A Whole-Farm Profitability Analysis of Organic and Conventional Cropping Systems

Replaced with revised version of paper 05/26/11.Organic Farming, Profitability, Farm Size, Machinery Cost, Crop Production/Industries, Farm Management, Risk and Uncertainty,

Bi-Directional SIFT Predicts a Subset of Activating Mutations

Advancements in sequencing technologies have empowered recent efforts to identify polymorphisms and mutations on a global scale. The large number of variations and mutations found in these projects requires high-throughput tools to identify those that are most likely to have an impact on function. Numerous computational tools exist for predicting which mutations are likely to be functional, but none that specifically attempt to identify mutations that result in hyperactivation or gain-of-function. Here we present a modified version of the SIFT (Sorting Intolerant from Tolerant) algorithm that utilizes protein sequence alignments with homologous sequences to identify functional mutations based on evolutionary fitness. We show that this bi-directional SIFT (B-SIFT) is capable of identifying experimentally verified activating mutants from multiple datasets. B-SIFT analysis of large-scale cancer genotyping data identified potential activating mutations, some of which we have provided detailed structural evidence to support. B-SIFT could prove to be a valuable tool for efforts in protein engineering as well as in identification of functional mutations in cancer

Effect of insulin on glucose metabolism in the dog after portacaval transposition

The effect of insulin on hepatic glucose metabolism was studied by a multiple-catheter technique in unanesthetized dogs with Eck fistula and with portacaval transposition. With the latter preparation, blood entering and leaving the liver was sampled from peripherally inserted catheters. In the unanesthetized Eck-fistula animals, insulin infusion produced a decrease in the hepatic glucose output. In the dogs with portacaval transposition, a constant infusion of insulin was given alternately by systemic and by intraportal routes. There was no significant difference between the effects of insulin administered by the two routes. During insulin infusion, glucose concentration differences across the liver were reduced, hepatic plasma flow was transiently elevated, and hepatic glucose output was decreased. After discontinuance of insulin, there was a transient rise of hepatic glucose output to above control values. </jats:p

Comparative embryotoxicity of a pentabrominated diphenyl ether mixture to common terns (\u3ci\u3eSterna hirundo\u3c/i\u3e) and American kestrels (\u3ci\u3eFalco sparverius\u3c/i\u3e)

Concentrations of polybrominated diphenyl ethers (PBDEs) in Forster’s tern (Sterna forsteri) eggs from San Francisco Bay have been reported to range up to 63 µg g-1 lipid weight. This value exceeds the lowest-observed-adverse-effect level (1.8 µg g-1 egg wet weight; ~32 µg g-1 lipid weight) reported in an embryotoxicity study with American kestrels (Falco sparverius). As a surrogate for Forster’s terns, common tern (Sterna hirundo) eggs were treated by air cell injection with corn oil vehicle (control) or a commercial penta-BDE formulation (DE-71) at nominal concentrations of 0.2, 2, and 20 µg g-1 egg. As a positive control, kestrel eggs received vehicle or 20 µg DE-71 g-1 egg. In terns, there were no effects of DE-71 on embryonic survival, and pipping or hatching success; however, treated eggs hatched later (0.44 d) than controls. Organ weights, organ-to-body weight ratios, and bone lengths did not differ, and histopathological observations were unremarkable. Several measures of hepatic oxidative stress in hatchling terns were not affected by DE-71, although there was some evidence of oxidative DNA damage (8-hydroxy-deoxyguanosine; 8-OH-dG). Although DE-71 did not impair pipping and hatching of kestrels, it did result in a delay in hatch, shorter humerus length, and reduced total thyroid weight. Concentrations of oxidized glutathione, reduced glutathione, thiobarbituric acid reactive substances, and 8-OH-dG in liver were greater in DE-71-treated kestrels compared to controls. Our findings suggest common tern embryos, and perhaps other tern species, are less sensitive to PBDEs than kestrel embryos

Chesapeake Bay Fish–Osprey (\u3ci\u3ePandion Haliaetus\u3c/i\u3e) Food Chain: Evaluation Of Contaminant Exposure And Genetic Damage

From 2011 to 2013, a large-scale ecotoxicological study was conducted in several Chesapeake Bay (USA) tributaries (Susquehanna River and flats, the Back, Baltimore Harbor/Patapsco Rivers, Anacostia/ middle Potomac, Elizabeth and James Rivers) and Poplar Island as a mid-Bay reference site. Osprey (Pandion haliaetus) diet and the transfer of contaminants from fish to osprey eggs were evaluated. The most bioaccumulative compounds (biomagnification factor\u3e5) included p,p’-dichlorodiphenyldichloroethylene (DDE), total polychlorinated biphenyls (PCBs), total polybrominated diphenyl ethers (PBDEs), and bromodiphenyl ether (BDE) congeners 47, 99, 100, and 154. This analysis suggested that alternative brominated flame retardants and other compounds (methoxytriclosan) are not appreciably biomagnifying. A multivariate analysis of similarity indicated that major differences in patterns among study sites were driven by PCB congeners 105, 128, 156, 170/190, and 189, and PBDE congeners 99 and 209. An integrative redundancy analysis showed that osprey eggs from Baltimore Harbor/Patapsco River and the Elizabeth River had high residues of PCBs and p,p’-DDE, with PBDEs making a substantial contribution to overall halogenated contamination on the Susquehanna and Anacostia/middle Potomac Rivers. The redundancy analysis also suggested a potential relation between PBDE residues in osprey eggs and oxidative DNA damage in nestling blood samples. The results also indicate that there is no longer a discernible relation between halogenated contaminants in osprey eggs and their reproductive success in Chesapeake Bay. Osprey populations are thriving in much of the Chesapeake, with productivity rates exceeding those required to sustain a stable population

Towards enduring autonomous robots via embodied energy.

Autonomous robots comprise actuation, energy, sensory and control systems built from materials and structures that are not necessarily designed and integrated for multifunctionality. Yet, animals and other organisms that robots strive to emulate contain highly sophisticated and interconnected systems at all organizational levels, which allow multiple functions to be performed simultaneously. Herein, we examine how system integration and multifunctionality in nature inspires a new paradigm for autonomous robots that we call Embodied Energy. Whereas most untethered robots use batteries to store energy and power their operation, recent advancements in energy-storage techniques enable chemical or electrical energy sources to be embodied directly within the structures and materials used to create robots, rather than requiring separate battery packs. This perspective highlights emerging examples of Embodied Energy in the context of developing autonomous robots

A comparison of the hypoglycemic effect of insulin with systemic venous and portal venous administration

The hyperglycemic effect of insulin by prolonged intraportal and systemic infusion was measured in unanesthetized dogs with a modified portacaval transposition. There was no significant difference in response with the two routes of administration. The relation of these results to research directed to surgical therapy of diabetes is discussed. © 1963 W. B. Saunders Company

The effects of the 2004 Tsunami on mainland India and the Andaman and Nicobar Islands

Mortality from the tsunamis was high, with more than 7,000 deaths in the Nicobar group alone (the final number may never be known as many indigenous people on remote islands may have perished). On the mainland, there were a similar number of fatalities ; The greatest losses were in fishing communities although the waves destroyed roads, jetties, other basic infrastructure and entire villages; There was major damage to the coastal resources of southeast India, particularly to mangrove and coastal forests. On the Andaman and Nicobar Islands there was considerable damage to the coral reefs and beaches, as well as the forests; The earthquakes changed the bathymetry of the coral reefs and coasts of the Andaman and Nicobars: reefs in the South Andamans to the Nicobars subsided by 1 - 3 metres; many reefs in the northern Andamans were uplifted out of the water and died; and some beaches have almost disappeared, while new beaches have formed; There was major damage to large areas of coral reefs of the Andamans and Nicobars, particularly due to debris being washed off the land and smothering by sediments; Mainland coral reefs in the Gulf of Mannar and elsewhere suffered very minor, localised damage. Many mainland beaches were seriously eroded; and The affected reefs are expected to recover within 5-10 years, if there is effective resource management and enforcement of legislation controlling destructive fishing, coral mining, over-harvesting of reef resources, coastal development, sedimentation and pollution