Towards high-speed optical quantum memories

Quantum memories, capable of controllably storing and releasing a photon, are a crucial component for quantum computers and quantum communications. So far, quantum memories have operated with bandwidths that limit data rates to MHz. Here we report the coherent storage and retrieval of sub-nanosecond low intensity light pulses with spectral bandwidths exceeding 1 GHz in cesium vapor. The novel memory interaction takes place via a far off-resonant two-photon transition in which the memory bandwidth is dynamically generated by a strong control field. This allows for an increase in data rates by a factor of almost 1000 compared to existing quantum memories. The memory works with a total efficiency of 15% and its coherence is demonstrated by directly interfering the stored and retrieved pulses. Coherence times in hot atomic vapors are on the order of microsecond - the expected storage time limit for this memory.Comment: 13 pages, 5 figure

RNA secondary structure prediction from multi-aligned sequences

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in a chapter of the book `Methods in Molecular Biology'. Note that this version of the manuscript may differ from the published versio

Risk factors for cardiovascular diseases in patients received complex treatment for cranial and craniospinal tumors in childhood

Aim. To study the traditional risk factors for cardiovascular disease (CVD), indicators of endothelial function and exercise tolerance in patients received complex treatment for cranial and craniospinal tumors in childhood, including radiation therapy.Material and methods. We compared examination data of 48 patients who underwent treatment for brain tumors using cranial and craniospinal irradiation in childhood (mean age, 21,7±4,3 years, mean period after the end of treatment, 6,9±5,4 years), and 20 healthy volunteers. Examination methods included assessment of lipid profile, vascular stiffness and endothelial function using the Photoplethysmography and occlusion test, cardiopulmonary test, and in patients who underwent craniospinal irradiation, also echocardiography and duplex ultrasound of extracranial arteries.Results. Compared to healthy individuals, patients after a brain tumor were found to have lower blood pressure, higher heart rate (HR), significantly lower exercise performance (peak oxygen consumption, 19,8±6,4 ml×min-1×kg vs 30,3±5,8 ml×min-1×kg, p<0,0001) and a higher prevalence of dyslipidemia (56% vs 5%, p<0,0001), as well as an increase in the augmentation index, indicating higher stiffness of large vessels (-7,3±16,3 vs -20,3±7,9, p=0,001), and a trend towards a decrease in the occlusion index (p=0,051). Echocardiography and duplex ultrasound revealed no radiation-associated abnormalities.Conclusion. Determining the mechanisms and prognostic significance of the identified risk factors for CVD (dyslipidemia, decreased exercise tolerance, increased heart rate and vascular stiffness) in this category of patients requires further research. Regular monitoring of risk factors, primarily the lipid profile, and the use of preventive measures for individuals with an increased risk of CVD should be recommended

Pediatric bacteremia and CNS infections associated with <i>klebsiella pneumoniae</i>: molecular genetic characteristics and clinical features

Klebsiella pneumoniae is one of the most significant and life-threatening pathogen of nosocomial infections. This opportunistic microorganism can cause infections of the bloodstream, respiratory tract, urinary tract, skin and soft tissues, inflammation of meninges of the brain and spinal cord, leading to elevated hospital mortality. The purpose of our study was a retrospective analysis of molecular genetic characteristics of K. pneumoniae isolated from blood and liquor samples as well as to describe clinical features in bacteremia and CNS infections. According to the results of assessed clinical data, K. pneumoniae isolates were selected from 64 children suffered from surgical pathology (congenital heart defects — 30%, abdominal pathology — 39%, severe combined trauma — 12%) and somatic diseases accompanied by antibacterial and/or glucocorticosteroid therapy — 14%. The minimum suppressive concentrations of antibiotics were determined by the broth micro-dilution method. Carbapenemases were detected by real time polymerase chain reaction. Virulence genes and capsule serotypes K1/K2 were assessed by multiplex PCR. Biofilms were grown using flat-bottomed polystyrene plates, followed by coloring, fixation, elution and data detection. The population diversity was assessed by multilocus sequence typing. Bacteremia and CNS infections associated with K. pneumoniae were fatal in 25% of cases. A substantial portion of the isolates demonstrated the phenotype of extremely drug resistance (XDR) — 43%, the phenotype of multidrug resistance (MDR) was shown in 16% of the isolates. The blaCTX-M cephalosporinase gene was found in 85% of the strains. The main determinant of resistance to carbapenems was the blaOXA-48 gene (33%); the blaNDM gene was detected in 9% of strains. The combination of blaOXA-48 and blaNDM was found in 7% of isolates. The study of biofilm production showed that moderate ability to form biofilms was shown in 61%, strong — 21%, and weak — 15% isolates. Two isolates (3%) did not form biofilms. The virulence genes entB and mrkD were detected in 100% of isolates, ybtS — in 78%. The iutA gene was found in 18% of the strains. Two isolates showed the presence of the kfu gene. Seven isolates belonged to the K2 serotype. 27 different genotypes were found in K. pneumoniae isolates examined. The most common were: ST307 — 21%, ST395 — 12%, ST48 — 7%, ST39 — 6% and ST29 — 6%. Infections of the bloodstream and central nervous system associated with K. pneumoniae have great importance in clinical practice. This microorganism is able to long persist on biotic and abiotic surfaces, has a wide natural and acquired resistance to antibiotics

Analysis of the effectiveness of proximal arteriovenous fistulas in patients on chronic hemodialysis

The purpose of the study is to carry out a comparative analysis of the performance of the shoulder-head arteriovenous fistula and autovenous loop shoulder-head arteriovenous fistula at the top third of the forearm.Цель исследования – провести сравнительный анализ эффективности работы плечеголовных артериовенозных фистул и аутовенозных петлевых плечеголовных артериовенозных фистул в верхней трети предплечья

Optical Magnetometry

Some of the most sensitive methods of measuring magnetic fields utilize interactions of resonant light with atomic vapor. Recent developments in this vibrant field are improving magnetometers in many traditional areas such as measurement of geomagnetic anomalies and magnetic fields in space, and are opening the door to new ones, including, dynamical measurements of bio-magnetic fields, detection of nuclear magnetic resonance (NMR), magnetic-resonance imaging (MRI), inertial-rotation sensing, magnetic microscopy with cold atoms, and tests of fundamental symmetries of Nature.Comment: 11 pages; 4 figures; submitted to Nature Physic

Sustained Delivery of Activated Rho GTPases and BDNF Promotes Axon Growth in CSPG-Rich Regions Following Spinal Cord Injury

Background: Spinal cord injury (SCI) often results in permanent functional loss. This physical trauma leads to secondary events, such as the deposition of inhibitory chondroitin sulfate proteoglycan (CSPG) within astroglial scar tissue at the lesion. Methodology/Principal Findings: We examined whether local delivery of constitutively active (CA) Rho GTPases, Cdc42 and Rac1 to the lesion site alleviated CSPG-mediated inhibition of regenerating axons. A dorsal over-hemisection lesion was created in the rat spinal cord and the resulting cavity was conformally filled with an in situ gelling hydrogel combined with lipid microtubes that slowly released constitutively active (CA) Cdc42, Rac1, or Brain-derived neurotrophic factor (BDNF). Treatment with BDNF, CA-Cdc42, or CA-Rac1 reduced the number of GFAP-positive astrocytes, as well as CSPG deposition, at the interface of the implanted hydrogel and host tissue. Neurofilament 160kDa positively stained axons traversed the glial scar extensively, entering the hydrogel-filled cavity in the treatments with BDNF and CA-Rho GTPases. The treated animals had a higher percentage of axons from the corticospinal tract that traversed the CSPG-rich regions located proximal to the lesion site. Conclusion: Local delivery of CA-Cdc42, CA-Rac1, and BDNF may have a significant therapeutic role in overcoming CSPGmediate

Effect of synthetic hormones on reproduction in Mastomys natalensis

Rodent pest management traditionally relies on some form of lethal control. Developing effective fertility control for pest rodent species could be a major breakthrough particularly in the context of managing rodent population outbreaks. This laboratory-based study is the first to report on the effects of using fertility compounds on an outbreaking rodent pest species found throughout sub-Saharan Africa. Mastomys natalensis were fed bait containing the synthetic steroid hormones quinestrol and levonorgestrel, both singly and in combination, at three concentrations (10, 50, 100 ppm) for seven days. Consumption of the bait and animal body mass was mostly the same between treatments when analysed by sex, day and treatment. However, a repeated measures ANOVA indicated that quinestrol and quinestrol+levonorgestrel treatments reduced consumption by up to 45%, particularly at the higher concentrations of 50 and 100 ppm. Although there was no clear concentration effect on animal body mass, quinestrol and quinestrol+levonorgestrel lowered body mass by up to 20% compared to the untreated and levonorgestrel treatments. Quinestrol and quinestrol+levonorgestrel reduced the weight of male rat testes, epididymis and seminal vesicles by 60-80%, and sperm concentration and motility were reduced by more than 95%. No weight changes were observed to uterine and ovarian tissue; however, high uterine oedema was observed among all female rats consuming treated bait at 8 days and 40 days from trial start. Trials with mate pairing showed there were significant differences in the pregnancy rate with all treatments when compared to the untreated control group of rodents

ОТЕЧЕСТВЕННЫЕ ЭКСПЛАНТАТЫ «БАСЭКС» В РЕКОНСТРУКТИВНОЙ ХИРУРГИИ АОРТЫ И МАГИСТРАЛЬНЫХ АРТЕРИЙ

Purpose. The use of explants in cardiovascular surgery is often accompanied by infectious, thrombotic, hemorrhagic complications and the most severe complication of postoperative period represents the infection of the explants itself, which develops at a frequency of 1.5 to 6 % followed by a mortality rate of 75–100 %. Thrombosis of the explants after surgery occur with a frequency of 6 to 42 %. Materials and methods. From 1996 to 2015, explants of BASEKS were used in 3 600 patients. Implants of BASEKS were used in 75 patients with aortic valve malformation in combination with an aneurysm of the ascending aorta and prosthetic endocarditis and in 1 944 patients with reconstruction of the aorta and arteries.Results. Bacteriological studies have demonstrated a wide range of antimicrobial action of the modifying components covering the explant and patches. The most promising results were obtained for micro-organisms which most commonly caused infections of these explants. All the sample explants had antimicrobial property and the zone of lysis around these explants were maintained for a longer time (up to 30 days or more). The residual anti-microbial explants after surgery were studied in vitro in 5 patients who died from peritonitis, heart, lungs and kidney failure. Explants after sampling were placed on growth media seeded with clinical strains of microorganisms. Within 12–24 hours, zones (15–18 mm) that caused the delay of the growth of microorganisms were formed around the studied fragments, confirming the preservation of the residual antimicrobial activity of the explants after implantation. During the period of follow-up, in 1.9 % of the patients in immediate postoperative period and in 4.1 % of patients in later postoperative period occurred thrombosis of the explants. Surface festering of the postoperative wound was observed in 155 (4.3 %) patients, deep festering – in 51 (1.4 %), 98 (2.7 %) patients succumbed to postoperative complications.Conclusion. The explants and patches of BASEKS which is antimicrobial, thromb-resistant and impermeable, could be widely used in cardiovascular surgery.Применение эксплантатов в сердечно-сосудистой хирургии нередко сопровождается инфекционными, тромботическими, геморрагическими осложнениями, самым грозным из них является инфицирование протезов, развивающееся с частотой от 1,5 до 6 % и сопровождающееся летальностью от 75 до 100 %. Тромбозы эксплантатов в послеоперационном периоде встречаются с частотой от 6 до 42 %.Цель. Оценка эффективности и безопасности имплантации протезов «БАСЭКС» в сердечно-сосудистой хирургии.Материалы и методы. С 1996 по 2015 год эксплантаты и заплаты «БАСЭКС» были имплантированы у 3 600 больных: у 75 пациентов при пороке аортального клапана в сочетании с аневризмой восходящей аорты и протезном эндокардите, у 1944 – при реконструкции аорты и магистральных артерий.Результаты. Бактериологические исследования продемонстрировали широкий спектр действия антимикробных компонентов модифицирующего покрытия эксплантата и заплат. Все образцы эксплантата обладали антимикробными свойствами, что наблюдалось вплоть до 30 суток после имплантации. Остаточные антиинфекционные свойства эксплантатов после операции были изучены in vitro у 5 умерших пациентов от перитонита, сердечной, легочной и почечной недостаточности. Эксплантаты после забора были помещены на питательные среды, засеянные клиническими штаммами микроорганизмов. Через 12–24 ч зоны задержки роста микроорганизмов вокруг исследуемых фрагментов составляли 15–18 мм, подтверждая тем самым сохранение остаточной антимикробной активности эксплантатов после их имплантации. За период наблюдения у 1,9 % больных в ближайшем послеоперационном периоде и у 4,1 % пациентов в отдаленном периоде наступил тромбоз эксплантатов. Поверхностное нагноение послеоперационной раны отмечалось у 155 (4,3 %), глубокое нагноение – у 51 (1,4%) больных. Послеоперационная летальность составила 2,7%.Заключение. Эксплантаты «БАСЭКС» демонстрируют удовлетворительные антимикробные, тромборезистентные свойства и могут широко применяться в сердечно-сосудистой хирургии.

Derepression of the Plant Chromovirus LORE1 Induces Germline Transposition in Regenerated Plants

Transposable elements represent a large proportion of the eukaryotic genomes. Long Terminal Repeat (LTR) retrotransposons are very abundant and constitute the predominant family of transposable elements in plants. Recent studies have identified chromoviruses to be a widely distributed lineage of Gypsy elements. These elements contain chromodomains in their integrases, which suggests a preference for insertion into heterochromatin. In turn, this preference might have contributed to the patterning of heterochromatin observed in host genomes. Despite their potential importance for our understanding of plant genome dynamics and evolution, the regulatory mechanisms governing the behavior of chromoviruses and their activities remain largely uncharacterized. Here, we report a detailed analysis of the spatio-temporal activity of a plant chromovirus in the endogenous host. We examined LORE1a, a member of the endogenous chromovirus LORE1 family from the model legume Lotus japonicus. We found that this chromovirus is stochastically de-repressed in plant populations regenerated from de-differentiated cells and that LORE1a transposes in the male germline. Bisulfite sequencing of the 5′ LTR and its surrounding region suggests that tissue culture induces a loss of epigenetic silencing of LORE1a. Since LTR promoter activity is pollen specific, as shown by the analysis of transgenic plants containing an LTR::GUS fusion, we conclude that male germline-specific LORE1a transposition in pollen grains is controlled transcriptionally by its own cis-elements. New insertion sites of LORE1a copies were frequently found in genic regions and show no strong insertional preferences. These distinctive novel features of LORE1 indicate that this chromovirus has considerable potential for generating genetic and epigenetic diversity in the host plant population. Our results also define conditions for the use of LORE1a as a genetic tool