Nonrigid chiral soliton for the octet and decuplet baryons

Systematic treatment of the collective rotation of the nonrigid chiral soliton is developed in the SU(3) chiral quark soliton model and applied to the octet and decuplet baryons. The strangeness degrees of freedom are treated by a simplified bound-state approach which omits the locality of the kaon wave function. Then, the flavor rotation is divided into the isospin rotation and the emission and absorption of the kaon. The kaon Hamiltonian is diagonalized by the Hartree approximation. The soliton changes the shape according to the strangeness. The baryons appear as the rotational bands of the combined system of the soliton and the kaon.Comment: 11 pages(LaTex), 1 figures(eps

A prominent β-hairpin structure in the winged-helix domain of RECQ1 is required for DNA unwinding and oligomer formation

RecQ helicases have attracted considerable interest in recent years due to their role in the suppression of genome instability and human diseases. These atypical helicases exert their function by resolving a number of highly specific DNA structures. The crystal structure of a truncated catalytic core of the human RECQ1 helicase (RECQ149–616) shows a prominent β-hairpin, with an aromatic residue (Y564) at the tip, located in the C-terminal winged-helix domain. Here, we show that the β-hairpin is required for the DNA unwinding and Holliday junction (HJ) resolution activity of full-length RECQ1, confirming that it represents an important determinant for the distinct substrate specificity of the five human RecQ helicases. In addition, we found that the β-hairpin is required for dimer formation in RECQ149–616 and tetramer formation in full-length RECQ1. We confirmed the presence of stable RECQ149–616 dimers in solution and demonstrated that dimer formation favours DNA unwinding; even though RECQ1 monomers are still active. Tetramers are instead necessary for more specialized activities such as HJ resolution and strand annealing. Interestingly, two independent protein–protein contacts are required for tetramer formation, one involves the β-hairpin and the other the N-terminus of RECQ1, suggesting a non-hierarchical mechanism of tetramer assembly

Extended Hauser-Feshbach Method for Statistical Binary-Decay of Light-Mass Systems

An Extended Hauser-Feshbach Method (EHFM) is developed for light heavy-ion fusion reactions in order to provide a detailed analysis of all the possible decay channels by including explicitly the fusion-fission phase-space in the description of the cascade chain. The mass-asymmetric fission component is considered as a complex-fragment binary-decay which can be treated in the same way as the light-particle evaporation from the compound nucleus in statistical-model calculations. The method of the phase-space integrations for the binary-decay is an extension of the usual Hauser-Feshbach formalism to be applied to the mass-symmetric fission part. The EHFM calculations include ground-state binding energies and discrete levels in the low excitation-energy regions which are essential for an accurate evaluation of the phase-space integrations of the complex-fragment emission (fission). In the present calculations, EHFM is applied to the first-chance binary-decay by assuming that the second-chance fission decay is negligible. In a similar manner to the description of the fusion-evaporation process, the usual cascade calculation of light-particle emission from the highly excited complex fragments is applied. This complete calculation is then defined as EHFM+CASCADE. Calculated quantities such as charge-, mass- and kinetic-energy distributions are compared with inclusive and/or exclusive data for the $^{32}$S+$^{24}$Mg and $^{35}$Cl+$^{12}$C reactions which have been selected as typical examples. Finally, the missing charge distributions extracted from exclusive measurements are also successfully compared with the EHFM+CASCADE predictions.Comment: 34 pages, 6 Figures available upon request, Phys. Rev. C (to be published

Instability of the hedgehog shape for the octet baryon in the chiral quark soliton model

In this paper the stability of the hedgehog shape of the chiral soliton is studied for the octet baryon with the SU(3) chiral quark soliton model. The strangeness degrees of freedom are treated by a simplified bound-state approach, which omits the locality of the kaon wave function. The mean field approximation for the flavor rotation is applied to the model. The classical soliton changes shape according to the strangeness. The baryon appears as a rotational band of the combined system of the deformed soliton and the kaon.Comment: 24 pages, LaTeX, 8 eps file

Unforeseen misuses of bed nets in fishing villages along Lake Victoria

<p>Abstract</p> <p>Background</p> <p>To combat malaria, the Kenya Ministry of Health and nongovernmental organizations (NGOs) have distributed insecticide-treated nets (ITNs) for use over beds, with coverage for children under five years of age increasing rapidly. Nevertheless, residents of fishing villages have started to use these bed nets for drying fish and fishing in Lake Victoria. This study investigated the extent of bed net misuse in fishing villages.</p> <p>Methods</p> <p>Seven fishing villages along the lake were surveyed to estimate how widely bed nets were being used for fishing and drying fish. Villagers were asked why they used the bed nets for such purposes.</p> <p>Results</p> <p>In total, 283 bed nets were being used for drying fish. Of these, 239 were long-lasting insecticidal bed nets (LLIN) and 44 were non-long-lasting insecticidal bed nets (NLLIN). Further, 72 of the 283 bed nets were also being used for fishing. The most popular reasons were because the bed nets were inexpensive or free and because fish dried faster on the nets. LLINs were preferred to NLLINs for fishing and drying fish.</p> <p>Conclusion</p> <p>There is considerable misuse of bed nets for drying fish and fishing. Many villagers are not yet fully convinced of the effectiveness of LLINs for malaria prevention. Such misuses may hamper the efforts of NGOs and governmental health organizations.</p

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org

Association of Human Leukocyte Antigen with Interstitial Lung Disease in Rheumatoid Arthritis: A Protective Role for Shared Epitope

INTRODUCTION: Interstitial Lung Disease (ILD) is frequently associated with Rheumatoid Arthritis (RA) as one of extra-articular manifestations. Many studies for Human Leukocyte Antigen (HLA) allelic association with RA have been reported, but few have been validated in an RA subpopulation with ILD. In this study, we investigated the association of HLA class II alleles with ILD in RA. METHODS: An association study was conducted on HLA-DRB1, DQB1, and DPB1 in 450 Japanese RA patients that were or were not diagnosed with ILD, based on the findings of computed tomography images of the chest. RESULTS: Unexpectedly, HLA-DRB1*04 (corrected P [Pc] = 0.0054, odds ratio [OR] 0.57), shared epitope (SE) (P = 0.0055, OR 0.66) and DQB1*04 (Pc = 0.0036, OR 0.57) were associated with significantly decreased risk of ILD. In contrast, DRB1*16 (Pc = 0.0372, OR 15.21), DR2 serological group (DRB1*15 and *16 alleles) (P = 0.0020, OR 1.75) and DQB1*06 (Pc = 0.0333, OR 1.57, respectively) were significantly associated with risk of ILD. CONCLUSION: HLA-DRB1 SE was associated with reduced, while DR2 serological group (DRB1*15 and *16) with increased, risk for ILD in Japanese patients with RA

The Gypsy Database (GyDB) of mobile genetic elements

In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es

Distribution of a Knockdown Resistance Mutation (L1014S) in Anopheles gambiae s.s. and Anopheles arabiensis in Western and Southern Kenya

In Kenya, insecticide-treated mosquito nets (ITNs) distributed to pregnant women and children under 5 years old through various programs have resulted in a significant reduction in malaria deaths. All of the World Health Organization-recommended insecticides for mosquito nets are pyrethroids, and vector mosquito resistance to these insecticides is one of the major obstacles to an effective malaria control program. Anopheles gambiae s.s. and Anopheles arabiensis are major malaria vectors that are widely distributed in Kenya. Two point mutations in the voltage-gated sodium channel (L1014F and L1014S) are associated with knockdown resistance (kdr) to DDT and pyrethroids in An. gambiae s.s. While the same point mutations have been reported to be rare in An. arabiensis, some evidence of metabolic resistance has been reported in this species. In order to determine the distribution of the point mutation L1014S in An. gambiae s.s. and An. arabiensis in southern and western Kenya, we collected larvae and screened for the mutation by DNA sequencing. We found high allelic and homozygous frequencies of the L1014S mutation in An. gambiae s.s. The L1014S mutation was also widely distributed in An. arabiensis, although the allelic frequency was lower than in An. gambiae s.s. The same intron sequence (length: 57 base) found in both species indicated that the mutation was introgressed by hybridization. The allelic frequency of L1014S was higher in both species in western regions, demonstrating the strong selection pressure imposed by long-lasting insecticide-treated nets (LLITN)/ITN on the An. gambiae s.s. and An. arabiensis populations in those areas. The present contribution of the L1014S mutation to pyrethroid resistance in An. arabiensis may be negligible. However, the homozygous frequency could increase with continuing selection pressure due to expanded LLITN coverage in the future

How much locomotive activity is needed for an active physical activity level: analysis of total step counts

<p>Abstract</p> <p>Background</p> <p>Although physical activity recommendations for public health have focused on locomotive activity such as walking and running, it is uncertain how much these activities contribute to overall physical activity level (PAL). The purpose of the present study was to determine the contribution of locomotive activity to PAL using total step counts measured in a calorimeter study.</p> <p>Methods</p> <p>PAL, calculated as total energy expenditure divided by basal metabolic rate, was evaluated in 11 adult men using three different conditions for 24-hour human calorimeter measurements: a low-activity day (L-day) targeted at a low active level of PAL (1.45), and a high-frequency moderate activity day (M-day) or a high-frequency vigorous activity day (V-day) targeted at an active level of PAL (1.75). These subjects were permitted only light activities except prescribed activities. In a separate group of 41 adults, free-living PAL was evaluated using doubly-labeled water (DLW). In both experiments, step counts per day were also measured using an accelerometer.</p> <p>Results</p> <p>In the human calorimeter study, PAL and step counts were 1.42 ± 0.10 and 8,973 ± 543 steps/d (L-day), 1.82 ± 0.14 and 29,588 ± 1,126 steps/d (M-day), and 1.74 ± 0.15 and 23,755 ± 1,038 steps/d (V-day), respectively. In the DLW study, PAL and step counts were 1.73 ± 0.15 and 10,022 ± 2,605 steps/d, and there was no significant relationship between PAL and daily step counts.</p> <p>Conclusions</p> <p>These results indicate that an enormous number of steps are needed for an active level of PAL if individuals extend physical activity-induced energy expenditure by only locomotive activity. Therefore, non-locomotive activity such as household activity should also play a significant role in increasing PAL under free-living conditions.</p