An evolutionary driver of interspersed segmental duplications in primates

Background The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution. We investigate the evolution of LCR16a, a putative driver of this phenomenon that encodes one of the most rapidly evolving human–ape gene families, nuclear pore interacting protein (NPIP). Results Comparative analysis shows that LCR16a has independently expanded in five primate lineages over the last 35 million years of primate evolution. The expansions are associated with independent lineage-specific segmental duplications flanking LCR16a leading to the emergence of large interspersed duplication blocks at non-orthologous chromosomal locations in each primate lineage. The intron-exon structure of the NPIP gene family has changed dramatically throughout primate evolution with different branches showing characteristic gene models yet maintaining an open reading frame. In the African ape lineage, we detect signatures of positive selection that occurred after a transition to more ubiquitous expression among great ape tissues when compared to Old World and New World monkeys. Mouse transgenic experiments from baboon and human genomic loci confirm these expression differences and suggest that the broader ape expression pattern arose due to mutational changes that emerged in cis. Conclusions LCR16a promotes serial interspersed duplications and creates hotspots of genomic instability that appear to be an ancient property of primate genomes. Dramatic changes to NPIP gene structure and altered tissue expression preceded major bouts of positive selection in the African ape lineage, suggestive of a gene undergoing strong adaptive evolution

Dialect, interaction and class positioning at school: from deficit to difference to repertoire.

Sociolinguists have been fighting dialect prejudice since the 1960s, but deficit views of non-standard English are regaining currency in educational discourse. In this paper I argue that the traditional sociolinguistic response – stressing dialect systematicity and tolerance of ‘difference’ – may no longer be effective by questioning a key assumption that both deficit and difference approaches share, namely that there exist discrete varieties of English. Based on an empirical study of the language of working-class children in north-east England, I demonstrate that non-standard dialects of English do not have a discrete system of grammar that is isolated from other varieties; rather local dialect forms interact with a range of semiotic resources (including standard forms) within speakers’ repertoires. Interactional analyses of the children’s spontaneous speech highlight this hybridity, as well as the social meanings behind the linguistic choices children make. I conclude by addressing educational responses to non-standard dialect in the classroom, suggesting that it is not the presence or absence of non-standard forms in children’s speech that raises educational issues; rather, educational responses which problematise non-standard voices risk marginalising working-class speech, and may contribute to the alienation of working-class children, or significant groups of them, within the school system

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Use of LANDSAT Classified Pixels for Estimating Annual Livestock and Crop Inventories

The U.S. Department of Agriculture (USDA) has been exploring methods of using remote sensing as a basis for improving survey methodology. This paper discusses digital techniques employing computer classification of pixels with ground enumerated livestock inventories for the State of Iowa during 1978. The methods of analyses include discriminant functions for classification of LANDSAT tapes and regression methods for making estimates of livestock numbers based on double sampling employing an area sampling frame. The results were much less promising than for acreage estimates, but similar to results for crop yield forecasts. These small gains in estimating efficiencies may have, in part, been due to the time interval between the dependent variable (livestock numbers) and independent variables (classified pixels). However, the combined gains in crop acreages, yields, and production when added to modest gains expected for livestock indicate that the combined economic benefits for agriculture are important

World War II Prisoners of War Oral History Project

Interview with Huddleston Wright, an Army veteran (2nd Battalion, 131st Field Artillery, Texas National Guard) and a member of the "Lost Battalion," concerning his experiences as a prisoner-of-war of the Japanese during World War II. Wright discusses the fall of Java and his capture, Bicycle Camp in Batavia (1942), Changi Prison Camp in Singapore (1942), building the Burma-Thailand Death Railway (1942-1944), Kanchanaburi, Thailand (1944-1945), Phet Buri, Thailand (1945), and his liberation

Effect of Physical State of Non-Metallic Inclusions on the Accumulation Within Magnesia-Stabilized Zirconia Foam Filters

In foundry steelmaking, filtration is a common practice to lower the concentration of non-metallic inclusions in steel castings. Removal of non-metallic inclusions reduces the scrap rate and improves machinability, casting appearance and mechanical properties. Non-metallic inclusions are captured by different types of ceramic filters, the choice of which depends on the specific application and location in the process. Ceramic foam filters are commonly utilized in multiple positions in the gating system of sand molds and are effective by a deep bed filtration mechanism. Inclusions can be formed during the melting, pouring and casting and are separated into two main categories of endogenous and exogenous inclusions. Exogenous inclusions come from sources outside the refining process, such as worn refractories, slag, sand, or by reoxidation of the melt and are often much larger than endogenous inclusions. Endogenous inclusions are formed as consequence of the steelmaking and refining process and can be modified at different stages of steelmaking operation for effective removal. Depending on the deoxidizer used, the physical state of the inclusions can be both solid and liquid. Filtration of both solid (alumina) and liquid (manganese silicate) inclusions have been reported by several authors, however, the differences in the capture method have not been well documented. The equilibrium reactions during deoxidization of molten steel using aluminum and silicomanganese can be represented by equations 1 and 2

The Influence on Rural Communities of Interurban Transportation Systems. Appendix II, Exhibit 1 (CATS-RR-46)

More information about this work in the Center for Transportation Research Library catalog: https://library.ctr.utexas.edu/Presto/catalogid=32099"This memorandum is a by-product of the research effort currently being conducted under the topic, "The Influence of Interurban Transportation Systems on the Rural Environment." The first aim of the research is to produce two planning manuals, one for the use of the professional, the other for the lay person in small urban and rural communities. In order to develop these two documents, the research effort has been divided into several subareas, specifically including: planning resources and policies pertaining to rural areas and small communities; the growth potential of small communities in a regional context; the social and economic variables most relevant to interurban, transportation planning; and the techniques currently used in the various stages of the planning process, including techniques for citizen participation. The bibliography contained in this memorandum is a selected and annotated list of works reviewed by various members of the research team in the course of their separate investigations. It is divided into five sections, which reflect the areas of greatest relevance to the final planning documents. These are: I. Planning and Policy; II. Transportation and Regional Growth; III. Socio-Economic Variables in Transportation Planning; IV. Evaluation Techniques and Models; and V. Citizen Participation. The books and articles included do not constitute an exhaustive list, but rather a selected group representative of the diversity and of the state of the art in these five areas. These works were dealt with in some detail during the course of the research; it is hoped that the comments on each will be of use in guiding other researchers to works appropriate to their particular concerns." --IntroductionDepartment of Transportation Office of University Research (Washington D.C.)Center for Transportation ResearchSee this work in the Center for Transportation Research Library catalog