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Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146328/1/hep30137_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146328/2/hep30137.pd

Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed

Update on Prevention, Diagnosis, and Treatment of Chronic Hepatitis B: AASLD 2018 Hepatitis B Guidance

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/145507/1/cld728.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/145507/2/cld728_am.pd

Survival and hepatitis status among Asian Americans with hepatocellular carcinoma treated without liver transplantation

<p>Abstract</p> <p>Background</p> <p>Chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) are established causes of HCC. HCC patients are often diagnosed late and receive palliative therapies, however, the survival of Asian American patients with HCC treated without transplantation has not been well studied. We reviewed our institution's experience to determine predictors and rates of survival in Asian American HCC patients treated without transplantation.</p> <p>Methods</p> <p>We identified Asian American patients with HCC referred to M. D. Anderson Cancer Center. Patients were tested for HBV and HCV. Survival curves were generated by Kaplan-Meier method. Multivariate Cox proportional hazards regression was used to test the relationship between prognostic factors and survival.</p> <p>Results</p> <p>Of 82 Asian American HCC patients, most had advanced disease (65%) and received treatment (68%); however, only 11% had surgical resection. 94% had positive anti-HBc and 61% had positive HBsAg. 20% had positive anti-HCV. There were no significant changes in the rates of HBV and HCV over time. Male gender, high alpha-fetoprotein levels, and stage IV disease were associated with shorter survival Overall median survival was 9.2 months (95% CI 6.5–11.9), and the survival of HCV and HBV patients was not statistically different.</p> <p>Conclusion</p> <p>The survival rate of Asian American patients with advanced HCC, for whom transplantation was not available, was low. Timely hepatitis screening and interventions by primary care physicians may be the most logical solution to reduce the burden of hepatitis-associated HCC among Asian Americans.</p

Impact of the timing of hepatitis B virus identification and antiâ hepatitis B virus therapy initiation on the risk of adverse liver outcomes for patients receiving cancer therapy

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138209/1/cncr30729_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138209/2/cncr30729.pd

Symmetry Breaking in Few Layer Graphene Films

Recently, it was demonstrated that the quasiparticle dynamics, the layer-dependent charge and potential, and the c-axis screening coefficient could be extracted from measurements of the spectral function of few layer graphene films grown epitaxially on SiC using angle-resolved photoemission spectroscopy (ARPES). In this article we review these findings, and present detailed methodology for extracting such parameters from ARPES. We also present detailed arguments against the possibility of an energy gap at the Dirac crossing ED.Comment: 23 pages, 13 figures, Conference Proceedings of DPG Meeting Mar 2007 Regensburg Submitted to New Journal of Physic

Software Citation Checklist for Developers

This document provides a minimal, generic checklist that developers of software (either open or closed source) used in research can use to ensure they are following good practice around software citation. This will help developers get credit for the software they create, and improve transparency, reproducibility, and reuse

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles

Abstract: Background: Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night. Results: Here, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identify common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems, such as loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems that are convergent with other nocturnal avian orders. Additionally, we find that a suite of genes associated with vision and circadian rhythm are differentially expressed in blood tissue between nocturnal and diurnal raptors, possibly indicating adaptive expression change during the transition to nocturnality. Conclusions: Overall, raptor genomes show genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators