A burst of segmental duplications in the genome of the African great ape ancestor

It is generally accepted that the extent of phenotypic change between human and great apes is dissonant with the rate of molecular change. Between these two groups, proteins are virtually identical, cytogenetically there are few rearrangements that distinguish ape-human chromosomes, and rates of single-base-pair change and retrotransposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Studies of gene family evolution indicate that gene loss and gain are enriched within the primate lineage. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orang-utan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of base pairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single-base-pair mutations, there has been a genomic burst of duplication activity at this period during human evolution.

Iowa Comprehensive Annual Financial Report, 1999

In accordance with Iowa Code Section421.3(5), we are please to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ended June 30, 1999. The Department of Revenue and Finance is responsible for both the accuracy in all materials respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State's financial activity. This report is prepared in accordance with generally accepted accounting principles (GAAP) for governments Standards Board (GASB).

Iowa Comprehensive Annual Financial Report, 2009

We are pleased to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ended June 30, 2009. As required by State statute, this report has been prepared in accordance with U.S. Generally Accepted Accounting Principles (GAAP) for governments as promulgated by the Governmental Accounting Standards Board (GASB). The Department of Administrative Services and the Department of Management are responsible for both the accuracy of the presented data, and the completeness and fairness of the presentation. We believe the information presented is accurate in all material respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State’s financial activity.

Iowa Comprehensive Annual Financial Report, 2010

We are pleased to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ended June 30, 2010. As required by State statute, this report has been prepared in accordance with U.S. Generally Accepted Accounting Principles (GAAP) for governments as promulgated by the Governmental Accounting Standards Board (GASB). The Department of Administrative Services and the Department of Management are responsible for both the accuracy of the presented data, and the completeness and fairness of the presentation. We believe the information presented is accurate in all material respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State’s financial activity.

Iowa Comprehensive Annual Financial Report, 2008

In accordance with Iowa Code Section421.3(5), we are please to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ending in June 2008. The Department of Administrative Services is responsible for both the accuracy in all materials respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State's financial activity. This report is prepared in accordance with generally accepted accounting principles (GAAP) for governments Standards Board (GASB).

Anthropogenic radionuclides in atmospheric air over Switzerland during the last few decades.

The atmospheric nuclear testing in the 1950s and early 1960s and the burn-up of the SNAP-9A satellite led to large injections of radionuclides into the stratosphere. It is generally accepted that current levels of plutonium and caesium radionuclides in the stratosphere are negligible. Here we show that those radionuclides are present in the stratosphere at higher levels than in the troposphere. The lower content in the troposphere reveals that dry and wet deposition efficiently removes radionuclides within a period of a few weeks to months. Since the stratosphere is thermally stratified and separated from the troposphere by the tropopause, radioactive aerosols remain longer. We estimate a mean residence time for plutonium and caesium radionuclides in the stratosphere of 2.5-5 years. Our results also reveal that strong volcanic eruptions like Eyjafjallajökull in 2010 have an important role in redistributing anthropogenic radionuclides from the stratosphere to the troposphere.

A comprehensive analysis of human gene expression profiles identifies stromal immunoglobulin κ C as a compatible prognostic marker in human solid tumors.

PURPOSE: Although the central role of the immune system for tumor prognosis is generally accepted, a single robust marker is not yet available. EXPERIMENTAL DESIGN: On the basis of receiver operating characteristic analyses, robust markers were identified from a 60-gene B cell-derived metagene and analyzed in gene expression profiles of 1,810 breast cancer; 1,056 non-small cell lung carcinoma (NSCLC); 513 colorectal; and 426 ovarian cancer patients. Protein and RNA levels were examined in paraffin-embedded tissue of 330 breast cancer patients. The cell types were identified with immunohistochemical costaining and confocal fluorescence microscopy. RESULTS: We identified immunoglobulin κ C (IGKC) which as a single marker is similarly predictive and prognostic as the entire B-cell metagene. IGKC was consistently associated with metastasis-free survival across different molecular subtypes in node-negative breast cancer (n = 965) and predicted response to anthracycline-based neoadjuvant chemotherapy (n = 845; P < 0.001). In addition, IGKC gene expression was prognostic in NSCLC and colorectal cancer. No association was observed in ovarian cancer. IGKC protein expression was significantly associated with survival in paraffin-embedded tissues of 330 breast cancer patients. Tumor-infiltrating plasma cells were identified as the source of IGKC expression. CONCLUSION: Our findings provide IGKC as a novel diagnostic marker for risk stratification in human cancer and support concepts to exploit the humoral immune response for anticancer therapy. It could be validated in several independent cohorts and carried out similarly well in RNA from fresh frozen as well as from paraffin tissue and on protein level by immunostaining.

Iowa Comprehensive Annual Financial Report, 2014

We are pleased to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ended June 30, 2014. As required by State statute, this report has been prepared in accordance with U.S. Generally Accepted Accounting Principles (GAAP) for governments as promulgated by the Governmental Accounting Standards Board (GASB). The Department of Administrative Services and the Department of Management are responsible for both the accuracy of the presented data, and the completeness and fairness of the presentation. We believe the information presented is accurate in all material respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State’s financial activity.

Iowa Comprehensive Annual Financial Report, 2011

We are pleased to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ended June 30, 2011. As required by State statute, this report has been prepared in accordance with U.S. Generally Accepted Accounting Principles (GAAP) for governments as promulgated by the Governmental Accounting Standards Board (GASB). The Department of Administrative Services and the Department of Management are responsible for both the accuracy of the presented data, and the completeness and fairness of the presentation. We believe the information presented is accurate in all material respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State’s financial activity.

Iowa Comprehensive Annual Financial Report, 2012

We are pleased to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ended June 30, 2012. As required by State statute, this report has been prepared in accordance with U.S. Generally Accepted Accounting Principles (GAAP) for governments as promulgated by the Governmental Accounting Standards Board (GASB). The Department of Administrative Services and the Department of Management are responsible for both the accuracy of the presented data, and the completeness and fairness of the presentation. We believe the information presented is accurate in all material respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State’s financial activity.

Iowa Comprehensive Annual Financial Report, 2013

We are pleased to submit the Comprehensive Annual Financial Report (CAFR) for the State of Iowa for the fiscal year ended June 30, 2013. As required by State statute, this report has been prepared in accordance with U.S. Generally Accepted Accounting Principles (GAAP) for governments as promulgated by the Governmental Accounting Standards Board (GASB). The Department of Administrative Services and the Department of Management are responsible for both the accuracy of the presented data, and the completeness and fairness of the presentation. We believe the information presented is accurate in all material respects and the necessary disclosures have been made which enable the reader to obtain an understanding of the State’s financial activity.

Nanoparticles for fingermark detection: an insight into the reaction mechanism

This publication presents one of the first uses of silicon oxide nanoparticles to detect fingermarks. The study is not confined to showing successful detection of fingermarks, but is focused on understanding the mechanisms involved in the fingermark detection process. To gain such an understanding, various chemical groups are grafted onto the nanoparticle surface, and parameters such as the pH of the solutions or zeta potential are varied to study their influence on the detection. An electrostatic interaction has been the generally accepted hypothesis of interaction between nanoparticles and fingermarks, but the results of this research challenge that hypothesis, showing that the interaction is chemically driven. Carboxyl groups grafted onto the nanoparticle surfaces react with amine groups of the fingermark secretion. This formation of amide linkage between carboxyl and amine groups has further been favoured by catalyzing the reaction with a compound of diimide type. The research strategy adopted here ought to be applicable to all detection techniques using nanoparticles. For most of them the nature of the interaction remains poorly understood.

Transverse Joint Sealing with Various Sealants, HR-203, 1983

Iowa's first portland cement concrete pavement was constructed in 1904 in the City of LeMars. A portion of that pavement served traffic until 1974 at which time it was resurfaced. The first rural Iowa pee pavement (16' wide, 6" to 7" thick) was constructed under the direction of the Iowa State Highway Commission in 1913. Some of Iowa's early pavements had transverse joints at 25-foot spacings. At that time, joint spacings across the nation ranged from 24 to 100 ft. There have been many changes in joint design over the years with some pavements being constructed without transverse joints. Joint spacing on Iowa primary pavements has generally remained around 20 feet with this spacing having been adopted as an Iowa standard in 1954. Until 1978 it was common to specify a 40-foot joint spacing on secondary pavements. The performance of the pavements with joint spacings greater than 20 feet, and in some cases no contraction joints, generated a 1955 research project on joint spacing. This project was 16 miles long containing sections without contraction joints and sections with joints sawed at intervals of 20, 50 and 80 feet. Approximately half of the sawed joints were left unsealed. The results of this research supported the 20-foot spacing, but were inconclusive regarding the benefits of sealing. One of the desired characteristics of joint sealing material is that it should act as a moisture barrier and prevent the intrusion of surface water. It was generally accepted from past experience that the hot poured type joint seals did not provide this effective moisture barrier.

Investigation of Plastic Pipes for Highway Applications, HR-373A, Phase II, 1997

It is generally accepted that high density polyethylene pipe (HDPE) performs well under live loads with shallow cover, provided the backfill is well compacted. Although industry standards require carefully compacted backfill, poor inspection and/or faulty construction may result in soils that provide inadequate restraint at the springlines of the pipes thereby causing failure. The objectives of this study were: 1) to experimentally define a lower limit of compaction under which the pipes perform satisfactorily, 2) to quantify the increase in soil support as compaction effort increases, 3) to evaluate pipe response for loads applied near the ends of the buried pipes, 4) to determine minimum depths of cover for a variety of pipes and soil conditions by analytically expanding the experimental results through the use of the finite element program CANDE. The test procedures used here are conservative especially for low-density fills loaded to high contact stresses. The failures observed in these tests were the combined effect of soil bearing capacity at the soil surface and localized wall bending of the pipes. Under a pavement system, the pipes' performance would be expected to be considerably better. With those caveats, the following conclusions are drawn from this study. Glacial till compacted to 50% and 80% provides insufficient support; pipe failureoccurs at surface contact stresses lower than those induced by highway trucks. On the other hand, sand backfill compacted to more than 110 pcf (17.3 kN/m3) is satisfactory. The failure mode for all pipes with all backfills is localized wall bending. At moderate tire pressures, i.e. contact stresses, deflections are reduced significantly when backfill density is increased from about 50 pcf (7.9 kN/m^3) to 90 pcf (14.1 kN/m^3). Above that unit weight, little improvement in the soil-pipe system is observed. Although pipe stiffness may vary as much as 16%, analyses show that backfill density is more important than pipe stiffness in controlling both deflections at low pipe stresses and at the ultimate capacity of the soil-pipe system. The rate of increase in ultimate strength of the system increases nearly linearly with increasing backfill density. When loads equivalent to moderate tire pressures are applied near the ends of the pipes, pipe deflections are slighly higher than when loaded at the center. Except for low density glacial till, the deflections near the ends are not excessive and the pipes perform satisfactorily. For contact stresses near the upper limit of truck tire pressures and when loaded near the end, pipes fail with localized wall bending. For flowable fill backfill, the ultimate capacity of the pipes is nearly doubled and at the upper limit of highway truck tire pressures, deflections are negligible. All pipe specimens tested at ambient laboratory room temperatures satisfied AASHTO minimum pipe stiffness requirements at 5% deflection. However, nearly all specimens tested at elevated pipe surface temperatures, approximately 122°F (50°C), failed to meet these requirements. Some HDPE pipe installations may not meet AASHTO minimum pipe stiffness requirements when installed in the summer months (i.e. if pipe surface temperatures are allowed to attain temperatures similar to those tested here). Heating of any portion of the pipe circumference reduced the load carrying capacity of specimens. The minimum soil cover depths, determined from the CANOE analysis, are controlled by the 5% deflection criterion. The minimum soil cover height is 12 in. (305 mm). Pipes with the poor silt and clay backfills with less than 85% compaction require a minimum soil cover height of 24 in. (610 mm). For the sand at 80% compaction, the A36 HDPE pipe with the lowest moment of inertia requires a minimum of 24 in. (610 mm) soil cover. The C48 HDPE pipe with the largest moment of inertia and all other pipes require a 12 in. (305 mm) minimum soil cover.

Scour Around Bridge Piers and Abutments, HR-30 and Iowa Highway Research Board Bulletin No. 4, 1956

Man’s never-ending search for better materials and construction methods and for techniques of analysis and design has overcome most of the early difficulties of bridge building. Scour of the stream bed, however, has remained a major cause of bridge failures ever since man learned to place piers and abutments in the stream in order to cross wide rivers. Considering the overall complexity of field conditions, it is not surprising that no generally accepted principles (not even rules of thumb) for the prediction of scour around bridge piers and abutments have evolved from field experience alone. The flow of individual streams exhibits a manifold variation, and great disparity exists among different rivers. The alignment, cross section, discharge, and slope of a stream must all be correlated with the scour phenomenon, and this in turn must be correlated with the characteristics of the bed material ranging from clays and fine silts to gravels and boulders. Finally, the effect of the shape of the obstruction itself-the pier or abutment-must be assessed. Since several of these factors are likely to vary with time to some degree, and since the scour phenomenon as well is inherently unsteady, sorting out the influence of each of the various factors is virtually impossible from field evidence alone. The experimental approach was chosen as the investigative method for this study, but with due recognition of the importance of field measurements and with the realization that the results must be interpreted so as to be compatible with the present-day theories of fluid mechanics and sediment transportation. This approach was chosen because, on the one hand, the factors affecting the scour phenomenon can be controlled in the laboratory to an extent that is not possible in the field, and, on the other hand, the model technique can be used to circumvent the present inadequate understanding of the phenomenon of the movement of sediment by flowing water. In order to obtain optimum results from the laboratory study, the program was arranged at the outset to include a related set of variables in each of several phases into which the whole problem was divided. The phases thus selected were : 1. Geometry of piers and abutments, 2. Hydraulics of the stream, 3. Characteristics of the sediment, 4. Geometry of channel shape and alignment.