Breakdown of Magnetic Order in the Pressurized Kitaev Iridate β-Li_{2}IrO_{3}

Temperature-pressure phase diagram of the Kitaev hyperhoneycomb iridate β-Li_{2}IrO_{3} is explored using magnetization, thermal expansion, magnetostriction, and muon spin rotation measurements, as well as single-crystal x-ray diffraction under pressure and ab initio calculations. The Néel temperature of β-Li_{2}IrO_{3} increases with the slope of 0.9  K/GPa upon initial compression, but the reduction in the polarization field H_{c} reflects a growing instability of the incommensurate order. At 1.4 GPa, the ordered state breaks down upon a first-order transition, giving way to a new ground state marked by the coexistence of dynamically correlated and frozen spins. This partial freezing in the absence of any conspicuous structural defects may indicate the classical nature of the resulting pressure-induced spin liquid, an observation paralleled to the increase in the nearest-neighbor off-diagonal exchange Γ under pressure.

Incidence of contamination of live bird markets in Bangladesh with influenza A virus and subtypes H5, H7 and H9

In the absence of robust active surveillance of avian influenza viruses (AIV) affecting poultry in South Asian countries, monitoring of live bird markets (LBMs) can be an alternative. In a longitudinal study of 32 LBM, five environments were sampled as follows: market floor, stall floor, slaughter area, poultry holding cage and water used for meat processing. Samples were taken monthly for 5 months, September 2013-January 2014. Incidence rates (IRs) of LBM contamination with AIV and its subtypes H5, H7 and H9 were assessed. In 10 of the LBM selected, biosecurity measures had been implemented through FAO interventions: the other 22 were non-intervened. Standard procedures were applied to detect AIV and three subtypes in pooled samples (1:5). An LBM was considered positive for AIV or a subtype if at least one of the pooled samples tested positive. The incidence rates of LBM contamination with AIV, H5, H7 and H9 were 0.194 (95% confidence interval (CI) 0.136-0.276), 0.031 (95% CI 0.013-0.075), 0 and 0.175 (95% CI 0.12-0.253) per LBM-month at risk, respectively. The log IR ratio between the FAO-intervened and non-intervened LBM for contamination with AIV was -0.329 (95% CI -1.052 to -0.394, p = .372), 0.598 (95% CI -1.593 to 2.789, p = .593) with subtype H5 and -0.500 (95% CI -1.249 to 0.248, p = .190) with subtype H9, indicating no significant difference. The results obtained suggest that both H5 and H9 were circulating in LBM in Bangladesh in the second half of 2013. The incidence of contamination with H9 was much higher than with H5.

Designer interface peptide grafts target estrogen receptor alpha dimerization

The nuclear transcription factor estrogen receptor alpha (ERα), triggered by its cognate ligand estrogen, regulates a variety of cellular signaling events. ERα is expressed in 70% of breast cancers and is a widely validated target for anti-breast cancer drug discovery. Administration of anti-estrogen to block estrogen receptor activation is still a viable anti-breast cancer treatment option but anti-estrogen resistance has been a significant bottle-neck. Dimerization of estrogen receptor is required for ER activation. Blocking ERα dimerization is therefore a complementary and alternative strategy to combat anti-estrogen resistance. Dimer interface peptide "I-box" derived from ER residues 503-518 specifically blocks ER dimerization. Recently using a comprehensive molecular simulation we studied the interaction dynamics of ERα LBDs in a homo-dimer. Based on this study, we identified three interface recognition peptide motifs LDKITDT (ERα residues 479-485), LQQQHQRLAQ (residues 497-506), and LSHIRHMSNK (residues 511-520) and reported the suitability of using LQQQHQRLAQ (ER 497-506) as a template to design inhibitors of ERα dimerization. Stability and self-aggregation of peptide based therapeutics poses a significant bottle-neck to proceed further. In this study utilizing peptide grafted to preserve their pharmacophoric recognition motif and assessed their stability and potential to block ERα mediated activity in silico and in vitro. The Grafted peptides blocked ERα mediated cell proliferation and viability of breast cancer cells but did not alter their apoptotic fate. We believe the structural clues identified in this study can be used to identify novel peptidometics and small molecules that specifically target ER dimer interface generating a new breed of anti-cancer agents.

Unexpected genomic relationships between Bacillus anthracis strains from Bangladesh and Central Europe

The zoonosis anthrax caused by the bacterium Bacillus anthracis has a broad geographical distribution. Active enzootic areas are typically located away from central and northern Europe where cases of the disease occur only sporadically and in limited numbers. In contrast, a few out of the 64 districts of Bangladesh are hyper-endemic for anthrax and there the disease causes major losses in live-stock. In this study we genotyped eight strains of B. anthracis collected from the districts of Sirajganj and Tangail in 2013. All these strains belonged to canSNP group A.Br.001/002 Sterne differing only in a few of 31 tandem-repeat (MLVA)-markers. Whole genome sequences were obtained from five of these strains and compared with genomic information of B. anthracis strains originating from various geographical locations. Characteristic signatures were detected defining two "Bangladesh" clusters potentially useful for rapid molecular epidemiology. From this data high-resolution PCR assays were developed and subsequently tested on additional isolates from Bangladesh and Central Europe. Remarkably, this comparative genomic analysis focusing on SNP-discovery revealed a close genetic relationship between these strains from Bangladesh and historic strains collected between 1991 and 2008 in The Netherlands and Germany, respectively. Possible explanations for these phylogenetic relationships are discussed.

Genotype Analysis of Bacillus anthracis Strains Circulating in Bangladesh

In Bangladesh, anthrax, caused by the bacterium Bacillus anthracis, is considered an endemic disease affecting ruminants with sporadic zoonotic occurrences in humans. Due to the lack of knowledge about risks from an incorrect removal of infected carcasses, the disease is not properly monitored, and because of the socio-economic conditions, the situation is under-reported and under-diagnosed. For sensitive species, anthrax represents a fatal outcome with sudden death and sometimes bleeding from natural orifices. The most common source of infection for ruminants is ingestion of spores during grazing in contaminated pastures or through grass and water contaminated with anthrax spores. Domestic cattle, sheep and goats can also become infected through contaminated bone meal (used as feed) originating from anthrax-infected carcasses. The present investigation was conducted to isolate B. anthracis organisms from 169 samples (73 soil, 1 tissue, 4 bone and 91 bone meal samples) collected from 12 different districts of Bangladesh. The sampling was carried out from 2012 to 2015. Twelve samples resulted positive for B. anthracis. Biomolecular analyses were conducted starting from the Canonical Single Nucleotide Polymorphism (CanSNP) to analyze the phylogenetic origin of strains. The analysis of genotype, obtained through the Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) with the analysis of 15 Variable Number Tandem Repeats (VNTR), demonstrated four different genotypes: two of them were previously identified in the district of Sirajganj. The sub-genotyping, conducted with Single Nucleotide Repeats analysis, revealed the presence of eight subgenotypes. The data of the present study concluded that there was no observed correlation between imported cattle feed and anthrax occurrence in Bangladesh and that the remarkable genetic variations of B. anthracis were found in the soil of numerous outbreaks in this country.

Origin of the Spin-Orbital Liquid State in a Nearly J=0 Iridate Ba_{3}ZnIr_{2}O_{9}

We show using detailed magnetic and thermodynamic studies and theoretical calculations that the ground state of Ba_{3}ZnIr_{2}O_{9} is a realization of a novel spin-orbital liquid state. Our results reveal that Ba_{3}ZnIr_{2}O_{9} with Ir^{5+} (5d^{4}) ions and strong spin-orbit coupling (SOC) arrives very close to the elusive J=0 state but each Ir ion still possesses a weak moment. Ab initio density functional calculations indicate that this moment is developed due to superexchange, mediated by a strong intradimer hopping mechanism. While the Ir spins within the structural Ir_{2}O_{9} dimer are expected to form a spin-orbit singlet state (SOS) with no resultant moment, substantial frustration arising from interdimer exchange interactions induce quantum fluctuations in these possible SOS states favoring a spin-orbital liquid phase down to at least 100 mK.

Biosecurity and Circulation of Influenza A (H5N1) Virus in Live-Bird Markets in Bangladesh, 2012

Bangladesh has been considered as one of the five countries endemic with highly pathogenic avian influenza A subtype H5N1 (HPAI H5N1). Live-bird markets (LBMs) in south Asian countries are believed to play important roles in the transmission of HPAI H5N1 and others due to its central location as a hub of the poultry trading. Food and Agriculture Organization (FAO) of the United Nations has been promoting improved biosecurity in LBMs in Bangladesh. In 2012, by enrolling 32 large LBMs: 10 with FAO interventions and 22 without assistance, we assessed the virus circulation in the selected LBMs by applying standard procedures to investigate market floors, poultry stall floors, poultry-holding cases and slaughter areas and the overall biosecurity using a questionnaire-based survey. Relative risk (RR) was examined to compare the prevalence of HPAI H5N1 in the intervened and non-intervened LBMs. The measures practised in significantly more of the FAO-intervened LBMs included keeping of slaughter remnants in a closed container; decontamination of poultry vehicles at market place; prevention of crows' access to LBM, market/floor cleaning by market committee; wet cleaning; disinfection of floor/poultry stall after cleaning; and good supply of clean water at market (P < 0.05). Conversely, disposal of slaughter remnants elsewhere at market and dry cleaning were in operation in more of the FAO non-intervened LBMs (P < 0.05). The RR for HPAI H5N1 in the intervened and non-intervened LBMs was 1.1 (95% confidence interval 0.44-2.76), suggesting that the proportion positive of the virus in the two kinds of LBM did not vary significantly (P = 0.413). These observations suggest that the viruses are still maintained at the level of production in farms and circulating in LBMs in Bangladesh regardless of interventions, albeit at lower levels than in other endemic countries.

Direct evidence for a pressure-induced nodal superconducting gap in the Ba0.65Rb0.35Fe2As2 superconductor

The superconducting gap structure in iron-based high-temperature superconductors (Fe-HTSs) is non-universal. In contrast to other unconventional superconductors, in the Fe-HTSs both d-wave and extended s-wave pairing symmetries are close in energy. Probing the proximity between these very different superconducting states and identifying experimental parameters that can tune them is of central interest. Here we report high-pressure muon spin rotation experiments on the temperature-dependent magnetic penetration depth in the optimally doped nodeless s-wave Fe-HTS Ba0.65Rb0.35Fe2As2. Upon pressure, a strong decrease of the penetration depth in the zero-temperature limit is observed, while the superconducting transition temperature remains nearly constant. More importantly, the low-temperature behaviour of the inverse-squared magnetic penetration depth, which is a direct measure of the superfluid density, changes qualitatively from an exponential saturation at zero pressure to a linear-in-temperature behaviour at higher pressures, indicating that hydrostatic pressure promotes the appearance of nodes in the superconducting gap.

Isosorbide Mononitrate versus Misoprostol for Cervical Ripening and Induction of Labour at Term

To assess the efficacy and safety of isosorbide mononitrate (IMN) compared with misoprostol for cervical ripening and labour induction at term. In this comparative study two hundred term pregnant women with indication for induction of labour were randomly divided to receive either 40 mg IMN tablet vaginally (n=100) or 50 μg misoprostol tablet vaginally (n=100) every 6 hours interval for a maximum of 4 doses. Progress & outcome of cervical ripening, labour induction and adverse effects were assessed. Change in cervical score was higher in misoprostol group than IMN group. Time from start of medication to vaginal delivery in IMN group was significantly longer, 28.66 ± 5.283 hours, than in misoprostol group, 16.12 ± 5.581 hours. Vaginal delivery occurred in 77% in IMN group and 69% in misoprostol group. There were no tachysystole or uterine hyper stimulation in the IMN group while in misoprostol group it was 17% and 11% respectively. Maternal satisfaction was higher in IMN group. Cervical ripening is satisfactory with IMN. Though misoprostol is singly more effective than IMN but IMN with oxytocin results in more vaginal delivery. Fetal and maternal side effects are less in IMN group.

Direct observation of the spin texture in SmB6 as evidence of the topological Kondo insulator

Topological Kondo insulators have been proposed as a new class of topological insulators in which non-trivial surface states reside in the bulk Kondo band gap at low temperature due to strong spin-orbit coupling. In contrast to other three-dimensional topological insulators, a topological Kondo insulator is truly bulk insulating. Furthermore, strong electron correlations are present in the system, which may interact with the novel topological phase. By applying spin- and angle-resolved photoemission spectroscopy, here we show that the surface states of SmB6 are spin polarized. The spin is locked to the crystal momentum, fulfilling time reversal and crystal symmetries. Our results provide strong evidence that SmB6 can host topological surface states in a bulk insulating gap stemming from the Kondo effect, which can serve as an ideal platform for investigating of the interplay between novel topological quantum states with emergent effects and competing orders induced by strongly correlated electrons.

Inflammation-induced haemostatic response in layer chickens infected with Streptococcus equi subsp. zooepidemicus as evaluated by fibrinogen, prothrombin time and thromboelastography

Streptococcus zooepidemicus has recently been shown to be a severe pathogen in layer chickens, where it is able to cause serious lesions in the vascular system. To evaluate the haemostatic response, 10 layer chickens were inoculated intravenously with S. zooepidemicus. Four hypotheses were tested: that the infection-induced inflammation would increase the plasma fibrinogen (Fbg) concentration, would prolong the prothrombin time (PT) and would prompt hypercoagulability or hypocoagulability as assessed by whole-blood thromboelastography (TEG), and that a possible correlation would exist between one of the TEG values and Fbg/PT. Each parameter was measured at days 1, 3 and 6 post inoculation (p.i.), and compared with the values at day 0 from each individual bird and with values obtained from non-infected control chickens (n = 10). In the infected chickens, the mean (± standard error) of Fbg was higher at day 3 p.i. (9.4 ± 1.4 g/l) and day 6 p.i. (8.0 ± 0.7 g/l) and the PT was prolonged at day 6 p.i. (168.1 ± 21.0 sec) compared with the day 0 standards (2.6 ± 0.2 g/l and 104.6 ± 2.0 sec, respectively) (P < 0.05). The majority of infected chickens demonstrated a hypercoagulable TEG result with increased mean values of the clot formation rate (α-angle) and maximal amplitude (MA) of TEG tracing at day 3 p.i. (83.1 ± 0.7°, 83.8 ± 1.4 mm) and day 6 p.i. (84.0 ± 0.4°, 89.8 ± 1.0 mm) compared with the day 0 values (75.8 ± 2.2° and 66.9 ± 1.4 mm, respectively) (P < 0.05). In control birds, the means of Fbg (1.5 ± 0.1 g/l), PT (79.4 ± 6.4 sec), TEG-α (76.7 ± 1.5°) and TEG-MA (64.0 ± 2.3 mm) were lower at day 6 compared with values observed for the infected chickens (P < 0.05). A negative correlation coefficient (-0.71) was found between the clot formation time (TEG-K) and Fbg at day 1 in the control group (P = 0.02). In conclusion, infection with S. zooepidemicus following intravenous injection in layer chickens induced haemostatic alterations including hyperfibrinogenaemia, prolonged PT, and hypercoagulability as measured by increased TEG-α and TEG-MA.

Superconductivity in a new layered bismuth oxyselenide: LaO(0.5)F(0.5)BiSe₂

We report superconductivity at T(c) ≈ 2.6 K in a new layered bismuth oxyselenide LaO(0.5)F(0.5)BiSe2 with the ZrCuSiAs-type structure composed of alternating superconducting BiSe2 and blocking LaO layers. The superconducting properties of LaO(0.5)F(0.5)BiSe2 were investigated by means of dc magnetization, resistivity and muon-spin rotation experiments, revealing the appearance of bulk superconductivity with a rather large superconducting volume fraction of ≈ 70% at 1.8 K.

Regional variation in the prevalence of E. coli O157 in cattle: a meta-analysis and meta-regression

BACKGROUND

Escherichia coli O157 (EcO157) infection has been recognized as an important global public health concern. But information on the prevalence of EcO157 in cattle at the global and at the wider geographical levels is limited, if not absent. This is the first meta-analysis to investigate the point prevalence of EcO157 in cattle at the global level and to explore the factors contributing to variation in prevalence estimates.

METHODS

Seven electronic databases- CAB Abstracts, PubMed, Biosis Citation Index, Medline, Web of Knowledge, Scirus and Scopus were searched for relevant publications from 1980 to 2012. A random effect meta-analysis model was used to produce the pooled estimates. The potential sources of between study heterogeneity were identified using meta-regression.

PRINCIPAL FINDINGS

A total of 140 studies consisting 220,427 cattle were included in the meta-analysis. The prevalence estimate of EcO157 in cattle at the global level was 5.68% (95% CI, 5.16-6.20). The random effects pooled prevalence estimates in Africa, Northern America, Oceania, Europe, Asia and Latin America-Caribbean were 31.20% (95% CI, 12.35-50.04), 7.35% (95% CI, 6.44-8.26), 6.85% (95% CI, 2.41-11.29), 5.15% (95% CI, 4.21-6.09), 4.69% (95% CI, 3.05-6.33) and 1.65% (95% CI, 0.77-2.53), respectively. Between studies heterogeneity was evidenced in most regions. World region (p<0.001), type of cattle (p<0.001) and to some extent, specimens (p = 0.074) as well as method of pre-enrichment (p = 0.110), were identified as factors for variation in the prevalence estimates of EcO157 in cattle.

CONCLUSION

The prevalence of the organism seems to be higher in the African and Northern American regions. The important factors that might have influence in the estimates of EcO157 are type of cattle and kind of screening specimen. Their roles need to be determined and they should be properly handled in any survey to estimate the true prevalence of EcO157.

Performance of a commercial Chicken-Ovo-transferrin-ELISA on the serum of brown layer chickens infected with Gallibacterium anatis and Streptococcus zooepidemicus

To evaluate Ovo-transferrin (OTF), a positive acute-phase protein in chickens, as a diagnostic biomarker of selected bacterial infections we checked the performance of a commercial Chicken-OTF-ELISA (ICL, Inc., Portland, OR, USA) by analytical and overlap performances using two groups of serum samples obtained from 26 Gallibacterium anatis-infected and 20 Streptococcus zooepidemicus-infected brown layer chickens. In addition, sera from 14 apparently healthy and 19 negative control chickens were analysed in the Gallibacterium group whereas sera from 20 healthy and 11 negative control chickens from the Streptococcus group were analysed. All calibration curves revealed high coefficients of determination (≥ 0.97) between optical density (OD 450nm) and concentrations of OTF (mg/ml). OTF concentrations in high, medium and low pools (made of sera from a combination of infected and/or non-infected birds) were >6.4, >3.8 to <4.5 and <1.6 mg/ml in the Gallibacterium group, and >6.7, >3.5 to <3.7 and <1.1 mg/ml in the Streptococcus group, respectively. For each pool, low coefficients of intra-assay (7.8, 5.7 and 5.3) and inter-assay (15.8, 18.0 and 18.0) variations were obtained in the Gallibacterium study. In the Streptococcus study only the intra-assay variation was low (3.7, 3.8 and 6.2, respectively). The linearity check was acceptable demonstrating a straight line with slope and intercept, not deviating from one and zero, respectively, using the Gallibacterium sera, whereas the Streptococcus sera deviated from the linear line. Detection limits were low (Gallibacterium, 0.01 mg/ml; Streptococcus, 0.32 mg/ml). OTF concentrations (mean ± standard error of the mean) in overlap performances were elevated in the sera of infected chickens (Gallibacterium, 4.4 ± 0.3 mg/ml; Streptococcus, 3.2 ± 0.4 mg/ml) compared with negative controls (1.7 ± 0.1 mg/ml) (P < 0.05). In conclusion, the Chicken-OTF-ELISA can be used to measure reproducible serum OTF concentrations in brown layer chickens as a response to G. anatis infections, whereas an adjustment of dilution process is proposed to optimize to use in S. zooepidemicus-infected chickens.

Poultry as a possible source of non-typhoidal Salmonella enterica serovars in humans in Bangladesh

We investigated Salmonella enterica isolates from human clinical cases of gastroenteritis to determine the distribution of non-typhoidal Salmonella serovars in the human population, and compared them to isolates originating from poultry by serotyping, phage typing, plasmid profiling, pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) to evaluate the potential role of poultry in human non-typhoidal salmonellosis in Bangladesh. Nine different serovars were identified among the human isolates of which Salmonella Paratyphi B var Java (S. Java), S. Kentucky, S. Enteritidis, S. Virchow and S. Weltevreden also were commonly isolated from poultry. The poultry isolates belonging to S. Java, S. Kentucky and S. Enteritidis were indistinguishable from human isolates or genetically closely related, based on PFGE profiles and MLST. S. Kentucky clone ST198 and S. Java clone ST43 both well-known cause of human infections were also isolated from poultry.

Pathogenicity of wild-type and small-colony variants of Streptococcus equi subsp. zooepidemicus in layer chickens

Wild-type (WT) and small-colony-variant (SCV) strains of Streptococcus equi subsp. zooepidemicus have recently been isolated from a layer flock in Denmark experiencing high mortality. To investigate the disease-causing potential of SCV compared with WT, a 2-week long infection study was performed in 45-week-old brown layer chickens. Four groups of 11 chickens each were inoculated with a WT or SCV strain by the intravenous or intra-tracheal route: WT-IV, SCV-IV or WT-IT, SCV-IT, respectively. Clinical signs were observed in most chickens in the WT-IV group (9/11). Mortality was observed in the SCV-IV (4/11) and WT-IV (2/11) groups. Ten chickens in the WT-IV and WT-IT groups, respectively, developed gross lesions including oophoritis/peritonitis, hepatitis and airsacculitis cervicalis. Bronchopneumonia was common in the SCV-IT group (6/11), and valvular endocarditis in the SCV-IV group (4/11). Histological lesions in liver tissue were frequently observed in the chickens of the SCV-IV group (9/11), followed by the WT-IT (7/11), WT-IV (6/11), and SCV-IT (2/11) groups. The lesions in the SCV-IV group were dominated by deposition of eosinophilic material with infiltration of inflammatory cells (6/9). Bacteriological re-isolation of either strain type was achieved from all chickens of the WT-IV and WT-IT groups, and from nine and seven out of 11 chickens for each of the SCV-IV and SCV-IT groups, respectively. In summary, we were able to reproduce clinical signs and lesions as observed during the natural outbreak, which included an overall initial onset in WT-infected chickens as opposed to a late onset and possible recurring infection seen in the SCV-infected chickens.

Two-dimensional superfluid density in an alkali metal-organic solvent intercalated iron selenide superconductor Li(C5H5N)0.2Fe2Se2

We report the low-temperature electronic and magnetic properties of the alkali metal-organic solvent intercalated iron selenide superconductor Li(C5H5N)0.2Fe2Se2 using muon-spin-spectroscopy measurements. The zero-field muon spin relaxation (μSR) results indicate that nearly half of the sample is magnetically ordered and spatially phase separated from the superconducting region. The transverse-field μSR results reveal that the superfluid density of Li(C5H5N)0.2Fe2Se2 is two dimensional in nature. The temperature dependence of the penetration depth λ(T) can be explained using a two-gap s-wave model. This implies that, despite the 2D nature of the superfluid density, the symmetry of the superconducting gap remains unaltered to the parent compound FeSe.

Mortality rate and clinical features of highly pathogenic avian influenza in naturally infected chickens in Bangladesh

A retrospective study was performed to assess the mortality rates and clinical signs in commercial and backyard chickens naturally infected with the highly pathogenic avian influenza (HPAI) H5N1 virus in Bangladesh. All of the 33 commercial and 25 backyard farms, recorded during the first wave of HPAI outbreaks (January to November 2007) in Bangladesh, were enrolled in this study. The farm profile data, stock information and major clinical signs recognised by the farmers and/or farm attendants, were collected through a prototype questionnaire. The investigating veterinarians' retrospective appraisals of the clinical signs were recorded by interview. After the clinical onset, the incidence rates of mortality in breeder, commercial broiler, commercial layer and backyard chickens were, respectively: 0.0215, 0.0341, 0.0179 and 0.0703 per chicken-day at risk. The four major clinical signs observed were cyanotic combs and wattles, oedema of the head and face, drowsiness and huddling and ecchymotic discoloration of the leg shanks. The first sign (cyanotic combs and wattles) was equally observed in chickens from commercial and backyard farms (p = 0.44) but the second (oedema of the head and face) was more common in backyard farms (p = 0.03).

Molecular epidemiology of circulating highly pathogenic avian influenza (H5N1) virus in chickens, in Bangladesh, 2007-2010

Bangladesh has been severely hit by highly pathogenic avian influenza H5N1 (HPAI-H5N1). However, little is known about the genetic diversity and the evolution of the circulating viruses in Bangladesh. In the present study, we analyzed the hemagglutinin gene of 30 Bangladeshi chicken isolates from 2007 through 2010. We analyzed the polybasic amino acid sequence motif of the cleavage site and amino acid substitution pattern. Phylogenetic history was reconstructed using neighbor-joining and Bayesian time-scaled methods. In addition, we used Mantel correlation tests to analyze the relation between genetic relatedness and spatial and temporal distances. Neighbor-joining phylogeography revealed that virus circulating in Bangladesh from 2007 through 2010 belonged to clade 2.2. The results suggest that clade 2.2 viruses are firmly entrenched and have probably become endemic in Bangladesh. We detected several amino acid substitutions, but they are not indicative of adaptation toward human infection. The Mantel correlation test confirmed significant correlation between genetic distances and temporal distances between the viruses. The Bayesian tree shows that isolates from waves 3 and 4 derived from a subgroup of isolates from the previous waves grouping with a high posterior probability (pp=1.0). This indicates the possibility of formation of local subclades. One surprising finding of spatio-temporal analysis was that genetically identical virus caused independent outbreaks over a distance of more than 200 km and within 14 days of each other. This might indicate long distance dispersal through vectors such as migratory birds and vehicles, and challenges the effectiveness of movement restriction around 10 km radius of an outbreak. The study indicates possible endemicity of the clade 2.2 HPAI-H5N1 virus in Bangladesh. Furthermore, the formation of a subclade capable of transmission to humans cannot be ruled out. The findings of this study might provide valuable information for future surveillance, prevention and control programme.

Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution

Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic-spin-dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid quantum mechanical-molecular mechanical simulation to study the interaction of OH radicals with a guanine-deoxyribose-phosphate DNA molecular unit in the presence of water, where all of the water molecules and the deoxyribose-phosphate fragment are treated with the simplistic classical molecular mechanical scheme. Our result illustrates that the presence of water strongly alters the hydrogen-abstraction reaction as the hydrogen bonding of OH radicals with water restricts the relative orientation of the OH radicals with respect to the DNA base (here, guanine). This results in an angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen-abstraction mechanisms than previously anticipated for identical systems in vacuum. The method can easily be extended to single- and double-stranded DNA without any appreciable computational cost as these molecular units can be treated in the classical subsystem, as has been demonstrated here.

First-order reorientation transition of the flux-line lattice in CaAlSi

The flux-line lattice in CaAlSi has been studied by small-angle neutron scattering. A well-defined hexagonal flux-line lattice is seen just above H(c1) in an applied field of only 54 Oe. A 30° reorientation of this vortex lattice has been observed in a very low field of 200 Oe. This reorientation transition appears to be first-order and could be explained by nonlocal effects. The magnetic field dependence of the form factor is well-described by a single penetration depth of λ=1496(1) Å and a single coherence length of ξ=307(1) Å at 2 K. At 1.5 K, the penetration depth anisotropy is γ(λ)=2.7(1), with the field applied perpendicular to the c axis, and agrees with the coherence length anisotropy determined from critical field measurements.

Structural, spectroscopic, magnetic and electrical characterization of Ca-doped polycrystalline bismuth ferrite, Bi(1-x)Ca(x)FeO(3-x/2) (x ≤ 0.1)

The crystal structure and physical properties of multiferroic polycrystalline Ca(2+)-doped BiFeO(3) samples have been investigated. The present experimental investigation suggests that Bi(1-x)Ca(x)FeO(3-x/2) (x ≤ 0.1) can be considered as a solid solution between BiFeO(3) and CaFeO(2.5). The oxidation state of Fe in these materials is + 3 and charge balance occurs through the creation of oxygen vacancies. For each composition, two structural phase transitions are revealed as anomalies in the variable-temperature in situ x-ray diffraction data which is consistent with the well-established high-temperature structural transformation in pure BiFeO(3). All compositions studied show antiferromagnetic behaviour along with a ferromagnetic component that increases with Ca(2+) doping. The resistivities of the Bi(1-x)Ca(x)FeO(3-x/2) samples at room temperature are of the order of 10(9) Ω cm and decrease with increasing Ca(2+) content. Arrhenius plots of the resistivity show two distinct linear regions with activation energies in the range of 0.4-0.7 and 0.03-0.16 eV. A correlation has been established between the critical temperatures associated with the structural phase transitions and the multiferroic properties. A composition of x = 0.085 is predicted to show maximum magneto-electric coupling.

Risk for highly pathogenic avian influenza H5N1 virus infection in chickens in small-scale commercial farms, in a high-risk area, Bangladesh, 2008

Small-scale commercial chicken farms (FAO-defined system 3) with poor biosecurity predominate in developing countries including Bangladesh. By enroling fifteen highly pathogenic avian influenza (HPAI) cases occurring in such farms - (February - April 2008) and 45 control farms (March-May 2008) with similar set up, we conducted a case-control study to evaluate the risk factors associated with HPAI H5N1 virus infections in chickens reared in small-scale commercial farms in a spatially high-risk area in Bangladesh. Data collected by a questionnaire from the selected farms were analysed by univariable analysis and multivariable conditional logistic regression. The risk factors independently associated were 'dead crow seen at or near farm' [odds ratio (OR) 47.4, 95% confidence interval (CI) 4.7-480.3, P = 0.001], 'exchanging eggtrays with market vendors' (OR 20.4, 95% CI 1.9-225.5, P = 0.014) and 'mortality seen in backyard chicken reared nearby' (OR 19.4, 95% CI 2.8-131.9, P = 0.002). These observations suggest that improved biosecurity might reduce the occurrence of HPAI outbreaks in small-scale commercial farms in Bangladesh.

Carcinoma gallbladder

Carcinoma gallbladder (CaGb) is a rare disease. The aetiology of CaGb is yet not known. However the risk of CaGb is increased in anomalous pancreaticobiliary duct junction (APBDJ), gall stones, xanthogranulomatus cholecystitis, calcified or porcelain gallbladder, cholelithiasis with typhoid carriers, gallbladder adenoma, red meat consumption and tobacco uses. There are protective effects of vegetables on CaGb. Most of the cases present with advanced disease. In early carcinoma of a gallbladder sign and symptoms mimic benign disease. The diagnosis is established by ultrasonography, computerized tomography and guided fine needle aspiration cytology (FNAC). Biochemical tests are of very little value in making a diagnosis. The treatment depends on the clinical stage at presentation. Surgery offers the best chance of cure. In stage T1a, laparoscopic or open cholecystectomy alone is curative, and in T1b, cholecystectomy with hepatoduodenal lymph node dissection without combined resection of an adjacent organ is required. Segment S4a+5 hepatectomy combined with extrahepatic bile duct resection (BDR) and D2 lymph node dissection is a highly recommended operation for the treatment of T2 and T3 CaGb. The dye injection method is useful in determining the appropriate extent of hepatic resection for advanced CaGb. Resurgery is required only in those cases where tumour has invaded the serosa and/ or adjacent structures when diagnosed postoperatively. Biliary bypass is required for palliation. Prognosis depends on early diagnosis and appropriate surgical excision.

Risk factors for infection with highly pathogenic influenza A virus (H5N1) in commercial chickens in Bangladesh

A matched case-control study was carried out to identify risk factors for highly pathogenic avian influenza A virus (subtype H5N1) infection in commercial chickens in Bangladesh. A total of 33 commercial farms diagnosed with H5N1 before September 9, 2007, were enrolled as cases, and 99 geographically matched unaffected farms were enrolled as control farms. Farm data were collected using a pretested questionnaire, and analysed by matched-pair analysis and multivariate conditional logistic regression. Two factors independently and positively associated with H5N1 infection remained in the final model. They were 'farm accessible to feral and wild animals' (odds ratio [OR] 5.71, 95 per cent confidence interval [CI] 1.81 to 18.0, P=0.003) and 'footbath at entry to farm/shed' (OR 4.93, 95 per cent CI 1.61 to 15.1, P=0.005). The use of a designated vehicle for sending eggs to a vendor or market appeared to be a protective factor (OR 0.14, 95 per cent CI 0.02 to 0.88, P=0.036).