How to measure cortical folding from MR images: a step-by-step tutorial to compute local gyrification index.

Cortical folding (gyrification) is determined during the first months of life, so that adverse events occurring during this period leave traces that will be identifiable at any age. As recently reviewed by Mangin and colleagues(2), several methods exist to quantify different characteristics of gyrification. For instance, sulcal morphometry can be used to measure shape descriptors such as the depth, length or indices of inter-hemispheric asymmetry(3). These geometrical properties have the advantage of being easy to interpret. However, sulcal morphometry tightly relies on the accurate identification of a given set of sulci and hence provides a fragmented description of gyrification. A more fine-grained quantification of gyrification can be achieved with curvature-based measurements, where smoothed absolute mean curvature is typically computed at thousands of points over the cortical surface(4). The curvature is however not straightforward to comprehend, as it remains unclear if there is any direct relationship between the curvedness and a biologically meaningful correlate such as cortical volume or surface. To address the diverse issues raised by the measurement of cortical folding, we previously developed an algorithm to quantify local gyrification with an exquisite spatial resolution and of simple interpretation. Our method is inspired of the Gyrification Index(5), a method originally used in comparative neuroanatomy to evaluate the cortical folding differences across species. In our implementation, which we name local Gyrification Index (lGI(1)), we measure the amount of cortex buried within the sulcal folds as compared with the amount of visible cortex in circular regions of interest. Given that the cortex grows primarily through radial expansion(6), our method was specifically designed to identify early defects of cortical development. In this article, we detail the computation of local Gyrification Index, which is now freely distributed as a part of the FreeSurfer Software (http://surfer.nmr.mgh.harvard.edu/, Martinos Center for Biomedical Imaging, Massachusetts General Hospital). FreeSurfer provides a set of automated reconstruction tools of the brain's cortical surface from structural MRI data. The cortical surface extracted in the native space of the images with sub-millimeter accuracy is then further used for the creation of an outer surface, which will serve as a basis for the lGI calculation. A circular region of interest is then delineated on the outer surface, and its corresponding region of interest on the cortical surface is identified using a matching algorithm as described in our validation study(1). This process is repeatedly iterated with largely overlapping regions of interest, resulting in cortical maps of gyrification for subsequent statistical comparisons (Fig. 1). Of note, another measurement of local gyrification with a similar inspiration was proposed by Toro and colleagues(7), where the folding index at each point is computed as the ratio of the cortical area contained in a sphere divided by the area of a disc with the same radius. The two implementations differ in that the one by Toro et al. is based on Euclidian distances and thus considers discontinuous patches of cortical area, whereas ours uses a strict geodesic algorithm and include only the continuous patch of cortical area opening at the brain surface in a circular region of interest.

Decision Support Model for Assessing Archaeological Survey Needs for Bridge Replacement Projects in Iowa, 2006

The Bridges Decision Support Model is a geographic information system (GIS) that assembles existing data on archaeological sites, surveys, and their geologic contexts to assess the risk of bridge replacement projects encountering 13,000- to 150-year-old Native American sites. This project identifies critical variables for assessing prehistoric sites potential, examines the quality of available data about the variables, and applies the data to creating a decision support framework for use by the Iowa Department of Transportation (Iowa DOT) and others. An analysis of previous archaeological surveys indicates that subsurface testing to discover buried sites became increasingly common after 1980, but did not become routine until after the adoption of guidelines recommending such testing, in 1993. Even then, the average depth of testing has been relatively shallow. Alluvial deposits of sufficient age, deposited in depositional environments conducive to human habitation, are considerably thicker than archaeologists have routinely tested.

Development of LRFD Procedures for Bridge Pile Foundations in Iowa Final Report, June 2010

For well over 100 years, the Working Stress Design (WSD) approach has been the traditional basis for geotechnical design with regard to settlements or failure conditions. However, considerable effort has been put forth over the past couple of decades in relation to the adoption of the Load and Resistance Factor Design (LRFD) approach into geotechnical design. With the goal of producing engineered designs with consistent levels of reliability, the Federal Highway Administration (FHWA) issued a policy memorandum on June 28, 2000, requiring all new bridges initiated after October 1, 2007, to be designed according to the LRFD approach. Likewise, regionally calibrated LRFD resistance factors were permitted by the American Association of State Highway and Transportation Officials (AASHTO) to improve the economy of bridge foundation elements. Thus, projects TR-573, TR-583 and TR-584 were undertaken by a research team at Iowa State University’s Bridge Engineering Center with the goal of developing resistance factors for pile design using available pile static load test data. To accomplish this goal, the available data were first analyzed for reliability and then placed in a newly designed relational database management system termed PIle LOad Tests (PILOT), to which this first volume of the final report for project TR-573 is dedicated. PILOT is an amalgamated, electronic source of information consisting of both static and dynamic data for pile load tests conducted in the State of Iowa. The database, which includes historical data on pile load tests dating back to 1966, is intended for use in the establishment of LRFD resistance factors for design and construction control of driven pile foundations in Iowa. Although a considerable amount of geotechnical and pile load test data is available in literature as well as in various State Department of Transportation files, PILOT is one of the first regional databases to be exclusively used in the development of LRFD resistance factors for the design and construction control of driven pile foundations. Currently providing an electronically organized assimilation of geotechnical and pile load test data for 274 piles of various types (e.g., steel H-shaped, timber, pipe, Monotube, and concrete), PILOT (http://srg.cce.iastate.edu/lrfd/) is on par with such familiar national databases used in the calibration of LRFD resistance factors for pile foundations as the FHWA’s Deep Foundation Load Test Database. By narrowing geographical boundaries while maintaining a high number of pile load tests, PILOT exemplifies a model for effective regional LRFD calibration procedures.

Geochemical and H-O-Sr-Nd isotope evidence for magmatic processes and meteoric-water interactions in the basal complex of La Gomera, Canary Islands

The plutonic rocks of the Basal Complex of La Gomera, Canary Islands, Spain, were studied by means of major and trace element contents and by H-O-Sr-Nd isotope compositions in order to distinguish primary magmatic characteristics and late-stage alteration products. Deciphering the effects of alteration allowed us to determine primary, plume-related compositions that indicated D- and (18)O-depletion relative to normal upper mantle, supporting the conclusions of earlier studies on the plutonic rocks of Fuerteventura and La Palma. Late-stage alteration took place during the formation of the intrusive series induced by interaction with meteoric water. Inferred isotopic compositions of the meteoric water indicate that the water infiltrated into the rock edifice at a height of about 1500 m above sea level, suggesting the existence of a subaerial volcano which was active during the intrusive activity and that it has been either distroyed or remain buried by later volcanic and landslide events.

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer.

BACKGROUND: Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software. RESULTS: In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function. CONCLUSIONS: The possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. The possibility to do so without having to maintain a complex software/hardware installation on site brings this technology to experts and non-experts alike.

A LIBRARY IN THE MAKING: Pioneer History of the Territorial and State Library of Iowa,October 1912

The discovery of early manuscript reports of Territorial and State Librarians, buried in the mass of old official papers transferred from the several departments of State to the new Department of Archives in the Historical Building, has suggested the propriety of completing as far as possible, the historical record of Iowa's State Library, "from the earliest period to the present time." After a thorough research through the papers on file in the Archives Department, the published Journals and departmental reports in the State Library and documents and private papers loaned me by Mr. Newton R. Parvin, librarian of the Iowa Masonic Library, Cedar Rapids. I am now able to present the following historical sketch, Supplemented by the hitherto unpublished papers referred to this filling a gap in the history of a State institution which from very small beginnings has grown to large proportions and has made for itself a firm place in the respect and esteem of every citizen of Iowa.

Evaluating Roadway Subsurface Drainage Practices, 2013

The bearing capacity and service life of a pavement is affected adversely by the presence of undrained water in the pavement layers. In cold winter climates like in Iowa, this problem is magnified further by the risk of frost damage when water is present. Therefore, well-performing subsurface drainage systems form an important aspect of pavement design by the Iowa Department of Transportation (DOT). However, controversial findings are also reported in the literature regarding the benefits of subsurface drainage. The goal of this research was not to investigate whether subdrains are needed in Iowa pavements, but to conduct an extensive performance review of primary interstate pavement subdrains in Iowa, determine the cause of the problem if there are drains that are not functioning properly, and investigate the effect of poor subdrain performance due to improper design, construction, and maintenance on pavement surface distresses, if any. An extensive literature review was performed covering national-level and state-level research studies mainly focusing on the effects of subsurface drainage on performance of asphalt and concrete pavements. Several studies concerning the effects of a recycled portland cement concrete (RPCC) subbase on PCC pavement drainage systems were also reviewed. A detailed forensic test plan was developed in consultation with the project technical advisory committee (TAC) for inspecting and evaluating the Iowa pavement subdrains. Field investigations were conducted on 64 selected (jointed plain concrete pavement/JPCP and hot-mix asphalt/HMA) pavement sites during the fall season of 2012 and were mainly focused on the drainage outlet conditions. Statistical analysis was conducted on the compiled data from field investigations to further investigate the effect of drainage on pavement performance. Most Iowa subsurface drainage system outlet blockage is due to tufa, sediment, and soil. Although higher blockage rates reduce the flow rate of water inside outlet pipes, it does not always stop water flowing from inside the outlet pipe to outside the outlet pipe unless the outlet is completely blocked. Few pavement surface distresses were observed near blocked subsurface drainage outlet spots. More shoulder distresses (shoulder drop or cracking) were observed near blocked drainage outlet spots compared to open ones. Both field observations and limited performance analysis indicate that drainage outlet conditions do not have a significant effect on pavement performance. The use of RPCC subbase in PCC pavements results in tufa formation, a primary cause of drainage outlet blockage in JPCP. Several useful recommendations to potentially improve Iowa subdrain performance, which warrant detailed field investigations, were made

Evaluating Roadway Subsurface Drainage Practices: Tech Transfer Summary, 2013.

The bearing capacity and service life of a pavement is affected adversely by the presence of undrained water in the pavement layers. In cold winter climates like in Iowa, this problem is magnified further by the risk of frost damage when water is present. Therefore, well-performing subsurface drainage systems form an important aspect of pavement design by the Iowa Department of Transportation (DOT). However, controversial findings are also reported in the literature regarding the benefits of subsurface drainage. The goal of this research was not to investigate whether subdrains are needed in Iowa pavements, but to conduct an extensive performance review of primary interstate pavement subdrains in Iowa, determine the cause of the problem if there are drains that are not functioning properly, and investigate the effect of poor subdrain performance due to improper design, construction, and maintenance on pavement surface distresses, if any. An extensive literature review was performed covering national-level and state-level research studies mainly focusing on the effects of subsurface drainage on performance of asphalt and concrete pavements. Several studies concerning the effects of a recycled portland cement concrete (RPCC) subbase on PCC pavement drainage systems were also reviewed. A detailed forensic test plan was developed in consultation with the project technical advisory committee (TAC) for inspecting and evaluating the Iowa pavement subdrains. Field investigations were conducted on 64 selected (jointed plain concrete pavement/JPCP and hot-mix asphalt/HMA) pavement sites during the fall season of 2012 and were mainly focused on the drainage outlet conditions. Statistical analysis was conducted on the compiled data from field investigations to further investigate the effect of drainage on pavement performance. Most Iowa subsurface drainage system outlet blockage is due to tufa, sediment, and soil. Although higher blockage rates reduce the flow rate of water inside outlet pipes, it does not always stop water flowing from inside the outlet pipe to outside the outlet pipe unless the outlet is completely blocked. Few pavement surface distresses were observed near blocked subsurface drainage outlet spots. More shoulder distresses (shoulder drop or cracking) were observed near blocked drainage outlet spots compared to open ones. Both field observations and limited performance analysis indicate that drainage outlet conditions do not have a significant effect on pavement performance. The use of RPCC subbase in PCC pavements results in tufa formation, a primary cause of drainage outlet blockage in JPCP. Several useful recommendations to potentially improve Iowa subdrain performance, which warrant detailed field investigations, were made.

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors.

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.

Impacts on the deep-sea ecosystem by a severe coastal storm

Major coastal storms, associated with strong winds, high waves and intensified currents, and occasionally with heavy rains and flash floods, are mostly known because of the serious damage they can cause along the shoreline and the threats they pose to navigation. However, there is a profound lack of knowledge on the deep-sea impacts of severe coastal storms. Concurrent measurements of key parameters along the coast and in the deep-sea are extremely rare. Here we present a unique data set showing how one of the most extreme coastal storms of the last decades lashing the Western Mediterranean Sea rapidly impacted the deep-sea ecosystem. The storm peaked the 26th of December 2008 leading to the remobilization of a shallow-water reservoir of marine organic carbon associated with fine particles and resulting in its redistribution across the deep basin. The storm also initiated the movement of large amounts of coarse shelf sediment, which abraded and buried benthic communities. Our findings demonstrate, first, that severe coastal storms are highly efficient in transporting organic carbon from shallow water to deep water, thus contributing to its sequestration and, second, that natural, intermittent atmospheric drivers sensitive to global climate change have the potential to tremendously impact the largest and least known ecosystem on Earth, the deep-sea ecosystem.

A new method to estimate the infilling of alluvial sediment of glacial valleys using a sloping local base level

A new method is used to estimate the volumes of sediments of glacial valleys. This method is based on the concept of sloping local base level and requires only a digital terrain model and the limits of the alluvial valleys as input data. The bedrock surface of the glacial valley is estimated by a progressive excavation of the digital elevation model (DEM) of the filled valley area. This is performed using an iterative routine that replaces the altitude of a point of the DEM by the mean value of its neighbors minus a fixed value. The result is a curved surface, quadratic in 2D. The bedrock surface of the Rhone Valley in Switzerland was estimated by this method using the free digital terrain model Shuttle Radar Topography Mission (SRTM) (~92 m resolution). The results obtained are in good agreement with the previous estimations based on seismic profiles and gravimetric modeling, with the exceptions of some particular locations. The results from the present method and those from the seismic interpretation are slightly different from the results of the gravimetric data. This discrepancy may result from the presence of large buried landslides in the bottom of the Rhone Valley.

Time for change: a roadmap to guide the implementation of the World Anti-Doping Code 2015

A medical and scientific multidisciplinary consensus meeting was held from 29 to 30 November 2013 on Anti-Doping in Sport at the Home of FIFA in Zurich, Switzerland, to create a roadmap for the implementation of the 2015 World Anti-Doping Code. The consensus statement and accompanying papers set out the priorities for the antidoping community in research, science and medicine. The participants achieved consensus on a strategy for the implementation of the 2015 World Anti-Doping Code. Key components of this strategy include: (1) sport-specific risk assessment, (2) prevalence measurement, (3) sport-specific test distribution plans, (4) storage and reanalysis, (5) analytical challenges, (6) forensic intelligence, (7) psychological approach to optimise the most deterrent effect, (8) the Athlete Biological Passport (ABP) and confounding factors, (9) data management system (Anti-Doping Administration & Management System (ADAMS), (10) education, (11) research needs and necessary advances, (12) inadvertent doping and (13) management and ethics: biological data. True implementation of the 2015 World Anti-Doping Code will depend largely on the ability to align thinking around these core concepts and strategies. FIFA, jointly with all other engaged International Federations of sports (Ifs), the International Olympic Committee (IOC) and World Anti-Doping Agency (WADA), are ideally placed to lead transformational change with the unwavering support of the wider antidoping community. The outcome of the consensus meeting was the creation of the ad hoc Working Group charged with the responsibility of moving this agenda forward.

'Comfort Me With Apples': Ambivalent Allusion in Paradise Lost

Paradise Lost can be read on various levels, some of which challenge or even contradict others. The main, explicit narrative from Genesis chapters 2 and 3 is shadowed by many other related stories. Some of these buried tales question or subvert the values made explicit in the dominant narrative. An attentive reader needs to be alert to the ways in which such references introduce teasing complexities. The approach of Satan to Eve in the ninth book of Paradise Lost is loaded in just that way with allusion to the literature of Greece and Rome. The poem recovers for this long and intricately constructed passage the weight of classical reference, especially in similes, that it had during the first Satanic books. Gardens, both classical and biblical, disguised or transformed serpents, and the weight of allusions that Eve is required to bear, all threaten to undermine the meanings of the overt narrative. The narrator has difficulty rescuing Eve from the allusions she attracts, or the many stories told about her.

Retaining Wall - Modular Unit Reinforced Earth Tensar Geogrid Reinforcement, HR-549, 1998

This research, initiated in October 1992, was located at the intersection of Blairs Ferry Road and Lindale Drive in the City of Marion. The wall is located on the southeast corner of the intersection. Reinforced retaining wall construction started with a five inch base of roadstone with one inch of sand for leveling purposes. One and one-half to two feet of one inch clean stone was placed behind the blocks. A four inch perforated plastic pipe was placed approximately nine inches from the bottom of the one inch clean stone. The Tenswal, tensar geogrid was placed at every third layer. Openings in the Tenswal are hooked over plastic dowels in the blocks. The tenswal reaches from the face of the wall back 5' to 8'. The cost for constructing this wall was $124,400. The wall has performed well for the past five years. The wall improves the aesthetics of a high traffic volume intersection of an urban area. Many positive comments have been received by the city regarding its appearance. The City of Marion has been pleased with the wall and has used this type of wall on subsequent projects.