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The Wednesday wars
During the 1967 school year, on Wednesday afternoons when all his classmates go to either Catechism or Hebrew school, seventh-grader Holling Hoodhood stays in Mrs. Baker's classroom where they read the plays of William Shakespeare and Holling learns much of value about the world in which he lives.
Book
Gut microbiota and IBD: causation or correlation?
Key Points
Alterations in intestinal microbial composition have long been associated with chronic inflammation; however, a definitive cause–effect relationship between dysbiosis and IBD has been difficult to prove, especially in humans
Dysbiosis alters not only the composition of the intestinal microbiota, but also its metabolome, thereby exerting a wide range of effects on the host
While the microbiota plays a key pathogenic role in IBD, chronic inflammation, in turn, promotes dysbiosis by altering the oxidative and metabolic environment of the gut
Animal studies have elucidated key immunological pathways in the pathogenesis of IBD, established both pro-inflammatory and anti-inflammatory roles of the gut microbiota, and shown that the gut microbiota is indispensable for pathogenesis in most colitis models
Microbial-based treatments will likely have a role in the future management of IBD; however, many questions remain regarding the bacterial composition, timing of administration, and patient selection for such therapies
Changes in the composition and metabolic function of the gut microbiota have been linked to IBD, but a direct causal association has yet to be established in humans. This Review discusses the evidence supporting dysbiosis in the gut microbiota in Crohn's disease and ulcerative colitis, exploring evidence from animal models and the translation to human disease.
A general consensus exists that IBD is associated with compositional and metabolic changes in the intestinal microbiota (dysbiosis). However, a direct causal relationship between dysbiosis and IBD has not been definitively established in humans. Findings from animal models have revealed diverse and context-specific roles of the gut microbiota in health and disease, ranging from protective to pro-inflammatory actions. Moreover, evidence from these experimental models suggest that although gut bacteria often drive immune activation, chronic inflammation in turn shapes the gut microbiota and contributes to dysbiosis. The purpose of this Review is to summarize current associations between IBD and dysbiosis, describe the role of the gut microbiota in the context of specific animal models of colitis, and discuss the potential role of microbiota-focused interventions in the treatment of human IBD. Ultimately, more studies will be needed to define host–microbial relationships relevant to human disease and amenable to therapeutic interventions.
Journal Article
Okay for now
As a fourteen-year-old who just moved to a new town, with no friends, an abusive father, and a louse for an older brother, Doug Swieteck has all the stats stacked against him until he finds an ally in Lil Spicer, a fiery young lady. Together, they find a safe haven in the local library, inspiration in learning about the plates of John James Audubon's birds, and a hilarious adventure on a Broadway stage.
Book
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Gene-set enrichment analysis is a useful technique to help functionally characterize large gene lists, such as the results of gene expression experiments. This technique finds functionally coherent gene-sets, such as pathways, that are statistically over-represented in a given gene list. Ideally, the number of resulting sets is smaller than the number of genes in the list, thus simplifying interpretation. However, the increasing number and redundancy of gene-sets used by many current enrichment analysis software works against this ideal.
To overcome gene-set redundancy and help in the interpretation of large gene lists, we developed \"Enrichment Map\", a network-based visualization method for gene-set enrichment results. Gene-sets are organized in a network, where each set is a node and edges represent gene overlap between sets. Automated network layout groups related gene-sets into network clusters, enabling the user to quickly identify the major enriched functional themes and more easily interpret the enrichment results.
Enrichment Map is a significant advance in the interpretation of enrichment analysis. Any research project that generates a list of genes can take advantage of this visualization framework. Enrichment Map is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software (http://baderlab.org/Software/EnrichmentMap/).
Journal Article
Practices and Applications of Convolutional Neural Network-Based Computer Vision Systems in Animal Farming: A Review
Convolutional neural network (CNN)-based computer vision systems have been increasingly applied in animal farming to improve animal management, but current knowledge, practices, limitations, and solutions of the applications remain to be expanded and explored. The objective of this study is to systematically review applications of CNN-based computer vision systems on animal farming in terms of the five deep learning computer vision tasks: image classification, object detection, semantic/instance segmentation, pose estimation, and tracking. Cattle, sheep/goats, pigs, and poultry were the major farm animal species of concern. In this research, preparations for system development, including camera settings, inclusion of variations for data recordings, choices of graphics processing units, image preprocessing, and data labeling were summarized. CNN architectures were reviewed based on the computer vision tasks in animal farming. Strategies of algorithm development included distribution of development data, data augmentation, hyperparameter tuning, and selection of evaluation metrics. Judgment of model performance and performance based on architectures were discussed. Besides practices in optimizing CNN-based computer vision systems, system applications were also organized based on year, country, animal species, and purposes. Finally, recommendations on future research were provided to develop and improve CNN-based computer vision systems for improved welfare, environment, engineering, genetics, and management of farm animals.
Journal Article
Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data
Single-cell RNA sequencing (scRNA-seq) can map cell types, states and transitions during dynamic biological processes such as tissue development and regeneration. Many trajectory inference methods have been developed to order cells by their progression through a dynamic process. However, when time series data is available, most of these methods do not consider the available time information when ordering cells and are instead designed to work only on a single scRNA-seq data snapshot. We present Tempora, a novel cell trajectory inference method that orders cells using time information from time-series scRNA-seq data. In performance comparison tests, Tempora inferred known developmental lineages from three diverse tissue development time series data sets, beating state of the art methods in accuracy and speed. Tempora works at the level of cell clusters (types) and uses biological pathway information to help identify cell type relationships. This approach increases gene expression signal from single cells, processing speed, and interpretability of the inferred trajectory. Our results demonstrate the utility of a combination of time and pathway information to supervise trajectory inference for scRNA-seq based analysis.
Journal Article
The Oxford Gothic grammar
This volume provides a comprehensive reference grammar of Gothic, the earliest attested language of the Germanic family (apart from runic inscriptions), dating to the fourth century. The bulk of the extant Gothic corpus is a translation of the Bible, of which only a portion remains, and which has been the focus of most previous works. This book is the first in English to also draw on the recently discovered Bologna fragment and Crimean graffiti, original Gothic texts that provide more insights into the language. Following an overview of the history of the Goths and the origin of the Gothic language, Gary Miller explores all the major topics in Gothic grammar, beginning with the alphabet and phonology, and proceeding through subjects such as case functions, prepositions and particles, compounding, derivation, and verbal and sentential syntax. He also presents a selection of Gothic texts with notes and vocabulary, and ends with a chapter on linearization, including an overview of Gothic in its Germanic context. The Oxford Gothic Grammar will be an invaluable reference for all Indo-Europeanists, Germanic scholars, and historical linguists, from advanced undergraduate level upwards.
Book
Rapid evolution of the human gut virome
Humans are colonized by immense populations of viruses, which metagenomic analysis shows are mostly unique to each individual. To investigate the origin and evolution of the human gut virome, we analyzed the viral community of one adult individual over 2.5 y by extremely deep metagenomic sequencing (56 billion bases of purified viral sequence from 24 longitudinal fecal samples). After assembly, 478 well-determined contigs could be identified, which are inferred to correspond mostly to previously unstudied bacteriophage genomes. Fully 80% of these types persisted throughout the duration of the 2.5-y study, indicating long-term global stability. Mechanisms of base substitution, rates of accumulation, and the amount of variation varied among viral types. Temperate phages showed relatively lower mutation rates, consistent with replication by accurate bacterial DNA polymerases in the integrated prophage state. In contrast, Microviridae, which are lytic bacteriophages with single-stranded circular DNA genomes, showed high substitution rates (>10 ⁻⁵ per nucleotide each day), so that sequence divergence over the 2.5-y period studied approached values sufficient to distinguish new viral species. Longitudinal changes also were associated with diversity-generating retroelements and virus-encoded Clustered Regularly Interspaced Short Palindromic Repeats arrays. We infer that the extreme interpersonal diversity of human gut viruses derives from two sources, persistence of a small portion of the global virome within the gut of each individual and rapid evolution of some long-term virome members.
Journal Article