frailtypack: An R Package for the Analysis of Correlated Survival Data with Frailty Models Using Penalized Likelihood Estimation or Parametrical Estimation

Frailty models are very useful for analysing correlated survival data, when observations are clustered into groups or for recurrent events. The aim of this article is to present the new version of an R package called frailtypack. This package allows to fit Cox models and four types of frailty models (shared, nested, joint, additive) that could be useful for several issues within biomedical research. It is well adapted to the analysis of recurrent events such as cancer relapses and/or terminal events (death or lost to follow-up). The approach uses maximum penalized likelihood estimation. Right-censored or left-truncated data are considered. It also allows stratification and time-dependent covariates during analysis

Does the Locally-Adaptive Model of Archaeological Potential (LAMAP) work for hunter-gatherer sites? A test using data from the Tanana Valley, Alaska

We report an assessment of the ability of the Locally-Adaptive Model of Archaeological Potential (LAMAP) to estimate archaeological potential in relation to hunter-gatherer sites. The sample comprised 182 known sites in the Tanana Valley, Alaska, which was occupied solely by hunter-gatherers for about 14,500 years. To estimate archaeological potential, we employed physiographic variables such as elevation and slope, rather than variables that are known to vary on short time scales, like vegetation cover. Two tests of LAMAP were carried out. In the first, we used the location of a random selection of 90 sites from all time periods to create a LAMAP model. We then evaluated the model with the remaining 92 sites. In the second test, we built a LAMAP model from 12 sites that pre-date 10,000 cal BP. This model was then tested with sites that post-date 10,000 cal BP. In both analyses, areas predicted to have higher archaeological potential contained higher frequencies of validation sites. The performance of LAMAP in the two tests was comparable to its performance in previous tests using archaeological sites occupied by agricultural societies. Thus, the study extends the use of LAMAP to the task of estimating archaeological potential of landscapes in relation to hunter-gatherer sites

Exposing Pharmacy Students to Public Health Concepts through Volunteering in the Medical Reserve Corps

Pharmacy students at the University of Kansas School of Pharmacy’s regional campus were exposed to the Medical Reserve Corps (MRC), a volunteer-based network that organizes locally to improve the health and safety of their communities. The school partnered with the local Medical Reserve Corps to provide students’ opportunities to fulfill co-curricular requirements and facilitate an application-based learning environment for public health concepts. The objective of the study was to explore the relationship between volunteering in the MRC and pharmacy students’ ability to meet educational outcomes and reinforce beliefs about their profession’s role in public health. Twenty-one students completed a survey addressing their ability to meet educational outcomes and identify the role of pharmacists in public health. Pharmacy students strongly agreed their past participation (mean 4.57) and future volunteering (mean 4.48) within the MRC would continue to help them better understand their role in public health. Pharmacy students strongly agreed (means ranging from 4.43 to 4.71) that they were able to fulfill educational outcomes related to knowledge, skills, and attitudes pharmacy graduates should possess. The positive responses gathered warrants expanding the partnership to include more student healthcare disciplines as well as looking for further opportunities to engage students in public health initiatives. Pharmacy schools should look to adopt similar partnerships with MRC units

Seeps, springs and wetlands: San Juan Basin, Colorado. Social-ecological climate resilience project

Prepared for: North Centeral Climate Adaptation Science Center.Social-Ecological Climate Resilience Project, 2016.Includes bibliographical references

Social Ecological Climate Resilience Project - 2016

Prepared for: North Central Climate Science Center, Fort Collins, Colorado.February 2017.Includes bibliographical references.Climate change is already having impacts on nature, ecosystem services and people in southwestern Colorado and is likely to further alter our natural landscapes in the coming decades. Understanding the potential changes and developing adaptation strategies can help ensure that natural landscapes and human communities remain healthy in the face of a changing climate. An interdisciplinary team consisting of social, ecological and climate scientists developed an innovative climate planning framework and worked with the Social‐Ecological Climate Resilience Project (SECR) and other stakeholders in Colorado’s San Juan River watershed to develop adaptation strategies for two significant landscapes, pinyon juniper woodlands and seeps, springs, and wetland resources under three climate scenarios between 2035 and 2050. This report summarizes the planning framework and results for the pinyon‐juniper landscape (the seeps, springs and wetlands results will be provided separately). This framework can be utilized to develop strategies for other landscapes at local, state, and national scales. Diagrams, narrative scenarios, and maps that depict climate scenarios and the social‐ecological responses help us portray the climate impact in the face of an uncertain future. Interviews and focus group workshops with agency staff and stakeholders who are users of public lands identified several important opportunities to improve the adaptation planning process for developing strategies that meet both social and ecological needs. Planning techniques that include or directly relate to specific resources, such as water and forage, or to activities, such as recreation or grazing, provide avenues for engaging diverse stakeholders into the process. Utilizing the scenarios to understand the impacts to our social and ecological landscapes, three overarching landscape‐scale adaptation strategies were developed. Each of these strategies has a suite of potential actions required to reach a desired future condition. The three key strategies are: 1) identify and protect persistent ecosystems as refugia, 2) proactively manage for resilience, and 3) accept, assist, and allow for transformation in non‐climate refugia sites. If the framework and strategies from this project are adopted by the local community, including land managers, owners, and users, the climate change impacts can be reduced, allowing for a more sustainable human and natural landscape

Forming low-cost, high quality carbon tows for automotive application.

Carbon fiber reinforced composites are widely used in many industries due to their high performance. Its application in the aerospace industry has increased significantly, however, in mass produced automobile sector it is still limited. The current production of carbon fiber tow is slow and capital intensive. Thus, carbon manufactures produce higher tow counts to increase production rate to reduce its cost. In order to offset the higher cost of carbon fiber composite, an innovative and unique approach has been developed. The higher tow count carbon spools are split into smaller tow counts. Due to the delicate nature of carbon fiber, it is important to control the filamentation during that process. Different splitting process line strategies have been developed in this research work for understanding the process limitations and challenges involved. The process was made feasible for production by developing a fully automated process line with a laser feedback system. The system splits a 12K spool into two 6K tows. The quality of the 6K split tows has been determined statistically by recording real time data from the laser during the splitting process. It was demonstrated that the proposed process effectively controls filamentation and produces consistent tow quality.Company research funding by Bentley Motors Limite

New proaporphines from the bark of Phoebe scortechinii

The phytochemical study of the bark of Malaysian Phoebe scortechinii (Lauraceae) has resulted in the isolation and identification of two new proaporphine alkaloids; (+)-scortechiniine A (1) and (+)-scortechiniine B (2) together with two known proaporphines; (−)-hexahydromecambrine A (3), (−)-norhexahydromecambrine A (4), and one aporphine; norboldine (5). Structural elucidations of these alkaloids were performed using spectroscopic methods especially 1D and 2D 1H and 13C NMR

Sagebrush landscape: Upper Gunnison River Basin, Colorado Social-Ecological Climate Resilience Project

Prepared with: The Gunnison Climate Working Group and Stakeholders in Gunnison, Colorado for: the North Central Climate Science Center, Ft. Collins, Colorado.April 30, 2017.Includes bibliographical references.Utilizing climate stories to understand the social and ecological impacts to the sagebrush landscape, the team worked with stakeholders to develop three overarching landscape‐scale adaptation strategies. Each of the strategies has a suite of potential actions required to reach a desired future condition. The three key strategies are: 1) identify and protect climate refugia sites (persistent areas), 2) maintain or enhance the resilience of the climate refugia sites, and 3) accept, assist and allow for transformation in non‐climate refugia sites. If adopted by the local community, including land managers and landowners, the framework and strategies resulting from this project can help to reduce the adverse impacts of climate change, allowing for a more sustainable human and natural landscape

Regulatory Processes That Control Haploid Expression of Salmon Sperm mRNAs

Objective  Various stages of mRNA processing are necessary for functionally important genes required during late-stage sperm differentiation. Protein–RNA complexes form that edit, stabilize, store, deliver, localize and regulate translation of sperm mRNAs. These regulatory processes are often directed by recognition sequence elements and the particular composition of the proteins associated with the mRNAs. Previous work has shown that the cAMP response element modulator (CREM), estrogen receptor-alpha (ERα) and forkhead box L2A (FOXL2A) proteins are present in late-stage salmon sperm. Here we investigate whether these and other regulatory proteins might control processing of mRNAs not expressed until the haploid stage of development. We also examine regulatory processes that prepare and present mRNAs that generate unique products essential for differentiating sperm (i.e. for flagellar assembly and function). Results  We provide evidence for potential sperm-specific recognition elements in 5′-untranslated regions (utrs) that may bind CREM, ERα, FOXL2A, Y-box and other proteins. We show that changes within the 5′-utrs and open reading frames of some sperm genes lead to distinct protein termini that may provide specific interfaces necessary for localization and function within the paternal gamete

Phase diagram of insulating crystal and quantum Hall states in ABC-stacked trilayer graphene

In the presence of a perpendicular magnetic field, ABC-stacked trilayer graphene's chiral band structure supports a 12-fold degenerate N=0 Landau level (LL). Along with the valley and spin degrees of freedom, the zeroth LL contains additional quantum numbers associated with the LL orbital index $$. Remote inter-layer hopping terms and external potential difference $\Delta_{B}$ between the layers lead to LL splitting by introducing a gap $$ between the degenerate zero-energy triplet LL orbitals. Assuming that the spin and valley degrees of freedom are frozen, we study the phase diagram of this system resulting from competition of the single particle LL splitting and Coulomb interactions within the Hartree-Fock approximation at integer filling factors. Above a critical value $\Delta_{LL}^{c}$ of the external potential difference i,e, for $|\Delta_{LL}| >\Delta_{LL}^{c}$, the ground state is a uniform quantum Hall state where the electrons occupy the lowest unoccupied LL orbital index. For $|\Delta_{LL}| <\Delta_{LL}^{c}$ (which corresponds to large positive or negative values of $\Delta_{B}$) the uniform QH state is unstable to the formation of a crystal state at integer filling factors. This phase transition should be characterized by a Hall plateau transition as a function of $\Delta_{LL}$ at a fixed filling factor. We also study the properties of this crystal state and discuss its experimental detection.Comment: 16 pages with 13 figure