Narrow-band search of continuous gravitational-wave signals from Crab and Vela pulsars in Virgo VSR4 data

In this paper we present the results of a coherent narrow-band search for continuous gravitational-wave signals from the Crab and Vela pulsars conducted on Virgo VSR4 data. In order to take into account a possible small mismatch between the gravitational-wave frequency and two times the star rotation frequency, inferred from measurement of the electromagnetic pulse rate, a range of 0.02 Hz around two times the star rotational frequency has been searched for both the pulsars. No evidence for a signal has been found and 95% confidence level upper limits have been computed assuming both that polarization parameters are completely unknown and that they are known with some uncertainty, as derived from x-ray observations of the pulsar wind torii. For Vela the upper limits are comparable to the spin-down limit, computed assuming that all the observed spin-down is due to the emission of gravitational waves. For Crab the upper limits are about a factor of 2 below the spin-down limit, and represent a significant improvement with respect to past analysis. This is the first time the spin-down limit is significantly overcome in a narrow-band search.

Directed search for gravitational waves from Scorpius X-1 with initial LIGO data

We present results of a search for continuously emitted gravitational radiation, directed at the brightest low-mass x-ray binary, Scorpius X-1. Our semicoherent analysis covers 10 days of LIGO S5 data ranging from 50-550 Hz, and performs an incoherent sum of coherent F-statistic power distributed amongst frequency-modulated orbital sidebands. All candidates not removed at the veto stage were found to be consistent with noise at a 1% false alarm rate. We present Bayesian 95% confidence upper limits on gravitational-wave strain amplitude using two different prior distributions: a standard one, with no a priori assumptions about the orientation of Scorpius X-1; and an angle-restricted one, using a prior derived from electromagnetic observations. Median strain upper limits of 1.3 x 10(-24) and 8 x 10(-25) are reported at 150 Hz for the standard and angle-restricted searches respectively. This proof-of-principle analysis was limited to a short observation time by unknown effects of accretion on the intrinsic spin frequency of the neutron star, but improves upon previous upper limits by factors of similar to 1.4 for the standard, and 2.3 for the angle-restricted search at the sensitive region of the detector.

Revision of Hawaiian, Australasian, Oriental, and Japanese Parandrinae (Coleoptera, Cerambycidae)

A comprehensive revision of the Subfamily Parandrinae (Coleoptera, Cerambycidae) from the Hawaiian, Australasian, Oriental, and Japanese regions is presented. Seven (7) new genera are described: Komiyandra, Melanesiandra, Papuandra, Storeyandra, Hawaiiandra, Caledonandra, and Malukandra. All known, indigenous species from these regions are assigned to new genera resulting in the following new combinations: Komiyandra janus (Bates, 1875), K. shibatai (Hayashi, 1963), K. formosana (Miwa and Mitono, 1939), K. lanyuana (Hayashi, 1981), Melanesiandra striatifrons (Fairmaire, 1879), M. solomonensis (Arigony, 1983), Caledonandra austrocaledonica (Montrouzier, 1861), C. passandroides (Thomson, 1867), Hawaiiandra puncticeps (Sharp, 1878), Malukandra heterostyla (Lameere, 1902), Storeyandra frenchi (Blackburn, 1895), and Papuandra araucariae (Gressitt, 1959). Thirty-one (31) new species are described: Komiyandra javana, K. nayani, K. ohbayashii, K. luzonica, K. philippinensis, K. mindanao, K. mehli, K. vivesi, K. lombokia, K. sulawesiana, K. irianjayana, K. menieri, K. sangihe, K. mindoro, K. niisatoi, K. drumonti, K. cabigasi, K. koni, K. johkii, K. poggii, K. uenoi, Melanesiandra bougainvillensis, M. birai, Papuandra gressitti, P. weigeli, P. queenslandensis, P. norfolkensis, P. rothschildi, P. oberthueri, Malukandra jayawijayana and M. hornabrooki. A lectotype is designated for Parandra janus Bates, 1875. Komiyandra janus (Bates, 1875) is excluded from nearly all previously reported locations, even one location given in the original description, and is now only known from Sulawesi. A paralectotype of Parandra janus Bates, 1875, is designated as a paratype for Komiyandra menieri, new species. Komiyandra formosana is excluded from the Japanese (Ryukyu Is.) fauna. Parandra vitiensis Nonfried, 1894, is again placed in synonymy with P. striatifrons Fairmaire (now Melanesiandra striatifrons). A neotype is designated for Parandra austrocaledonica Montrouzier, 1861. A lectotype is designated for Parandra janus Bates, 1875. The lectotype of Parandra gabonica Thomson, 1858, designated by Quentin and Villiers (1975) is considered invalid. Papuandra araucariae (Gressitt, 1959) is excluded from the fauna of Norfolk Island. The African species Stenandra kolbei (Lameere, 1903) is reported for the first time from Asia (N. Vietnam). Keys are presented to separate worldwide genera of Parandrini and all species within the study regions. Illustrations are provided for all species including many special characters to differentiate genera and species.

Genome of the host-cell transforming parasite Theileria annulata compared with T. parva

Theileria annulata and T. parva are closely related protozoan parasites that cause lymphoproliferative diseases of cattle. We sequenced the genome of T. annulata and compared it with that of T. parva to understand the mechanisms underlying transformation and tropism. Despite high conservation of gene sequences and synteny, the analysis reveals unequally expanded gene families and species-specific genes. We also identify divergent families of putative secreted polypeptides that may reduce immune recognition, candidate regulators of host-cell transformation, and a Theileria-specific protein domain [frequently associated in Theileria (FAINT)] present in a large number of secreted proteins.

Impact of viral E2-gene status on outcome after radiotherapy for patients with human papillomavirus 16-positive cancer of the uterine cervix

PURPOSE: Integration of high-risk papillomavirus DNA has been considered an important step in oncogenic progression to cervical carcinoma. Disruption of the human papillomavirus (HPV) genome within the E2 gene is frequently a consequence. This study investigated the influence of episomal viral DNA on outcome in patients with advanced cervical cancer treated with primary radiotherapy. METHODS AND MATERIALS: Paraffin-embedded biopsies of 82 women with locally advanced cervical cancer could be analyzed for HPV infection by multiplex polymerase chain reaction (PCR) by use of SPF1/2 primers. E2-gene intactness of HPV-16-positive samples was analyzed in 3 separate amplification reactions by use of the E2A, E2B, E2C primers. Statistical analyses (Kaplan-Meier method; log-rank test) were performed for overall survival (OS), disease-free survival (DFS), local progression-free survival (LPFS), and distant metastases-free survival (DMFS). RESULTS: Sixty-one (75%) of 82 carcinomas were HPV positive, 44 of them for HPV-16 (72%). Seventeen of the 44 HPV-16-positive tumors (39%) had an intact E2 gene. Patients with a HPV-16-positive tumor and an intact E2 gene showed a trend for a better DFS (58% vs. 38%, p = 0.06) compared with those with a disrupted E2 gene. A nonsignificant difference occurred regarding OS (87% vs. 66%, p = 0.16) and DMFS (57% vs. 48%, p = 0.15). CONCLUSION: E2-gene status may be a promising new target, but more studies are required to elucidate the effect of the viral E2 gene on outcome after radiotherapy in HPV-positive tumors.

Camel Streptococcus agalactiae populations are associated with specific disease complexes and acquired the tetracycline resistance gene tetM via a Tn916-like element

Camels are the most valuable livestock species in the Horn of Africa and play a pivotal role in the nutritional sustainability for millions of people. Their health status is therefore of utmost importance for the people living in this region. Streptococcus agalactiae, a Group B Streptococcus (GBS), is an important camel pathogen. Here we present the first epidemiological study based on genetic and phenotypic data from African camel derived GBS. Ninety-two GBS were characterized using multilocus sequence typing (MLST), capsular polysaccharide typing and in vitro antimicrobial susceptibility testing. We analysed the GBS using Bayesian linkage, phylogenetic and minimum spanning tree analyses and compared them with human GBS from East Africa in order to investigate the level of genetic exchange between GBS populations in the region. Camel GBS sequence types (STs) were distinct from other STs reported so far. We mapped specific STs and capsular types to major disease complexes caused by GBS. Widespread resistance (34%) to tetracycline was associated with acquisition of the tetM gene that is carried on a Tn916-like element, and observed primarily among GBS isolated from mastitis. The presence of tetM within different MLST clades suggests acquisition on multiple occasions. Wound infections and mastitis in camels associated with GBS are widespread and should ideally be treated with antimicrobials other than tetracycline in East Africa.

The need for transparency and good practices in the qPCR literature

Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.

Pinus nigra (European black pine) as the dominant species of the last glacial pinewoods in south-western to central Iberia: a morphological study of modern and fossil pollen

Aim Our aim was to discriminate different species of Pinus via pollen analysis in order to assess the responses of particular pine species to orbital and millennial-scale climate changes, particularly during the last glacial period. Location Modern pollen grains were collected from current pine populations along transects from the Pyrenees to southern Iberia and the Balearic Islands. Fossil pine pollen was recovered from the south-western Iberian margin core MD95-2042. Methods We measured a set of morphological traits of modern pollen from the Iberian pine species Pinus nigra, P. sylvestris, P. halepensis, P. pinea and P. pinaster and of fossil pine pollen from selected samples of the last glacial period and the early to mid-Holocene. Classification and regression tree (CART) analysis was used to establish a model from the modern dataset that discriminates pollen from the different pine species and allows identification of fossil pine pollen at the species level. Results The CART model was effective in separating pollen of P. nigra and P. sylvestris from that of the Mediterranean pine group (P. halepensis, P. pinea and P. pinaster). The pollen of Pinus nigra diverged from that of P. sylvestris by having a more flattened corpus. Predictions using this model suggested that fossil pine pollen is mainly from P. nigra in all the samples analysed. Pinus sylvestris was more abundant in samples from Greenland stadials than Heinrich stadials, whereas Mediterranean pines increased in samples from Greenland interstadials and during the early to mid-Holocene. Main conclusions Morphological parameters can be successfully used to increase the taxonomic resolution of fossil pine pollen at the species level for the highland pines (P. nigra and P. sylvestris) and at the group of species level for the Mediterranean pines. Our study indicates that P. nigra was the dominant component of the last glacial south-western/central Iberian pinewoods, although the species composition of these woodlands varied in response to abrupt climate changes.

Mineralogy micromorphology, and geochemistry at DSDP Site 89-585

At Site 585 of Deep Sea Drilling Project Leg 89 more than 500 m of volcaniclastic to argillaceous middle-Late Cretaceous sediments were recovered. Analyses by X-ray diffraction (bulk sediment and clay fraction), transmission electron microscopy, molecular and atomic absorption, and electron microprobe were done on Site 585 samples. We identify four successive stages and interpret them as the expression of environments evolving under successive influences: Stage 1, late Aptian to early Albian - subaerial and proximal volcanism, chiefly expressed by the presence of augite, analcite, olivine, celadonite, small and well-shaped transparent trioctahedral saponite, Al hydroxides, Na, Fe, Mg, and various trace elements (Mn, Ni, Cr, Co, Pb, V, Zn, Ti). Stage 2, early to middle Albian - submarine and less proximal volcanic influence, characterized by dioctahedral and hairy Mg-beidellites, a paucity of analcite and pyroxenes, the presence of Mg and K, and local alteration of Mg-smectites to Mg-chlorites. Stage 3, middle Albian to middle Campanian - early marine diagenesis, marked by the development of recrystallization from fleecy smectites to lathed ones (all of alkaline Si-rich Fe-beidellite types), by the development of opal CT and clinoptilolite, and by proximal to distal volcanic influences (Na parallel to Ti, K). Local events consist of the supply of reworked palygorskite during the Albian-Cenomanian, and the recurrence of proximal volcanic activity during the early Campanian. Stage 4, late Campanian to Maestrichtian - development of terrigenous supply resulting from the submersion of topographic barriers; this terrigenous supply is associated with minor diagenetic effects and is marked by a clay diversification (beidellite, illite, kaolinite, palygorskite), the rareness of clay recrystallizations, and the disappearance of volcanic markers.