ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Adsorption of glyphosate in chilean soils and its relationship with unoccupied phosphate binding sites

The objective of this work was to investigate glyphosate adsorption by soils and its relationship with unoccupied binding sites for phosphate adsorption. Soil samples of three Chilean soils series - Valdivia (Andisol), Clarillo (Inceptisol) and Chicureo (Vertisol) - were incubated with different herbicide concentrations. Glyphosate remaining in solution was determined by adjusting a HPLC method with a UV detector. Experimental maximum adsorption capacity were 15,000, 14,300 and 4,700 mg g¹ for Valdivia, Clarillo, and Chicureo soils, respectively. Linear, Freundlich, and Langmuir models were used to describe glyphosate adsorption. Isotherms describing glyphosate adsorption differed among soils. Maximum adjusted adsorption capacity with the Langmuir model was 231,884, 17,874 and 5,670 mg g-1 for Valdivia, Clarillo, and Chicureo soils, respectively. Glyphosate adsorption on the Valdivia soil showed a linear behavior at the range of concentrations used and none of the adjusted models became asymptotic. The high glyphosate adsorption capacity of the Valdivia soil was probably a result of its high exchangeable Al, extractable Fe, and alophan and imogolite clay type. Adsorption was very much related to phosphate dynamics in the Valdivia soil, which showed the larger unoccupied phosphate binding sites. However relationship between unoccupied phosphate binding sites and glyphosate adsorption in the other two soils (Clarillo and Chicureo) was not clear.

Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (Nomascus leucogenys, NLE) in the form of high-quality BAC insert sequences (4.2 Mbp). While there is a significant deficit of breakpoints in genes, we identified seven human gene structures involved in signaling pathways (DEPDC4, GNG10), phospholipid metabolism (ENPP5, PLSCR2), beta-oxidation (ECH1), cellular structure and transport (HEATR4), and transcription (ZNF461), that have been disrupted in the NLE gibbon lineage. Notably, only three of these genes show the expected evolutionary signatures of pseudogenization. Sequence analysis of the breakpoints suggested both nonclassical nonhomologous end-joining (NHEJ) and replication-based mechanisms of rearrangement. A substantial number (11/24) of human-NLE gibbon breakpoints showed new insertions of gibbon-specific repeats and mosaic structures formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements. Analysis of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution.

Multi-Purpose ESS/ITS Data Collection Sites, SPR72-00-0003-042, 2014

This document presents the results of a state-of-practice survey of transportation agencies that are installing intelligent transportation sensors (ITS) and other devices along with their environmental sensing stations (ESS) also referred to as roadway weather information system (RWIS) assets.

A randomised controlled pilot study comparing Mepitel(®) and SurfaSoft(®) on paediatric donor sites treated with Recell(®).

This randomized controlled pilot study examined the effects of a silicone net dressing (Mepitel(®)) and a monofilament polyamide woven dressing (SurfaSoft(®)) on the rate of epithelialisation and epidermal maturation, pain, and ease of dressing removal on paediatric donor sites treated with epithelial cell suspension (ReCell(®)). Fifteen children (1-15 years) admitted for acute or reconstructive burns procedures in a tertiary referral hospital in Australia were randomly assigned to the experimental group, Mepitel(®) (n=8) and to the control group, SurfaSoft(®) (n=7). All donor sites were treated with ReCell(®) and covered with the assigned dressing. Measurements of rate of epithelialisation and epidermal maturation, pain, and ease of dressing removal were recorded every two days until the wound was healed. Results showed that there was no difference in the rate of epidermal maturation between the two groups. Less pain and force to remove the dressing was shown in the Mepitel(®) group when compared to SurfaSoft(®). The rate of epithelialisation was found to be an unreliable measure. Although additional research is required to support the results of this study, these results suggest that Mepitel's(®) pliable, self-adhesive and atraumatic properties may improve healing of ReCell(®) treated donor sites with less pain at dressing changes. This pilot study provides a strong base for further research in this area.

Audit report on America’s Agricultural Industrial Heritage Landscape, Inc., d/b/a Silos and Smokestacks National Heritage Area and Silos and Smokestacks Natural Heritage Area Foundation in Waterloo, Iowa for the years ended December 31, 2014 and 2013

Audit report on America’s Agricultural Industrial Heritage Landscape, Inc., d/b/a Silos and Smokestacks National Heritage Area and Silos and Smokestacks Natural Heritage Area Foundation in Waterloo, Iowa for the years ended December 31, 2014 and 2013

Cross-species analysis of the replication complex of Old World arenaviruses reveals two nucleoprotein sites involved in L protein function.

Lassa virus (LASV) causing hemorrhagic Lassa fever in West Africa, Mopeia virus (MOPV) from East Africa, and lymphocytic choriomeningitis virus (LCMV) are the main representatives of the Old World arenaviruses. Little is known about how the components of the arenavirus replication machinery, i.e., the genome, nucleoprotein (NP), and L protein, interact. In addition, it is unknown whether these components can function across species boundaries. We established minireplicon systems for MOPV and LCMV in analogy to the existing LASV system and exchanged the components among the three systems. The functional and physical integrity of the resulting complexes was tested by reporter gene assay, Northern blotting, and coimmunoprecipitation studies. The minigenomes, NPs, and L proteins of LASV and MOPV could be exchanged without loss of function. LASV and MOPV L protein was also active in conjunction with LCMV NP, while the LCMV L protein required homologous NP for activity. Analysis of LASV/LCMV NP chimeras identified a single LCMV-specific NP residue (Ile-53) and the C terminus of NP (residues 340 to 558) as being essential for LCMV L protein function. The defect of LASV and MOPV NP in supporting transcriptional activity of LCMV L protein was not caused by a defect in physical NP-L protein interaction. In conclusion, components of the replication complex of Old World arenaviruses have the potential to functionally and physically interact across species boundaries. Residue 53 and the C-terminal domain of NP are important for function of L protein during genome replication and transcription.

Thin Maintenance Surfaces for Municipalities, TR-507, 2007

As streets age, officials must deal with rehabilitating and reconstructing these pavements to maintain a safe and comfortable ride. In light of nationwide budget shortfalls, cost-effective methods of extending pavement service life must be developed or the overall condition of street systems will continue to fall. Thin maintenance surfaces (TMSs) are a set of cost-effective preventive maintenance surfacing techniques that can be used to extend the life of bituminous pavement—pavement built with hot mix asphalt, hot mix asphalt overlays of portland cement concrete pavements, built-up seal coat (chip seal), stabilized materials, or a combination of these. While previous phases of TMS research have provided information about the uses of thin maintenance surfaces in rural settings, urban areas have different road maintenance challenges that should be considered separately. This research provides city street officials with suggestions for TMS techniques that street departments can easily test and include into their current programs. This research project facilitated the construction of TMS test sections in Cedar Rapids, Council Bluffs, and West Des Moines (all urban settings in Iowa). Test section sites and surfaces were selected to suit the needs of municipalities and were applied to roads with an array of various distresses and maintenance needs. Condition surveys of each test section were performed before construction, after construction, and after the first winter to record the amount and severity of existing distress and calculate the pavement condition index. Because conditions of the test sections varied greatly, determining which surface was most successful by comparing case studies was not feasible. However, some general conclusions can be made from this research. TMSs are suitable preventive maintenance techniques for a municipal street department’s program for preserving existing pavements. Careful attention should be paid to proper planning, quality control during construction, aggregate and binder selection, and aggregate embedment in order to support successful TMS application.

Quantitative Mapping of Waterways Characteristics at Bridge Sites, TR-569, 2008

Iowa state, county, and city engineering offices expend considerable effort monitoring the state’s approximately 25,000 bridges, most of which span small waterways. In fact, the need for monitoring is actually greater for bridges over small waterways because scour processes are exacerbated by the close proximity of abutments, piers, channel banks, approach embankments, and other local obstructions. The bridges are customarily inspected biennially by the county’s road department bridge inspectors. It is extremely time consuming and difficult to obtain consistent, reliable, and timely information on bridge-waterway conditions for so many bridges. Moreover, the current approaches to gather survey information is not uniform, complete, and quantitative. The methodology and associated software (DIGIMAP) developed through the present project enable a non-intrusive means to conduct fast, efficient, and accurate inspection of the waterways in the vicinity of the bridges and culverts using one technique. The technique combines algorithms image of registration and velocimetry using images acquired with conventional devices at the inspection site. The comparison of the current bridge inspection and monitoring methods with the DIGIMAP methodology enables to conclude that the new procedure assembles quantitative information on the waterway hydrodynamic and morphologic features with considerable reduced effort, time, and cost. It also improves the safety of the bridge and culvert inspections conducted during normal and extreme hydrologic events. The data and information are recorded in a digital format, enabling immediate and convenient tracking of the waterway changes over short or long time intervals.

Asian/Pacific American heritage month, May 2005 (Asian/Pacific Americans in Iowa 2005)

Demographic profile of the Iowa population Asian and Pacific Islander descent.

Latinos in Iowa 2005 (Hispanic Heritage Month, September 2005: Latinos in Iowa

Statistical snapshot and demographic profile of Iowa's Latino population in Census statistics.

Latinos in Iowa 2006 (Hispanic Heritage Month, September 2006: Latinos in Iowa

Statistical snapshot and demographic profile of Iowa's Latino population in Census statistics.