Should Networks Supplant Tree Building?

Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical. Second is the argument tree building approaches are circular—you ask for a tree and you get one, which pins a verificationist label on tree building that, if correct, should be the end of phylogenetic analysis as we currently know it. In this review, we examine these questions and suggest that rumors of the death of the bacterial tree of life are exaggerated at best

VUE: Civic Investment in Public Education Winter 2012, Number 32

The Annenberg Institute for School Reform (AISR) at Brown University partnered with Public Education Network to highlight the findings of PEN's National Commission on Civic Investment in Public Education, which met for 18 months and issued its final report in May, 2011. AISR dedicated its Winter 2012 issue of Voices in Urban Education (VUE) to the topic of civic investment in public education. The fifteen members of the National Commission for Civic Investment in Public Education have performed an extraordinary service for this nation and for America's schoolchildren. The Commission's work was ably led by co-chairs Richard W. Riley, former U.S. Secretary of Education (1993 -- 2001) and Linda Darling-Hammond, world-renowned education scholar and professor of education at Stanford University. Other members included leaders from the corporate, philanthropic, and nonprofit sectors; educators; researchers; and public education support organization leaders from around the country. Together they shared a commitment to expand civic knowledge and support of public education through citizen involvement. Contents:The National Commission for Civic Investment in Public Education by Wendy PuriefoyReaffirming the Dream: The Case for Civic Investment by Richard W. Riley and Linda Darling-HammondA Story of Civic Investment in Public Education by Susan V. BerresfordThe Right Funds for Reinvestment by Erwin de LeonA Failure of Philanthropy: American Charity Shortchanges the Poor, and Public Policy is Partly to Blame by Rob Reic

Determination of the Processes Driving the Acquisition of Immunity to Malaria Using a Mathematical Transmission Model

Acquisition of partially protective immunity is a dominant feature of the epidemiology of malaria among exposed individuals. The processes that determine the acquisition of immunity to clinical disease and to asymptomatic carriage of malaria parasites are poorly understood, in part because of a lack of validated immunological markers of protection. Using mathematical models, we seek to better understand the processes that determine observed epidemiological patterns. We have developed an age-structured mathematical model of malaria transmission in which acquired immunity can act in three ways (“immunity functions”): reducing the probability of clinical disease, speeding the clearance of parasites, and increasing tolerance to subpatent infections. Each immunity function was allowed to vary in efficacy depending on both age and malaria transmission intensity. The results were compared to age patterns of parasite prevalence and clinical disease in endemic settings in northeastern Tanzania and The Gambia. Two types of immune function were required to reproduce the epidemiological age-prevalence curves seen in the empirical data; a form of clinical immunity that reduces susceptibility to clinical disease and develops with age and exposure (with half-life of the order of five years or more) and a form of anti-parasite immunity which results in more rapid clearance of parasitaemia, is acquired later in life and is longer lasting (half-life of >20 y). The development of anti-parasite immunity better reproduced observed epidemiological patterns if it was dominated by age-dependent physiological processes rather than by the magnitude of exposure (provided some exposure occurs). Tolerance to subpatent infections was not required to explain the empirical data. The model comprising immunity to clinical disease which develops early in life and is exposure-dependent, and anti-parasite immunity which develops later in life and is not dependent on the magnitude of exposure, appears to best reproduce the pattern of parasite prevalence and clinical disease by age in different malaria transmission settings. Understanding the effector mechanisms underlying these two immune functions will assist in the design of transmission-reducing interventions against malaria

An Evaluation of the Diagnostic Accuracy of the Grade of Preoperative Biopsy Compared to Surgical Excision in Chondrosarcoma of the Long Bones

Chondrosarcoma is the second most common primary malignant bone tumour. Distinguishing between grades is not necessarily straightforward and may alter the disease management. We evaluated the correlation between histological grading of the preoperative image-guided needle biopsy and the resection specimen of 78 consecutive cases of chondrosarcoma of the femur, humerus, and tibia. In 11 instances, there was a discrepancy in histological grade between the biopsy and surgical specimen. Therefore, there was an 85.9% (67/78) accuracy rate for pre-operative histological grading of chondrosarcoma, based on needle biopsy. However, the accuracy of the diagnostic biopsy to distinguish low-grade from high-grade chondrosarcoma was 93.6% (73/78). We conclude that accurate image-guided biopsy is a very useful adjunct in determining histological grade of chondrosarcoma and the subsequent treatment plan. At present, a multidisciplinary approach, comprising experienced orthopaedic surgeons, radiologists, and pathologists, offers the most reliable means of accurately diagnosing and grading of chondrosarcoma of long bones

CO2GeoNet, the unique role of the European scientific body on CO2 geological storage

CO2GeoNet is a Network of Excellence on the geological storage of CO2, initiated by the EC's 6th research framework programme in 2004 and integrating Europe's key research institutes to create a scientific reference body dedicated to the development of CO2 geological storage as a viable option for mitigating climate change. It has gained international recognition through bodies such as CSLF and IEA-GHG. It emerges as the world's largest integrated scientific community on this theme. In 2008, the network has been transformed into a legally registered Association, thus reinforcing its identity as a durable entity engaged for the safe and reliable deployment of CO2 geological storage. CO2GeoNet's activities encompass joint research, training, scientific advice, and information and communication on CO2 geological storage. © 2009 Elsevier Ltd. All rights reserved

The Heritage Landscape of Plymouth, MA Greenway Planning and Cultural Design

In anticipation of the 400th anniversary of the Pilgrim’s landing in 1620, this studio combined greenway planning and cultural landscape design and interpretation to revitalize the public landscape of Plymouth, Massachusetts and convey the significance of these historic places to visitors and residents. Through the use of landscape research combining GIS data and analysis with historical narratives and maps, this fourteen-week senior BSLA capstone studio developed a regional and town-scale greenway plan along with detailed designs of individual public landscapes in historic downtown Plymouth

Mechanical properties of tungsten following rhenium ion and helium plasma exposure

Mechanical properties of Tungsten (W) samples irradiated with 2 MeV Rhenium (Re) ions and helium (He) plasma were investigated using nanoindentation. It was found that there was an increase in hardness for all samples following separate irradiation with both Re ion and He plasma. A slight increase in hardness was obtained for combined exposures. A comparable increase in hardness was observed for a pure He plasma with a sample temperature of 473 K and 1273 K. Optical interferometry was employed to compare surface modification of the samples. Grazing incidence small angle x-ray scattering confirmed He nano-bubble formation of approximately 1 nm diameter in the higher temperature sample, which was not observed with samples at the lower temperaturesPK, CC and JB acknowledge support from the Future Fellowship Scheme of the Australian Research Council (FT120100289, FT100100825 and FT130101355). This research has also been supported by the Science and Industry Endowment Fund grant (PS034)

Disk, Corona, Jet Connection in the Intermediate State of MAXI J1820+070 Revealed by NICER Spectral-timing Analysis

We analyze five epochs of Neutron star Interior Composition Explorer (NICER) data of the black hole X-ray binary MAXI J1820+070 during the bright hard-to-soft state transition in its 2018 outburst with both reflection spectroscopy and Fourier-resolved timing analysis. We confirm the previous discovery of reverberation lags in the hard state, and find that the frequency range where the (soft) reverberation lag dominates decreases with the reverberation lag amplitude increasing during the transition, suggesting an increasing X-ray emitting region, possibly due to an expanding corona. By jointly fitting the lag-energy spectra in a number of broad frequency ranges with the reverberation model reltrans, we find the increase in reverberation lag is best described by an increase in the X-ray coronal height. This result, along with the finding that the corona contracts in the hard state, suggests a close relationship between spatial extent of the X-ray corona and the radio jet. We find the corona expansion (as probed by reverberation) precedes a radio flare by ~5 days, which may suggest that the hard-to-soft transition is marked by the corona expanding vertically and launching a jet knot that propagates along the jet stream at relativistic velocities

Hepatic Uptake in the Dog: Comparison of Uptake in Hepatocytes and Human Embryonic Kidney Cells Expressing Dog Organic Anion-Transporting Polypeptide 1B4

ABSTRACT: Although the dog is frequently used in pharmacological, pharmacokinetic, and drug safety studies, little is known about canine drug transporters. Dog organic anion-transporting polypeptide (Oatp1b4) has recently been cloned (Comp Biochem Physiol C Toxicol Pharmacol 151:393-399, 2010), but the contribution of Oatp1b4 to hepatic uptake has yet to be clarified. This study compares the transport characteristics of dog Oatp1b4 with those of human OATP1B1/1B3 and demonstrates the importance of Oatp1b4 in the uptake of anionic compounds in dog hepatocytes. Oatp1b4 is the predominant Oatp in dog liver with expression levels double and 30 times those of Oatp2b1 and Oatp1a2, respectively. Uptake of a range of typical OATP substrates by Oatp1b4-expressing HEK293 cells was compared with that in fresh dog hepatocytes. All compounds tested were transported by Oatp1b4 and uptake intrinsic clearance (CL int, uptake ) in dog hepatocytes in sodium-free buffer was correlated significantly with CL int, uptake in Oatp1b4-expressing cells. Dog in vivo clearance for five substrates was predicted more accurately from CL int, uptake than from metabolic intrinsic clearance (CL int, met ), indicating that uptake governs the overall in vivo hepatic clearance of these anionic compounds in dog. The substrate specificities of dog Oatp1b4 appear to be similar to those of human OATP1B1/OATP1B3, whereas the relative uptake clearance of substrates for Oatp1b4 correlate better with OATP1B3 than with the more abundant hepatic analog OATP1B1