R package regmedint: extension of regression-based causal mediation analysis with effect measure modification by covariates

This is the supplementary document of R package regmedint that implements the extension of the regression-based causal mediation analysis first proposed by Valeri and VanderWeele (2013, 2015). It supports including effect measure modification by covariates (treatment-covariate and mediator-covariate product terms in mediator and outcome regression models), and also accommodates the original SAS macro and PROC CAUSALMED procedure in SAS when there is no effect measure modification.

Pierre Teilhard de Chardin: a visionary in controversy

Teilhard de Chardin developed an evolutionary vision of our planetary future, currently developing from a sphere of life, or biosphere towards a sphere of mind, or noosphere. As a visionary, Teilhard was not only on the brink of formulating the internet, but he also anticipated current academic efforts to understand globalization, as well as human, cultural and technological evolution. However, his ideas are sources of enduring controversies in both scientific and theological circles. Here I uncover some of the core reasons why his ways of thinking and writing are often problematic, and propose a way forward. This note aims to introduce Teilhard’s central article about the noosphere (The Formation of the Noosphere, 1947), but can also be read as an independent introduction to Teilhard’s system of thought. A detailed exegesis of Teilhard’s article is available as a supplementary document.

Revisiting Integrated Coastal and Marine Management in Canada: Opportunities in the Bay of Fundy

Limited progress has been made in implementing integrated coastal and marine management (ICM) policies globally. A renewed commitment to ICM in Canada offers an opportunity to implement lessons from previous efforts over the past 20 years. This study applies three core ICM characteristics identified from the literature (formal structures; meaningful inclusion; and, innovative mechanisms) to identify opportunities for operationalizing ICM from participants’ lived experiences in Atlantic Canada. These characteristics are employed to assess and compare ICM initiatives across two case studies in the Upper Bay and the Lower Bay of Fundy. The assessments are based on semi-structured interviews conducted with key participants and a supplementary document analysis. The following insights for future ICM policies were identified: adaptive formal structures are required for avoiding previous mistakes; a spectrum of approaches will support meaningful engagement in ICM; local capacity is needed for effective innovative mechanisms; and, policy recommendations should be implemented in parallel. Although these insights are relevant to each of the two sub-regional case studies, the paths taken to incorporating and realizing them appear to be location-specific. To account for these site-specific differences, we suggest more attention be given to strategies that incorporate local history, unique capacity of actor groups and location-specific social-ecological systems objectives. We provide the following recommendations on policy instruments to assist in moving toward enhanced regional ICM in the Bay of Fundy, and that may also be transferable to international ICM efforts: update policy statements to incorporate lessons from previous experiences; strengthen commitment to ICM in Federal law; create a regional engagement strategy to enhance involvement of local actor groups; and, enhance the role of municipal governments to support local capacity building and appropriate engagement of local actors in ICM processes.

CAREC Gender Assessment: Supplementary Document for the CAREC Gender Strategy 2030

Этот документ представляет собой диагностическую основу для анализа уровня гендерного равенства в странах Центральноазиатского регионального экономического сотрудничества (ЦАРЭС). Он также служит основой для разработки Гендерной стратегии ЦАРЭС до 2030 года и оценки эффективности Программы ЦАРЭС по включению гендерного фактора в ее операции. Анализ включает сравнение ключевых гендерных глобальных показателей, а также сквозных гендерных вопросов и вопросов человеческого развития – в особенности, таких как доступ женщин к достойной работе, экономическим возможностям, образованию и обучению, услугам здравоохранения, информационным и коммуникационным технологиям, а также инфраструктуре и государственным услугам, и участие женщин в принятии решений. Репрезентативная выборка из 107 проектов ЦАРЭС была проанализирована для выявления передовой практики, пробелов и упущенных возможностей в области учета гендерной проблематики.

A Sensitivity-Based Three-Phase Weather-Dependent Power Flow Algorithm for Networks with Local Controllers—Supplementary

This supplementary document is part of the original 2-Part manuscript titled “A SensitivityBased Three-Phase Weather-Dependent Power Flow Algorithm for Networks with Local Controllers.” This research focuses on proposing a novel sensitivity-based three-phase weather-dependent power flow algorithm for distribution networks with local voltage controllers (LVCs). The proposed algorithm has four distinct characteristics: a) it considers the three-phase unbalanced nature of distribution systems, b) the operating state of LVCs is calculated using sensitivity parameters, which accelerates the convergence speed of the algorithm, c) it considers the precise switching sequence of LVCs based on their reaction time delays, and d) the nonlinear influence of weather variations in the power flow is also taken into consideration. In this supplementary document, the relevant derivations of the sensitivity parameters are presented to complement the original 2-Part manuscript.

A Sensitivity-Based Three-Phase Weather-Dependent Power Flow Algorithm for Networks with Local Controllers—Supplementary

This supplementary document is part of the original 2-Part manuscript titled “A SensitivityBased Three-Phase Weather-Dependent Power Flow Algorithm for Networks with Local Controllers.” This research focuses on proposing a novel sensitivity-based three-phase weather-dependent power flow algorithm for distribution networks with local voltage controllers (LVCs). The proposed algorithm has four distinct characteristics: a) it considers the three-phase unbalanced nature of distribution systems, b) the operating state of LVCs is calculated using sensitivity parameters, which accelerates the convergence speed of the algorithm, c) it considers the precise switching sequence of LVCs based on their reaction time delays, and d) the nonlinear influence of weather variations in the power flow is also taken into consideration. In this supplementary document, the relevant derivations of the sensitivity parameters are presented to complement the original 2-Part manuscript.

A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction

Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities. High-throughput DNA sequencing platforms oversample mixture components to provide massive amounts of reads whose relative positions can be determined by mapping the reads to a known reference genome; assembly of the components, however, requires discovery of the reads' origin – an NP-hard problem that the existing methods struggle to solve with the required level of accuracy. In this paper, we present a learning framework based on a graph auto-encoder designed to exploit structural properties of sequencing data. The algorithm is a neural network which essentially trains to ignore sequencing errors and infers the posterior probabilities of the origin of sequencing reads. Mixture components are then reconstructed by finding consensus of the reads determined to originate from the same genomic component. Results on realistic synthetic as well as experimental data demonstrate that the proposed framework reliably assembles haplotypes and reconstructs viral communities, often significantly outperforming state-of-the-art techniques. Source codes, datasets and supplementary document are available at https://github.com/WuLoli/GAEseq.

SELEN⁴ (SELEN version 4.0): a Fortran program for solving the gravitationally and topographically self-consistent sea-level equation in glacial isostatic adjustment modeling

We present SELEN4 (SealEveL EquatioN solver), an open-source program written in Fortran 90 that simulates the glacial isostatic adjustment (GIA) process in response to the melting of the Late Pleistocene ice sheets. Using a pseudo-spectral approach complemented by a spatial discretization on an icosahedron-based spherical geodesic grid, SELEN4 solves a generalized sea-level equation (SLE) for a spherically symmetric Earth with linear viscoelastic rheology, taking the migration of the shorelines and the rotational feedback on sea level into account. The approach is gravitationally and topographically self-consistent, since it considers the gravitational interactions between the solid Earth, the cryosphere, and the oceans, and it accounts for the evolution of the Earth's topography in response to changes in sea level. The SELEN4 program can be employed to study a broad range of geophysical effects of GIA, including past relative sea-level variations induced by the melting of the Late Pleistocene ice sheets, the time evolution of paleogeography and of the ocean function since the Last Glacial Maximum, the history of the Earth's rotational variations, present-day geodetic signals observed by Global Navigation Satellite Systems, and gravity field variations detected by satellite gravity missions like GRACE (the Gravity Recovery and Climate Experiment). The “GIA fingerprints” constitute a standard output of SELEN4. Along with the source code, we provide a supplementary document with a full account of the theory, some numerical results obtained from a standard run, and a user guide. Originally, the SELEN program was conceived by Giorgio Spada (GS) in 2005 as a tool for students eager to learn about GIA, and it has been the first SLE solver made available to the community.

Targeted need’s assessment: Medical ethics in MBBS curriculum of Pakistan

Objective: To assess the learner need’s assessment of medical ethics in undergraduate medical curriculum of Pakistan. Methods: To establish an actual need, three methods were employed during October 2018. The first included a review of the curriculum for medical ethics as designed by the Pakistan Medical and Dental College (PMDC). A supplementary document “Code of Ethics”, published by Pakistan Medical and Dental College (PMDC), was also reviewed. In the second method, a self-administered questionnaire was distributed to all 500 undergraduate medical students at Poonch Medical College. Data analysis was performed through SPSS v 23.0 (IBM Corporation, Armonk, NY, US) at 95% CI. The results were expressed in the form of frequencies. The third method employed was an extensive review of literature to identify gaps and to propose learning strategies. Results: In the section on guiding principles in the curriculum, Ethics is considered as an optional subject. Bioethics is designated to be taught in the 3rd year of the MBBS, as part of Forensic Medicine. The agreement to study Medical Ethics Principles as part of the curriculum among final-year medical students saw numbers almost double to 84.61%. The highest majority was seen among final year medical students where 84.6% of the students agreed to study principles of medical ethics as part of their curriculum. Conclusions: Data and the PMDC curriculum support the incorporation of medical ethics in undergraduate education. Thus, an effective educational program based on the assessment of needs could be developed for medical ethics. doi: https://doi.org/10.12669/pjms.35.5.873 How to cite this:Javaeed A. Targeted need’s assessment: Medical ethics in MBBS curriculum of Pakistan. Pak J Med Sci. 2019;35(5):---------. doi: https://doi.org/10.12669/pjms.35.5.873 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.