its sensitivity to anatomical variations, proton therapy is expected to benefit greatly from integration with magnetic resonance imaging for online anatomy monitoring during irradiation. Such an integration raises several challenges, as both systems mutually interact. The proton beam will experience quasi-continuous energy loss and energy-dependent electromagnetic deflection at the same time, giving rise to a deflected beam trajectory and an altered dose distribution with a displaced Bragg peak. So far, these effects have only been predicted using Monte Carlo and analytical models, but no clear consensus has been reached and experimental benchmark data are lacking. We measured proton beam trajectories and Bragg peak displacement in a homogeneous phantom placed inside a magnetic field and compared them to simulations. METHODS: Planar dose distributions of proton pencil beams (80-180 MeV) traversing the field of a 0.95 T NdFeB permanent magnet while depositing energy in a PMMA slab phantom were measured using EBT3 radiochromic films and simulated using the Geant4 toolkit. Deflected beam trajectories and the Bragg peak displacement were extracted from the measured planar dose distributions and compared against the simulations. RESULTS: The lateral beam deflection was clearly visible on the EBT3 films and ranged from 1 to 10 mm for 80 to 180 MeV, respectively. Simulated and measured beam trajectories and Bragg peak displacement agreed within 0.8 mm for all studied proton energies. CONCLUSIONS: These results prove that the magnetic field-induced Bragg peak displacement is both measurable and accurately predictable in a homogeneous phantom at 0.95 T, and allows Monte Carlo simulations to be used as gold standard for proton beam trajectory prediction in similar frameworks for MR-integrated proton therapy.

All-optical structuring of laser-driven proton beam profiles.

Extreme field gradients intrinsic to relativistic laser-interactions with thin solid targets enable compact MeV proton accelerators with unique bunch characteristics. Yet, direct control of the proton beam profile is usually not possible. Here we present a readily applicable all-optical approach to imprint detailed spatial information from the driving laser pulse onto the proton bunch. In a series of experiments, counter-intuitively, the spatial profile of the energetic proton bunch was found to exhibit identical structures as the fraction of the laser pulse passing around a target of limited size. Such information transfer between the laser pulse and the naturally delayed proton bunch is attributed to the formation of quasi-static electric fields in the beam path by ionization of residual gas. Essentially acting as a programmable memory, these fields provide access to a higher level of proton beam manipulation.

Developmental validation of QIAGEN Investigator® 24plex QS Kit and Investigator® 24plex GO! Kit: Two 6-dye multiplex assays for the extended CODIS core loci.

The original CODIS database based on 13 core STR loci has been overwhelmingly successful for matching suspects with evidence. In order to increase the power of discrimination, reduce the possibility of adventitious matches, and expand global data sharing, the CODIS Core Loci Working Group determined the expansion of the CODIS core loci to 20 STR plus three additional "highly recommended" loci (SE33, DY391, Amelogenin) Hares, 2015, 2012 [1,2]. The QIAGEN Investigator 24plex QS and Investigator 24plex GO! Kits are 6-dye multiplex assays that contain all markers of the expanded 23 CODIS core loci along with a unique internal performance control that is co-amplified with the STR markers. The "Quality Sensor" generates additional information for quality control and performance checks. Investigator 24plex QS is designed for purified DNA from casework and reference samples, whereas 24plex GO! is dedicated to direct amplification of reference samples, like blood or buccal cells on FTA or swabs. A developmental validation study was performed on both assays. Here, we report the results of this study which followed the recommendations of the European Network of Forensic Science Institutes (ENFSI) [3] and the Revised Validation Guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM) [4]. Data included are for PCR-based procedures e.g. reaction conditions, effects of PCR annealing temperature variations, amplification cycles or cyclers, sensitivity (also in the context of the Quality Sensor), performance with simulated inhibition, stability and efficiency, precision, reproducibility, mixture study, concordance, stutter, species specificity, and case-type samples. The validation results demonstrate that the Investigator 24plex QS and Investigator 24plex GO! Kits are robust and reliable identification assays as required for forensic DNA typing in forensic casework analysis and databasing.

Efficient laser-driven proton acceleration from cylindrical and planar cryogenic hydrogen jets.

We report on recent experimental results deploying a continuous cryogenic hydrogen jet as a debris-free, renewable laser-driven source of pure proton beams generated at the 150 TW ultrashort pulse laser Draco. Efficient proton acceleration reaching cut-off energies of up to 20 MeV with particle numbers exceeding 109 particles per MeV per steradian is demonstrated, showing for the first time that the acceleration performance is comparable to solid foil targets with thicknesses in the micrometer range. Two different target geometries are presented and their proton beam deliverance characterized: cylindrical (∅ 5 µm) and planar (20 µm × 2 µm). In both cases typical Target Normal Sheath Acceleration emission patterns with exponential proton energy spectra are detected. Significantly higher proton numbers in laser-forward direction are observed when deploying the planar jet as compared to the cylindrical jet case. This is confirmed by two-dimensional Particle-in-Cell (2D3V PIC) simulations, which demonstrate that the planar jet proves favorable as its geometry leads to more optimized acceleration conditions.

The crystal structures of apo and cAMP-bound GlxR from Corynebacterium glutamicum reveal structural and dynamic changes upon cAMP binding in CRP/FNR family transcription factors.

The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator) transcriptional regulators that play central roles in bacterial metabolic regulatory networks. In C. glutamicum, which is widely used for the industrial production of amino acids and serves as a non-pathogenic model organism for members of the Corynebacteriales including Mycobacterium tuberculosis, the GlxR homodimer controls the transcription of a large number of genes involved in carbon metabolism. GlxR therefore represents a key target for understanding the regulation and coordination of C. glutamicum metabolism. Here we investigate cylic AMP and DNA binding of GlxR from C. glutamicum and describe the crystal structures of apo GlxR determined at a resolution of 2.5 Å, and two crystal forms of holo GlxR at resolutions of 2.38 and 1.82 Å, respectively. The detailed structural analysis and comparison of GlxR with CRP reveals that the protein undergoes a distinctive conformational change upon cyclic AMP binding leading to a dimer structure more compatible to DNA-binding. As the two binding sites in the GlxR homodimer are structurally identical dynamic changes upon binding of the first ligand are responsible for the allosteric behavior. The results presented here show how dynamic and structural changes in GlxR lead to optimization of orientation and distance of its two DNA-binding helices for optimal DNA recognition.

Citrate synthase in Corynebacterium glutamicum is encoded by two gltA transcripts which are controlled by RamA, RamB, and GlxR.

Citrate synthase (CS) is located at a major branch point in the metabolism and is required for both tricarboxylic acid and glyoxylic acid cycle activity. Here we show that the CS gene gltA of Corynebacterium glutamicum is monocistronic, but that two transcripts are formed with their transcript initiation sites located 121 bp and 357 bp upstream of the translational start codon, respectively. Northern blot analyses revealed that during growth on acetate the short transcript prevails, whereas during growth on glucose the long transcript is dominant. Further Northern blots, reporter gene fusions, and CS activity measurements in mutants devoid of the transcriptional regulators RamA and RamB or with the global regulator GlxR overexpressed revealed a complex involvement of these regulators in gltA transcription. This was confirmed by demonstrating the direct interaction of isolated RamA, RamB and GlxR proteins with specific gltA promoter regions in vitro. The combined analyses point to an elaborate control of gltA transcript formation, which is possibly required as a dedicated mechanism to balance the total CS activity according to the physiological requirements.

Transcriptional control of the succinate dehydrogenase operon sdhCAB of Corynebacterium glutamicum by the cAMP-dependent regulator GlxR and the LuxR-type regulator RamA.

In experiments performed to identify transcriptional regulators of the tricarboxylic acid cycle of Corynebacterium glutamicum, the cAMP-dependent regulator GlxR and the regulators of acetate metabolism RamA and RamB were enriched by DNA affinity chromatography with the promoter region of the sdhCAB operon encoding succinate dehydrogenase. The binding of purified GlxR, RamA and RamB was verified by electrophoretic mobility shift assays and the regulatory effects of these proteins on sdhCAB gene expression were tested by promoter activity assays and SDH activity measurements. Evidence was obtained that GlxR functions as a repressor and RamA as an activator of sdhCAB expression, whereas RamB had no obvious influence under the conditions tested.