Prospects for Observing and Localizing Gravitational-Wave Transients with Advanced LIGO and Advanced Virgo

We present a possible observing scenario for the Advanced LIGO and Advanced Virgo gravitational-wave detectors over the next decade, with the intention of providing information to the astronomy community to facilitate planning for multi-messenger astronomy with gravitational waves. We determine the expected sensitivity of the network to transient gravitational-wave signals, and study the capability of the network to determine the sky location of the source. We report our findings for gravitational-wave transients, with particular focus on gravitational-wave signals from the inspiral of binary neutron-star systems, which are considered the most promising for multi-messenger astronomy. The ability to localize the sources of the detected signals depends on the geographical distribution of the detectors and their relative sensitivity, and 90% credible regions can be as large as thousands of square degrees when only two sensitive detectors are operational. Determining the sky position of a significant fraction of detected signals to areas of 5 deg2 to 20 deg2 will require at least three detectors of sensitivity within a factor of ∼ 2 of each other and with a broad frequency bandwidth. Should the third LIGO detector be relocated to India as expected, a significant fraction of gravitational-wave signals will be localized to a few square degrees by gravitational-wave observations alone.

Improved upper limits on the stochastic gravitational-wave background from 2009-2010 LIGO and Virgo data

Gravitational waves from a variety of sources are predicted to superpose to create a stochastic background. This background is expected to contain unique information from throughout the history of the Universe that is unavailable through standard electromagnetic observations, making its study of fundamental importance to understanding the evolution of the Universe. We carry out a search for the stochastic background with the latest data from the LIGO and Virgo detectors. Consistent with predictions from most stochastic gravitational-wave background models, the data display no evidence of a stochastic gravitational-wave signal. Assuming a gravitational-wave spectrum of Ω_{GW}(f)=Ω_{α}(f/f_{ref})^{α}, we place 95% confidence level upper limits on the energy density of the background in each of four frequency bands spanning 41.5-1726 Hz. In the frequency band of 41.5-169.25 Hz for a spectral index of α=0, we constrain the energy density of the stochastic background to be Ω_{GW}(f)<5.6×10^{-6}. For the 600-1000 Hz band, Ω_{GW}(f)<0.14(f/900  Hz)^{3}, a factor of 2.5 lower than the best previously reported upper limits. We find Ω_{GW}(f)<1.8×10^{-4} using a spectral index of zero for 170-600 Hz and Ω_{GW}(f)<1.0(f/1300  Hz)^{3} for 1000-1726 Hz, bands in which no previous direct limits have been placed. The limits in these four bands are the lowest direct measurements to date on the stochastic background. We discuss the implications of these results in light of the recent claim by the BICEP2 experiment of the possible evidence for inflationary gravitational waves.

Search for gravitational waves associated with γ-ray bursts detected by the interplanetary network

We present the results of a search for gravitational waves associated with 223 γ-ray bursts (GRBs) detected by the InterPlanetary Network (IPN) in 2005-2010 during LIGO's fifth and sixth science runs and Virgo's first, second, and third science runs. The IPN satellites provide accurate times of the bursts and sky localizations that vary significantly from degree scale to hundreds of square degrees. We search for both a well-modeled binary coalescence signal, the favored progenitor model for short GRBs, and for generic, unmodeled gravitational wave bursts. Both searches use the event time and sky localization to improve the gravitational wave search sensitivity as compared to corresponding all-time, all-sky searches. We find no evidence of a gravitational wave signal associated with any of the IPN GRBs in the sample, nor do we find evidence for a population of weak gravitational wave signals associated with the GRBs. For all IPN-detected GRBs, for which a sufficient duration of quality gravitational wave data are available, we place lower bounds on the distance to the source in accordance with an optimistic assumption of gravitational wave emission energy of 10(-2)M⊙c(2) at 150 Hz, and find a median of 13 Mpc. For the 27 short-hard GRBs we place 90% confidence exclusion distances to two source models: a binary neutron star coalescence, with a median distance of 12 Mpc, or the coalescence of a neutron star and black hole, with a median distance of 22 Mpc. Finally, we combine this search with previously published results to provide a population statement for GRB searches in first-generation LIGO and Virgo gravitational wave detectors and a resulting examination of prospects for the advanced gravitational wave detectors.

Search for gravitational waves associated with γ-ray bursts detected by the interplanetary network

We present the results of a search for gravitational waves associated with 223 γ-ray bursts (GRBs) detected by the InterPlanetary Network (IPN) in 2005-2010 during LIGO's fifth and sixth science runs and Virgo's first, second, and third science runs. The IPN satellites provide accurate times of the bursts and sky localizations that vary significantly from degree scale to hundreds of square degrees. We search for both a well-modeled binary coalescence signal, the favored progenitor model for short GRBs, and for generic, unmodeled gravitational wave bursts. Both searches use the event time and sky localization to improve the gravitational wave search sensitivity as compared to corresponding all-time, all-sky searches. We find no evidence of a gravitational wave signal associated with any of the IPN GRBs in the sample, nor do we find evidence for a population of weak gravitational wave signals associated with the GRBs. For all IPN-detected GRBs, for which a sufficient duration of quality gravitational wave data are available, we place lower bounds on the distance to the source in accordance with an optimistic assumption of gravitational wave emission energy of 10(-2)M⊙c(2) at 150 Hz, and find a median of 13 Mpc. For the 27 short-hard GRBs we place 90% confidence exclusion distances to two source models: a binary neutron star coalescence, with a median distance of 12 Mpc, or the coalescence of a neutron star and black hole, with a median distance of 22 Mpc. Finally, we combine this search with previously published results to provide a population statement for GRB searches in first-generation LIGO and Virgo gravitational wave detectors and a resulting examination of prospects for the advanced gravitational wave detectors.

Constraints on cosmic strings from the LIGO-Virgo gravitational-wave detectors

Cosmic strings can give rise to a large variety of interesting astrophysical phenomena. Among them, powerful bursts of gravitational waves (GWs) produced by cusps are a promising observational signature. In this Letter we present a search for GWs from cosmic string cusps in data collected by the LIGO and Virgo gravitational wave detectors between 2005 and 2010, with over 625 days of live time. We find no evidence of GW signals from cosmic strings. From this result, we derive new constraints on cosmic string parameters, which complement and improve existing limits from previous searches for a stochastic background of GWs from cosmic microwave background measurements and pulsar timing data. In particular, if the size of loops is given by the gravitational backreaction scale, we place upper limits on the string tension Gμ below 10(-8) in some regions of the cosmic string parameter space.

Directional limits on persistent gravitational waves using LIGO S5 science data

The gravitational-wave (GW) sky may include nearby pointlike sources as well as stochastic backgrounds. We perform two directional searches for persistent GWs using data from the LIGO S5 science run: one optimized for pointlike sources and one for arbitrary extended sources. Finding no evidence to support the detection of GWs, we present 90% confidence level (C.L.) upper-limit maps of GW strain power with typical values between 2-20×10(-50)  strain(2) Hz(-1) and 5-35×10(-49)  strain(2) Hz(-1) sr(-1) for pointlike and extended sources, respectively. The latter result is the first of its kind. We also set 90% C.L. limits on the narrow-band root-mean-square GW strain from interesting targets including Sco X-1, SN 1987A and the Galactic center as low as ≈7×10(-25) in the most sensitive frequency range near 160 Hz.

Effect of regional climate warming on the phenology of butterflies in boreal forests in Manitoba, Canada

We examined the effect of regional climate warming on the phenology of butterfly species in boreal forest ecosystems in Manitoba, Canada. For the period 1971-2004, the mean monthly temperatures in January, September, and December increased significantly, as did the mean temperatures for several concurrent monthly periods. The mean annual temperature increased ≈ 0.05°C/yr over the study period. The annual number of frost-free days and degree-day accumulations increased as well. We measured the response of 19 common butterfly species to these temperature changes with the date of first appearance, week of peak abundance, and the length of flight period over the 33-yr period of 1972-2004. Although adult butterfly response was variable for spring and summer months, 13 of 19 species showed a significant (P < 0.05) increase in flight period extending longer into the autumn. Flight period extensions increased by 31.5 ± 13.9 (SD) d over the study period for 13 butterfly species significantly affected by the warming trend. The early autumn and winter months warmed significantly, and butterflies seem to be responding to this warming trend with a change in the length of certain life stages. Two species, Junonia coenia and Euphydryas phaeton, increased their northerly ranges by ≈ 150 and 70 km, respectively. Warmer autumns and winters may be providing opportunities for range extensions of more southerly butterfly species held at bay by past climatic conditions.

The Geneva prognostic score and mortality in patients diagnosed with pulmonary embolism by CT pulmonary angiogram

This study prospectively evaluates whether a previously established adverse outcome score (the Geneva prognostic score) predicts 3 and 12-month overall mortality among the patients diagnosed with pulmonary embolism (PE) by a CT pulmonary angiogram (CTPA). Five hundred twenty-three consecutive patients who had CTPA for suspected PE were recruited prospectively from March 2003 to October 2004. The Geneva prognostic score was calculated for all patients. Twelve-month follow up was completed in all patients in December 2005. There were 105 patients diagnosed with PE. The mean score was 2.71 (standard deviation (SD) 1.25) for those patients who had died (n = 7) and 1.14 (SD 1.19) for those patients who were alive (n = 98) at 3-month follow up (P < 0.001). The mean scores were 2.69 (SD 0.95) for those who had died (n = 13) and 1.04 (SD 1.15) for those patients who were alive (n = 92) at 12-month follow up (P < 0.001). At 3-month follow up, among the 88 patients with a score of 2 or less, three patients (3.4%) died and among 17 patients with a score of greater than 2, four patients (23.5%) died (P = 0.01). At 12-month follow up, five patients (5.7%) with a score of 2 or less died and eight patients (47.1%) with a score of three or more died (P < 0.0001). The Geneva prognostic score stratifies patients with low and high risk for overall mortality at 3 and 12 months among patients diagnosed with PE by CTPA.

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.

Search for gravitational-wave bursts from soft gamma repeaters

We present a LIGO search for short-duration gravitational waves (GWs) associated with soft gamma ray repeater (SGR) bursts. This is the first search sensitive to neutron star f modes, usually considered the most efficient GW emitting modes. We find no evidence of GWs associated with any SGR burst in a sample consisting of the 27 Dec. 2004 giant flare from SGR 1806-20 and 190 lesser events from SGR 1806-20 and SGR 1900+14. The unprecedented sensitivity of the detectors allows us to set the most stringent limits on transient GW amplitudes published to date. We find upper limit estimates on the model-dependent isotropic GW emission energies (at a nominal distance of 10 kpc) between 3x10;{45} and 9x10;{52} erg depending on waveform type, detector antenna factors and noise characteristics at the time of the burst. These upper limits are within the theoretically predicted range of some SGR models.

Withholding anticoagulation after a negative computed tomography pulmonary angiogram as a stand-alone imaging investigation: a prospective management study

BACKGROUND

Accurate diagnosis of pulmonary embolism (PE) is essential and it is not clear whether a computed tomography pulmonary angiogram (CTPA) could be used as a stand-alone imaging investigation. The aim of the study was to test the accuracy of the clinical outcome of a negative CTPA as a stand-alone imaging investigation to exclude PE.

METHODS

Five hundred and thirty-four consecutive patients who had a CTPA for diagnosis or exclusion of PE were recruited from March 2003 to October 2004. Four hundred and ninety-four patients had a helical CTPA as a stand-alone imaging investigation for diagnosis or exclusion of PE. A 3-month post-CTPA follow up was carried out in all patients to establish the clinical outcome accuracy of a negative CTPA as a stand-alone imaging investigation.

RESULTS

There were 387 (78.3%) negative and 107 (21.7%) positive CTPA examinations. The average age of the patients was 57.16 years (standard deviation 18.57). Among those with a negative CTPA who survived, one patient had deep vein thrombosis and 342 patients had no evidence of an episode of venous thromboembolism or PE at the 3-month follow up. Thirty-eight patients died within the 3-month follow-up period and one patient's death was attributed to suspected PE. The negative predictive value of a CTPA is 99.5% (95% confidence interval 98.1-99.9%).

CONCLUSION

Helical negative CTPA examination excludes clinically significant PE as a stand-alone imaging investigation. Where concurrent deep vein thrombosis is suspected, lower limb needs to be imaged by ultrasound if the CTPA is negative.

Computed tomography pulmonary angiogram diagnosis of pulmonary embolism

Over the last decade, contrast-enhanced spiral CT has been established as a non-invasive alternative to catheter angiography and is now regarded as the first-line imaging investigation for the diagnosis of pulmonary embolism (PE). The reported sensitivities for the diagnosis of PE of spiral CT vary from 45 to 100% and the specificities vary from 78 to 100%. Prospective outcome studies have shown a high negative predictive value for a single-detector spiral CT for PE. Patients' outcomes were not adversely affected in these studies when anticoagulation was withheld after a negative CT pulmonary angiogram. The main limitation of single-detector spiral CT has been its limited ability to detect isolated subsegmental PE. However, multidetector spiral CT allows evaluation of pulmonary vessels down to sixth-order branches and significantly increases the rate of detection of PE in segmental and subsegmental levels. The interobserver correlations for diagnosis of subsegmental PE with multidetector spiral CT exceed the reproducibility of selective pulmonary angiography. If appropriate equipment is available (multidetector CT), then CT pulmonary angiogram is safe to be used as the first-line imaging investigation for the diagnosis of PE.

Otitis media and a neck lump--current diagnostic challenges for Paragonimus-like trematode infections

A 29 year-old Nigerian studying in the UK presented with a neck lump and otitis media. Paragonimus-like trematode eggs were found in the neck lump aspirate. Morphologically these eggs resembled Paragonimus uterobilateralis or Achillurbainia congolensis. We favoured the diagnosis of achillurbainiasis over extrapulmonary paragonimiasis on the basis of clinical features and because we could not amplify DNA sequences using PCR primers specific for Paragonimus species. We discuss current diagnostic challenges for this rare parasitic infection.

Molecular discrimination of Perna (Mollusca: Bivalvia) species using the polymerase chain reaction and species-specific mitochondrial primers

This work was prompted by the need to be able to identify the invasive mussel species, Perna viridis, in tropical Australian seas using techniques that do not rely solely on morphology. DNA-based molecular methods utilizing a polymerase chain reaction (PCR) approach were developed to distinguish unambiguously between the three species in the genus Perna. Target regions were portions of two mitochondrial genes, cox1 and nad4, and the intergenic spacer between these that occurs in at least two Perna species. Based on interspecific sequence comparisons of the nad4 gene, a conserved primer has been designed that can act as a forward primer in PCRs for any Perna species. Four reverse primers have also been designed, based on nad4 and intergenic spacer sequences, which yield species-specific products of different lengths when paired with the conserved forward primer. A further pair of primers has been designed that will amplify part of the cox1 gene of any Perna species, and possibly other molluscs, as a positive control to demonstrate that the PCR is working.

High levels of type 2 cytokine-producing cells in chronic fatigue syndrome

The aetiology of chronic fatigue syndrome (CFS) is not known. However, it has been suggested that CFS may be associated with underlying immune activation resulting in a Th2-type response. We measured intracellular production of interferon (IFN)-gamma and interleukin (IL)-2; type 1 cytokines), IL-4 (type 2) and IL-10 (regulatory) by both polyclonally stimulated and non-stimulated CD4 and CD8 lymphocytes from patients with CFS and control subjects by flow cytometry. After polyclonal activation we found evidence of a significant bias towards Th2- and Tc2-type immune responses in CFS compared to controls. In contrast, levels of IFN-gamma, IL-2 and IL-10-producing cells were similar in both study groups. Non-stimulated cultures revealed significantly higher levels of T cells producing IFN-gamma or IL-4 in CFS patients. Concluding, we show evidence for an effector memory cell bias towards type 2 responsiveness in patients with CFS, as well as ongoing type 0 immune activation in unstimulated cultures of peripheral blood cells.

A quantitative description of the diffusion of noradrenaline in the media of blood vessels following its release from sympathetic varicosities

A quantitative model is provided which describes how noradrenaline (NAd), released from varicosities at the adventitial surface of an artery, either diffuses into the media of the vessel to reach the intimal surface, diffuses into the volume of solution surrounding the artery, or is removed by the uptake 1 process in the varicosities. These predictions are then compared with experimental evaluations of the extent of changes in NAd to be found at the adventitial and intimal surfaces of the rat-tail artery, during and after trains of impulses, as determined using amperometry. In the model of the blood vessel there is a sequential decrease in the diffusion constant of NAd from the surrounding solution, to the adventitia, to the media, to the endothelium, to rise again in the lumen of the vessel; there is also an uptake 1 NAd pump in the varicosities described by Michaelis-Menten kinetics. This model is shown to provide a quantitative account of the spatial and temporal changes in NAd observed following trains of impulses at different frequencies of stimulation (5-40 Hz) for different periods of times (10-40 s). Changes in the spatio-temporal distribution of NAd observed following block of the uptake 1 NAd pump were also successfully predicted by the model. It is concluded that, within the context of the model, there is no need to evoke special mechanisms of buffering at the sympathetic varicosities, nor distinctions on the basis that only secreting varicosities utilize the uptake 1 mechanism, in order to describe the dynamics of NAd distribution in arteries during nerve activity.

Gene sequencing for identification of Paragonimus eggs from a human case

OBJECTIVE

To identify the etiologic agent from a paragonimiasis patient using molecular techniques.

METHODS

The complete nuclear ribosomal DNA second internal transcribed spacer (ITS2) gene sequence of eggs in sputum from a paragonimiasis patient was obtained by directly auto-sequencing its PCR product. ITS2 genes from eggs of Paragonimus westermani and Pagumogonimus skrjabini (both from animal hosts) were also sequenced for comparison. In addition, morphological comparisons were made with the eggs of the two species.

RESULTS

The ITS2 gene from the human case was 100% identical with the sequence from the eggs of P. westermani from an experimentally infected dog but only 92% identical with the sequence from the eggs of P. skrjabini. Morphologically, the eggs from the human case more resembled those from P. westermani infected dog.

CONCLUSION

The patient was diagnosed to be suffered from paragonimiasis westermani by gene sequence analysis.

Revisiting the question of limited genetic variation within Schistosoma japonicum

Recent electrophoretic data have indicated that Schistosoma japonicum in mainland China may be a species complex, with the existence of a cryptic species being predicted from the analysis of schistosome populations from Sichuan province. To investigate the Sichuan form of S. japonicum, 4.9 kbp of mitochondrial DNA from each of three samples of the parasite from China (two from Sichuan and one from Hunan) and one from Sorsogon in the Philippines were amplified, sequenced and characterized. The sequence data were compared with those from the related South-east Asian species of S. mekongi (Khong Island, Laos) and S. mlayensis (Baling, Malaysia) and that from S. japonicm from Anhui (China). At both the nucleotide and amino-acid levels, the variation among the five S. japonicum samples was limited (< 1%). This was consistent with the conclusions drawn from previous molecular studies, in which minimal variation among S. japonicum populations was also detected. In contrast, S. mekongi and S. malayensis, species recognized as separate but closely related, differ from each other by about 10%, and each differs by 25%-26% from S. japonicum. Phylogenetic trees provided a graphic representation of these differences, showing all S. japonicum sequences to be very tightly clustered and distant from S. mekongi and S. malayensis, the last two being clearly distinct from each other. The results thus indicate no significant intra-specific genetic variation among S. japonicum samples collected from different geographical areas and do not support the idea of a distinct form in Sichuan.

Affinities between Asian non-human Schistosoma species, the S. indicum group, and the African human schistosomes

Schistosoma species have traditionally been arranged in groups based on egg morphology, geographical origins, and the genus or family of snail intermediate host. One of these groups is the 'S. indicum group' comprising species from Asia that use pulmonate snails as intermediate hosts. DNA sequences were obtained from the four members of this group (S. indicum, S. spindale, S. nasale and S. incognitum) to provide information concerning their phylogenetic relationships with other Asian and African species and species groups. The sequences came from the second internal transcribed spacer (ITS2) of the ribosomal gene repeat, part of the 28S ribosomal RNA gene (28S), and part of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene. Tree analyses using both distance and parsimony methods showed the S. indicum group not to be monophyletic. Schistosoma indicum, S. spindale and S. nasale were clustered among African schistosomes, while S. incognitum was placed as sister to the African species (using ITS2 and 28S nucleotide sequences and CO1 amino acid sequences), or as sister to all other species of Schistosoma (CO1 nucleotide sequences). Based on the present molecular data, a scenario for the evolution of the S. indicum group is discussed.

Evolutionary relationships between trematodes and snails emphasizing schistosomes and paragonimids

Snails and digeneans have been associated for at least 200 million years. Their inter-relationships over such a time-span must have been complex and varied. Few studies have attempted to explore these relationships in the light of knowledge of the phylogeny of both host and parasite groups. Here we focus on two important families of digeneans, the Schistosomatidae and the Paragonimidae, for which molecular phylogenies are available. We investigate the types of evolutionary relationships between host and parasite, operating at different phylogenetic depths, that might explain current host specificity and distributions of both associates. Both families of parasites utilise a number of highly diverged gastropod families, indicating that host extensions have featured in their histories. However, schistosomatids and paragonimids show different patterns of association with their snail hosts. As befits the apparently more ancient group, schistosomatids utilise snails from across a wide phylogenetic range within the Gastropoda. The genus Schistosoma itself has experienced one long-range host switch between pulmonates and caenogastropods. By contrast, paragonimids are restricted to two superfamilies of caenogastropods. Despite these differences, modern schistosomatid species appear to be more host specific than are paragonimids and host additions, at the level of host family, are far less common among species of schistosomatids than among paragonimids. Some species of Paragonimus exhibit remarkably low levels of host specificity, with different populations utilising snails of different families. Existing knowledge relating to the phenomenon will be presented in the context of phylogenies of schistosomatids, paragonimids, and their snail hosts. Discussion focuses on the usefulness of current theories of snail-digenean coevolution for interpreting these findings. In the past, much emphasis has been placed on the idea that digeneans engage in a one-to-one arms race with their snail host. We consider that phylogenetic tracking rather than an arms-race relationship might be a common alternative. Not being bound by the restrictions imposed by an arms race, some digeneans might be able to extend to new host species more easily than the literature suggests. Switches into related host taxa are most likely. However, ecologically equivalent but unrelated gastropod hosts may also be exploited. Given the right ecological setting, digeneans are able to switch across considerable phylogenetic distances. Examples from the Paragonimidae and Schistosomatidae are given.

Complete mitochondrial genomes confirm the distinctiveness of the horse-dog and sheep-dog strains of Echinococcus granulosus

Unlike other members of the genus, Echinococcus granulosus is known to exhibit considerable levels of variation in biology, physiology and molecular genetics. Indeed, some of the taxa regarded as 'genotypes' within E. granulosus might be sufficiently distinct as to merit specific status. Here, complete mitochondrial genomes are presented of 2 genotypes of E. granulosus (G1-sheep-dog strain: G4-horse-dog strain) and of another taeniid cestode, Taenia crassiceps. These genomes are characterized and compared with those of Echinococcus multilocularis and Hymenolepis diminuta. Genomes of all the species are very similar in structure, length and base-composition. Pairwise comparisons of concatenated protein-coding genes indicate that the G1 and G4 genotypes of E. granulosus are almost as distant from each other as each is from a distinct species, E. multilocularis. Sequences for the variable genes atp6 and nad3 were obtained from additional genotypes of E. granulosus, from E. vogeli and E. oligarthrus. Again, pairwise comparisons showed the distinctiveness of the G1 and G4 genotypes. Phylogenetic analyses of concatenated atp6, nad1 (partial) and cox1 (partial) genes from E. multilocularis, E. vogeli, E. oligarthrus, 5 genotypes of E. granulosus, and using T. crassiceps as an outgroup, yielded the same results. We conclude that the sheep-dog and horse-dog strains of E. granulosus should be regarded as distinct at the specific level.

Paragonimiasis in Yongjia County, Zhejiang Province, China: clinical, parasitological and karyotypic studies on Paragonimus westermani

Paragonimiasis in Yongjia County, Zhejiang Province, China, has been of such public health concern that a specialized Institute for Paragonimiasis Control has been established there. The study reported here involved both parasitological research on Paragonimus westermani in the endemic areas and a clinical analysis of 94 cases of paragonimiasis. Eggs were found in sputum, feces and brain tissue in 45 cases. Twenty patients, 19 of whom where children under 10 years of age, showed hepatic injury. Treatment with praziquantel or bithionol had satisfactory results in all cases. Dimensions of the parasite eggs, metacercariae from freshwater crabs and adult flukes suggested that the form of P. westermani in Yongjia is the 'small type': a suggestion supported by karyotypic studies on gonad cells from adult flukes collected from experimentally infected animals as all were found to be diploid. In conclusion, the 'small type' or diploid form of P. westermani is the cause of paragonimiasis pulmonary symptoms in Yongjia.

Complete DNA sequence and gene organization of the mitochondrial genome of the liverfluke, Fasciola hepatica L. (Platyhelminthes; Trematoda)

The complete nucleotide sequence of the mitochondrial (mt) DNA molecule of the liverfluke, Fasciola hepatica (phylum Platyhelminthes, class Trematoda, family Fasciolidae), was determined. It comprises 14462 bp, contains 12 protein-encoding, 2 ribosomal and 22 transfer RNA genes, and is the second complete flatworm (and the first trematode) mitochondrial sequence to be described in detail. All of the genes are transcribed from the same strand. Of the genes typically found in mitochondrial genomes of eumetazoans, only atp8 is absent. The nad4L and nad4 genes overlap by 40 nt. Most intergenic sequences are very short. Two larger non-coding regions are present. The longer one (817 nt) is located between trnG and cox3 and consists of 8 identical tandem repeats of 85 nt, rich in G and C, followed by 1 imperfect repeat. The shorter non-coding region (187 nt) exhibits no special features and is separated from the longer region by trnG. The gene arrangement resembles that of some other trematodes including the eastern Asian Schistosoma species (and cyclophyllidean cestode species) but it is strikingly different from that of the African schistosomes, represented by Schistosoma mansoni. The genetic code is as inferred previously for flatworms. Transfer RNA genes range in length from 58 to 70 nt, their products producing characteristic 'clover leaf' structures, except for tRNA(S(UNC)) and tRNA(S(AGN)) lacking the DHU arm.

Mitochondrial gene content, arrangement and composition compared in African and Asian schistosomes

Complete sequences were obtained for the coding portions of the mitochondrial (mt) genomes of Schistosoma mansoni (NMRI strain, Puerto Rico; 14 415 bp), S. japonicum (Anhui strain, China; 14 085 bp) and S. mekongi (Khong Island, Laos; 14 072 bp). Each comprises 36 genes: 12 protein-encoding genes (cox1-3, nad1-6, nad4L, atp6 and cob); two ribosomal RNAs, rrnL (large subunit rRNA or 16S) and rrnS (small subunit rRNA or 12S); as well as 22 transfer RNA (tRNA) genes. The atp8 gene is absent. A large segment (9.6 kb) of the coding region (comprising 14 tRNAs, eight complete and two incomplete protein-encoding genes) for S. malayensis (Baling, Malaysian Peninsula) was also obtained. Each genome also possesses a long non-coding region that is divided into two parts (a small and a large non-coding region, the latter not fully sequenced in any species) by one or more tRNAs. The protein-encoding genes are similar in size, composition and codon usage in all species except for cox1 in S. mansoni (609 aa) and cox2 in S. mekongi (219 aa), both of which are longer than homologues in other species. An unexpected finding in all the Schistosoma species was the presence of a leucine zipper motif in the nad4L gene. The gene order in S. mansoni is strikingly different from that seen in the S. japonicum group and other flatworms. There is a high level of identity (87-94% at both the nucleotide and amino acid levels) for all protein-encoding genes of S. mekongi and S. malayensis. The identity between genes of these two species and those of S. japonicum is less (56-83% for amino acids and 73-79% for nucleotides). The identity between the genes of S. mansoni and the Asian schistosomes is far less (33-66% for amino acids and 54-68% for nucleotides), an observation consistent with the known phylogenetic distance between S. mansoni and the other species.

A leucine zipper protein of mitochondrial origin

Sequence-specific DNA-binding proteins are characterised by short coiled-coil structural domains classified as zinc finger/RING finger, leucine zipper (L-Zip) or helix-loop-helix (HLH) motifs. The L-Zip proteins are defined by a pattern of at least four leucine (L) residues repeated every seventh amino acid that mediates protein dimerisation through the formation of parallel alpha-helical dimers. Usually the zipper is incorporated into a helix-loop-helix conformation called the basic helix-loop-helix-leucine zipper (bHLH/Zip). To date, all of the several hundred proteins reported as containing the L-Zip and/or bHLH/Zip motifs are nuclear-encoded. No leucine zipper polypeptide has, hitherto, been reported as mitochondrial in origin. Here we report such a polypeptide, the nicotinamide dehydrogenase subunit 4L (nad4L). We first identified this in human blood flukes of the genus Schistosoma (phylum Platyhelminthes; class Trematoda) but show that this is a common feature in other eucaryotes as well. Therefore, in addition to their well recognised role in oxidative phosphorylation, nad4L proteins may be pivotally involved in a range of other biological processes such as transcription and/or replication activation or as signal transmitters in communication with the nucleus and other cellular organelles. This may indicate a link between transcription regulation and respiration in mitochondria. We have also identified L-Zip-like motifs in nuoK, the procaryotic equivalent of the nad4L mitochondrial protein.

Urinary free cortisol in chronic fatigue syndrome

OBJECTIVE

The authors measured 24-hour urinary free cortisol in a group of well-characterized patients with chronic fatigue syndrome.

METHOD

They obtained 24-hour urine collections from 121 consecutive clinic patients with chronic fatigue syndrome and 64 comparison subjects without the syndrome.

RESULTS

Urinary free cortisol was significantly lower in the subjects with chronic fatigue syndrome regardless of the presence or absence of current or past comorbid psychiatric illness. Lower levels of urinary free cortisol were not related to medication use, sleep disturbance, or disability levels.

CONCLUSIONS

There is mild hypocortisolism in chronic fatigue syndrome. Whether a primary feature or secondary to other factors, hypocortisolism may be one factor contributing to the symptoms of chronic fatigue syndrome.

Mitochondrial genomes of human helminths and their use as markers in population genetics and phylogeny

To date, over 100 complete metazoan mitochondrial (mt) genomes of different phyla have been reported. Here, we briefly summarise mt gene organisation in the Metazoa and review what is known of the mt genomes of nematodes and flatworms parasitic in humans. The availability of complete or almost complete mtDNA sequences for several parasitic helminths provides a rich source of genetic markers for phylogenetic analysis and study of genetic variability in helminth groups. Examples of the application of mtDNA in studies on Ascaris, Onchocerca, Schistosoma, Fasciola, Paragonimus, Echinostoma, Echinococcus and Taenia are described.

Molecular phylogeographic studies on Paragonimus westermani in Asia

The lung fluke, Paragonimus westermani (Kerbert, 1878), is widely distributed in Asia, and exhibits much variation in its biological properties. Previous phylogenetic studies using DNA sequences have demonstrated that samples from north-east Asia form a tight group distinct from samples from south Asia (Philippines, Thailand, Malaysia). Among countries from the latter region, considerable molecular diversity was observed. This was investigated further using additional DNA sequences (partial mitochondrial cytochrome c oxidase subunit 1 (COI) and the second internal transcribed spacer of the nuclear ribosomal gene repeat (ITS2)) from additional samples of P. westermani. Phylogenies inferred from these again found three or four groups within P. westermani, depending on the method of analysis. Populations of P. westermani from north-east Asia use snail hosts of the family Pleuroceridae and differ in other biological properties from populations in south Asia (that use snail hosts of the family Thiaridae). It is considered that the populations we sampled can be divided into two species, one in north-east Asia and the other in south Asia.

Multiple lineages of the mitochondrial gene NADH dehydrogenase subunit 1 (ND1) in parasitic helminths: implications for molecular evolutionary studies of facultatively anaerobic eukaryotes

The task of using partial ND1 sequences to infer a phylogeny for species of the genus Paragonimus (Trematoda: Digenea) was complicated by the discovery of at least two ND1 lineages within individual worms. The divergence of the ND1 lineages is shown by phylogenetic analysis not only to predate the divergence of the three Paragonimus species or species groups investigated but also the divergence of some trematode families. Some sequences are clearly pseudogenes as they contain single base deletions and/or premature termination codons. The presence of both pseudogenes and/or mitochondrial heteroplasmy are invoked to explain the presence of multiple and divergent ND1 lineages in these trematodes, which have two distinct cytochemical types of mitochondria. The implications for phylogenetic studies generally and of parasitic helminths specifically, using ND1 sequence data, are discussed. The ability of these organisms to adapt their metabolic processes to the variable availability of oxygen as an electron acceptor are proposed to explain some of the molecular diversity observed in parasitic helminths and possibly also in other anaerobically adapted eukaryotes.

The distribution of P2X receptor clusters on individual neurons in sympathetic ganglia and their redistribution on agonist activation

The distribution of P2X receptors on neurons in rat superior cervical ganglia and lability of P2X receptors on exposure to agonists were determined. Antibody labeling of each P2X subtype P2X(1)-P2X(7) showed neurons isolated into culture possessed primarily P2X(2) subunits with others occurring in order P2X(7) > P2X(6) > P2X(3) > P2X(1) > P2X(5) > P2X(4). Application of ATP and alpha,beta-meATP to neurons showed they possessed a predominantly nondesensitizing P2X receptor type insensitive to alpha,beta-meATP, consistent with immunohistochemical observations. P2X(1)-green fluorescent protein (GFP) was used to study the time course of P2X(1) receptor clustering in plasma membranes of neurons and internalization of receptors following prolonged exposure to ATP. At 12-24 h after adenoviral infection, P2X(1)-GFP formed clusters about 1 microm diameter in the neuron membrane. Application of ATP and alpha,beta-meATP showed these neurons possessed a predominantly desensitizing P2X receptor type sensitive to alpha,beta-meATP. Infection converted the major functional P2X receptor type in the membrane to P2X(1). Exposure of infected neurons to alpha,beta-meATP for less than 60 s led to the disappearance of P2X(1)-GFP fluorescence from the cell surface that was blocked by monensin, indicating the chimera is normally endocytosed into these organelles on exposure to agonist.

Respiratory distress secondary to both amphotericin B deoxycholate and lipid complex formulation

A 73-y-old female with a history of adenocarcinoma of colon and refractory anemia developed febrile neutropenia following chemotherapy. Therapy with iv infusion of amphotericin B deoxycholate (AmBd) was initiated on day 8 of hospital admission. Premedications included acetaminophen, diphenhydramine and meperidine. Patient developed rigor, chill and elevated temperature approximately 100 min into the infusion. The infusion was temporarily discontinued and rigors subsided following administration of 25 mg meperidine im. Infusion was continued after cessation of the rigors with no further sequelae. During each infusion of AmBd over the next 3 d, the patient developed rigor, chill and elevated temperature which was managed with meperidine. However, on day 4 she developed respiratory distress, bronchospasm and visible cyanosis with oxygen saturation of 88% while on 2 L oxygen. The infusion was stopped and the symptoms subsided with administration of albuterol via nebulizer. Amphotericin lipid formulation infusion was reinstituted after 3 d because of the patient's worsening clinical status. However, the patient developed severe respiratory distress approximately 130 min into the infusion. The infusion was discontinued and she was treated with albuterol via nebulizer. Itraconazole therapy was instituted without any adverse sequelae. Clinicians should be aware of this potential adverse event since it can occur with all formulation of amphotericin.

Patterns in thin vibrated granular layers: interfaces, hexagons, and superoscillons

A theoretical and experimental study of patterns in vibrated granular layers is presented. An order parameter model based on the parametric Ginzburg-Landau equation is used to describe strongly nonlinear excitations including hexagons, interfaces between flat antiphase domains, and new localized objects, superoscillons. The experiments confirm the existence of superoscillons and bound states of superoscillons and interfaces. On the basis of the order parameter model we predict analytically and confirm experimentally that additional subharmonic driving results in the controlled motion of interfaces.

Genomes of Paragonimus westermani and related species: current state of knowledge

There have been few investigations of genomes of Paragonimus westermani and related species. Most studies have focussed on questions such as the identities of species and relationships among them, origins and relationships of strains with different ploidy states, and the characterisation of genes producing immunologically significant proteins. In the context of these questions, work on the karyotypes, nuclear and mitochondrial genomes is reviewed.

Electrostatically driven granular media: phase transitions and coarsening

We report the experimental and theoretical study of electrostatically driven granular material. We show that the charged granular medium undergoes a hysteretic phase transition from the immobile condensed state (granular solid) to a fluidized dilated state (granular gas) with a changing applied electric field. In addition we observe a spontaneous precipitation of dense clusters from the gas phase and subsequent coarsening-coagulation of these clusters. Molecular dynamics simulations show qualitative agreement with experimental results.

Analysis of Mycobacterium tuberculosis transmission patterns in a homeless shelter outbreak

SETTING

From July 1997 through May 1998, ten tuberculosis (TB) cases were reported among men in a Syracuse New York homeless shelter for men.

OBJECTIVE AND DESIGN

Investigation to determine extent of, and prevent further, transmission of Mycobacterium tuberculosis.

RESULTS

Epidemiologic and laboratory evidence suggests that eight of the ten cases were related. Seven cases had isolates with matching six-band IS6110 DNA fingerprints; the isolate from another case had a closely related fingerprint pattern and this case was considered to be caused by a variant of the same strain. Isolates from eight cases had identical spoligotypes. The source case had extensive cavitary disease and stayed at the shelter nightly, while symptomatic, for almost 8 months before diagnosis. A contact investigation was conducted among 257 shelter users and staff, 70% of whom had a positive tuberculin skin test, including 21 with documented skin test conversions.

CONCLUSIONS

An outbreak of related TB cases in a high-risk setting was confirmed through the use of IS6110 DNA fingerprinting in conjunction with spoligotyping and epidemiologic evidence. Because of the high rate of infection in the homeless population, routine screening for TB and preventive therapy for eligible persons should be considered in shelters.

Mitochondrial DNA sequences of human schistosomes: the current status

Sequences generated from the mitochondrial genome provide useful molecular markers for defining population groups, for tracing the genetic history of an individual or a particular group of related individuals, and for constructing deep-branch taxonomic phylogenies. There is every reason to believe that the mitochondrial genome will be as valuable in studies on flatworms, such as the human schistosomes, as it has been for other taxa. To date, however, our knowledge of mitochondrial genomes of flatworms remains limited, and this review summarises the currently available information. In particular, details of the recent sequence obtained for cloned Schistosoma mansoni mitochondrial DNA fragments spanning over half of the mitochondrial genome of this species are emphasised. This and other information, available as a result of the Schistosome Genome Project, provide the basis for obtaining the complete mitochondrial DNA sequence and gene order of S. mansoni and the other human schistosomes. The availability of complete mitochondrial DNA sequences from the different species will facilitate much more in-depth study of genetic diversity and host specificity in schistosomes and the interrelationships between the various forms infecting humans and between these and other flatworms.