CAPTION Young citizen scientists locate and collect leaves with symptoms of sudden oak death, using the SODmap mobile application. More than 1,600 trained volunteers, from high school students to firefighters, have helped track the disease in California over a six-year period. CREDIT Photo by Douglas Schmidt, UC Berkeley

Six-year sudden oak death project shows promise of crowdsourced research

Crowdsourced science helped predict the path of a deadly plant disease over a six-year period, demonstrating the contributions that trained citizen scientists can make in large-scale geographic tracking projects. That's the conclusion of a study of sudden oak death monitoring in California, published today in Frontiers in Ecology and the Environment.

"Sudden oak death is the Ebola of the plant world, the most serious disease threat to nonagricultural plants," says lead author Ross Meentemeyer, director of the Center for Geospatial Analytics at North Carolina State University. The disease, which has killed millions of oak and tanoak trees in California and Oregon, can infect more than 100 susceptible host plants and can spread from nursery stock to residential landscapes.

Starting in 2008, University of California, Berkeley researchers expanded their sudden oak death monitoring efforts exponentially, thanks to 1,600 trained volunteers who collected leaf samples from trees in metropolitan and urban-wildland areas.

"We were able to get data from backyards in the Bay Area, along with other undersampled locations," says Meentemeyer, who specializes in geographic information system analysis. "That data was used to develop accurate computer models for the disease's spread, showing that properly trained and educated citizen scientists can collect data that's just as reliable as that of professionals."

The crowdsource approach could be adopted for other large-scale research projects, from tracking wildlife populations to fighting human disease outbreaks.

Accurate predictions about sudden oak death's spread allowed scientists to target treatments to the most vulnerable areas, says Matteo Garbelotto, a UC Berkeley extension specialist and adjunct professor who directs the Forest Pathology and Mycology Laboratory. Follow-up evaluation showed that trained citizen scientists were as effective as experts in identifying and collecting diseased tree leaves, whether or not they reported having a professional background in science.

The annual Sudden Oak Death Blitz, which includes extensive publicity during peak periods for the disease, involves high school students, homeowners, tree specialists, firefighters, teachers and others.

"To answer many science questions, we need the efforts of a large number of people - and the general public can help," says Sam Scheiner, National Science Foundation director for the NSF-NIH-USDA Ecology and Evolution of Infectious Diseases Program, which funded the research. "This study shows that asking local residents to report on the location of outbreaks of sudden oak death can provide critical information. The result is a better understanding of the spread of this serious plant disease."

Rice University computer scientist Moshe Vardi has joined the elite group of scientists who have been elected to both the National Academy of Sciences and the National Academy of Engineering.

Vardi, Rice’s Karen Ostrum George Distinguished Service Professor of Computational Engineering and professor of computer science, is among 84 new National Academy of Sciencesmembers announced today. He was elected to the National Academy of Engineering in 2002.

The National Academy of Sciences, National Academy of Engineering and Institute of Medicine (whose name will change July 1 to National Academy of Medicine) are private, nonprofit membership organizations that elect the country’s leading scientists, engineers and medical professionals and engage in a wide variety of activities to advance research and knowledge in science, engineering and medicine. Fewer than 5 percent of National Academy members have dual membership in multiple academies.

“Moshe is very worthy of this distinctive honor, which reflects the high caliber of Rice University faculty,” Provost George McLendon said. 

“Recognition by one’s peer is the goal of every scientist,” said Vardi, who also serves as director of Rice’s Ken Kennedy Institute for Information Technology. “Getting elected to the National Academy of Sciences is the ultimate peer recognition.”

Vardi joined Rice’s faculty in 1993. His research interests include applications of logic to computer science, database systems, computational complexity theory, multiagent systems and specification and verification of hardware and software. He is the author or co-author of more than 500 technical articles and of two books, “Reasoning about Knowledge” and “Finite Model Theory and Its Applications.”

Vardi is a member of the American Academy of Arts and Sciences, the European Academy of Sciences and the Academia Europaea. He is a fellow of the Association of Computing Machinery, the Institute for Electrical and Electronics Engineers (IEEE) and the Society for Industrial and Applied Mathematics. Among his prior honors are the Southeastern Universities Research Association’s 2013 Distinguished Scientist Award, the 2011 IEEE Computer Society Harry H. Goode Award, the 2008 Blaise Pascal Medal for Computer Science by the European Academy of Sciences and the 2000 Goedel Prize for outstanding papers in the area of theoretical computer science.

Dual-academy membership is an honor Vardi shares with only five other faculty members throughout Rice’s 103-year history.

Fall Plugfest Follows the Most Successful-to-Date Plugfest Held Last Spring Where More Than 200 Cables and Devices Were Tested

  • IBTA 16th Compliance and Interoperability Plugfest
  • OpenFabrics Alliance 8th Interoperability Event
  • Supercomputing 2009

The InfiniBand Trade Association (IBTA)  today announced the 16th Compliance and Interoperability Plugfest. The Plugfest will take place October 12-16, 2009 in the University of New Hampshire’s Interoperability Lab. The event provides an opportunity for InfiniBand device and cable vendors to test their products for compliance with the InfiniBand architecture specification, as well as interoperability with other InfiniBand products.

This event will include testing of both double data rate (DDR) 20Gb/s devices and quad data rate (QDR) 40Gb/s devices. There is a new test procedure for the recently released 120Gb/s 12x Small Form-Factor Pluggable (CXP) Interface Specification for cables, along with a new memory map test procedure for the EEPROMs included with QSFP and CXP active cables. The updated Wave Dispersion Penalty (WDP) testing will also be included.

The October Plugfest will include interoperability test procedures using Mellanox, QLogic and Voltaire products. The test procedures ensure that InfiniBand products are both compliant and interoperable, which in turn ensures the trouble-free deployment of InfiniBand clusters. More information on test procedures is available for IBTA members at: http://members.infinibandta.org/apps/org/workgroup/ciwg/documents.php?folder_id=298#folder_298

Plugfest registration is free for IBTA members; non-members need to pay a special fee. More information is available on the IBTA website at: www.infinibandta.org.

The Plugfest program has been a significant contributor to the growth of InfiniBand in both the enterprise data center and the high-performance computing markets. According to the June 2009 TOP500 list, InfiniBand is now the leading server interconnect in the Top100 with 59 clusters.

The Integrators’ List has grown from 115 products in October 2008, to 297 products as of the last Plugfest event in April 2009. End users and OEMs frequently reference this list prior to the deployment of InfiniBand-related systems, including both small clusters and large-scale clusters of 1,000 nodes or more. Many OEMs use this list as a gateway in the procurement process.

Fall Plugfest follows the highly successful Spring ‘09 Plugfest

The Spring ‘09 Plugfest was the most successful in IBTA history with more than 20 cable and device vendors in attendance. During the event, over 200 cables and 14 devices were tested. The number of devices qualifying for inclusion on the Integrators’ List has steadily increased; the list now includes more than 297 products.

Vendors recently adding products to the IBTA Integrators’ List include: Amphenol, Avago Technologies, Cinch Connectors, Emcore, LSI, Luxtera, Mellanox, Molex, Obsidian Research, Panduit, Quellan Inc (Intersil), Tyco Electronics, Volex, Voltaire and W.L. Gore. Several additional vendors will attend the October 2009 Plugfest, including QLogic, FCI and Hitachi.

Following Plugfest: OpenFabrics Alliance’s Eighth Interoperability Event

Following the IBTA Plugfest, the OpenFabrics Alliance will be conducting their 8th Interoperability event from Oct. 15-23, 2009. This session will focus on industry-wide interoperability using the OpenFabrics Alliance Software Stack. This event requires separate eligibility, cost and registration. For more information, please visit: http://www.iol.unh.edu/services/testing/ofa/events/Invitation_2009-10_OFA.php

IBTA to Celebrate 10-Year Anniversary at Supercomputing 2009

The IBTA will celebrate its 10-year anniversary at Supercomputing 2009 in Portland, Ore. on November 14-20. The IBTA will host InfiniBand demonstrations and an InfiniBand presentation theater. The IBTA invites all attendees to stop by booth number 139 at the show.

 

Over the last six years Enabling Grids for E-sciencE (EGEE) has grown to become the world's largest multi-disciplinary grid infrastructure, with tens of thousands of users. In Barcelona this month the flagship EC-funded project meets for its final annual conference. Next year will see the inauguration of EGEE's successor, the European Grid Initiative (EGI), and this pivotal gathering of the grid community will allow for reflection on the successes of the project, as well as marking a major step forward on the path towards a nationally-focused sustainable grid infrastructure, to benefit all European researchers for years to come. The transition from EGEE to EGI represents a welcome move from short-term project funding to sustained support on a national and international level, which will enable users to continue using grid infrastructures – now and in the future.

Successes have been numerous and EGEE already caters for a multitude of disciplines. This final annual conference is an opportunity for the user communities to showcase their work and achievements, and demonstrate the power of grid technology. There will be live demonstrations from diverse scientific research fields, including many from medical research - notably neuGrid, studying degenerative diseases such as Alzheimer's, RadioTherapy Grid optimising the use of radiotherapy in cancer treatment and EUAsiaGrid helping research into monitoring future flu pandemics.

While the medical community has benefited greatly it is not the only one to increasingly rely on grids. The computing power and data storage offered by EGEE has allowed scientists to think big - from modelling weather using the grid with WRF4G, predicting the distribution of marine life with AquaMaps, to EUAsiaGrid’s software helping authorities to cope in the aftermath of an earthquake. The breadth and quality of scientific research supported by EGEE is a testament to the versatility of computing grids.

It is this versatility that has attracted industry. EGEE has worked with the business community since the early days of grids. Each year, the dedicated business track increases the collaboration between EGEE and industry.  This year is no different, demonstrating the evolution of grid computing by highlighting not only key areas such as cloud computing and service level agreements, but also unveiling prime examples of technology transfer from science and academia to commercialisation.

With cloud computing generating increasing excitement in the business community, EGEE is working to integrate the two services. Two sessions at EGEE’09 will present a range of projects working on grids and clouds, such as StratusLab which is bringing grids and clouds together to create benefits for both science and industry.

As in previous years, the conference has attracted major grid computing figures from around the world as keynote speakers, including locally-based speaker Gonzalo Merino from PIC, who is in charge of Spain’s Tier-1 data centre for the Large Hadron Collider, Jennifer Schopf, from the National Science Foundation’s Office of CyberInfrastructure in the US and Kostas Glinos, who leads the Géant & e-Infrastructures Unit of the Directorate General for Information Society and Media at the European Commission. EGEE’09 will also be a key milestone in the preparations of pan-European projects defined within the European Strategy Forum on Research Infrastructures (ESFRI), presented at the conference by Professor John Wood, chair of the European Research Area Board and former Chair of ESFRI.

Streamlines of flow within an idealized Arterio-Venous Fistulae. The color of the lines corresponds to the speed of the blood—red being highest, and blue lowest.

Supercomputing software from the aerospace industry has allowed an interdisciplinary team of U.K. researchers to design Arterio-Venous Fistulae with better, less unnatural flow patterns, which may reduce failure rates and improve clinical outcomes for patients with kidney failure who require dialysis.

A team of researchers in the United Kingdom has found a way to redesign an artificial connection between an artery and vein, known as an Arterio-Venous Fistulae, which surgeons form in the arms of people with end-stage renal disease so that those patients can receive routine dialysis, filtering their blood and keeping them alive after their kidneys fail.

The new design, described in the journal Physics of Fluids, from AIP Publishing, may decrease the likelihood of blockages in Arterio-Venous Fistulae, which is a major complication of dialysis.

While the AVF would have to prove effective in clinical trials before they could be deemed a success, the researchers are enthusiastic about their approach, which used software from the aerospace industry to design the novel configurations.

"At the moment, the process of creating an Arterio-Venous Fistulae for dialysis is rather 'one-size-fits-all'," said Peter Vincent, a senior lecturer and EPSRC early career fellow in the Department of Aeronautics at Imperial College London. "Our ultimate aim is to use computational simulation tools to design tailored, patient-specific Arterio-Venous Fistulae configurations that won't block and fail."

Dialysis and Chronic Kidney Disease

Dialysis is a life-saving treatment for end-stage renal disease -- the last stage of chronic kidney disease -- a serious and often fatal health condition in which a person's kidneys become damaged and can no longer filter blood as effectively as healthy kidneys. As a result, wastes from the blood remain within the body and often lead to other health problems such as cardiovascular disease, anemia and bone disease.

Chronic kidney disease is a global health challenge. For perspective, in the United States alone, the Centers for Disease Control and Prevention estimates that more than 20 million adults -- more than 10 percent of the U.S. adult population -- may have the disease, although many are undiagnosed. Kidney disease is now the 9th leading cause of death in the U.S.

Once a person's kidney's fail, they require either a kidney transplant or regular treatment via a dialysis machine to keep filtering the blood like a kidney. Transplant surgeries often have very good outcomes, but the procedures are limited by the availability of donated kidneys, and only a few thousand become available every year in the United States, while tens of thousands of people are on the waiting list for a kidney transplant. People often wait for a new kidney transplant for years, having to undergo periodic dialysis the entire time. 

One problem that arises with dialysis is that the connections made between the body and a dialysis machine via an Arterio-Venous Fistulae frequently become blocked and fail shortly after they are created -- leading to unfavorable clinical outcomes and a significant additional cost burden for healthcare systems worldwide.

So an interdisciplinary team of U.K. researchers -- including members from aeronautics, bioengineering, computational engineering, medical imaging and clinical medicine -- from Imperial College London, Imperial College Renal and Transplant Centre at Hammersmith Hospital, and St. Mary's Hospital set out to design an Arterio-Venous Fistulae with reduced failure rates.

Design Based on Aerospace Software

To do this, the researchers first needed to gain a better understanding of how arterial curvature affects blood flow and oxygen transport patterns within Arterio-Venous Fistula.

Blood flow patterns within AVF are "inherently 'un-natural,' and it's thought that these unnatural flow patterns lead to their ultimate failure," explained Vincent.

By using computational simulation software originally developed for the aerospace sector, the team is able to simulate and predict flow patterns in various Arterio-Venous Fistula configurations. "This allows us to design Arterio-Venous Fistula with much more natural flow patterns, which will hopefully reduce failure rates," Vincent said.

The team "identified ways of constructing Arterio-Venous Fistula such that the flow is stabilized," he added. "We discovered that if an Arterio-Venous Fistulae is formed via connection of a vein onto the outside of an arterial bend, it stabilizes the flow."

The implications of this work are tremendous, because it may now finally be possible to design an Arterio-Venous Fistulae with reduced failure rates -- offering improved clinical outcomes for patients with kidney failure who require dialysis.

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