Local perturbations of periodic systems. Chemisorption and point defects by GoGreenGo

We present a software package GoGreenGo-an overlay aimed to model local perturbations of periodic systems due to either chemisorption or point defects. The electronic structure of an ideal crystal is obtained by worldwide-distributed standard quantum physics/chemistry codes, and then processed by various tools performing projection to atomic orbital basis sets. Starting from this, the perturbation is addressed by GoGreenGo with use of the Green's functions formalism, which allows evaluating its effect on the electronic structure, density matrix, and energy of the system. In the present contribution, the main accent is made on processes of chemical nature, such as chemisorption or doping. We address a general theory and its computational implementation supported by a series of test calculations of the electronic structure perturbations for benchmark model solids: simple, face-centered, and body-centered cubium systems. In addition, more realistic problems of local perturbations in graphene lattice, such as lattice substitution, vacancy, and "on-top" chemisorption, are considered.

X-ray micro-computed tomography in the assessment of penile cavernous fibrosis in a rabbit castration model

BACKGROUND

Current assessment methods of penile cavernous fibrosis in animal models have limitations due to the inability to provide complex and volume analysis of fibrotic alterations.

OBJECTIVE

The aim was to evaluate micro-computed tomography (micro-CT) for assessment of cavernous fibrosis and compare it with histological, histochemical, immunohistochemical, and RT-PCR analysis.

MATERIALS AND METHODS

A controlled trial was performed involving 25 New Zealand male rabbits with induced testosterone deficiency by orchidectomy. Penile samples were obtained before and after 7, 14, 21, 84 days from orchidectomy. We consistently performed: a) gray value analysis of corpora cavernosa 3D models reconstructed after micro-CT; b) morphometry of smooth muscles/connective tissue ratio, collagen type I/III ratio, and area of TGF-beta-1 expression in corpora cavernosa; c) RT-PCR of TGF-beta-1 expression.

RESULTS

Micro-CT allowed visualization of penile structures at the resolution comparable to light microscopy. Gray values of corpora cavernosa decreased from 1673 (1512-1773) on the initial day to 1184 (1089-1232) on 21 day (p < 0,005); however, on 84 day, it increased to 1610 (1551-1768). At 21 and 84 days, there were observed a significant decrease in smooth muscle/connective tissue ratio and a significant increase in collagen type I/III ratio (p < 0,05). TGF-beta1 expression increased on 84 day according to immunohistochemistry (p < 0,005). RT-PCR was impossible to conduct due to the absence of RNA in obtained samples after micro-CT.

DISCUSSION AND CONCLUSIONS

Micro-CT provided 3D visualization of entire corpora cavernosa and assessment of radiodensity alterations by gray value analysis in fibrosis progression. We speculate that gray value changes at early and late fibrosis stages could be related to tissue reorganization. RT-PCR is impossible to conduct on tissue samples studied by micro-CT due to RNA destruction. We also suggest that micro-CT could negatively affect the immunohistochemical outcome, as a significant increase of TGF-beta-1 expression occurs later than histological fibrotic signs. This article is protected by copyright. All rights reserved.

Genome assembly using quantum and quantum-inspired annealing

Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a reference, require solving tasks of high computational complexity. Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the [Formula: see text]X 174 bacteriophage. Our results pave a way for a significant increase in the efficiency of solving bioinformatics problems with the use of quantum computing technologies and, in particular, quantum annealing might be an effective method. We expect that the new generation of quantum annealing devices would outperform existing techniques for de novo genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques.

Relative stability of diamond and graphite as seen through bonds and hybridizations

The relative stability of the two most important forms of elemental carbon, diamond and graphite, is readdressed from a newly developed perspective as derived from historically well-known roots. Unlike other theoretical studies mostly relying on numerical methods, we consider an analytical model to gain fundamental insight into the reasons for the quasi-degeneracy of diamond and graphite despite their extremely different covalent bonding patterns. We derive the allotropes' relative energies and provide a qualitative picture predicting a quasi-degenerate electronic ground state for graphite (graphene) and diamond at zero temperature. Our approach also gives numerical estimates of the energy difference and interatomic separations in good agreement with experimental data and recent results of hybrid DFT modeling, although obtained with a much smaller numerical but highly transparent effort. An attempt to extend this treatment to the lowest energy allotropes of silicon proves to be successful as well.

Deductive molecular mechanics of four-coordinated carbon allotropes

We propose a semi-quantitative quantum-chemical model ranging the energies of four-coordinated carbon allotropes on the energy scale and providing efficient and precise estimates of their structure and elastic properties (hardness).

[Sensitivity of the diamagnetic condensed matter to weak magnetic fields]

It is shown that, under the influence of magnetic field, rotational moments of the same direction appear for all charged particles having the same sign of their charge and freely moving in a thermal fluctuational electromagnetic field in a diamagnetic condensed matter. The magnitude of this rotational moment is proportional to the thermal energy kT and can be substantially increased when the conditions for cyclotron resonance are satisfied. The moments of positively charged particles are directed oppositely to the vector of the magnetic field induction. The so-called "kT problem" has been solved. The evidence for magnetosensitivity is the appearance of rotational moments acting on the particles from the thermal field in the presence of an external magnetic field as a small factor.

[Structure of the metaepiphyseal growth plate cartilage in conditions of total isolation from cellular and humoral influences after its transplantation into soft tissues (an experimental study)]

The aim of this study was to determine the effect of a skeletal muscle on the cartilage of growth plate of metaepiphyseal explants of tubular bones of growing and mature Chinchilla rabbits (n = 18) under conditions of their isolation from cellular and humoral influences. In experimental animals, metaepiphyseal explants of metatarsal bones, containing growth plate, were sealed in polyethylene film and were placed, under local anesthesia, in the femoral muscles. One week later these grafts were removed and studied histologically. Despite the absence of the effects of biologically active substances and immunocompetent cells of the donor (foreign) organism, the exposure of the cartilage plate to the environment of the muscular tissue lead to some typical changes in its structure. The results obtained may indicate the susceptibility of the cartilage growth plates to the action of some distant factors, probably, of an electromagnetic nature. The detection of these factors is promising for the development of clinical methods of the stimulation of the damaged cartilage growth plates for the correction of bone deformities.

[Minor congenital malformations: prognostic indicator of ill-being of an infant born by alcoholic mother]

This work presents the results of a comparative analysis of risk factors and phenotypical characteristics of 228 children with fetal alcohol syndrome and of 347 children with hypoxicischemic encepalopathy. The study of a phenotype detected that an average number of minor congenital malformations in children with fetal alcohol syndrome was equal to 12.2 while in comparison group it was equal to 7.3. High prevalence of stigmata was associated with an increased frequency congenital malformations of internal organs and mental disorders in children by the age of 4.

[Reparative bone regeneration after aseptic necrosis of the femoral head as influenced by 1-chloromethylsilatrane treatment]

The aim of this work was to study the effect of 1-chloromethyisilatranum on the processes of reparative bone regeneration in experimentally induced aseptic femoral head necrosis. Aseptic femoral head necrosis was modeled in 4 Chinchilla rabbits by destruction of spongy substance of femoral neck and cutting of ligamentum teres of its head. Rabbits of the experimental group were injected with 0.4 ml of 1% solution of 1-chloromethylsilatranum on postoperational days 5, 10, 15 and 20 into the damaged femoral head and close to the damaged joint. Animal were sacrificed by air embolism 5 weeks from the start of an experiment. Necrotic and repair processes in hip joints from damaged and intact sides were assessed radiologically and histologically prior to sacrifice. In rabbits of both control and experimental groups extensive aseptic necrosis of hip joints was found. The osseous tissue of damaged hip joints of experimental animals contained the chains of osteoblasts actively producing new bone matrix. Foci of bone regeneration were found both in the deep and peripheral regions of the epiphysis, which is indicative of active processes of bone repair. The results obtained suggest that administration of organic-silicon drug 1-chloromethylsilatranum stimulates (optimizes) the processes of repair osteogenesis following aseptic femoral head necrosis in experimental animals. Application of this preparation appears to be very promising.

[Terminology: Why were small congenital anomalies called degenerative stigmas or small signs of birth defects?]

The problem of small developmental anomalies has once again become actual not only for geneticists but also for practical public health. Before using complicated and expensive laboratory methods of investigation the surgeon, orthopedist, traumatologist and neurologist should carefully and thoughtfully examine the external signs of pathology of the patient. Having detected "small" anomalies the doctor may start looking for a "large" pathology--a serious disease of internal organs, locomotor system and nervous system. It seems to be of importance under conditions of insurance medicine when many laboratory investigations are expensive or not available.

[A rare complication of conduction anesthesia in the treatment of finger injury]

At the present time novocain still remains the anesthetic of choice in ambulatory surgery and traumatology. In practical work the 2% and 0.5% solutions are used. The 2% solution of novocain can in some cases (in patients prone to angiodystonic reactions) cause a persistent spasm of digital arteries that results in irreversible alterations in finger tissues down to the development of gangrene. This fact was confirmed in experiments with 2% solutions of novocain. It is proposed to follow the recommendations on using the 0.5% and 1% solutions of novocain for regional anesthesia in fingers. Such anesthetics as Lidocain and Trimecain should be used more widely since they possess more pronounced and continuous anesthetizing properties.

[Comparative study of centralized and decentralized outpatient surgical services]

The results of work of decentralized and centralized out-patient surgical service in two regions of the city of Novokuznetsk are compared. The authors make a conclusion that the centralized out-patient surgical service has a number of advantages as compared with the decentralized service since it allows to concentrate the material resources, to improve the staff of specialists, to widen the volume and spectrum of the medical care and makes prerequisites for profitable work of the institution under conditions of the market relations and competition.

[Quality of life in patients after coloesophagoplasty, performed in childhood]

Based on questionnaire, the authors analyze long-term results of coloesophagoplasty in 32 patients operated from 1990 to 2000. At the moment of operation age of the children ranged from 3 months to 14 years (5 years, on the average). 1 (3.1%) patient died at the age of 15 years, 9 years after esophageal plasty. Long-term results were evaluated in 31 respondents. Most respondents (81.3%) evaluate their state late after coloesophagoplasty as good and satisfactory. All the respondents take meal without assistance 74% patients don't keep a diet. Respondents with severe concomitant diseases (VACNERL--syndrome, bullous epidermolisis, CNS disorders) evaluate their state as unsatisfactory. In children after coloesophagoplasty falling behind growth (48%) and weight (62%) was revealed due to disease and low living standard. 89.5% respondents evaluate their quality of life as satisfactory.