Statics and dynamics of single DNA molecules confined in nanochannels

The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics

Climate geoengineering: issues of path-dependence and socio-technical lock-in

As academic and policy interest in climate geoengineering grows, the potential irreversibility of technological developments in this domain has been raised as a pressing concern. The literature on socio-technical lock-in and path dependence is illuminating in helping to situate current concerns about climate geoengineering and irreversibility in the context of academic understandings of historical socio-technical development and persistence. This literature provides a wealth of material illustrating the pervasiveness of positive feedbacks of various types (from the discursive to the material) leading to complex socio-technical entanglements which may resist change and become inflexible even in the light of evidence of negative impacts. With regard to climate geoengineering, there are concerns that geoengineering technologies might contribute so-called ‘carbon lock-in’, or become irreversibly ‘locked-in’ themselves. In particular, the scale of infrastructures that geoengineering interventions would require, and the issue of the so-called ‘termination effect’ have been discussed in these terms. Despite the emergent and somewhat ill-defined nature of the field, some authors also suggest that the extant framings of geoengineering in academic and policy literatures may already demonstrate features recognizable as forms of cognitive lock-in, likely to have profound implications for future developments in this area. While the concepts of path-dependence and lock-in are the subject of ongoing academic critique, by drawing analytical attention to these pervasive processes of positive feedback and entanglement, this literature is highly relevant to current debates around geoengineering

Evaluating the effects of increasing physical activity to optimize rehabilitation outcomes in hospitalized older adults (MOVE Trial): Study protocol for a randomized controlled trial

Background: Older adults who have received inpatient rehabilitation often have significant mobility disability at discharge. Physical activity levels in rehabilitation are also low. It is hypothesized that providing increased physical activity to older people receiving hospital-based rehabilitation will lead to better mobility outcomes at discharge. Methods/Design: A single blind, parallel-group, multisite randomized controlled trial with blinded assessment of outcome and intention-to-treat analysis. The cost effectiveness of the intervention will also be examined. Older people (age >60 years) undergoing inpatient rehabilitation to improve mobility will be recruited from geriatric rehabilitation units at two Australian hospitals. A computer-generated blocked stratified randomization sequence will be used to assign 198 participants in a 1:1 ratio to either an 'enhanced physical activity' (intervention) group or a 'usual care plus' (control) group for the duration of their inpatient stay. Participants will receive usual care and either spend time each week performing additional physical activities such as standing or walking (intervention group) or performing an equal amount of social activities that have minimal impact on mobility such as card and board games (control group). Self-selected gait speed will be measured using a 6-meter walk test at discharge (primary outcome) and 6 months follow-up (secondary outcome). The study is powered to detect a 0.1 m/sec increase in self-selected gait speed in the intervention group at discharge. Additional measures of mobility (Timed Up and Go, De Morton Mobility Index), function (Functional Independence Measure) and quality of life will be obtained as secondary outcomes at discharge and tertiary outcomes at 6 months follow-up. The trial commenced recruitment on 28 January 2014. Discussion: This study will evaluate the efficacy and cost effectiveness of increasing physical activity in older people during inpatient rehabilitation. These results will assist in the development of evidenced-based rehabilitation programs for this population. Trial registration: Australian New Zealand Clinical Trials Registry ACTRN12613000884707(Date of registration 08 August 2013); ClinicalTrials.gov Identifier NCT01910740(Date of registration 22 July 2013)

The Rule of Law is Dead! Long Live the Rule of Law!

Polls show that a significant proportion of the public considers judges to be political. This result holds whether Americans are asked about Supreme Court justices, federal judges, state judges, or judges in general. At the same time, a large majority of the public also believes that judges are fair and impartial arbiters, and this belief also applies across the board. In this paper, I consider what this half-law-half-politics understanding of the courts means for judicial legitimacy and the public confidence on which that legitimacy rests. Drawing on the Legal Realists, and particularly on the work of Thurman Arnold, I argue against the notion that the contradictory views must be resolved in order for judicial legitimacy to remain intact. A rule of law built on contending legal and political beliefs is not necessarily fair or just. But it can be stable. At least in the context of law and courts, a house divided may stand

Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion

Zinc-finger nucleases (ZFNs) have been successfully used for rational genome engineering in a variety of cell types and organisms. ZFNs consist of a non-specific FokI endonuclease domain and a specific zinc-finger DNA-binding domain. Because the catalytic domain must dimerize to become active, two ZFN subunits are typically assembled at the cleavage site. The generation of obligate heterodimeric ZFNs was shown to significantly reduce ZFN-associated cytotoxicity in single-site genome editing strategies. To further expand the application range of ZFNs, we employed a combination of in silico protein modeling, in vitro cleavage assays, and in vivo recombination assays to identify autonomous ZFN pairs that lack cross-reactivity between each other. In the context of ZFNs designed to recognize two adjacent sites in the human HOXB13 locus, we demonstrate that two autonomous ZFN pairs can be directed simultaneously to two different sites to induce a chromosomal deletion in ∼10% of alleles. Notably, the autonomous ZFN pair induced a targeted chromosomal deletion with the same efficacy as previously published obligate heterodimeric ZFNs but with significantly less toxicity. These results demonstrate that autonomous ZFNs will prove useful in targeted genome engineering approaches wherever an application requires the expression of two distinct ZFN pairs

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin