Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution

Background: Chemoreception is a widespread mechanism that is involved in critical biologic processes, including individual and social behavior. The insect peripheral olfactory system comprises three major multigene families: the olfactory receptor (Or), the gustatory receptor (Gr), and the odorant-binding protein (OBP) families. Members of the latter family establish the first contact with the odorants, and thus constitute the first step in the chemosensory transduction pathway.Results: Comparative analysis of the OBP family in 12 Drosophila genomes allowed the identification of 595 genes that encode putative functional and nonfunctional members in extant species, with 43 gene gains and 28 gene losses (15 deletions and 13 pseudogenization events). The evolution of this family shows tandem gene duplication events, progressive divergence in DNA and amino acid sequence, and prevalence of pseudogenization events in external branches of the phylogenetic tree. We observed that the OBP arrangement in clusters is maintained across the Drosophila species and that purifying selection governs the evolution of the family; nevertheless, OBP genes differ in their functional constraints levels. Finally, we detect that the OBP repertoire evolves more rapidly in the specialist lineages of the Drosophila melanogaster group (D. sechellia and D. erecta) than in their closest generalists.Conclusion: Overall, the evolution of the OBP multigene family is consistent with the birth-and-death model. We also found that members of this family exhibit different functional constraints, which is indicative of some functional divergence, and that they might be involved in some of the specialization processes that occurred through the diversification of the Drosophila genus.

Feasibility Study on Proposed Amtrak service from Chicago, to Iowa City, Iowa via Quad Cities, December 5, 2007

Soon after the Illinois Department of Transportation (“Ill. DOT”) requested Amtrak to conduct a feasibility study on proposed Amtrak service between Chicago and the Illinois Quad Cities, the Iowa Department of Transportation (“Iowa DOT”) asked that the study be extended to Iowa City and later to Des Moines. This report examines the feasibility of extending service to Iowa City. The completed report for the proposed Chicago – Quad Cities’ service was delivered to Ill. DOT in early January 2008. It assumes a stand-alone train operation strictly within the State of Illinois and makes no reference to extending the service into the State of Iowa. Therefore, there is no discussion about potential cost sharing allocations for capital improvements or operating losses between the two states which will become a matter of future negotiations between the two jurisdictions. That being said, this report on extending the service to Iowa City is simply an addendum to the Quad Cities report and covers such topics as additional capital infrastructure improvements that would be required in Iowa, impacts on operating expenses, revised ridership and revenue projections, and the like. With one minor exception, the recommended level of capital improvements within Illinois will still be required if the service to Iowa City is initiated. It is thus important for the readers of this report to refer to the Illinois study for detailed information on that state’s portion of the route alternatives.

Extinction debt of high-mountain plants under 21st-century climate change

Quantitative estimates of the range loss of mountain plants under climate change have so far mostly relied on static geographical projections of species' habitat shifts(1-3). Here, we use a hybrid model(4) that combines such projections with simulations of demography and seed dispersal to forecast the climate-driven spatio-temporal dynamics of 150 high-mountain plant species across the European Alps. This model predicts average range size reductions of 44-50% by the end of the twenty-first century, which is similar to projections from the most 'optimistic' static model (49%). However, the hybrid model also indicates that population dynamics will lag behind climatic trends and that an average of 40% of the range still occupied at the end of the twenty-first century will have become climatically unsuitable for the respective species, creating an extinction debt(5,6). Alarmingly, species endemic to the Alps seem to face the highest range losses. These results caution against optimistic conclusions from moderate range size reductions observed during the twenty-first century as they are likely to belie more severe longer-term effects of climate warming on mountain plants.

Precast Concrete Elements for Accelerated Bridge Construction Final Report, Volume 1-1. Laboratory Testing of Precast Substructure Components: Boone County Bridge, January 2009

In July 2006, construction began on an accelerated bridge project in Boone County, Iowa that was composed of precast substructure elements and an innovative, precast deck panel system. The superstructure system consisted of full-depth deck panels that were prestressed in the transverse direction, and after installation on the prestressed concrete girders, post-tensioned in the longitudinal direction. Prior to construction, laboratory tests were completed on the precast abutment and pier cap elements. The substructure testing was to determine the punching shear strength of the elements. Post-tensioning testing and verification of the precast deck system was performed in the field. The forces in the tendons provided by the contractor were verified and losses due to the post-tensioning operation were measured. The stress (strain) distribution in the deck panels due to the post-tensioning was also measured and analyzed. The entire construction process for this bridge system was documented. Representatives from the Boone County Engineers Office, the prime contractor, precast fabricator, and researchers from Iowa State University provided feedback and suggestions for improving the constructability of this design.

First day of an oil spill on the open sea: early mass transfers of hydrocarbons to air and water.

During the first hours after release of petroleum at sea, crude oil hydrocarbons partition rapidly into air and water. However, limited information is available about very early evaporation and dissolution processes. We report on the composition of the oil slick during the first day after a permitted, unrestrained 4.3 m(3) oil release conducted on the North Sea. Rapid mass transfers of volatile and soluble hydrocarbons were observed, with >50% of ≤C17 hydrocarbons disappearing within 25 h from this oil slick of <10 km(2) area and <10 μm thickness. For oil sheen, >50% losses of ≤C16 hydrocarbons were observed after 1 h. We developed a mass transfer model to describe the evolution of oil slick chemical composition and water column hydrocarbon concentrations. The model was parametrized based on environmental conditions and hydrocarbon partitioning properties estimated from comprehensive two-dimensional gas chromatography (GC×GC) retention data. The model correctly predicted the observed fractionation of petroleum hydrocarbons in the oil slick resulting from evaporation and dissolution. This is the first report on the broad-spectrum compositional changes in oil during the first day of a spill at the sea surface. Expected outcomes under other environmental conditions are discussed, as well as comparisons to other models.

Visualization Resources for Iowa State University and the Iowa DOT: An Automated Design Model to Simulator Converter, November 2012

This project developed an automatic conversion software tool that takes input a from an Iowa Department of Transportation (DOT) MicroStation three-dimensional (3D) design file and converts it into a form that can be used by the University of Iowa’s National Advanced Driving Simulator (NADS) MiniSim. Once imported into the simulator, the new roadway has the identical geometric design features as in the Iowa DOT design file. The base roadway appears as a wireframe in the simulator software. Through additional software tools, textures and shading can be applied to the roadway surface and surrounding terrain to produce the visual appearance of an actual road. This tool enables Iowa DOT engineers to work with the universities to create drivable versions of prospective roadway designs. By driving the designs in the simulator, problems can be identified early in the design process. The simulated drives can also be used for public outreach and human factors driving research.

Inside IPERS and Pensioners’ Post, Winter 2004-2005

I am pleased to send you this special edition newsletter, which includes a fi nancial summary on pages 2 and 3. Providing you fi nancial and performance information refl ects my commitment to accountability. IPERS’ performance continues to be strong, as does the commitment of the Governor, Legislature, employers, members, the Investment Board, the Benefi ts Advisory Committee (BAC), and staff to maintaining a good retirement plan. Unfortunately, IPERS’ good performance and everyone’s commitment does not eliminate the need for a contribution rate increase. There are many reasons for this. We must make up for losses from the recent bear markets. Also, our retirees are living longer; therefore, they are drawing pensions longer.

Allergo-immunologie : 1. Dans quelles situations doit-on penser au syndrome des antiphospholipides? [When should consider antiphospholipid syndrome?]

En pratique courante, les événements thrombotiques ne sont pas rares. Dans le suivi des grossesses, les gynécologues ont souvent affaire à des pertes foetles chez leurs patientes. Jusqu'à quel point ces événements peuvent-ils être considérés comme "banals" ? Quand et sur quels critères doit-on considérer la possibilité d'un syndrome des antiphospholipides ? Des efforts ont été réalisés ces dernières années en vue de mieux codifier ce syndrome, tant sur le plan du laboratoire, que clinique. En vue d'uniformiser ces éléments, une première conférence de consensus a eu lieu en 1999 à Sapporo, avec mise à jour en 2004 à Sydney. Ces quelques lignes font le point sur les éléments nouveaux liés à la classification actuelle et sur les éléments diagnostiques en découlant, en vue de retenir le diagnostic de syndrome des antiphospholipides de manière rigoureuse, et d'initier le traitement adéquat dans les différentes situations liées à ce syndrome. In current practice, the occurrence of thrombosis--venous or arterial--is not rare. Moreover, during the follow-up of pregnancies, gynecologists often have to deal with fetal losses of their patients. Up to which point can these events be considered as "ordinary"? When and on which criteria can we consider an antiphospholipid syndrome? Efforts have been put these last years to better codify the diagnosis of this syndrome, so much on the laboratory side as on the clinical side. With a view to standardize these elements, a first consensus conference took place in 1999 in Sapporo, with an update in 2004 in Sydney, that has recently been published. The goal of these lines is to focus on new elements connected to the actual classification and on the resulting diagnosis elements, with the aim of obtaining a diagnosis of antiphospholipid syndrome in a rigorous way, and to initiate the appropriate treatment in different situations linked to this syndrome

Determination of entrance loss coefficients for pre-cast reinforced Concrete Box Culverts, December 2012

There is an increased interest in constructing Pre-Cast (PC) Twin and Triple Reinforced Concrete Box (RCB) culverts in Iowa due to the efficiency associated with their production in controlled environment and decrease of the construction time at the culvert sites. The design of the multi-barrel PC culverts is, however, based on guidelines for single-barrel cast-inplace (CIP) culverts despite that the PC and CIP culverts have different geometry. There is scarce information for multiplebarrel RCB culverts in general and even fewer on culverts with straight wingwalls as those designed by Iowa DOT. Overall, the transition from CIP to PC culverts requires additional information for improving the design specifications currently in use. Motivated by the need to fill these gaps, an experimental study was undertaken by IIHR-Hydroscience & Engineering. The goals of the study are to document flow performance curves and head losses at the culvert entrance for a various culvert geometry, flow conditions, and settings. The tests included single-, double- and triple-barrel PC and CIP culverts with two span-to-rise ratios set on mild and steep slopes. The tests also included optimization of the culvert geometry entrance by considering various configurations for the top bevel. The overall conclusion of the study is that by and large the current Iowa DOT design specifications for CIP culverts can be used for multi-barrel PC culvert design. For unsubmerged flow conditions the difference in the hydraulic performance curves and headloss coefficients for PC and CIP culverts are within the experimental uncertainty. Larger differences (specified by the study) are found for submerged conditions when the flow is increasingly constricted at the entrance in the culvert. The observed differentiation is less important for multi-barrel culverts as the influence of the wingwalls decreases with the increase of the number of barrels.

Western Iowa Missouri River Flooding -- Geo-Infrastructure Damage Assessment, Repair and Mitigation Strategies, TR-638, 2013

The 2011 Missouri River flooding caused significant damage to many geo-infrastructure systems including levees, bridge abutments/foundations, paved and unpaved roadways, culverts, and embankment slopes in western Iowa. The flooding resulted in closures of several interchanges along Interstate 29 and of more than 100 miles of secondary roads in western Iowa, causing severe inconvenience to residents and losses to local businesses. The main goals of this research project were to assist county and city engineers by deploying and using advanced technologies to rapidly assess the damage to geo-infrastructure and develop effective repair and mitigation strategies and solutions for use during future flood events in Iowa. The research team visited selected sites in western Iowa to conduct field reconnaissance, in situ testing on bridge abutment backfills that were affected by floods, flooded and non-flooded secondary roadways, and culverts. In situ testing was conducted shortly after the flood waters receded, and several months after flooding to evaluate recovery and performance. Tests included falling weight deflectometer, dynamic cone penetrometer, three-dimensional (3D) laser scanning, ground penetrating radar, and hand auger soil sampling. Field results indicated significant differences in roadway support characteristics between flooded and non-flooded areas. Support characteristics in some flooded areas recovered over time, while others did not. Voids were detected in culvert and bridge abutment backfill materials shortly after flooding and several months after flooding. A catalog of field assessment techniques and 20 potential repair/mitigation solutions are provided in this report. A flow chart relating the damages observed, assessment techniques, and potential repair/mitigation solutions is provided. These options are discussed for paved/unpaved roads, culverts, and bridge abutments, and are applicable for both primary and secondary roadways.

Consumption of macrophytes by invertebrates in Tancada lagoon (NE Spain)

Gammarus aequicauda and Sphaeroma hookeri are the most abundant macroinvertebrates on Ruppia cirrhosa (1275 and 1290 individuals.m-2) and Potamogeton pectinatus (140 and 680 individuals. m-2) in Tancada lagoon, a Mediterranean coastal lagoon in the Ebro Delta (NE Spain). Consumption and assimilation efficiencies were calculated from bell jar experiments. Gammarus grazing effects are higher than Sphaeroma on both Ruppia cirrhosa and Potamogeton pectinatus. Green Ruppia leaves lost 0.3 mg per mg Gammarus per day, while Potamogeton leaves lost 0.2 mg per mg Gammarus per day. Decomposing Ruppia leaves lost 0.35-0.54 mg per mg Gammarus per day. Losses of weight by both Ruppia and Potamogeton due to Sphaeroma feeding were less than half those by Gammarus. Assimilation efficiencies are higher for Gammarus (44-78% feeding on Ruppia 2% feeding on Potamogeton) than for Sphaeroma (26-48%) feeding on Ruppia). These assimilation efficiencies were higher than those reported by other authors working at higher latitudes perhaps because of the higher temperature under which the experiments were carried out.

Evidence-Based Recommendations for Optimal Dietary Protein Intake in Older People: A Position Paper From the PROT-AGE Study Group.

New evidence shows that older adults need more dietary protein than do younger adults to support good health, promote recovery from illness, and maintain functionality. Older people need to make up for age-related changes in protein metabolism, such as high splanchnic extraction and declining anabolic responses to ingested protein. They also need more protein to offset inflammatory and catabolic conditions associated with chronic and acute diseases that occur commonly with aging. With the goal of developing updated, evidence-based recommendations for optimal protein intake by older people, the European Union Geriatric Medicine Society (EUGMS), in cooperation with other scientific organizations, appointed an international study group to review dietary protein needs with aging (PROT-AGE Study Group). To help older people (>65 years) maintain and regain lean body mass and function, the PROT-AGE study group recommends average daily intake at least in the range of 1.0 to 1.2 g protein per kilogram of body weight per day. Both endurance- and resistance-type exercises are recommended at individualized levels that are safe and tolerated, and higher protein intake (ie, ≥1.2 g/kg body weight/d) is advised for those who are exercising and otherwise active. Most older adults who have acute or chronic diseases need even more dietary protein (ie, 1.2-1.5 g/kg body weight/d). Older people with severe kidney disease (ie, estimated GFR <30 mL/min/1.73m(2)), but who are not on dialysis, are an exception to this rule; these individuals may need to limit protein intake. Protein quality, timing of ingestion, and intake of other nutritional supplements may be relevant, but evidence is not yet sufficient to support specific recommendations. Older people are vulnerable to losses in physical function capacity, and such losses predict loss of independence, falls, and even mortality. Thus, future studies aimed at pinpointing optimal protein intake in specific populations of older people need to include measures of physical function.

Five essays on bankruptcy

Chapter 2 Bankruptcy Initiation In The New Era of Chapter 11 2.1 Abstract The bankruptcy act of 1978 placed corporate managers (as debtor in possession) in control of the bankruptcy process. Between 2000 and 2001 managers apparently lost this control to secured creditors. This study examines financial ratios of firms filing for bankruptcy between 1993 and 2004 and tests the hypothesis that the change from manager to creditor control created or exacerbated the managerial (and dominant creditor) incentive to delay bankruptcy filing. We find a clear deterioration in the financial conditions of firms filing after 2001. This is consistent with managers (or creditors who control them) delaying filing for bankruptcy. We also observe patterns of operating losses and liquidations that suggest adverse economic consequences from such delay. Chapter 3 Bankruptcy Resolution: Priority of Claims with the Secured Creditor in Control 3.1 Abstract We present new evidence on the violation of priority of claims in bankruptcy using a sample of 222 firms that tiled for Chapter 11 bankruptcy over the 1993-2004 period. Our study reveals a dramatic reduction in the violations of priority of claims compared to research on prior periods. These results are consistent with changes in both court practices and laws transferring power to the secured creditors over our sample period. We also find an increase in the time from the date of a bankruptcy filing to reaching plan confirmation where priority is not violated. Chapter 4 Bankruptcy Resolution: Speed, APR Violations and Delaware 4.1 Abstract We analyze speed of bankruptcy resolution on a sample of 294 US firms filing for bankruptcy in the 1993-2004 period. We find strong association between type of Chapter II filing and speed of bankruptcy resolution. We also find that violations to the absolute priority rule reduce the time from bankruptcy filing to plan confirmation. This is consistent with the hypothesis that creditors are willing to grant concessions in exchange for faster bankruptcy resolution. Furthermore, after controlling for the type of filing and violations to the absolute priority rule, we do not find any difference in the duration of the bankruptcy process for firms filing in Delaware, New York, or other bankruptcy districts. Chapter 5 Financial Distress and Corporate Control 5.1 Abstract We examine the replacement rates of directors and executives in 63 firms filing for bank ruptcy during the 1995-2002 period. We find that over 76% of directors and executives are replaced in the four year period from the year prior to the bankruptcy filing through three years after. These rates are higher than those found in prior research and is consistent with changes in bankruptcy procedures and practice (i.e. the increased secured creditors control over the process due to both DIP financing and changes in the Uniform Commercial Code) having a significant impact on the corporate governance of firms in financial distress. Chapter 6 Financial Statement Restatements: Decision to File for Bankruptcy 6.1 Abstract On a sample of 201 firms that restated their financial statements we analyze the process of regaining investor trust in a two year period after the restatement. We find that 20% of firms that restate their financial statements tile for bankruptcy or restructure out of court. Our results also indicate that the decisions to change auditor or management is correlated with a higher probability of failure. Increased media attention appears to partly explain the decision of firms to restructure their debt or tile for bankruptcy.

Feasibility of Cooperative Development of Wetland Mitigation Projects, TR-526, 2006

The Iowa Department of Transportation (Iowa DOT) currently performs wetland mitigation on a project-by-project basis. At the same time, other agencies like the Iowa Department of Natural Resources and Natural Resource Conservation Service are performing wetland restoration projects, and counties and cities may be mitigating wetland losses as well. This project examined the feasibility of developing cooperative wetland mitigation projects in order to utilize state and local resources more efficiently to benefit both Iowa and local communities. The project accomplished the following objectives: (1) Identified and characterized cooperative wetland mitigation programs nationwide; (2) Developed a needs assessment through a survey of state, county, and large city agencies in Iowa to describe wetland mitigation programs and determine challenges with mitigation and program improvements, including long-term risks associated with maintenance and monitoring programs; (3) Surveyed state, county, and city agencies and organizations to identify resources available for developing cooperative mitigation projects and procedures; (4) Developed a conceptual framework for cooperative wetland mitigation.

Determination of the critical period of weed control in corn using a thermal basis

Field studies were conducted over 3 years in southeast Buenos Aires, Argentina, to determine the critical period of weed control in maize (Zea mays L.). The treatments consisted of two different periods of weed interference, a critical weed-free period, and a critical time of weed removal. The Gompertz and logistic equations were fitted to relative yields representing the critical weed-free and the critical time of weed removal, respectively. Accumulated thermal units were used to describe each period of weed-free or weed removal. The critical weed-free period and the critical time of weed removal ranged from 222 to 416 and 128 to 261 accumulated thermal units respectively, to prevent yield losses of 2.5%. Weed biomass proved to be inverse to the crop yield for all the years studied. When weeds competed with the crop from emergence, a large increase in weed biomass was achieved 10 days after crop emergence. However, few weed seedlings emerged and prospered after the 5-6 leaf maize stage (10-20 days after emergence).