Evolutionary distance estimation and fidelity of pair wise sequence alignment

BACKGROUND: Evolutionary distances are a critical measure in comparative genomics and molecular evolutionary biology. A simulation study was used to examine the effect of alignment accuracy of DNA sequences on evolutionary distance estimation. RESULTS: Under the studied conditions, distance estimation was relatively unaffected by alignment error (50% or more of the sites incorrectly aligned) as long as 50% or more of the sites were identical among the sequences (observed P-distance < 0.5). Beyond this threshold, the alignment procedure artificially inflates the apparent sequence identity, skewing distance estimates, and creating alignments that are essentially indistinguishable from random data. This general result was independent of substitution model, sequence length, and insertion and deletion size and rate. CONCLUSION: Examination of the estimated sequence identity may yield some guidance as to the accuracy of the alignment. Inaccurate alignments are expected to have large effects on analyses dependent on site specificity, but analyses that depend on evolutionary distance may be somewhat robust to alignment error as long as fewer than half of the sites have diverged

Doxycycline or Ofloxacin for Outpatient Chlamydial Pelvic Inflammatory Disease? A Cost-Benefit and Cost-Effectiveness Analysis

Objective: The current Centers for Disease Control and Prevention (CDC) guidelines include 2 drugs, doxycycline and ofloxacin, for treatment of the chlamydial component of outpatient pelvic inflammatory disease (PID). Although ofloxacin costs about $90 more than doxycycline, doxycycline is frequently associated with side effects and patient compliance with this drug is probably poor. Because clinicians have little information by which to judge the tradeoffs between price and compliance for these 2 antibiotics, we examined the impact of patient compliance in the evaluation of the costs and benefits of using each drug

Addressing Teacher Shortages in the COVID-19 Landscape: Viewing Teacher Candidates as Assets

COVID-19 continues to impose dire consequences on all sectors of our public education system. Many students, particularly those from vulnerable populations, are receiving reduced amounts of direct instruction and are experiencing significant losses in learning. At the same time, educator preparation programs (EPPs) are struggling to ensure that teacher candidates have ample opportunities to apply their newly acquired pedagogical skills in high quality clinical placements. In this article we describe and provide exemplars as to how teacher candidates can serve as assets to school districts as they complete their field placements. We also offer specific strategies and practices for EPPs and school districts to maximize the productive and efficient integration of teacher candidates in both virtual and in-person environments

Survey of the Federal Circuit\u27s Patent Law Decisions in 2006: A New Chapter in the Ongoing Dialogue with the Supreme Court

In 2006, the Federal Circuit decided only one portion of one patent case en banc, and that was done mainly as a procedural matter (the entire case was not argued to an en banc court) in order to reconcile prior conflicting precedent on the issue of induced patent infringement with the recent Supreme Court decision in Metro-Goldwyn-Mayer Studios, Inc. v. Grokster, Ltd., involving induced copyright infringement. But in light of the Supreme Court’s much more muscular review of the Federal Circuit’s patent cases—which may not even reflect the full extent of the Court’s interest in the Federal Circuit’s patent decisions—the relative paucity of en banc decisions in 2006 is understandable, and in many ways irrelevant to gaining a better understanding of the Federal Circuit’s patent law jurisprudence. In the pages that follow, we will address these and many other developments reflected in the Federal Circuit’s patent jurisprudence of 2006. And, as we did in our article surveying the Federal Circuit’s year 2000 jurisprudence, we again conclude with an addendum that discusses the statistical output of the Federal Circuit and its judges

Survey of the Federal Circuit\u27s Patent Law Decisions in 2006: A New Chapter in the Ongoing Dialogue with the Supreme Court

In 2006, the Federal Circuit decided only one portion of one patent case en banc, and that was done mainly as a procedural matter (the entire case was not argued to an en banc court) in order to reconcile prior conflicting precedent on the issue of induced patent infringement with the recent Supreme Court decision in Metro-Goldwyn-Mayer Studios, Inc. v. Grokster, Ltd., involving induced copyright infringement. But in light of the Supreme Court’s much more muscular review of the Federal Circuit’s patent cases—which may not even reflect the full extent of the Court’s interest in the Federal Circuit’s patent decisions—the relative paucity of en banc decisions in 2006 is understandable, and in many ways irrelevant to gaining a better understanding of the Federal Circuit’s patent law jurisprudence. In the pages that follow, we will address these and many other developments reflected in the Federal Circuit’s patent jurisprudence of 2006. And, as we did in our article surveying the Federal Circuit’s year 2000 jurisprudence, we again conclude with an addendum that discusses the statistical output of the Federal Circuit and its judges

An integrated sequence stratigraphic, palaeoenvironmental, and chronostratigraphic analysis of the Tangahoe Formation, southern Taranaki coast, with implications for mid-Pliocene (c. 3.4–3.0 Ma) glacio-eustatic sea-level changes

Sediments of the mid-Pliocene (c. 3.4–3.0 Ma) Tangahoe Formation exposed in cliffs along the South Taranaki coastline of New Zealand comprise a 270 m thick, cyclothemic shallow-marine succession that has been gently warped into a north to south trending, low angle anticline. This study examines the sedimentologic, faunal, and petrographic characteristics of 10 Milankovitch-scale (6th order), shallow-marine depositional sequences exposed on the western limb of the anticline. The sequences are recognised on the basis of the cyclic vertical stacking of their constituent lithofacies, which are bound by sharp wave cut surfaces produced during transgressive shoreface erosion. Each sequence comprises three parts: (1) a 0.2–2 m thick, deepening upwards, basal suite of reworked bioclastic lag deposits (onlap shellbed) and/or an overlying matrix supported, molluscan shellbed of offshore shelf affinity (backlap shellbed); (2) a 5–20 m thick, gradually shoaling, aggradational siltstone succession; and (3) a 5–10 m thick, strongly progradational, well sorted “forced regressive” shoreline sandstone. The three-fold subdivision corresponds to transgressive, highstand, and regressive systems tracts (TSTs, HSTs, and RSTs) respectively, and represents deposition during a glacio-eustatic sea-level cycle. Lowstand systems tract sediments are not recorded because the outcrop is situated c. 100 km east of the contemporary shelf edge and was subaerially exposed at that time. Well developed, sharp- and gradational-based forced regressive sandstones contain a variety of storm-emplaced sedimentary structures, and represent the rapid and abrupt basinward translation of the shoreline on to a storm dominated, shallow shelf during eustatic sea-level fall. Increased supply of sediment from north-west South Island during “forced regression” is indicated from petrographic analyses of the heavy mineralogy of the sandstones. A chronology based on biostratigraphy and the correlation of a new magnetostratigraphy to the magnetic polarity timescale allows: (1) identification of the Mammoth (C2An.2r) and Kaena (C2An.1r) subchrons; (2) correlation of the coastal section to the Waipipian Stage; and (3) estimation of the age of the coastal section as 3.36–3.06 Ma. Qualitative assessment of foraminiferal census data and molluscan palaeoecology reveals cyclic changes in water depth from shelf to shoreline environments during the deposition of each sequence. Seven major cycles in water depth of between 20 and 50m have been correlated to individual 40 ka glacio-eustatic sea-level cycles on the marine oxygen isotope timescale. The coastal Tangahoe Formation provides a shallow-marine record of global glacio-eustasy prior to the development of significant ice sheets on Northern Hemisphere continents, and supports evidence from marine δ18O archives that changes in Antarctic ice volume were occurring during the Pliocene

Enhancing Classroom Management Skills: Efficacy of a Supplemental Multi-Platform Intervention for Preservice Teachers

Many teachers are ill-prepared to apply practices that can both preempt and address challenging behaviors that interfere with academic instruction. We evaluated the efficacy of a supplemental multi-platform (direct instruction, guided practice, and mixed reality simulations) intervention designed for preservice teachers who do not have opportunities to participate in formal classroom management courses. Efficacy of the intervention was assessed through the quality of classroom management plans, the presentation and implementation of the plan in the virtual classroom, and classroom management self-efficacy. Results indicated that preservice teachers successfully developed quality proactive classroom management plans but struggled to present and implement their plans. However, self-efficacy increased indicating that participants believed they were better able to manage classroom behavior than they did prior to the intervention. Implications of these outcomes are discussed with an emphasis on how adequate opportunities to practice acquired classroom management skills are included in budget-challenged teacher preparation programs

Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia

Homologous meiotic recombination occurs in most sexually reproducing organisms, yet its evolutionary advantages are elusive. Previous research explored recombination in the honeybee, a eusocial hymenopteran with an exceptionally high genome-wide recombination rate. A comparable study in a non-social member of the Hymenoptera that would disentangle the impact of sociality from Hymenoptera-specific features such as haplodiploidy on the evolution of the high genome-wide recombination rate in social Hymenoptera is missing. Utilizing single-nucleotide polymorphisms (SNPs) between two Nasonia parasitoid wasp genomes, we developed a SNP genotyping microarray to infer a high-density linkage map for Nasonia. The map comprises 1,255 markers with an average distance of 0.3 cM. The mapped markers enabled us to arrange 265 scaffolds of the Nasonia genome assembly 1.0 on the linkage map, representing 63.6% of the assembled N. vitripennis genome. We estimated a genome-wide recombination rate of 1.4-1.5 cM/Mb for Nasonia, which is less than one tenth of the rate reported for the honeybee. The local recombination rate in Nasonia is positively correlated with the distance to the center of the linkage groups, GC content, and the proportion of simple repeats. In contrast to the honeybee genome, gene density in the parasitoid wasp genome is positively associated with the recombination rate; regions of low recombination are characterized by fewer genes with larger introns and by a greater distance between genes. Finally, we found that genes in regions of the genome with a low recombination frequency tend to have a higher ratio of non-synonymous to synonymous substitutions, likely due to the accumulation of slightly deleterious non-synonymous substitutions. These findings are consistent with the hypothesis that recombination reduces interference between linked sites and thereby facilitates adaptive evolution and the purging of deleterious mutations. Our results imply that the genomes of haplodiploid and of diploid higher eukaryotes do not differ systematically in their recombination rates and associated parameters.Publisher PDFPeer reviewe

Imaging Active Infection in vivo Using D-Amino Acid Derived PET Radiotracers.

Occult bacterial infections represent a worldwide health problem. Differentiating active bacterial infection from sterile inflammation can be difficult using current imaging tools. Present clinically viable methodologies either detect morphologic changes (CT/ MR), recruitment of immune cells (111In-WBC SPECT), or enhanced glycolytic flux seen in inflammatory cells (18F-FDG PET). However, these strategies are often inadequate to detect bacterial infection and are not specific for living bacteria. Recent approaches have taken advantage of key metabolic differences between prokaryotic and eukaryotic organisms, allowing easier distinction between bacteria and their host. In this report, we exploited one key difference, bacterial cell wall biosynthesis, to detect living bacteria using a positron-labeled D-amino acid. After screening several 14C D-amino acids for their incorporation into E. coli in culture, we identified D-methionine as a probe with outstanding radiopharmaceutical potential. Based on an analogous procedure to that used for L-[methyl-11C]methionine ([11C] L-Met), we developed an enhanced asymmetric synthesis of D-[methyl-11C]methionine ([11C] D-Met), and showed that it can rapidly and selectively differentiate both E. coli and S. aureus infections from sterile inflammation in vivo. We believe that the ease of [11C] D-Met radiosynthesis, coupled with its rapid and specific in vivo bacterial accumulation, make it an attractive radiotracer for infection imaging in clinical practice