Bayesian classification of vegetation types with Gaussian mixture density fitting to indicator values.

Question: Is it possible to mathematically classify relevés into vegetation types on the basis of their average indicator values, including the uncertainty of the classification? Location: The Netherlands. Method: A large relevé database was used to develop a method for predicting vegetation types based on indicator values. First, each relevé was classified into a phytosociological association on the basis of its species composition. Additionally, mean indicator values for moisture, nutrients and acidity were computed for each relevé. Thus, the position of each classified relevé was obtained in a three-dimensional space of indicator values. Fitting the data to so called Gaussian Mixture Models yielded densities of associations as a function of indicator values. Finally, these density functions were used to predict the Bayesian occurrence probabilities of associations for known indicator values. Validation of predictions was performed by using a randomly chosen half of the database for the calibration of densities and the other half for the validation of predicted associations. Results and Conclusions: With indicator values, most relevés were classified correctly into vegetation types at the association level. This was shown using confusion matrices that relate (1) the number of relevés classified into associations based on species composition to (2) those based on indicator values. Misclassified relevés belonged to ecologically similar associations. The method seems very suitable for predictive vegetation models

HEPA respirators and tuberculosis in hospital workers

Adal et al. (July 21 issue)1 demonstrate that at the University of Virginia Hospital, where the incidence of tuberculosis is low, the infection controls already instituted may be sufficient and the cost of adding respirators with high-efficiency particulate air filters (HEPA respirators) for their 3852 workers is impressively high. The situation is different at our hospital, Lincoln Medical and Mental Health Center in South Bronx, New York. In contrast to their figure of 11 patients with documented tuberculosis per year, we have over 160 such patients per year, of whom approximately 30 percent have multidrug-resistant tuberculosis

An Analytical Model for Rotator Cuff Repairs

Background: Currently, natural and synthetic scaffolds are being explored as augmentation devices for rotator cuff repair. When used in this manner, these devices are believed to offer some degree of load sharing; however, no studies have quantified this effect. Furthermore, the manner in which loads on an augmented rotator cuff repair are distributed among the various components of the repair is not known, nor is the relative biomechanical importance of each component. The objectives of this study are to (1) develop quasi-static analytical models of simplified rotator cuff repairs, (2) validate the models, and (3) predict the degree of load sharing provided by an augmentation scaffold. Methods: The individual components of the repair constructs were modeled as non-linear springs, and the model equations were formulated based on the physics of springs in series and parallel. The model was validated and used to predict the degree of load sharing provided by a scaffold. Parametric sensitivity analysis was used to identify which of the component(s)/parameter(s) most influenced the mechanical behavior of the augmented repair models. Findings: The validated models predict that load will be distributed ~70-80% to the tendon repair and ~20-30% to the augmentation component. The sensitivity analysis suggests that the greatest improvements in the force carrying capacity of a tendon repair may be achieved by improving the properties of the bone-suture-tendon interface. Future studies will perform parametric simulation to illustrate the manner in which changes to the individual components of the repair, representing different surgical techniques and scaffold devices, may influence the biomechanics of the repair construct

The ^4He trimer as an Efimov system

We review the results obtained in the last four decades which demonstrate the Efimov nature of the $^4$He three-atomic system.Comment: Review article for a special issue of the Few-Body Systems journal devoted to Efimov physic

The effect on melanoma risk of genes previously associated with telomere length.

Telomere length has been associated with risk of many cancers, but results are inconsistent. Seven single nucleotide polymorphisms (SNPs) previously associated with mean leukocyte telomere length were either genotyped or well-imputed in 11108 case patients and 13933 control patients from Europe, Israel, the United States and Australia, four of the seven SNPs reached a P value under .05 (two-sided). A genetic score that predicts telomere length, derived from these seven SNPs, is strongly associated (P = 8.92x10(-9), two-sided) with melanoma risk. This demonstrates that the previously observed association between longer telomere length and increased melanoma risk is not attributable to confounding via shared environmental effects (such as ultraviolet exposure) or reverse causality. We provide the first proof that multiple germline genetic determinants of telomere length influence cancer risk.This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/jnci/dju26

A deep dive into the ecology of Gamay (Botany Bay, Australia): current knowledge and future priorities for this highly modified coastal waterway

Context: Gamay is a coastal waterway of immense social, cultural and ecological value. Since European settlement, it has become a hub for industrialisation and human modification. There is growing desire for ecosystem-level management of urban waterways, but such efforts are often challenged by a lack of integrated knowledge. Aim and methods: We systematically reviewed published literature and traditional ecological knowledge (TEK), and consulted scientists to produce a review of Gamay that synthesises published knowledge of Gamay’s aquatic ecosystem to identify knowledge gaps and future research opportunities. Key results: We found 577 published resources on Gamay, of which over 70% focused on ecology. Intertidal rocky shores were the most studied habitat, focusing on invertebrate communities. Few studies considered multiple habitats or taxa. Studies investigating cumulative human impacts, long-term trends and habitat connectivity are lacking, and the broader ecological role of artificial substrate as habitat in Gamay is poorly understood. TEK of Gamay remains a significant knowledge gap. Habitat restoration has shown promising results and could provide opportunities to improve affected habitats in the future. Conclusion and implications: This review highlights the extensive amount of knowledge that exists for Gamay, but also identifies key gaps that need to be filled for effective management

Intratumor heterogeneity of the estrogen receptor and the long-term risk of fatal Breast cancer

Background: Breast cancer patients with estrogen receptor (ER)–positive disease have a continuous long-term risk for fatal Breast cancer, but the biological factors influencing this risk are unknown. We aimed to determine whether high intratumor heterogeneity of ER predicts an increased long-term risk (25 years) of fatal Breast cancer. Methods: The STO-3 trial enrolled 1780 postmenopausal lymph node–negative Breast cancer patients randomly assigned to receive adjuvant tamoxifen vs not. The fraction of cancer cells for each ER intensity level was scored by Breast cancer pathologists, and intratumor heterogeneity of ER was calculated using Rao’s quadratic entropy and categorized into high and low heterogeneity using a predefined cutoff at the second tertile (67%). Long-term Breast cancer-specific survival analyses by in-tra-tumor heterogeneity of ER were performed using Kaplan-Meier and multivariable Cox proportional hazard modeling adjusting for patient and tumor characteristics. Results: A statistically significant difference in long-term survival by high vs low intratumor heterogeneity of ER was seen for all ER-positive patients (P < .001) and for patients with luminal A subtype tumors (P ¼ .01). In multivariable analyses, patients with high intratumor heterogeneity of ER had a twofold increased long-term risk as compared with patients with low intratumor heterogeneity (ER-positive: hazard ratio [HR] ¼ 1.98, 95% confidence interval [CI] ¼ 1.31 to 3.00; luminal A subtype tumors: HR ¼ 2.43, 95% CI ¼ 1.18 to 4.99). Conclusions: Patients with high intratumor heterogeneity of ER had an increased long-term risk of fatal Breast cancer. Interestingly, a similar long-term risk increase was seen in patients with luminal A subtype tumors. Our findings suggest that intratumor heterogeneity of ER is an independent long-term prognosticator with potential to change clinical management, especially for patients with luminal A tumors

Calabi-Yau Volumes and Reflexive Polytopes

We study various geometrical quantities for Calabi–Yau varieties realized as cones over Gorenstein Fano varieties, obtained as toric varieties from reflexive polytopes in various dimensions. Focus is made on reflexive polytopes up to dimension 4 and the minimized volumes of the Sasaki–Einstein base of the corresponding Calabi–Yau cone are calculated. By doing so, we conjecture new bounds for the Sasaki–Einstein volume with respect to various topological quantities of the corresponding toric varieties. We give interpretations about these volume bounds in the context of associated field theories via the AdS/CFT correspondence

Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent Cross-Reactive Neutralizing Human Monoclonal Antibody

The henipaviruses, represented by Hendra (HeV) and Nipah (NiV) viruses are highly pathogenic zoonotic paramyxoviruses with uniquely broad host tropisms responsible for repeated outbreaks in Australia, Southeast Asia, India and Bangladesh. The high morbidity and mortality rates associated with infection and lack of licensed antiviral therapies make the henipaviruses a potential biological threat to humans and livestock. Henipavirus entry is initiated by the attachment of the G envelope glycoprotein to host cell membrane receptors. Previously, henipavirus-neutralizing human monoclonal antibodies (hmAb) have been isolated using the HeV-G glycoprotein and a human naïve antibody library. One cross-reactive and receptor-blocking hmAb (m102.4) was recently demonstrated to be an effective post-exposure therapy in two animal models of NiV and HeV infection, has been used in several people on a compassionate use basis, and is currently in development for use in humans. Here, we report the crystal structure of the complex of HeV-G with m102.3, an m102.4 derivative, and describe NiV and HeV escape mutants. This structure provides detailed insight into the mechanism of HeV and NiV neutralization by m102.4, and serves as a blueprint for further optimization of m102.4 as a therapeutic agent and for the development of entry inhibitors and vaccines