The Hyperfine Spin Splittings In Heavy Quarkonia

The hyperfine spin splittings in heavy quarkonia are studied using the recently developed renormalization group improved spin-spin potential which is independent of the scale parameter $\mu$. The calculated energy difference between the $J/\psi$ and the $\eta_c$ fits the experimental data well, while the predicted energy difference $\Delta M_p$ between the center of the gravity of $1^3P_{0,1,2}$ states and the $1^1P_1$ state of charmonium has the correct sign but is somewhat larger than the experimental data. This is not surprising since there are several other contributions to $\Delta M_p$, which we discuss, that are of comparable size ($\sim 1$ MeV) that should be included, before precise agreement with the data can be expected. The mass differences of the $\psi'-\eta_c'$, $\Upsilon(1S)-\eta_b$, $\Upsilon(2S)-\eta_b'$, and $B_c^*-B_c$ are also predicted.Comment: 17 page

Developing a predictive modelling capacity for a climate change-vulnerable blanket bog habitat: Assessing 1961-1990 baseline relationships

Aim: Understanding the spatial distribution of high priority habitats and developing predictive models using climate and environmental variables to replicate these distributions are desirable conservation goals. The aim of this study was to model and elucidate the contributions of climate and topography to the distribution of a priority blanket bog habitat in Ireland, and to examine how this might inform the development of a climate change predictive capacity for peat-lands in Ireland. Methods: Ten climatic and two topographic variables were recorded for grid cells with a spatial resolution of 1010 km, covering 87% of the mainland land surface of Ireland. Presence-absence data were matched to these variables and generalised linear models (GLMs) fitted to identify the main climatic and terrain predictor variables for occurrence of the habitat. Candidate predictor variables were screened for collinearity, and the accuracy of the final fitted GLM was evaluated using fourfold cross-validation based on the area under the curve (AUC) derived from a receiver operating characteristic (ROC) plot. The GLM predicted habitat occurrence probability maps were mapped against the actual distributions using GIS techniques. Results: Despite the apparent parsimony of the initial GLM using only climatic variables, further testing indicated collinearity among temperature and precipitation variables for example. Subsequent elimination of the collinear variables and inclusion of elevation data produced an excellent performance based on the AUC scores of the final GLM. Mean annual temperature and total mean annual precipitation in combination with elevation range were the most powerful explanatory variable group among those explored for the presence of blanket bog habitat. Main conclusions: The results confirm that this habitat distribution in general can be modelled well using the non-collinear climatic and terrain variables tested at the grid resolution used. Mapping the GLM-predicted distribution to the observed distribution produced useful results in replicating the projected occurrence of the habitat distribution over an extensive area. The methods developed will usefully inform future climate change predictive modelling for Irelan

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement In Accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

Multicentric Reticulohistiocytosis : a Critical Review

The literature reports approximately 300 cases of multicentric reticulohistiocytosis (MRH) worldwide, mostly women of Caucasian origin. MRH manifests as a symmetric erosive polyarthritis mimicking rheumatoid arthritis with the subsequent appearance of typical papulonodular skin lesions. The disease may rapidly progress towards mutilans arthritis in the majority of cases, but it generally remits spontaneously in 10\ua0years. The only diagnostic hallmark for MRH is the observation at histology of numerous histiocytes and multinucleated giant cells and ground glass eosinophilic cytoplasm. Despite its rarity, clinical and pathogenetic challenging features characterize the condition. First, the differential diagnosis with other forms of arthritis and the frequent coexistence of neoplasms or autoimmune diseases warrant a careful evaluation of suspected cases. Second, data from isolated MRH cases are consistent in supporting a role for monocyte/macrophage cells and for an enhanced osteoclastic activity in the affected tissues. Third, beside anti-inflammatory treatments, promising reports suggest that biologics targeting TNF-alpha and bisphosphonates may prove beneficial in MRH. Based on these observations, we are convinced that our understanding of this rare condition may prove beneficial in mechanistic advancement for other more prevalent inflammatory conditions such as arthritidies and other bone diseases

Zooplankton dynamics in a mesoscale eddy-jet system off California

Zooplankton in the central jet of the California Current and an adjacent mesoscale cyclonic eddy centered at 125.1°W, 38.4°N were studied in early July, 1993, using a SeaSoar-mounted Optical Plankton Counter. Within 3 d after the 2 d survey of these mesoscale features we completed a MOCNESS transect across the study area. Zooplankton in the rapidly moving (>40 cm s-1 near surface) jet were negatively correlated with the vertical distribution of phytoplankton biomass, which displayed strong fluorescence maxima in the upper 200 m. Zooplankton in the recirculating eddy, however, were positively correlated with fluorescence maxima at the pycnocline (ca 50 m) and at 150 m. Euphausiids, dominated by Euphausia pacifica, and the copepod Calanus pacificus accounted for most of the zooplankton in the upper 50 m of the eddy, while the copepod Metridia pacifica dominated the abundance maximum of medium size zooplankton at 150 m. These species were also present in the jet, but male:female ratios of the 2 copepod species differed greatly, suggesting that populations within the jet and the eddy were distinct from one another. Earlier observations of the cyclonic eddy indicate that it departed California coastal waters in April; resident zooplankton populations may have gone through several generations before they reached the position at which we found it in July. Waters of the jet, by contrast, probably departed from the California coastal region in mid-June, so that its populations of zooplankton may have been essentially the same as those advected to our sampling location

Zooplankton dynamics in a mesoscale eddy-jet system off California

Zooplankton in the central jet of the California Current and an adjacent mesoscale cyclonic eddy centered at 125.1°W, 38.4°N were studied in early July, 1993, using a SeaSoar-mounted Optical Plankton Counter. Within 3 d after the 2 d survey of these mesoscale features we completed a MOCNESS transect across the study area. Zooplankton in the rapidly moving (>40 cm s-1 near surface) jet were negatively correlated with the vertical distribution of phytoplankton biomass, which displayed strong fluorescence maxima in the upper 200 m. Zooplankton in the recirculating eddy, however, were positively correlated with fluorescence maxima at the pycnocline (ca 50 m) and at 150 m. Euphausiids, dominated by Euphausia pacifica, and the copepod Calanus pacificus accounted for most of the zooplankton in the upper 50 m of the eddy, while the copepod Metridia pacifica dominated the abundance maximum of medium size zooplankton at 150 m. These species were also present in the jet, but male:female ratios of the 2 copepod species differed greatly, suggesting that populations within the jet and the eddy were distinct from one another. Earlier observations of the cyclonic eddy indicate that it departed California coastal waters in April; resident zooplankton populations may have gone through several generations before they reached the position at which we found it in July. Waters of the jet, by contrast, probably departed from the California coastal region in mid-June, so that its populations of zooplankton may have been essentially the same as those advected to our sampling location

Medical Complications of Tattoos: A Comprehensive Review

Tattoos are defined as the introduction of exogenous pigments into the dermis in order to produce a permanent design. This process may occur unintentional or may be deliberately administered for cosmetic or medical reasons. Tattoos have been around for over 5000 years and over time have evolved to represent a common cosmetic practice worldwide. Currently, adverse reactions are relatively rare and generally unpredictable and predominantly include immune-mediated reactions and skin infections. Along with better healthcare standards and more stringent public health mandates such as the provision of disposable needles, major infectious complications related to hepatitis and human retroviral infections have decreased significantly. When they do occur, skin infections are most frequently associated with Staphylococcus aureus or Streptococcus pyogenes. The aim of this study is to review the types and rates of medical complications of permanent tattoos. PubMed search and search dates were open ended. Acute local inflammation is the most common complication, but infections, allergic contact dermatitis, and other inflammatory or immune responses that are not well-characterized may occur. As many patients with immune reactions to tattoos do not react on skin or patch testing, it is postulated that the antigens contained in dyes or pigments are such small molecules that they need to be haptenized in order to become immunogenic. Red ink is associated more frequently with long-term reactions, including granulomatous and pseudolymphomatous phenomena or morphea-like lesions and vasculitis. Exacerbation of preexisting psoriasis, atopic dermatitis, and pyoderma gangrenosum may occur after tattooing. There is no well-defined association between cancer and tattoos. The treatment of tattoo-related complications may include local destructive measures (cryotherapy, electro-surgery, dermabrasion, chemical destruction, ablative laser destruction), surgical excision, and thermolysis of the pigment using Q-switched laser therapy