The corporate literature on reengineering has much to offer academic libraries. This article describes how reengineering can be applied in library settings, trends affecting library user services ...operations, and the reengineering effort that is ongoing at Rice University where user services operations have been transformed through collaborative reengineering efforts between the library and computing.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The graduation rates of 1,642 M student athletes at Michigan State U during a 25-year period are compared by sport, decade of matriculation, race, & athletic success. The data, collected by ...unobtrusive means from various U records & files, also are examined against comparable national data for student athletes, & against comparable data for the general student population at Michigan State U. All M athletes (letter-winners or not) who played football, basketball, baseball, or hockey are included. The results support the position that intercollegiate athletics has a positive influence on the educational attainment of participating athletes, since the graduation rates for athletes were found to be higher than or comparable to those of the general student population. However, across all sports, black athletes were found to have higher attrition & lower graduation rates than their white counterparts. 3 Tables, 4 References. Modified AA.
Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is ...exacerbated by the exclusion of codon-based models from commonly employed model selection techniques, presumably due to the computational cost associated with codon models. We investigated an efficient alternative to standard nucleotide substitution models, in which codon position (CP) is incorporated into the model. We determined the most appropriate model for alignments of 177 RNA virus genes and 106 yeast genes, using 11 substitution models including one codon model and four CP models. The majority of analyzed gene alignments are best described by CP substitution models, rather than by standard nucleotide models, and without the computational cost of full codon models. These results have significant implications for phylogenetic inference of coding sequences as they make it clear that substitution models incorporating CPs not only are a computationally realistic alternative to standard models but may also frequently be statistically superior.
Abstract
It is regarded as best practice in phylogenetic reconstruction to perform relative model selection to determine an appropriate evolutionary model for the data. This procedure ranks a set of ...candidate models according to their goodness of fit to the data, commonly using an information theoretic criterion. Users then specify the best-ranking model for inference. Although it is often assumed that better-fitting models translate to increase accuracy, recent studies have shown that the specific model employed may not substantially affect inferences. We examine whether there is a systematic relationship between relative model fit and topological inference accuracy in protein phylogenetics, using simulations and real sequences. Simulations employed site-heterogeneous mechanistic codon models that are distinct from protein-level phylogenetic inference models, allowing us to investigate how protein models performs when they are misspecified to the data, as will be the case for any real sequence analysis. We broadly find that phylogenies inferred across models with vastly different fits to the data produce highly consistent topologies. We additionally find that all models infer similar proportions of false-positive splits, raising the possibility that all available models of protein evolution are similarly misspecified. Moreover, we find that the parameter-rich GTR (general time reversible) model, whose amino acid exchangeabilities are free parameters, performs similarly to models with fixed exchangeabilities, although the inference precision associated with GTR models was not examined. We conclude that, although relative model selection may not hinder phylogenetic analysis on protein data, it may not offer specific predictable improvements and is not a reliable proxy for accuracy.
Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the ...genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming.
Here we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5 h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding.
SRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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