Analyzing X-Ray Pulsar Profiles: Geometry and Beam Pattern of Her X-1

We report on our analysis of a large sample of energy dependent pulse profiles of the X-ray binary pulsar Hercules X-1. We find that all data are compatible with the assumption of a slightly distorted magnetic dipole field as sole cause of the asymmetry of the observed pulse profiles. Further the analysis provides evidence that the emission from both poles is equal. We determine an angle of 20 deg between the rotation axis and the local magnetic axis. One pole has an offset of 5 deg from the antipodal position of the other pole. The beam pattern shows structures that can be interpreted as pencil- and fan-beam configurations. Since no assumptions on the polar emission are made, the results can be compared with various emission models. A comparison of results obtained from pulse profiles of different phases of the 35-day cycle indicates different attenuation of the radiation from the poles being responsible for the change of the pulse shape during the main-on state. These results also suggest the resolution of an ambiguity within a previous analysis of pulse profiles of Cen X-3, leading to a unique result for the beam pattern of this pulsar as well. The analysis of pulse profiles of the short-on state indicates that a large fraction of the radiation cannot be attributed to the direct emission from the poles. We give a consistent explanation of both the evolution of the pulse profile and the spectral changes with the 35-day cycle in terms of a warped precessing accretion disk.Comment: 24 pages, 12 figures. To appear in ApJ 529 #2, 1 Feb 200

A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins

Gauging the systemic effects of non-synonymous single nucleotide polymorphisms (nsSNPs) is an important topic in the pursuit of personalized medicine. However, it is a non-trivial task to understand how a change at the protein structure level eventually affects a cell's behavior. This is because complex information at both the protein and pathway level has to be integrated. Given that the idea of integrating both protein and pathway dynamics to estimate the systemic impact of missense mutations in proteins remains predominantly unexplored, we investigate the practicality of such an approach by formulating mathematical models and comparing them with experimental data to study missense mutations. We present two case studies: (1) interpreting systemic perturbation for mutations within the cell cycle control mechanisms (G2 to mitosis transition) for yeast; (2) phenotypic classification of neuron-related human diseases associated with mutations within the mitogen-activated protein kinase (MAPK) pathway. We show that the application of simplified mathematical models is feasible for understanding the effects of small sequence changes on cellular behavior. Furthermore, we show that the systemic impact of missense mutations can be effectively quantified as a combination of protein stability change and pathway perturbation

Digital receivers for low-frequency radio telescopes UTR-2, URAN, GURT

This paper describes digital radio astronomical receivers used for decameter and meter wavelength observations. This paper describes digital radio astronomical receivers used for decameter and meter wavelength observations. Since 1998, digital receivers performing on-the-fly dynamic spectrum calculations or waveform data recording without data loss have been used at the UTR-2 radio telescope, the URAN VLBI system, and the GURT new generation radio telescope. Here we detail these receivers developed for operation in the strong interference environment that prevails in the decameter wavelength range. Data collected with these receivers allowed us to discover numerous radio astronomical objects and phenomena at low frequencies, a summary of which is also presented.Comment: 24 pages, 15 figure

Complex experiment on studying the microphysical, chemical, and optical properties of aerosol particles and estimating the contribution of atmospheric aerosol-to-earth radiation budget

The primary objective of this complex aerosol experiment was the measurement of microphysical, chemical, and optical properties of aerosol particles in the surface air layer and free atmosphere. The measurement data were used to retrieve the whole set of aerosol optical parameters, necessary for radiation calculations. Three measurement cycles were performed within the experiment during 2013: in spring, when the aerosol generation is maximal; in summer (July), when atmospheric boundary layer altitude and, hence, mixing layer altitude are maximal; and in late summer/early autumn, during the period of nucleation of secondary particles. Thus, independently obtained data on the optical, meteorological, and microphysical parameters of the atmosphere allow intercalibration and inter-complement of the data and thereby provide for qualitatively new information which explains the physical nature of the processes that form the vertical structure of the aerosol field

Source contributions to Northern Hemisphere CO and black carbon during spring and summer 2008 from POLARCAT and START08/preHIPPO observations and MOZART-4

International audienceAnthropogenic pollution and wildfires are main producers of carbon monoxide (CO) and black carbon (BC) in the Northern Hemisphere. High concentrations of these compounds are transported into the Arctic troposphere, influencing the ecosystem in high northern latitudes and the global climate. The global chemical transport model MOZART-4 is used to quantify the seasonal evolution of the contribution of CO and BC from different source regions in spring and summer 2008 by tagging their emissions. Aircraft observations from the POLARCAT experiments, in particular NASA ARCTAS, NOAA ARCPAC, POLARCAT-France, DLR GRACE and YAK-AEROSIB, as well as the NSF START08/preHIPPO experiments during Spring-Summer 2008 are combined to quantify the representation of simulated tracer characteristics in anthropogenic and fire plumes. In general, the model reproduces CO and BC well. Based on aircraft measurements and FLEXPART back-trajectories, the altitude contribution of emissions coming from different source regions is well captured in the model. Uncertainties of the MOZART-4 model are identified by comparing the data with model results on the flight tracks and using MOPITT satellite observations. Anthropogenic emissions are underestimated by about 10% in high northern latitudes in spring, and shortcomings exist in simulating fire plumes. The remote impact of East-Siberian fire emissions is underestimated for spring, whereas the impact of Southeast Asian fire emissions to mid-latitude CO values is overestimated by the model. In summer, mid-latitude CO values agree well between model and observations, whereas summer high latitude East-Siberian fire emissions in the model are overestimated by 20% in comparison to observations in the region. On the other hand, CO concentrations are underestimated by about 30% over Alaska and Canada at altitudes above 4 km. BC values are overestimated by the model at altitudes above 4 km in summer. Based on MOZART-4, with tagged CO and BC tracers, anthropogenic emissions of Asia, Europe and the US have the largest contribution to the CO and BC in mid- and high latitudes in spring and summer. Southeast Asian, Chinese and Indian fires have a large impact on CO pollution in spring in low latitudes with a maximum between 20° and 30°, whereas Siberian fires contribute largely to the pollution in high latitudes, up to 10% in spring and up to 30% in summer. The largest contributions to BC values in high latitudes are from anthropogenic emissions (about 70%). CO and BC have larger mass loadings in April than in July, as a result of photochemistry and dynamics

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

Abstract Background Understanding how biomolecules interact is a major task of systems biology. To model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical property of amino acids and evolutionary information in terms of position-specific scoring matrix (PSSM), have been used for DNA or RNA-binding site prediction. However, PSSM is rather designed for PSI-BLAST searches, and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences. Results In the present study, several new descriptors of evolutionary information have been developed and evaluated for sequence-based prediction of DNA and RNA-binding residues using support vector machines (SVMs). The new descriptors were shown to improve classifier performance. Interestingly, the best classifiers were obtained by combining the new descriptors and PSSM, suggesting that they captured different aspects of evolutionary information for DNA and RNA-binding site prediction. The SVM classifiers achieved 77.3% sensitivity and 79.3% specificity for prediction of DNA-binding residues, and 71.6% sensitivity and 78.7% specificity for RNA-binding site prediction. Conclusions Predictions at this level of accuracy may provide useful information for modelling protein-nucleic acid interactions in systems biology studies. We have thus developed a web-based tool called BindN+ (http://bioinfo.ggc.org/bindn+/) to make the SVM classifiers accessible to the research community

Coordinated integral and optical observations of SS433

Results of simultaneous INTEGRAL and optical observations of galactic microquasar SS433 in May 2003 are presented. The analysis of the X-ray and optical eclipse duration and hard X-ray spectra obtained by INTEGRAL together with optical spectroscopy obtained on the 6-m telescope allows us to construct a model of SS433 as a massive X-ray binary. X-ray eclipse in hard X-rays has a depth of ∼ 80% and extended wings. The optical spectroscopy allows us to identify the optical companion as a A5-A7 supergiant and to measure its radial velocity semiamplitude Kv = 132 km/s. A strong heating effect in the optical star atmosphere is discovered spectroscopically. The observed broadband X-ray spectrum 2-100 keV can be described by emission from optically thin thermal plasma with kT ∼ 15 - 20keV

Характеристика пациентов с активным онкологическим процессом и венозными тромбоэмболическими осложнениями, получающих курс химиотерапии (по данным реальной клинической практики ГБУЗ «МГОБ №62 ДЗМ»)

Introduction. Pulmonary embolism (PE) accounts for about 10% in the mortality pattern among cancer patients, which is the second most frequent cause of death.Aim. To identify and characterize patients with active cancer and VTEC receiving chemotherapy (CT) based on the retrospective review of medical records provided by Moscow City Oncology Hospital No. 62 (MCOH No. 62) for the period from 01.2018 to 04.2020.Materials and methods. Medical records of 3,912 patients receiving chemotherapy treatment cycles in the departments of MCOH No. 62 were reviewed. 227 (5.8%) patients in whom the underlying disease course was complicated by VTEC were selected. Sites of primary tumours, n (%): stomach – 37 (16.3); colon and rectum – 36 (15.9); uterus, cervix, ovaries – 31 (13.7); lungs – 23 (10.1); kidneys, ureters and bladder, testicles – 19 (8.4); pancreas – 18 (7.9); soft tissues – 14 (6.2); mammary gland – 13 (5.7); lymphoma, myeloma – 8 (3.5); Ear Nose Throat (ENT) tumours – 7 (3); others – 21 (9.3).Results. The majority of patients (176 (77.5%)) had a sum Khorana score <3, 51 (22.5%) patients had Khorana scores ≥ 3, which corresponds to a high thrombotic risk. 29 (12.7%) patients died. The hospital physicians assessed the causes of death as follows: 16 patients died from pulmonary embolism, of which 13 (81%) had a sum Khorana score <3; 13 patients died due to progression of cancer.Conclusions. VTEC most commonly occurred in patients with gastrointestinal cancer (32.2%) and genito-urinary system cancer (22.1%). Half (54.5%) of VTEC occurred in the first 3 months of chemotherapy treatment. The Khorana scale is non-perfect in ‘real-life’ clinical practice (only 22.5% of patients with verified VTEC had a high thrombotic risk, and 81% of patients who died due to PE had a low and medium risk of VTEC).Введение. В структуре смертности онкобольных на тромбоэмболию легочной артерии (ТЭЛА) приходится около 10%, что является второй по частоте причиной смерти. Цель исследования. На основе ретроспективного анализа медицинской документации МГОБ №62 за период с 01.2018 по 04.2020 г. найти и охарактеризовать пациентов с активным раком и ВТЭО, получающих химиотерапию (ХТ). Материалы и методы. Были проанализированы случаи лечения 3 912 пациентов, получавших циклические курсы ХТ в отделениях МГОБ №62. Были отобраны 227 (5,8%) пациентов, у которых течение основного заболевания осложнилось ВТЭО. Локализация первичной опухоли, n (%): желудок – 37 (16,3); толстая и прямая кишка – 36 (15,9); матка, шейка матки, яичники – 31 (13,7); легкие – 23 (10,1); почки, мочеточники и мочевой пузырь, яички – 19 (8,4); поджелудочная железа – 18 (7,9); мягкие ткани – 14 (6,2); молочная железа – 13 (5,7); лимфома, миелома – 8 (3,5); опухоли лор-органов – 7 (3); другие – 21 (9,3). Результаты. Сумма баллов по шкале Khorana < 3 отмечалась у большинства пациентов – 176 (77,5%), ≥ 3 баллов по шкале Khorana – у 51 (22,5%) пациента, что соответствует высокому тромботическому риску. Умерли 29 (12,7%) пациентов. Оценка причин смерти, по мнению лечащих врачей: 16 пациентов – от ТЭЛА, из них у 13 (81%) сумма баллов по шкале Khorana < 3 баллов; у 13 пациентов причина смерти – прогрессирование онкологического заболевания. Выводы. Чаще всего ВТЭО возникали у больных раком ЖКТ (32,2%) и раком МПС (22,1%). Половина (54,5%) ВТЭО возникали в первые 3 мес. ХТ. Шкала Khoranа несовершенна в реальной клинической практике (только 22,5% больных с верифицированным ВТЭО имели высокий тромботический риск, а 81% больных, умерших от ТЭЛА, имели низкий и средний риск ВТЭО)

The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures

Repeat-proteins are made up of near repetitions of 20– to 40–amino acid stretches. These polypeptides usually fold up into non-globular, elongated architectures that are stabilized by the interactions within each repeat and those between adjacent repeats, but that lack contacts between residues distant in sequence. The inherent symmetries both in primary sequence and three-dimensional structure are reflected in a folding landscape that may be analyzed as a quasi–one-dimensional problem. We present a general description of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction energetics in and between foldons, whose collective ensemble are treated as spin variables. The overall folding properties of a complete “domain” (the stability and cooperativity of the repeating array) can be derived from this microscopic description. The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (ΔGwater) and the cooperativity of denaturation (m-value), which do not ordinarily apply for globular proteins. We show how the parameters for the “coarse-grained” description in terms of foldon spin variables can be extracted from more detailed folding simulations on perfectly funneled landscapes. To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR) repeat proteins and quantitatively relate the results to the experimentally observed folding transitions. Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are “poised” at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions

INTEGRAL observations of SS433: Results of a coordinated campaign

Results of simultaneous INTEGRAL and optical observations of the galactic microquasar SS433 in May 2003 and INTEGRAL/RXTE observations in March 2004 are presented. Persistent precessional variability with a maximum to minimum uneclipsed hard X-ray flux ratio of ∼4 is discovered. The 18-60 keV X-ray eclipse is found to be in phase with optical and near infrared eclipses. The orbital eclipse observed by INTEGRAL in May 2003 is at least two times deeper and apparently wider than in the soft X-ray band. The broadband 2-100 keV X-ray spectrum simultaneously detected by RXTE/INTEGRAL in March 2004 can be explained by bremsstrahlung emission from optically thin thermal plasma with kT ∼ 30 keV. Optical spectroscopy with the 6-m SAO BTA telescope confirmed the optical companion to be an A5-A7 supergiant. For the first time, spectorscopic indications of a strong heating effect in the optical star atmosphere are found. The measurements of absorption lines which are presumably formed on the non-illuminated side of the supergiant yield its radial velocity semi-amplitude Kv = 132 ±9 km s-1. The analysis of the observed hard X-ray light curve and the eclipse duration, combined with the spectroscopically determined optical star radial velocity corrected for the strong heating effect, allows us to model SS433 as a massive X-ray binary. Assuming that the hard X-ray source in SS433 is eclipsed by the donor star that exactly fills its Roche lobe, the masses of the optical and compact components in SS433 are suggested to be Mv ≈ 30 M⊙ and Mx ≈ 9 M⊙, respectively. This provides further evidence that SS433 is a massive binary system with supercritical accretion onto a black hole. © ESO 2005