Non-traumatic chronic shoulder pain is not associated with changes in rotator cuff interval tendon thickness

To determine whether the thickness of the rotator interval tendons is different when comparing both symptomatic and non-symptomatic sides in people with chronic shoulder pain, and to those free of pain. Furthermore, to calculate the level of association between the rotator interval tendon thicknesses and perceived shoulder pain-function. A cross-sectional, observational study. The supraspinatus, subscapularis and biceps brachii tendon thickness of sixty two patients with chronic shoulder pain were determined from standardized ultrasonography measures performed on both shoulders, whereas only the dominant arm was measured for the control subjects. Supraspinatus, subscapularis and biceps brachii tendon thickness was comparable between sides in the symptomatic group and was also comparable between the symptomatic and asymptomatic participants. In addition, the correlation between the tendon thickness and shoulder pain-function was non-significant. Tendon thickness was unaltered in people with chronic shoulder pain. These findings do not rule out the possibility that other changes in the tendon are present such as changes in the elastic properties and cell population and this should be explored in future studies

Anthropogenic impact on amorphous silica pools in temperate soils

Human land use changes perturb biogeochemical silica (Si) cycling in terrestrial ecosystems. This directly affects Si mobilisation and Si storage and influences Si export from the continents, although the magnitude of the impact is unknown. A major reason for our lack of understanding is that very little information exists on how land use affects amorphous silica (ASi) storage in soils. We have quantified and compared total alkali-extracted (PSi<sub>a</sub>) and easily soluble (PSi<sub>e</sub>) Si pools at four sites along a gradient of anthropogenic disturbance in southern Sweden. Land use clearly affects ASi pools and their distribution. Total PSi</sub>a</sub> and PSi<sub>e</sub> for a continuous forested site at Siggaboda Nature Reserve (66 900 ± 22 800 kg SiO<sub>2</sub> ha<sup>−1</sup> and 952 ± 16 kg SiO<sub>2</sub> ha<sup>−1</sup>) are significantly higher than disturbed land use types from the Råshult Culture Reserve including arable land (28 800 ± 7200 kg SiO<sub>2</sub> ha<sup>−1</sup> and 239 ± 91 kg SiO<sub>2</sub> ha<sup>−1</sup>), pasture sites (27 300 ± 5980 kg SiO<sub>2</sub> ha<sup>−1</sup> and 370 ± 129 kg SiO<sub>2</sub> ha<sup>−1</sup>) and grazed forest (23 600 ± 6370 kg SiO<sub>2</sub> ha<sup>−1</sup> and 346 ± 123 kg SiO<sub>2</sub> ha<sup>−1</sup>). Vertical PSi<sub>a</sub> and PSi<sub>e</sub> profiles show significant (<i>p</i> < 0.05) variation among the sites. These differences in size and distribution are interpreted as the long-term effect of reduced ASi replenishment, as well as changes in ecosystem specific pedogenic processes and increased mobilisation of the PSi<sub>a</sub> in disturbed soils. We have also made a first, though rough, estimate of the magnitude of change in temperate continental ASi pools due to human disturbance. Assuming that our data are representative, we estimate that total ASi storage in soils has declined by ca. 10 % since the onset of agricultural development (3000 BCE). Recent agricultural expansion (after 1700 CE) may have resulted in an average additional export of 1.1 ± 0.8 Tmol Si yr<sup>−1</sup> from the soil reservoir to aquatic ecosystems. This is ca. 20 % to the global land-ocean Si flux carried by rivers. It is necessary to update this estimate in future studies, incorporating differences in pedology, geology and climatology over temperate regions, but data are currently not sufficient. Yet, our results emphasize the importance of human activities for Si cycling in soils and for the land-ocean Si flux

Applying modern pain neuroscience in clinical practice: criteria for the classification of central sensitization pain

Background: The awareness is growing that central sensitization is of prime importance for the assessment and management of chronic pain, but its classification is challenging clinically since no gold standard method of assessment exists. Objectives: Designing the first set of classification criteria for the classification of central sensitization pain. Methods: A body of evidence from original research papers was used by 18 pain experts from 7 different countries to design the first classification criteria for central sensitization pain. Results: It is proposed that the classification of central sensitization pain entails 2 major steps: the exclusion of neuropathic pain and the differential classification of nociceptive versus central sensitization pain. For the former, the International Association for the study of Pain diagnostic criteria are available for diagnosing or excluding neuropathic pain. For the latter, clinicians are advised to screen their patients for 3 major classification criteria, and use them to complete the classification algorithm for each individual patient with chronic pain. The first and obligatory criterion entails disproportionate pain, implying that the severity of pain and related reported or perceived disability are disproportionate to the nature and extent of injury or pathology (i.e., tissue damage or structural impairments). The 2 remaining criteria are 1) the presence of diffuse pain distribution, allodynia, and hyperalgesia; and 2) hypersensitivity of senses unrelated to the musculoskeletal system (defined as a score of at least 40 on the Central Sensitization Inventory). Limitations: Although based on direct and indirect research findings, the classification algorithm requires experimental testing in future studies. Conclusion: Clinicians can use the proposed classification algorithm for differentiating neuropathic, nociceptive, and central sensitization pain

Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors

We investigate the application of hierarchical classification schemes to the annotation of gene function based on several characteristics of protein sequences including phylogenic descriptors, sequence based attributes, and predicted secondary structure. We discuss three Bayesian models and compare their performance in terms of predictive accuracy. These models are the ordinary multinomial logit (MNL) model, a hierarchical model based on a set of nested MNL models, and a MNL model with a prior that introduces correlations between the parameters for classes that are nearby in the hierarchy. We also provide a new scheme for combining different sources of information. We use these models to predict the functional class of Open Reading Frames (ORFs) from the E. coli genome. The results from all three models show substantial improvement over previous methods, which were based on the C5 algorithm. The MNL model using a prior based on the hierarchy outperforms both the non-hierarchical MNL model and the nested MNL model. In contrast to previous attempts at combining these sources of information, our approach results in a higher accuracy rate when compared to models that use each data source alone. Together, these results show that gene function can be predicted with higher accuracy than previously achieved, using Bayesian models that incorporate suitable prior information

Expression of CXCL10 is associated with response to radiotherapy and overall survival in squamous cell carcinoma of the tongue

Five-year survival for patients with oral cancer has been disappointingly stable during the last decades, creating a demand for new biomarkers and treatment targets. Lately, much focus has been set on immunomodulation as a possible treatment or an adjuvant increasing sensitivity to conventional treatments. The objective of this study was to evaluate the prognostic importance of response to radiotherapy in tongue carcinoma patients as well as the expression of the CXC-chemokines in correlation to radiation response in the same group of tumours. Thirty-eight patients with tongue carcinoma that had received radiotherapy followed by surgery were included. The prognostic impact of pathological response to radiotherapy, N-status, T-stage, age and gender was evaluated using Cox's regression models, Kaplan-Meier survival curves and chi-square test. The expression of 23 CXC-chemokine ligands and their receptors were evaluated in all patients using microarray and qPCR and correlated with response to treatment using logistic regression. Pathological response to radiotherapy was independently associated to overall survival with a 2-year survival probability of 81 % for patients showing a complete pathological response, while patients with a non-complete response only had a probability of 42 % to survive for 2 years (p = 0.016). The expression of one CXC-chemokine, CXCL10, was significantly associated with response to radiotherapy and the group of patients with the highest CXCL10 expression responded, especially poorly (p = 0.01). CXCL10 is a potential marker for response to radiotherapy and overall survival in patients with squamous cell carcinoma of the tongue

Effect of land use on carbon-, nitrogen- and silica soil stocks in the South African bushveld

Anthropogenic land use alters soil properties and influences biological transformations in the root zone, thereby affecting the distribution and supply of soil nutrients. It is generally acknowledged that human land-use activities such as intensive cattle farming and cultivation of citrus products lead to a homogenization of soil nutrients. This research aims at investigating the heterogeneity in soil nutrient stocks and BSi stocks (a beneficial plant element) within the Savannah biome of South Africa. In this study, C-N-Si stocks and their ratios were quantified in the soil of five different land use types, common in South Africa. The five different land use types are i) bush savannahs, ii) mopane-dominated woodlands, iii) annually burned land, iv) communal grazing land and v) citrus orchards. Empirical research however could not fully validate this hypothesis. In particular fire management and game farming (natural land use type) led to more variability in nutrient pools, with occasional occurrences of C-N-Si hotspots. Our results suggest that when ecosystem analysis of soil nutrient and carbon stocks is handled as a homogeneous unit potentially large mistakes are made, even in anthropogenic landscapes previously hypothesized with uniform nutrient distributions

Post Hoc Analysis Of The Patricia Randomized Trial Of The Efficacy Of Human Papillomavirus Type 16 (hpv-16)/hpv-18 As04-adjuvanted Vaccine Against Incident And Persistent Infection With Nonvaccine Oncogenic Hpv Types Using An Alternative Multiplex Type-specific Pcr Assay For Hpv Dna

The efficacy of the human papillomavirus type 16 (HPV-16)/HPV-18 AS04-adjuvanted vaccine against cervical infections with HPV in the Papilloma Trial against Cancer in Young Adults (PATRICIA) was evaluated using a combination of the broad-spectrum L1-based SPF10 PCR-DNA enzyme immunoassay (DEIA)/line probe assay (LiPA(25)) system with type-specific PCRs for HPV-16 and -18. Broad-spectrum PCR assays may underestimate the presence of HPV genotypes present at relatively low concentrations in multiple infections, due to competition between genotypes. Therefore, samples were retrospectively reanalyzed using a testing algorithm incorporating the SPF10 PCR-DEIA/LiPA(25) plus a novel E6-based multiplex type-specific PCR and reverse hybridization assay (MPTS12 RHA), which permits detection of a panel of nine oncogenic HPV genotypes (types 16, 18, 31, 33, 35, 45, 52, 58, and 59). For the vaccine against HPV types 16 and 18, there was no major impact on estimates of vaccine efficacy (VE) for incident or 6-month or 12-month persistent infections when the MPTS12 RHA was included in the testing algorithm versus estimates with the protocol-specified algorithm. However, the alternative testing algorithm showed greater sensitivity than the protocol-specified algorithm for detection of some nonvaccine oncogenic HPV types. More cases were gained in the control group than in the vaccine group, leading to higher point estimates of VE for 6-month and 12-month persistent infections for the nonvaccine oncogenic types included in the MPTS12 RHA assay (types 31, 33, 35, 45, 52, 58, and 59). This post hoc analysis indicates that the per-protocol testing algorithm used in PATRICIA underestimated the VE against some nonvaccine oncogenic HPV types and that the choice of the HPV DNA testing methodology is important for the evaluation of VE in clinical trials.222235244GlaxoSmithKline Biologicals SAGSKSanofi Pasteur MSDMerck Co.QiagenCSLSpeakers Burea

Opal-CT precipitation in a clayey soil explained by geochemical transport model of dissolved Si (Blégny, Belgium)

Opal-CT precipitation controlling dissolved Si export Dissolved Si (DSi) exported by rivers are controlled by geological, hydrological and biological cycle processes [1]. The DSi concentrations measured in a river of an upstream catchment in eastern Belgium (Blégny, Land of Herve) don’t vary seasonally (6.91±0.94mgL-1; n=363). Si concentrations in pore water are often higher and vary more (8.65±3.65mgL-1; n=128). The decrease of DSi along the flowpath of water is due to sink processes, i.e. precipitation, adsorption or uptake by vegetation. As the DSi in the river does not show any seasonal variation, uptake by vegetation can be ruled out [1] whereas precipitation or adsorption can control the DSi drained by the stream water. This hypothesis is confirmed by XRD and DeMaster analysis. At 0.1m depth the soil is constituted of 62% quartz, 7% K-feldspar, 6% plagioclase, 3.2% carbonates, 18.9% Al-clay, 1.47% Kaolinite, 0.63% Chlorite and 0.2% amorphous Si, probably of biogenic origin. At 1.5m depth, the amounts of several minerals (35.8% quartz, 0.6% K-feldspars, 0.9% plagioclase, Al-clay 14.7%) drop drastically. Carbonates, chlorite and kaolinite are absent whereas 40.4% opal-CT appears. The precipitation of opal-CT controls the DSi export of this catchment. Development of geochemical transport model To descripe DSi export from a catchment a geochemical transport model is developped in HP1 which couples the water flux model Hydrus with the geochemical model PHREEQC [2]. Our model is based on the conceptual model developped in [3]. First results show different DSi export dynamics in the unsaturated zone than in the aquifer due to different pCO2 values and varying soil moisture conditions. Further development of the model will help to find out the reason of opal-CT precipitation in this setting. [1]Fulweiler, Nixon (2005) Biogeochemistry 74:115–130. [2] Simunek, Jacques, van Genuchten, Mallants (2006) JAWRA 42:1537-1547. [3] Ronchi et al. (2013). Silicon, 5(1), 115–133

Predicting gene function using hierarchical multi-label decision tree ensembles

<p>Abstract</p> <p>Background</p> <p><it>S. cerevisiae</it>, <it>A. thaliana </it>and <it>M. musculus </it>are well-studied organisms in biology and the sequencing of their genomes was completed many years ago. It is still a challenge, however, to develop methods that assign biological functions to the ORFs in these genomes automatically. Different machine learning methods have been proposed to this end, but it remains unclear which method is to be preferred in terms of predictive performance, efficiency and usability.</p> <p>Results</p> <p>We study the use of decision tree based models for predicting the multiple functions of ORFs. First, we describe an algorithm for learning hierarchical multi-label decision trees. These can simultaneously predict all the functions of an ORF, while respecting a given hierarchy of gene functions (such as FunCat or GO). We present new results obtained with this algorithm, showing that the trees found by it exhibit clearly better predictive performance than the trees found by previously described methods. Nevertheless, the predictive performance of individual trees is lower than that of some recently proposed statistical learning methods. We show that ensembles of such trees are more accurate than single trees and are competitive with state-of-the-art statistical learning and functional linkage methods. Moreover, the ensemble method is computationally efficient and easy to use.</p> <p>Conclusions</p> <p>Our results suggest that decision tree based methods are a state-of-the-art, efficient and easy-to-use approach to ORF function prediction.</p

High export of dissolved silica from the Greenland Ice Sheet

Silica is an essential element for marine life and plays a key role in the biogeochemistry of the ocean. Glacial activity stimulates rock weathering, generating dissolved silica that is exported to coastal areas along with meltwater. The magnitude of the dissolved silica export from large glacial areas such as the Greenland Ice Sheet is presently poorly quantified and not accounted for in global budgets. Here we present data from two fjord systems adjacent to the Greenland Ice Sheet which reveal a large export of dissolved silica by glacial meltwater relative to other macronutrients. Upscaled to the entire Greenland Ice Sheet, the export of dissolved silica equals 22 ± 10 Gmol Si yr−1. When the silicate-rich meltwater mixes with upwelled deep water, either inside or outside Greenland's fjords, primary production takes place at increased silicate to nitrate ratios. This likely stimulates the growth of diatoms relative to other phytoplankton groups