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Wicked Cool Perl Scripts
Most Perl programmers have been frustrated at one time or another because the system just wouldn't do what they wanted it to do. There was that one simple and obvious utility that was missing that would make life so much easier: A tool to get a stock quote, show off a photograph collection, or even display a collection of favorite comics. Wicked Cool Perl Scripts is about writing those utilities quickly and easily. A collection of handy utilities that solves difficult problems, Wicked Cool Perl Scripts is a great resource for the savvy Perl programmer.
eBook
Application of clearance strategies for extractables and leachables and advances in process modeling
Single-use devices made from plastic materials and used in the manufacturing of pharmaceutical products were identified as sources of extractables and potentially process equipment-related leachables (PERLs), which may interfere with process performance and product quality. In this contribution, the sinks of PERLs in biopharmaceutical processes are explored and the underlying physical-chemical mechanisms are discussed. This includes an overview of studies on leachable clearance with ultrafiltration/diafiltration operations (UF/DF) and chromatographic steps, filter rinsing, and adsorption. Literature reveals that dilution and phase separation are the main drivers for reducing PERL exposure along a process. Integrating extractables release and established physical processes of dynamic dilution and phase separation allows to set up and populate mathematical models which can predict the fate of PERLs in batch and continuous bioprocessing. Integrating the fate of PERLs improves process understanding, supports process qualification studies, and, ultimately, strengthens the patient safety assessment.
Key points
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It is possible to demonstrate that biopharmaceutical processes can significantly reduce PERLs
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Various process operation steps are identified as sinks for PERLs, and the fate of PERLs is predictable with simple mathematical models
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Using PERL exposure models improves process understanding and enhances the safety assessments for single-use devices used in bioprocessing
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Journal Article
The Beginnings of Modern Jewish Literature
This short article introduces this special issue of Prooftexts, The Beginnings of Modern Jewish Literature in Europe. It is divided into two parts. The first part historicizes and analyzes the debate about when modern Jewish Literature began, focusing on the major literary historiographies of the twentieth century (Klausner, Lachower, Slouschz, Weinreich, and Zinberg). The second connects this debate to the scholarship of the contributors to this volume and provides a short summary of the content of their articles.
Journal Article
ENMTools 1.0: an R package for comparative ecological biogeography
The ENMTools software package was introduced in 2008 as a platform for making measurements on environmental niche models (ENMs, frequently referred to as species distribution models or SDMs), and for using those measurements in the context of newly developed Monte Carlo tests to evaluate hypotheses regarding niche evolution. Additional functionality was later added for model selection and simulation from ENMs, and the software package has been quite widely used. ENMTools was initially implemented as a Perl script, which was also compiled into an executable file for various platforms. However, the package had a number of significant limitations; it was only designed to fit models using Maxent, it relied on a specific Perl distribution to function, and its internal structure made it difficult to maintain and expand. Subsequently, the R programming language became the platform of choice for most ENM studies, making ENMTools less usable for many practitioners. Here we introduce a new R version of ENMTools that implements much of the functionality of its predecessor as well as numerous additions that simplify the construction, comparison and evaluation of niche models. These additions include new metrics for model fit, methods of measuring ENM overlap, and methods for testing evolutionary hypotheses. The new version of ENMTools is also designed to work within the expanding universe of R tools for ecological biogeography, and as such includes greatly simplified interfaces for analyses from several other R packages.
Journal Article
Current Approaches to Tactical Performance Analyses in Soccer Using Position Data
Tactical match performance depends on the quality of actions of individual players or teams in space and time during match-play in order to be successful. Technological innovations have led to new possibilities to capture accurate spatio-temporal information of all players and unravel the dynamics and complexity of soccer matches. The main aim of this article is to give an overview of the current state of development of the analysis of position data in soccer. Based on the same single set of position data of a high-level 11 versus 11 match (Bayern Munich against FC Barcelona) three different promising approaches from the perspective of dynamic systems and neural networks will be presented: Tactical performance analysis revealed inter-player coordination, inter-team and inter-line coordination before critical events, as well as team-team interaction and compactness coefficients. This could lead to a multi-disciplinary discussion on match analyses in sport science and new avenues for theoretical and practical implications in soccer.
Journal Article
MUMmer4: A fast and versatile genome alignment system
The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major release of MUMmer version 3 in 2004, it has been applied to many types of problems including aligning whole genome sequences, aligning reads to a reference genome, and comparing different assemblies of the same genome. Despite its broad utility, MUMmer3 has limitations that can make it difficult to use for large genomes and for the very large sequence data sets that are common today. In this paper we describe MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query sequences. With a theoretical limit on the input size of 141Tbp, MUMmer4 can now work with input sequences of any biologically realistic length. We show that as a result of these enhancements, the nucmer program in MUMmer4 is easily able to handle alignments of large genomes; we illustrate this with an alignment of the human and chimpanzee genomes, which allows us to compute that the two species are 98% identical across 96% of their length. With the enhancements described here, MUMmer4 can also be used to efficiently align reads to reference genomes, although it is less sensitive and accurate than the dedicated read aligners. The nucmer aligner in MUMmer4 can now be called from scripting languages such as Perl, Python and Ruby. These improvements make MUMer4 one the most versatile genome alignment packages available.
Journal Article