Using landscape history to predict biodiversity patterns in fragmented landscapes

Landscape ecology plays a vital role in understanding the impacts of land-use change on biodiversity, but it is not a predictive discipline, lacking theoretical models that quantitatively predict biodiversity patterns from first principles. Here, we draw heavily on ideas from phylogenetics to fill this gap, basing our approach on the insight that habitat fragments have a shared history. We develop a landscape ‘terrageny’, which represents the historical spatial separation of habitat fragments in the same way that a phylogeny represents evolutionary divergence among species. Combining a random sampling model with a terrageny generates numerical predictions about the expected proportion of species shared between any two fragments, the locations of locally endemic species, and the number of species that have been driven locally extinct. The model predicts that community similarity declines with terragenetic distance, and that local endemics are more likely to be found in terragenetically distinctive fragments than in large fragments. We derive equations to quantify the variance around predictions, and show that ignoring the spatial structure of fragmented landscapes leads to over-estimates of local extinction rates at the landscape scale. We argue that ignoring the shared history of habitat fragments limits our ability to understand biodiversity changes in human-modified landscape

The Lantern, 2012-2013

• How They Run • What Was Said in Boston • On the Last Day of the Month • An Angel Tries to Surprise Humans • I Wonder if God Modeled Boys After Books • Marred with Modern Scars • Feather Bed • Ode to a Pen • Objet Petit A • Breaking News: Grownups Fear Return of Disco • Neuroscience • New Document • We Were Stars, and the Sky was Our Grass • About a Man • Trojan • An Ode • Yr Body Sour • That Lake in Jamaica • Live While Chiefs are Still Fighting • Lament for Mathematics • The Robert Frost House • People Fell in Love on Me • Sunday Review • Looks Silly in Tiny Desk Chairs • Two Years Later • Better Than Nothing • Istanbul • Packs of Cigarettes • Sonnet • Outside King of Steaks • Obstinance • Coffee Grinds • Autumn Equinox • Homecoming • Oh, San Francisco • Slide: A Beginning • Slowly Last Summer • Of Dogs and Men • Letters Not Sent • Before the Race • The Little Things • Tarpon Springs • Payment for Rebellion • Wednesday • When is President\u27s Day? • Heartless Parallels and Perpendiculars • Railway • Presto Agitato • Easier Said Than Done • Waves • Four White Women • Rope • Alter Ego Self Portrait • Pebbles • Coney Island • Guanjuanto • Growth • Evolve • Winter Blackout • Honeybee • Frames • Wanderlust • Guiding Light 1 • Frick\u27s Lock • The Ones That Never Leave • In Memoriam: Rachel Blunthttps://digitalcommons.ursinus.edu/lantern/1179/thumbnail.jp

De-Novo Transcriptome Sequencing of a Normalized cDNA Pool from Influenza Infected Ferrets

The ferret is commonly used as a model for studies of infectious diseases. The genomic sequence of this animal model is not yet characterized, and only a limited number of fully annotated cDNAs are currently available in GenBank. The majority of genes involved in innate or adaptive immune response are still lacking, restricting molecular genetic analysis of host response in the ferret model. To enable de novo identification of transcriptionally active ferret genes in response to infection, we performed de-novo transcriptome sequencing of animals infected with H1N1 A/California/07/2009. We also included splenocytes induced with bacterial lipopolysaccharide to allow for identification of transcripts specifically induced by Gram-negative bacteria. We pooled and normalized the cDNA library in order to delimit the risk of sequencing only highly expressed genes. While normalization of the cDNA library removes the possibility of assessing expression changes between individual animals, it has been shown to increase identification of low abundant transcripts. In this study, we identified more than 19000 partial ferret transcripts, including more than 1000 gene orthologs known to be involved in the innate and the adaptive immune response

Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection

Although scarce after annual influenza vaccination, B cells producing antibodies capable of neutralizing multiple influenza strains are abundant in humans infected with pandemic 2009 H1N1 influenza

Panel of Prototypical Raltegravir-Resistant Infectious Molecular Clones in a Novel Integrase-Deleted Cloning Vector▿

We created an HIV-1 cloning vector, pNL4.3ΔIN, to generate recombinant infectious molecular clones for analysis of patient-derived HIV-1 integrase coding regions. Using this vector, we constructed a panel of clinically derived viruses with the canonical patterns of raltegravir resistance mutations and submitted the panel to the NIH AIDS Research and Reference Reagent Program. Investigational integrase inhibitors with activity against these clones are likely to retain activity against the most clinically relevant raltegravir-resistant variants

Exposure therapy for OCD from an acceptance and commitment therapy (ACT) framework

This article addresses the use of exposure therapy for OCD as informed by an acceptance and commitment therapy (ACT) framework. The model on which ACT is based is covered, including its philosophy, basic research, targeted process of change, individual treatment components, and general manual. Specific suggestions for how to prepare, select, set up, and conclude exposure exercises from an ACT perspective are included and illustrated using the case of Monica as an example. Empirical support for this approach is briefly covered

Adding Acceptance and Commitment Therapy to Exposure and Response Prevention for Obsessive-Compulsive Disorder: A Randomized Controlled Trial

The objective of this study was to test whether treatment acceptability, exposure engagement, and completion rates could be increased by integrating acceptance and commitment therapy (ACT) with traditional exposure and response prevention (ERP). 58 adults (68% female) diagnosed with obsessive-compulsive disorder (OCD; M age = 27, 80% white) engaged in a multisite randomized controlled trial of 16 individual twice-weekly sessions of either ERP or ACT + ERP. Assessors unaware of treatment condition administered assessments of OCD, depression, psychological flexibility, and obsessional beliefs at pretreatment, posttreatment, and six-month follow-up. Treatment acceptability, credibility/expectancy, and exposure engagement were also assessed. Exposure engagement was high in both conditions and there were no significant differences in exposure engagement, treatment acceptability, or dropout rates between ACT + ERP and ERP. OCD symptoms, depression, psychological flexibility, and obsessional beliefs decreased significantly at posttreatment and were maintained at follow-up in both conditions. No between-group differences in outcome were observed using intent to treat and predicted data from multilevel modeling. ACT + ERP and ERP were both highly effective treatments for OCD, and no differences were found in outcomes, processes of change, acceptability, or exposure engagement