Twisted speckle entities inside wavefront reversal mirrors

The previously unknown property of the optical speckle pattern reported. The interference of a speckle with an oppositely moving phase-conjugated speckle wave produces a randomly distributed ensemble of a twisted entities (ropes) surrounding optical vortex lines. These entities appear in a wide range of randomly chosen speckle parameters inside the phase-conjugating mirrors regardless to an internal physical mechanism of the wavefront reversal. These numerically generated interference patterns are relevant to a Brillouin $\bf PC$-mirrors and to a four-wave mixing $\bf PC$-mirrors based upon laser trapped ultracold atomic cloud.Comment: 4 pages,3 figures, Accepted to Physical Review

Creation, doubling, and splitting, of vortices in intracavity second harmonic generation

We demonstrate generation and frequency doubling of unit charge vortices in a linear astigmatic resonator. Topological instability of the double charge harmonic vortices leads to well separated vortex cores that are shown to rotate, and become anisotropic, as the resonator is tuned across resonance

Excitonic effects on the two-color coherent control of interband transitions in bulk semiconductors

Quantum interference between one- and two-photon absorption pathways allows coherent control of interband transitions in unbiased bulk semiconductors; carrier population, carrier spin polarization, photocurrent injection, and spin current injection may all be controlled. We extend the theory of these processes to include the electron-hole interaction. Our focus is on photon energies that excite carriers above the band edge, but close enough to it so that transition amplitudes based on low order expansions in $\mathbf{k}$ are applicable; both allowed-allowed and allowed-forbidden two-photon transition amplitudes are included. Analytic solutions are obtained using the effective mass theory of Wannier excitons; degenerate bands are accounted for, but envelope-hole coupling is neglected. We find a Coulomb enhancement of two-color coherent control process, and relate it to the Coulomb enhancements of one- and two-photon absorption. In addition, we find a frequency dependent phase shift in the dependence of photocurrent and spin current on the optical phases. The phase shift decreases monotonically from $\pi /2$ at the band edge to 0 over an energy range governed by the exciton binding energy. It is the difference between the partial wave phase shifts of the electron-hole envelope function reached by one- and two-photon pathways.Comment: 31 pages, 4 figures, to be published in Phys. Rev.

A Database of Weed Plants in the European Part of Russia

Weeds are plants that, although not specially cultivated, grow and often adapt to growing in arable lands. They form an ecological variant of flora, as a historically-formed set of species growing on cultivated soils. For the rational use of the chemical and biological crop protection products and to produce safe and high-quality food, up-to-date data on the floristic diversity of weeds and the patterns of its geographical change are required. The need for a weeds' database arises that allows many specialists to work together independently. However, the great value of any database lies not in its existence, but in the accumulation of data that can be used to analyse the factors affecting the species diversity of weeds. New information A dataset of weed species diversity and their distribution in the European part of Russia, based on the results of the authors' own research from 1999 to 2019, has been created. The dataset includes 24,284 observations of occurrences of weed plants, which were obtained on the basis of 2,049 relevés of segetal plant communities in seven regions of the European part of Russia. In total, the dataset includes information about 329 species of vascular plants growing in 65 farmlands: cereals, spring and winter crops, industrial crops, row crops and perennial grasses (Tretyakova et al. 2020). © Tretyakova A et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Funding: This work was supported by Russian public funds (AAAA-A18-118011990151-7) in the framework of implementation of the State task on the “Vascular plants of Eurasia: taxonomy, ora, plant resources” (AAAA-A19-119031290052-1), by the Competitiveness of the Ural Federal University (Russian Federation Government Regulation no. 211, contract no. 02. A03.21.0006) and partially by the Russian Foundation for Basic Research (project nos. 17-44-020402 and 19-016-00135)

Ribonucleolytic activity of mycoplasmas

Mycoplasmas are incapable of de novo synthesis of nucleotides and must therefore secrete nucleases in order to replenish the pool of nucleic acid precursors. The nucleolytic activity of mycoplasmas is an important factor in their pathogenicity. Bacterial ribonucleases (RNases) may produce a broad spectrum of biological effects, including antiviral and antitumor activity. Mycoplasma RNases are therefore of interest. In the present work, the capacity of Acholeplasma laidlawii and Mycoplasma hominis for RNase synthesis and secretion was studied. During the stationary growth phase, these organisms were found to synthesize Mg2+-dependent RNases, with their highest activity detected outside the cells. Localization of A. laidlawii RNases was determined: almost 90% of the RNase activity was found to be associated with the membrane vesicles. Bioinformational analysis revealed homology between the nucleotide sequences of 14 Bacillus subtilis genes encoding the products with RNase activity and the genes of the mycoplasmas under study. Amino acid sequences of 4 A. laidlawii proteins with ribonuclease activity and the Bsn RNase were also established. © 2014 Pleiades Publishing, Ltd

An efficient algorithm for systematic analysis of nucleotide strings suitable for siRNA design

<p>Abstract</p> <p>Background</p> <p>The "off-target" silencing effect hinders the development of siRNA-based therapeutic and research applications. Existing solutions for finding possible locations of siRNA seats within a large database of genes are either too slow, miss a portion of the targets, or are simply not designed to handle a very large number of queries. We propose a new approach that reduces the computational time as compared to existing techniques.</p> <p>Findings</p> <p>The proposed method employs tree-based storage in a form of a modified truncated suffix tree to sort all possible short string substrings within given set of strings (i.e. transcriptome). Using the new algorithm, we pre-computed a list of the best siRNA locations within each human gene ("siRNA seats"). siRNAs designed to reside within siRNA seats are less likely to hybridize off-target. These siRNA seats could be used as an input for the traditional "set-of-rules" type of siRNA designing software. The list of siRNA seats is available through a publicly available database located at <url>http://web.cos.gmu.edu/~gmanyam/siRNA_db/search.php</url></p> <p>Conclusions</p> <p>In attempt to perform top-down prediction of the human siRNA with minimized off-target hybridization, we developed an efficient algorithm that employs suffix tree based storage of the substrings. Applications of this approach are not limited to optimal siRNA design, but can also be useful for other tasks involving selection of the characteristic strings specific to individual genes. These strings could then be used as siRNA seats, as specific probes for gene expression studies by oligonucleotide-based microarrays, for the design of molecular beacon probes for Real-Time PCR and, generally, any type of PCR primers.</p

Challenges in QCD matter physics --The scientific programme of the Compressed Baryonic Matter experiment at FAIR

Substantial experimental and theoretical efforts worldwide are devoted to explore the phase diagram of strongly interacting matter. At LHC and top RHIC energies, QCD matter is studied at very high temperatures and nearly vanishing net-baryon densities. There is evidence that a Quark-Gluon-Plasma (QGP) was created at experiments at RHIC and LHC. The transition from the QGP back to the hadron gas is found to be a smooth cross over. For larger net-baryon densities and lower temperatures, it is expected that the QCD phase diagram exhibits a rich structure, such as a first-order phase transition between hadronic and partonic matter which terminates in a critical point, or exotic phases like quarkyonic matter. The discovery of these landmarks would be a breakthrough in our understanding of the strong interaction and is therefore in the focus of various high-energy heavy-ion research programs. The Compressed Baryonic Matter (CBM) experiment at FAIR will play a unique role in the exploration of the QCD phase diagram in the region of high net-baryon densities, because it is designed to run at unprecedented interaction rates. High-rate operation is the key prerequisite for high-precision measurements of multi-differential observables and of rare diagnostic probes which are sensitive to the dense phase of the nuclear fireball. The goal of the CBM experiment at SIS100 (sNN= 2.7--4.9 GeV) is to discover fundamental properties of QCD matter: the phase structure at large baryon-chemical potentials (μB&gt; 500 MeV), effects of chiral symmetry, and the equation of state at high density as it is expected to occur in the core of neutron stars. In this article, we review the motivation for and the physics programme of CBM, including activities before the start of data taking in 2024, in the context of the worldwide efforts to explore high-density QCD matter

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

Genome-wide association study of angioedema induced by angiotensin-converting enzyme inhibitor and angiotensin receptor blocker treatment

Angioedema in the mouth or upper airways is a feared adverse reaction to angiotensin-converting enzyme inhibitor (ACEi) and angiotensin receptor blocker (ARB) treatment, which is used for hypertension, heart failure and diabetes complications. This candidate gene and genome-wide association study aimed to identify genetic variants predisposing to angioedema induced by these drugs. The discovery cohort consisted of 173 cases and 4890 controls recruited in Sweden. In the candidate gene analysis, ETV6, BDKRB2, MME, and PRKCQ were nominally associated with angioedema (p < 0.05), but did not pass Bonferroni correction for multiple testing (p < 2.89 × 10−5). In the genome-wide analysis, intronic variants in the calcium-activated potassium channel subunit alpha-1 (KCNMA1) gene on chromosome 10 were significantly associated with angioedema (p < 5 × 10−8). Whilst the top KCNMA1 hit was not significant in the replication cohort (413 cases and 599 ACEi-exposed controls from the US and Northern Europe), a meta-analysis of the replication and discovery cohorts (in total 586 cases and 1944 ACEi-exposed controls) revealed that each variant allele increased the odds of experiencing angioedema 1.62 times (95% confidence interval 1.05–2.50, p = 0.030). Associated KCNMA1 variants are not known to be functional, but are in linkage disequilibrium with variants in transcription factor binding sites active in relevant tissues. In summary, our data suggest that common variation in KCNMA1 is associated with risk of angioedema induced by ACEi or ARB treatment. Future whole exome or genome sequencing studies will show whether rare variants in KCNMA1 or other genes contribute to the risk of ACEi- and ARB-induced angioedema