How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.

Primary Fallopian tube carcinoma:occurrence, risk and prognostic factors

The aim of the study was to clarify the occurrence, and etiological and prognostic factors of primary fallopian tube carcinoma (PFTC). We studied the sociodemographic determinants of the incidence of PFTC in Finland and the role of chlamydial infections and human papillomavirus infections as risk factors for PFTC. Serum tumor markers were studied as prognostic factors for PFTC. We also evaluated selected reproductive factors (parity, sterilization and hysterectomy) as risk or protective factors of PFTC. The risks of second primary cancers after PFTC were also studied. The age-adjusted incidence of PFTC in Finland increased to 5.4 / 1,000,000 in 1993 97. The incidence rate was higher in the cities, but the relative rise was higher in rural areas. Women in the two highest social classes showed a 1.8 fold incidence compared with those in the lowest. Women in agriculture and those not working outside the home showed only half the PFTC incidence of those in higher socioeconomic occupations. Pretreatment serum concentrations of hCGβ, CA125 and TATI were evaluated as prognostic markers for PFTC. Elevated hCGβ values (above the 75th percentile, 3.5 pmol/L; OR 2.49, 95% CI 1.22 5.09), stage and histology were strong independent prognostic factors for PFTC. The effects of parity, sterilization and hysterectomy on the risk of PFTC were studied in a case control-study with 573 PFTC cases from the Finnish Cancer Registry. In multivariate analysis parity was the only significant protective factor as regards PFTC, with increasing protection associated with increasing number of deliveries. In univariate analysis sterilization gave borderline protection against PFTC and the protective effect increased with time since the operation. In multivariate analysis the protection did not reach statistical significance. Chlamydial and human papillomavirus (HPV) infections were studied in two separate seroepidemiological case-control studies with 78 PFTC patients. The incidence of women with positive HPV or chlamydial serology was the same in PFTC patients and in the control group and was not found to be a risk factor for PFTC. Finally, the possible risk of a second primary cancer after diagnosis and treatment of PFTC in a cohort of 2084 cases from 13 cancer registries followed for second primary cancers within the period 1943 2000 was studied. In PFTC patients, second primary cancers were 36% more common than expected (SIR 1.36, 95% CI 1.13 1.63). In conclusion, the incidence of PFTC has increased in Finland, especially in higher social classes and among those in certain occupations. Elevated serum hCGβ reflect a worsened prognosis. Parity is a clear protective factor, as is previous sterilization. After PFTC there is a risk of second primary cancers, especially colorectal, breast, lung and bladder cancers and non-lymphoid leukemia. The excess of colorectal and breast cancers after PFTC may indicate common effects of earlier treatments, or they could reflect common effects of lifestyle or genetic, immunological or environmental background.

Avian diversification patterns across the K-Pg boundary: Influence of calibrations, datasets, and model misspecification

Birds represent the most diverse extant tetrapod clade, with ca. 10,000 extant species, and the timing of the crown avian radiation remains hotly debated. The fossil record supports a primarily Cenozoic radiation of crown birds, whereas molecular divergence dating analyses generally imply that this radiation was well underway during the Cretaceous. Furthermore, substantial differences have been noted between published divergence estimates. These have been variously attributed to clock model, calibration regime, and gene type. One underappreciated phenomenon is that disparity between fossil ages and molecular dates tends to be proportionally greater for shallower nodes in the avian Tree of Life. Here, we explore potential drivers of disparity in avian divergence dates through a set of analyses applying various calibration strategies and coding methods to a mitochondrial genome dataset and an 18-gene nuclear dataset, both sampled across 72 taxa. Our analyses support the occurrence of two deep divergences (i.e., the Palaeognathae/Neognathae split and the Galloanserae/Neoaves split) well within the Cretaceous, followed by a rapid radiation of Neoaves near the K-Pg boundary. However, 95% highest posterior density intervals for most basal divergences in Neoaves cross the boundary, and we emphasize that, barring unreasonably strict prior distributions, distinguishing between a rapid Early Paleocene radiation and a Late Cretaceous radiation may be beyond the resolving power of currently favored divergence dating methods. In contrast to recent observations for placental mammals, constraining all divergences within Neoaves to occur in the Cenozoic does not result in unreasonably high inferred substitution rates. Comparisons of nuclear DNA (nDNA) versus mitochondrial DNA (mtDNA) datasets and NT- versus RY-coded mitochondrial data reveal patterns of disparity that are consistent with substitution model misspecifications that result in tree compression/tree extension artifacts, which may explain some discordance between previous divergence estimates based on different sequence types. Comparisons of fully calibrated and nominally calibrated trees support a correlation between body mass and apparent dating error. Overall, our results are consistent with (but do not require) a Paleogene radiation for most major clades of crown birds.

IMIA working group on health record banking - How complex systems can cooperate towards having individual's consolidated data

This workshop aims at discussing alternative approaches to resolving the problem of health information fragmentation, partially resulting from difficulties of health complex systems to semantically interact at the information level. In principle, we challenge the current paradigm of keeping medical records where they were created and discuss an alternative approach in which an individual's health data can be maintained by new entities whose sole responsibility is the sustainability of individual-centric health records. In particular, we will discuss the unique characteristics of the European health information landscape. This workshop is also a business meeting of the IMIA Working Group on Health Record Banking.

Germination biology and occurrence of pol-yembryony in two forms of cats claw creeper vine, Dolichandra unguis-cati (Bignonia-ceae): implications for its invasiveness and management

Cat’s claw creeper, Dolichandra unguis-cati (L.) Lohmann (syn. Macfadyena unguis-cati (L.) Gentry) is a major environmental weed in Australia. Two forms (‘long’ and ‘short’ pod) of the weed occur in Australia. This investigation aimed to evaluate and compare germination behavior and occurrence of polyembryony in the two forms of the weed. Seeds were germinated in growth chambers set to 10/20 °C, 15/25 °C, 20/30 °C, 30/45 °C and 25 °C. Germination and polyembryony were monitored over a period of 12 weeks. For all the treatments in this study, seeds from the short pod form exhibited significantly higher germination rates and higher occurrence of polyembryony than those from the long pod form. Seeds from the long pod form did not germinate at the lowest temperature of 10/20 °C; in contrast, those of the short pod form germinated under this condition, albeit at a lower rate. Results from this study could explain why the short pod form of D. unguis-cati is the more widely distributed form in Australia, while the long pod form is confined to a few localities. The results have implication in predicting future ranges of both forms of the invasive D. unguis-cati, as well as inform management decisions for control of the weed.

Iron and manganese in groundwater in Finland : Occurrence in glacifluvial aquifers and removal by biofiltration

Yhteenveto: Rauta ja mangaani Suomen glasifluviaalisten akviferien pohjavedessä ja poisto biosuodatuksella

Occurrence of Lipid Peroxidation in Brain Microsomes in the Presence of NADH and Vanadate

Oxidation of NADH by rat brain microsomes was stimulated severalfold on addition of vanadate. During the reaction, vanadate was reduced, oxygen was consumed, and H2O2 was generated with a stoichiometry of 1:1 for NADH/O2, as in the case of other membranes. Extra oxygen was found to be consumed over that needed for H2O2 generation specifically when brain microsomes were used. This appears to be due to the peroxidation of lipids known to be accompanied by a large consumption of oxygen. Occurrence of lipid peroxidation in brain microsomes in the presence of NADH and vanadate has been demonstrated. This activity was obtained specifically with the polymeric form of vanadate and with NADH, and was inhibited by the divalent cations Cu2+, Mn2+, and Ca2+, by dihydroxy-phenolic compounds, and by hemin in a concentration-dependent fashion. In the presence of a small concentration of vanadate, addition of an increasing concentration of Fe2+ gave increasing lipid peroxidation. After undergoing lipid peroxidation in the presence of NADH and vanadate, the binding of quinuclidinyl benzylate, a muscarinic antagonist, to brain membranes was decreased.

Assessment of insect occurrence in boreal forests based on satellite imagery and field measurements.

The presence/absence data of twenty-seven forest insect taxa (e.g. Retinia resinella, Formica spp., Pissodes spp., several scolytids) and recorded environmental variation were used to investigate the applicability of modelling insect occurrence based on satellite imagery. The sampling was based on 1800 sample plots (25 m by 25 m) placed along the sides of 30 equilateral triangles (side 1 km) in a fragmented forest area (approximately 100 km2) in Evo, S Finland. The triangles were overlaid on land use maps interpreted from satellite images (Landsat TM 30 m multispectral scanner imagery 1991) and digitized geological maps. Insect occurrence was explained using either environmental variables measured in the field or those interpreted from the land use and geological maps. The fit of logistic regression models varied between species, possibly because some species may be associated with the characteristics of single trees while other species with stand characteristics. The occurrence of certain insect species at least, especially those associated with Scots pine, could be relatively accurately assessed indirectly on the basis of satellite imagery and geological maps. Models based on both remotely sensed and geological data better predicted the distribution of forest insects except in the case of Xylechinus pilosus, Dryocoetes sp. and Trypodendron lineatum, where the differences were relatively small in favour of the models based on field measurements. The number of species was related to habitat compartment size and distance from the habitat edge calculated from the land use maps, but logistic regressions suggested that other environmental variables in general masked the effect of these variables in species occurrence at the present scale.

Occurrence of 1-methyladenosine and absence of ribothymidine in transfer ribonucleic acid of Mycobacterium smegmatis

The minor base composition of Mycobacterium smegmatis tRNA has been studied. Thin-layer chromatographic patterns of a ribonuclease T2 digest of mycobacterial tRNA indicated the presence of appreciable amounts of 1-methyladenosine (which is commonly present only in eucaryotic tRNA), dihydrouridine, and 7-methylguanosine. Ribothymidine was absent. The S-adenosylmethionine-dependent tRNA methylases of M. smegmatis catalyzed the formation of 1-methyladenosine when Escherichia coli tRNA was used as acceptor. Similarly, E. coli extracts methylated the tRNA of M. smegmatis, forming ribothymidine.

Occurrence of maximum Tc at an optimal carrier concentration in superconducting bismuth and thallium cuprates

The superconducting transition temperatures in Bi2Ca1−xLnxSr2Cu2O8+δ, TlCa1−xLnxSr2Cu2O6+δ, and Tl0.8Ca1−xLnxBa2Cu23O6+δ (Ln=Y or rare earth) vary with composition and show a maximum at a specific value of x or δ. This observation suggests that an optimal carrier concentration is required to attain maximum Tc in such cuprates which seem to be two‐band systems

A delta13C record of late Quaternary climate change from tropical peats in southern India

STABLE-ISOTOPE ratios of carbon in soils or lake sediments1-3 and of oxygen and hydrogen in peats4,5 have been found to reflect past moisture variations and hence to provide valuable palaeoclimate records. Previous applications of the technique to peat have been restricted to temperate regions, largely because tropical climate variations are less pronounced, making them harder to resolve. Here we present a deltaC-13 record spanning the past 20 kyr from peats in the Nilgiri hills, southern India. Because the site is at high altitude (>2,000 m above sea level), it is possible to resolve a clear climate signal. We observe the key climate shifts that are already known to have occurred during the last glacial maximum (18 kyr ago) and the subsequent deglaciation. In addition, we observe an arid phase from 6 to 3.5 kyr ago, and a short, wet phase about 600 years ago. The latter appears to correspond to the Mediaeval Warm Period, which previously was believed to be confined to Europe and North America6,7. Our results therefore suggest that this event may have extended over the entire Northern Hemisphere.

Paleoseismological evidence of surface faulting along the northeastern Himalayan front, India: Timing, size, and spatial extent of great earthquakes

The similar to 2500 km long Himalayan arc has experienced three large to great earthquakes of M-w 7.8 to 8.4 during the past century, but none produced surface rupture. Paleoseismic studies have been conducted during the last decade to begin understanding the timing, size, rupture extent, return period, and mechanics of the faulting associated with the occurrence of large surface rupturing earthquakes along the similar to 2500 km long Himalayan Frontal Thrust (HFT) system of India and Nepal. The previous studies have been limited to about nine sites along the western two-thirds of the HFT extending through northwest India and along the southern border of Nepal. We present here the results of paleoseismic investigations at three additional sites further to the northeast along the HFT within the Indian states of West Bengal and Assam. The three sites reside between the meizoseismal areas of the 1934 Bihar-Nepal and 1950 Assam earthquakes. The two westernmost of the sites, near the village of Chalsa and near the Nameri Tiger Preserve, show that offsets during the last surface rupture event were at minimum of about 14 m and 12 m, respectively. Limits on the ages of surface rupture at Chalsa (site A) and Nameri (site B), though broad, allow the possibility that the two sites record the same great historical rupture reported in Nepal around A.D. 1100. The correlation between the two sites is supported by the observation that the large displacements as recorded at Chalsa and Nameri would most likely be associated with rupture lengths of hundreds of kilometers or more and are on the same order as reported for a surface rupture earthquake reported in Nepal around A.D. 1100. Assuming the offsets observed at Chalsa and Nameri occurred synchronously with reported offsets in Nepal, the rupture length of the event would approach 700 to 800 km. The easternmost site is located within Harmutty Tea Estate (site C) at the edges of the 1950 Assam earthquake meizoseismal area. Here the most recent event offset is relatively much smaller (<2.5 m), and radiocarbon dating shows it to have occurred after A.D. 1100 (after about A.D. 1270). The location of the site near the edge of the meizoseismal region of the 1950 Assam earthquake and the relatively lesser offset allows speculation that the displacement records the 1950 M-w 8.4 Assam earthquake. Scatter in radiocarbon ages on detrital charcoal has not resulted in a firm bracket on the timing of events observed in the trenches. Nonetheless, the observations collected here, when taken together, suggest that the largest of thrust earthquakes along the Himalayan arc have rupture lengths and displacements of similar scale to the largest that have occurred historically along the world's subduction zones.

HLA-B*57 and Gender Influence the Occurrence of Tuberculosis in HIV Infected People of South India

Background. Substantial evidence exists for HLA and other host genetic factors being determinants of susceptibility or resistance to infectious diseases. However, very little information is available on the role of host genetic factors in HIV-TB coinfection. Hence, a longitudinal study was undertaken to investigate HLA associations in a cohort of HIV seropositive individuals with and without TB in Bangalore, South India. Methods. A cohort of 238 HIV seropositive subjects were typed for HLA-A, B, and DR by PCR-SSP and followed up for 5 years or till manifestation of Tuberculosis. HLA data of 682 HIV Negative healthy renal donors was used as control. Results. The ratio of males and females in HIV cohort was comparable (50.4% and 49.6%). But the incidence of TB was markedly lower in females (12.6%,) than males (25.6%). Further, HLA-B* 57 frequency in HIV cohort was significantly higher among females without TB (21.6%, 19/88) than males (1.7%, 1/59); P = 0.0046; OR = 38. CD4 counts also were higher among females in this cohort. Conclusion. This study suggests that HIV positive women with HLA-B* 57 have less occurrence of TB as compared to males.