Photoionization Suppression by Continuum Coherence: Experiment and Theory

We present experimental and theoretical results of a detailed study of laser-induced continuum structures (LICS) in the photoionization continuum of helium out of the metastable state 2s $^1S_0$. The continuum dressing with a 1064 nm laser, couples the same region of the continuum to the {4s $^1S_0$} state. The experimental data, presented for a range of intensities, show pronounced ionization suppression (by as much as 70% with respect to the far-from-resonance value) as well as enhancement, in a Beutler-Fano resonance profile. This ionization suppression is a clear indication of population trapping mediated by coupling to a contiuum. We present experimental results demonstrating the effect of pulse delay upon the LICS, and for the behavior of LICS for both weak and strong probe pulses. Simulations based upon numerical solution of the Schr\"{o}dinger equation model the experimental results. The atomic parameters (Rabi frequencies and Stark shifts) are calculated using a simple model-potential method for the computation of the needed wavefunctions. The simulations of the LICS profiles are in excellent agreement with experiment. We also present an analytic formulation of pulsed LICS. We show that in the case of a probe pulse shorter than the dressing one the LICS profile is the convolution of the power spectra of the probe pulse with the usual Fano profile of stationary LICS. We discuss some consequences of deviation from steady-state theory.Comment: 29 pages, 17 figures, accepted to PR

The effects of forest age, forest edge and landscape factors on the occupancy and cover of the Micarea globulosella lichen in a Swedish boreal forest

Lichens are sensitive indicators of changes in environmental factors such as moisture, light intensity and air pollution. They are easily affected by forest fragmentation and by recent increases in forest edges as a result of intensive use of forest resources. The aim of this study was to describe previously unknown ecological characteristics of the Micarea globulosella lichen by (1) comparing the occupancy and cover of M. globulosella in old and young forest production stands, (2) investigating whether M. globulosella is affected by stand edges and (3) exploring the effect of high M. globulosella occupancy in old stands on lichen regeneration in young stands. The impacts of other landscape factors on M. globulosella, including altitude and latitude, were also tested. Most profoundly, M. globulosella was found in young forest stands. This contradicts current information which states that the lichen predominantly grows in old-growth forests with long tree continuity. Lichen occupancy and cover increased with stand age. M. globulosella responded to forest edges. In old South facing stands, there was a significant increase in occupancy with increasing distance from the stand edge towards the forest interior. In young North facing stands, lichen occupancy decreased significantly with increasing distance from the stand edge towards the forest interior of the young stand. In young South facing stands, contrary to expectations, there was a significant decrease in lichen occupancy with an increasing distance from the stand edge towards the forest interior of the young stand. A positive correlation between high lichen occupancy in old stands and increased lichen occupancy in the directly adjacent young stands was found. This study’s findings suggest that M. globulosella regeneration and occupancy is affected by both microclimate and dispersal interactions

Molecular epidemiology and antimicrobial resistance of Clostridioides difficile in Germany, 2014-2019

Clostridioides difficile is a Gram positive spore-forming rod and mainly responsible for nosocomial diarrhea in developed nations. Molecular and antimicrobial surveillance is important for monitoring the strain composition including genotypes of high epidemiological importance such as ribotype 027 (RT027) and corresponding resistance patterns. 1535 isolates obtained from samples sent between 2014 and 2019 to the German National Reference Center (NRC) for diagnostic reasons (NRC strain set), and 1143 isolates from a Tertiary Care University Center in Saarland, Germany (non-NRC strain set), were evaluated using antibiotic susceptibility testing and ribotyping. In the NRC strain set, RT027 overtook RT001, the main RT found in the preceding studies, and dominated with 36.2%, followed by RT001 (13.3%), and RT014 (8.5%). Of note, since 2016 a constant decrease of RT027 could be noticed. In the non-NRC strain set a large strain diversity was present with RT014 (18%) and RT001 (8.9%) being most prevalent. In NRC samples, resistance towards metronidazole, vancomycin, moxifloxacin, clarithromycin and rifampicin was 2.7%, 0%, 57.1%, 53.2% and 19.2%, respectively. Metronidazole resistance was almost exclusively found in RT027 isolates. Rifampicin resistance was also observed predominantly in isolates of RT027, constituting an almost four-fold increase, when compared to preceeding studies in this region. In conclusion these data demonstrate that RT027 is a driver for rifampicin and metronidazole resistance, underlining the importance of continuous surveillance efforts

Principles for the definition of design structures

Different kinds of design structure are created and used in engineering design and development processes. Function structures, design grammars and bills of materials are common examples. However, there is a lack of clarity regarding distinctions and similarities between different kinds of structure and systematic ways to articulate them. This paper brings together research on product structuring and shape computation to inform the specification of principles for the definition of design structures. The principles draw together findings reported in the computational geometry and product definition literature with research from a range of companies and industry sectors that encompasses enterprise and process structures. The potential value of the principles to computer integrated manufacturing and through-life support is demonstrated through application to four case studies

Simple Questionnaires to Improve Pooling Strategies for SARS-CoV-2 Laboratory Testing

Background: Liberal PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is key to contain the coronavirus disease 2019 (COVID-19) pandemic. Combined multi-sample testing in pools instead of single tests might enhance laboratory capacity and reduce costs, especially in low- and middle-income countries. Objective: The purpose of our study was to assess the value of a simple questionnaire to guide and further improve pooling strategies for SARS-CoV-2 laboratory testing. Methods: Pharyngeal swabs for SARS-CoV-2 testing were obtained from healthcare and police staff, hospital inpatients, and nursing home residents in the southwestern part of Germany. We designed a simple questionnaire, which included questions pertaining to a suggestive clinical symptomatology, recent travel history, and contact with confirmed cases to stratify an individual’s pre-test probability of having contracted COVID-19. The questionnaire was adapted repeatedly in face of the unfolding pandemic in response to the evolving epidemiology and observed clinical symptomatology. Based on the response patterns, samples were either tested individually or in multi-sample pools. We compared the pool positivity rate and the number of total PCR tests required to obtain individual results between this questionnaire-based pooling strategy and randomly assembled pools. Findings: Between March 11 and July 5, 2020, we processed 25,978 samples using random pooling (n = 6,012; 23.1%) or questionnaire-based pooling (n = 19,966; 76.9%). The overall prevalence of SARS-CoV-2 was 0.9% (n = 238). Pool positivity (14.6% vs. 1.2%) and individual SARS-CoV-2 prevalence (3.4% vs. 0.1%) were higher in the random pooling group than in the questionnaire group. The average number of PCR tests needed to obtain the individual result for one participant was 0.27 tests in the random pooling group, as compared to 0.09 in the questionnaire-based pooling group, leading to a laboratory capacity increase of 73% and 91%, respectively, as compared to single PCR testing. Conclusions: Strategies that combine pool testing with a questionnaire-based risk stratification can increase laboratory testing capacities for COVID-19 and might be important tools, particularly in resource-constrained settings

Novel modulators of p53-signaling encoded by unknown genes of emerging viruses

The p53 transcription factor plays a key role both in cancer and in the cell-intrinsic response to infections. The ORFEOME project hypothesized that novel p53-virus interactions reside in hitherto uncharacterized, unknown, or hypothetical open reading frames (orfs) of human viruses. Hence, 172 orfs of unknown function from the emerging viruses SARS-Coronavirus, MERS-Coronavirus, influenza, Ebola, Zika (ZIKV), Chikungunya and Kaposi Sarcomaassociated herpesvirus (KSHV) were de novo synthesized, validated and tested in a functional screen of p53 signaling. This screen revealed novel mechanisms of p53 virus interactions and two viral proteins KSHV orf10 and ZIKV NS2A binding to p53. Originally identified as the target of small DNA tumor viruses, these experiments reinforce the notion that all viruses, including RNA viruses, interfere with p53 functions. These results validate this resource for analogous systems biology approaches to identify functional properties of uncharacterized viral proteins, long non-coding RNAs and micro RNAs

Multivalent S2-based vaccines provide broad protection against SARS-CoV-2 variants of concern and pangolin coronaviruses

Background: The COVID-19 pandemic continues to cause morbidity and mortality worldwide. Most approved COVID-19 vaccines generate a neutralizing antibody response that primarily targets the highly variable receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein. SARS-CoV-2 “variants of concern” have acquired mutations in this domain allowing them to evade vaccine-induced humoral immunity. Recent approaches to improve the breadth of protection beyond SARS-CoV-2 have required the use of mixtures of RBD antigens from different sarbecoviruses. It may therefore be beneficial to develop a vaccine in which the protective immune response targets a more conserved region of the S protein. Methods: Here we have developed a vaccine based on the conserved S2 subunit of the S protein and optimized the adjuvant and immunization regimen in Syrian hamsters and BALB/c mice. We have characterized the efficacy of the vaccine against SARS-CoV-2 variants and other coronaviruses. Findings: Immunization with S2-based constructs elicited a broadly cross-reactive IgG antibody response that recognized the spike proteins of not only SARS-CoV-2 variants, but also SARS-CoV-1, and the four endemic human coronaviruses. Importantly, immunization reduced virus titers in respiratory tissues in vaccinated animals challenged with SARS-CoV-2 variants B.1.351 (beta), B.1.617.2 (delta), and BA.1 (omicron) as well as a pangolin coronavirus. Interpretation: These results suggest that S2-based constructs can elicit a broadly cross-reactive antibody response resulting in limited virus replication, thus providing a framework for designing vaccines that elicit broad protection against coronaviruses. Funding: NIH, Japan Agency for Medical Research and Development, Garry Betty/ V Foundation Chair Fund, and NSF

Human PrP90-231-induced cell death is associated with intracellular accumulation of insoluble and protease-resistant macroaggregates and lysosomal dysfunction

To define the mechanisms by which hPrP90-231 induces cell death, we analyzed its interaction with living cells and monitored its intracellular fate. Treatment of SH-SY5Y cells with fluorescein-5-isothiocyanate (FITC)-conjugated hPrP90-231 caused the accumulation of cytosolic aggregates of the prion protein fragment that increased in number and size in a time-dependent manner. The formation of large intracellular hPrP90-231 aggregates correlated with the activation of apoptosis. hPrP90-231 aggregates occurred within lysotracker-positive vesicles and induced the formation of activated cathepsin D (CD), indicating that hPrP90-231 is partitioned into the endosomal–lysosomal system structures, activating the proteolytic machinery. Remarkably, the inhibition of CD activity significantly reduced hPrP-90-231-dependent apoptosis. Internalized hPrP90-231 forms detergent-insoluble and SDS-stable aggregates, displaying partial resistance to proteolysis. By confocal microscopy analysis of lucifer yellow (LY) intracellular partition, we show that hPrP90-231 accumulation induces lysosome destabilization and loss of lysosomal membrane impermeability. In fact, although control cells evidenced a vesicular pattern of LY fluorescence (index of healthy lysosomes), hPrP90-231-treated cells showed diffuse cytosolic fluorescence, indicating LY diffusion through damaged lysosomes. In conclusion, these data indicate that exogenously added hPrP90-231 forms intralysosomal deposits having features of insoluble, protease-resistant aggregates and could trigger a lysosome-mediated apoptosis by inducing lysosome membrane permeabilization, followed by the release of hydrolytic enzymes

Roadmap on STIRAP applications

STIRAP (stimulated Raman adiabatic passage) is a powerful laser-based method, usually involving two photons, for efficient and selective transfer of populations between quantum states. A particularly interesting feature is the fact that the coupling between the initial and the final quantum states is via an intermediate state, even though the lifetime of the latter can be much shorter than the interaction time with the laser radiation. Nevertheless, spontaneous emission from the intermediate state is prevented by quantum interference. Maintaining the coherence between the initial and final state throughout the transfer process is crucial. STIRAP was initially developed with applications in chemical dynamics in mind. That is why the original paper of 1990 was published in The Journal of Chemical Physics. However, from about the year 2000, the unique capabilities of STIRAP and its robustness with respect to small variations in some experimental parameters stimulated many researchers to apply the scheme to a variety of other fields of physics. The successes of these efforts are documented in this collection of articles. In Part A the experimental success of STIRAP in manipulating or controlling molecules, photons, ions or even quantum systems in a solid-state environment is documented. After a brief introduction to the basic physics of STIRAP, the central role of the method in the formation of ultracold molecules is discussed, followed by a presentation of how precision experiments (measurement of the upper limit of the electric dipole moment of the electron or detecting the consequences of parity violation in chiral molecules) or chemical dynamics studies at ultralow temperatures benefit from STIRAP. Next comes the STIRAP-based control of photons in cavities followed by a group of three contributions which highlight the potential of the STIRAP concept in classical physics by presenting data on the transfer of waves (photonic, magnonic and phononic) between respective waveguides. The works on ions or ion strings discuss options for applications, e.g. in quantum information. Finally, the success of STIRAP in the controlled manipulation of quantum states in solid-state systems, which are usually hostile towards coherent processes, is presented, dealing with data storage in rare-earth ion doped crystals and in nitrogen vacancy (NV) centers or even in superconducting quantum circuits. The works on ions and those involving solid-state systems emphasize the relevance of the results for quantum information protocols. Part B deals with theoretical work, including further concepts relevant to quantum information or invoking STIRAP for the manipulation of matter waves. The subsequent articles discuss the experiments underway to demonstrate the potential of STIRAP for populating otherwise inaccessible high-lying Rydberg states of molecules, or controlling and cooling the translational motion of particles in a molecular beam or the polarization of angular-momentum states. The series of articles concludes with a more speculative application of STIRAP in nuclear physics, which, if suitable radiation fields become available, could lead to spectacular results