A Mutual Information Based Sequence Distance For Vertebrate Phylogeny Using Complete Mitochondrial Genomes

Traditional sequence distances require alignment. A new mutual information based sequence distance without alignment is defined in this paper. This distance is based on compositional vectors of DNA sequences or protein sequences from complete genomes. First we establish the mathematical foundation of this distance. Then this distance is applied to analyze the phylogenetic relationship of 64 vertebrates using complete mitochondrial genomes. The phylogenetic tree shows that the mitochondrial genomes are separated into three major groups. One group corresponds to mammals; one group corresponds to fish; and the last one is Archosauria (including birds and reptiles). The structure of the tree based on our new distance is roughly in agreement in topology with the current known phylogenies of vertebrates

Effect of air core on the shape and discharge of the outflow through a bottom outlet

AbstractExperiments were conducted to study the generation of air core and its effect on the outflow shape and discharge in a cylindrical water tank with a bottom well-designed outlet. Depending on the stages of the air core in the tank, the outflow shape can vary from a smooth water jet to a smooth spindle shape with air-core, and to water sprays. The diameter of the nozzle size also has influence on the outflow pattern. The existence of the penetrated air core can dramatically reduce the outflow discharge, with the discharge coefficient decreasing with the nozzle diameter

Autogeneic RNA-electroporated CD40-ligand activated B-cells from hepatocellular carcinoma patients induce CD8+ T-cell responses ex vivo

Since dendritic cells (DCs) constitute only 0.1–0.5% of human peripheral blood mononuclear cells (PBMCs), and generation of DCs from monocytes or stem cells is difficult and expensive, we choose B-lymphocytes as an alternative, cost-effective source of antigen presenting cells (APC). Aim: To induce specific CTLs response ex vivo by CD40L activated B-cells (CD40-B) transfected with hepatocellular carcinoma (HCC) total RNA. Methods: To induce CD40-B PBMCs of patients with HCC were isolated by Ficoll technique and cultured in RMPI 1640 supplemented with 10% fetal calf serum (FCS), sCD40L (2 µg/ml), recombinant human interleukin-4 (IL-4) (4 ng/ml). The expression of CD80 and CD86 was evaluated by flow cytometry. The level of interleukin-12 (IL-12) produced by cultured B-lymphocytes was measured using enzyme-linked immunosorbent assay (ELISA). HCC patient’s T-lymphocytes were obtained from PBMCs cultured in RMPI 1640 supplemented with 10% FCS, 2 ng/mL IL-4 and 10 ng/ml IL-7. CD40-B transfected with tumor total RNA isolated from HCC cells were used to induce specific CTL proliferation. The level of IFN-g was measured using ELISA and the expression of CD8 was determined by FCAS. Specific cytotoxicity was measured using MTT method. Results: The results show that the activated B-lymphocytes were easily expandable and formed large clones, and a high expression of CD80/CD86 and a high IL-12 secretion by CD40-B was registered. CD40-B transfected with tumor total RNA can induce CTLs to express CD8 and generate IFN-g at high levels. Compared to the control group, the specific cytotoxicity of CTLs was up-regulated. Conclusion: These findings demonstrate that CD40-B-cells electroporated with total RNA derived from carcinoma cells can be used as alternative APC for the induction of antigen-specific CD8+ T-cell responses, which might be used in HCC immunotherapy.Поскольку дендритные клетки (ДК) составляют только 0,1–0,5% мононуклеаров периферической крови (МПК) человека, и получение ДК из моноцитов и стволовых кроветворных клеток является трудоемкой и дорогостоящей процедурой, выбраны В-лимфоциты в качестве альтернативного источника антигенпрезентирующих клеток (АПК). Цель: изучить возможность активированных CD40-лигандом В-лимфоцитов (CD40-B), трансфецированных суммарной РНК, выделенной из клеток гепатоцеллюлярной карциномы, индуцировать специфический ответ цитотоксических Т-лимфоцитов ex vivo Методы: МПК пациентов с гепатоцеллюлярной карциномой изолировали на градиенте фиколла и культивировали в среде RMPI 1640 с 10% эмбриональной сыворотки телят (ЭСТ), sCD40 (2 мкг/мл) и рекомбинантным человеческим интерлейкином-4 (ИЛ-4, 4 нг/мл). Экспрессию СD80 и CD86 оценивали на проточном цитофлюориметре. Концентрацию интерлейкина-12, продуцируемого культивируемыми В-лимфоцитами, оценивали с помощью иммуноферментного анализа (ИФА). Т-лимфоциты получали из МПК пациентов с гепатоцеллюлярной карциномой и культивировали в среде RMPI 1640 с 10% ЭСТ, 2 нг/мл ИЛ-4 и 10 нг/мл ИЛ-7 и культивированы совместно с CD40- клетками, трансфецированными опухолевой РНК, для индукции пролиферации специфических цитотоксических Т-лимфоцитов. Уровень интерферона- (ИНФ-γ) определяли с помощью ИФА, а экспрессию CD8 на проточном цитофлуориметре. Специфическую цитотоксичность оценивали в МТТ тесте. Результаты: показано, что активированные in В-лимфоциты формируют большие колонии, на поверхности клеток отмечается высокая экспрессия антигенов CD80/CD86, и ими в повышенных количествах секретируется ИЛ-12. CD40-B-лимфоциты, трансфецированные опухолевой РНК, могут активировать CD + цитотоксические лимфоциты, которые продуцируют ИНФ-γ. Выводы: CD40-B-клетки, трансфецированные суммарной РНК, выделенной из опухолевых клеток больных с гепатоцеллюлярной карциномой, — это альтернативные АПК для индукции антигенспецифического CD + T-клеточного ответа, что может быть использовано для иммунотерапии пациентов с гепатоцеллюлярной карциномой

The mechanism of the polarization dependence of the optical transmission in subwavelength metal hole arrays

We investigate the mechanism of extraordinary optical transmission in subwave-length metal hole arrays. Experimental results for the arrays consisting of square or rectangle holes are well explained about the dependence of transmission strength on the polarization direction of the incident light. This polarization dependence occurs in each single-hole. For a hole array, there is in addition an interplay between the adjacent holes which is caused by the transverse magnetic field of surface plasmon polariton on the metal film surfaces. Based on the detailed study of a single-hole and two-hole structures, a simple method to calculate the total tranmissivity of hole arrays is proposed.Comment: 34 pages, 7 figure

Orbit- and Atom-Resolved Spin Textures of Intrinsic, Extrinsic and Hybridized Dirac Cone States

Combining first-principles calculations and spin- and angle-resolved photoemission spectroscopy measurements, we identify the helical spin textures for three different Dirac cone states in the interfaced systems of a 2D topological insulator (TI) of Bi(111) bilayer and a 3D TI Bi2Se3 or Bi2Te3. The spin texture is found to be the same for the intrinsic Dirac cone of Bi2Se3 or Bi2Te3 surface state, the extrinsic Dirac cone of Bi bilayer state induced by Rashba effect, and the hybridized Dirac cone between the former two states. Further orbit- and atom-resolved analysis shows that s and pz orbits have a clockwise (counterclockwise) spin rotation tangent to the iso-energy contour of upper (lower) Dirac cone, while px and py orbits have an additional radial spin component. The Dirac cone states may reside on different atomic layers, but have the same spin texture. Our results suggest that the unique spin texture of Dirac cone states is a signature property of spin-orbit coupling, independent of topology

Longitudinal bioimpedance vector plots add little value to fluid management of peritoneal dialysis patients

Bioimpedance (BI) has the potential to enable better management of fluid balance, which can worsen over time on peritoneal dialysis (PD) due to loss of residual kidney function and progressive muscle wasting. We undertook a prospective, randomized, open-label, blinded end-point controlled trial to determine whether availability of longitudinal BI measures as vector plots helped clinicians maintain stable fluid status over 12 months in 308 peritoneal dialysis patients from the United Kingdom and Shanghai, China. Patients were recruited into 4 groups nested within a single trial design according to country and residual kidney function. Nonanuric subjects from both countries demonstrated stable fluid volumes irrespective of randomization. Hydration worsened in control anuric patients in Shanghai with increased extracellular/total body water (ECW/TBW) ratio (0.04; 95% CI: 0.01, 0.06) and reduced TBW (-1.76 L 95% CI: -2.70, -0.82), but was stable in the BI intervention group whose dialysate glucose prescription was increased. However, multilevel analysis incorporating data from both countries showed worsening ECW/TBW in active and control anuric patients. Clinicians in the United Kingdom reduced target weight in the nonanuric BI intervention group causing a reduction in TBW without beneficial effects on ECW or blood pressure. Thus, routine use of longitudinal BI vector plots to improve clinical management of fluid status is not supported.Kidney International advance online publication, 14 October 2015; doi:10.1038/ki.2015.294