AbstractWhen using alternative metrics (altmetrics) to investigate the impact of a scholar's work, researchers and librarians are typically cautioned that altmetrics will be less useful for older works of scholarship. This is because it is difficult to collect social media and other attention retroactively, and the numbers will be lower if the work was published before social media marketing and promotion were widely accepted in a field. In this article, we argue that altmetrics can provide useful information about older works in the form of documenting renewed attention to past scholarship as part of a scholar's legacy. Using the altmetrics profile of the late Dr. Thomas E. Starzl, often referred to as "the father of modern transplantation", we describe two cases where altmetrics provided information about renewed interest in his works: a controversy about race and genetics, and posthumous remembrances by colleagues of his contributions to a field. Keywords: altmetrics, social media, preservation Introduction: Altmetrics and Social Media Altmetrics, a blend of the words “alternative” and “metrics,” show the use of an article beyond citation counts, which are a method traditionally used to evaluate the impact of an article. Altmetrics, when employed in conjunction with citations, can show a wider impact of scholarly work; citations track formal, acknowledged influence, and altmetrics track the informal and social attention given to an article  \cite{Priem2012,Cronin_2001}. Altmetrics do not directly correlate with citation counts; although some measures such as Mendeley readers may predict future citations \cite{Mohammadi_2015}, social media in particular is weakly related to citations \cite{Costas2015,de_Winter_2014} and may be influenced by factors like the extant digital footprint of the authors \cite{bar2012beyond}. Social media attention has been discussed often in the altmetrics literature. Analyses of social media often point to the fact social media attention is higher for more recently published or released work \cite{Peters_2016,Kwok_2013}. The presence of social media bots on platforms such as Twitter can impact the use of raw numbers for social media data, and researchers have cautioned that social media use must be examined and not taken at face value \cite{Haustein_2015}.  Furthermore, the promotional use of social media to share recently published papers, when done by the journal or the publisher, may have a bias effect on the social media numbers for a particular paper \cite{Bornmann_2014}. Finally, some have debated the meaningfulness of social media metrics, distinguishing between social media sharing and attention given to papers and arguing that there is little correlation between the act of sharing a paper and making an informed comment about a work of scholarship \cite{crotty2014altmetrics}. These considerations are all important when evaluating social attention given to a paper; however, examples of interesting and meaningful use of social media in academic contexts can help understand the ways that altmetrics can show social impact. By examining the altmetrics activity surrounding the works of researcher Dr. Thomas E. Starzl, a pioneer in the field of organ transplantation, we describe two cases where older articles received social media attention: a controversial discussion and the death of the author. Implications for archival practices are discussed. Background to the ProjectAfter his retirement from active surgery in 1992, Dr. Starzl donated his papers to the Archives Service Center at the University Library System, University of Pittsburgh, as a way to ensure that his work would be accessible and usable to future generations of scholars. In addition to processing over 400 boxes of his archival documents, a team of librarians (www.starzl.pitt.edu/contact.html) digitized his Curriculum Vitae (originally in the form of hand-written pages in a series of three-ring binders) and created metadata for his publications using Optical Character Recognition (OCR). These metadata records were hand-checked for completeness and correctness, and then the records for Dr. Starzl's publications were imported into the Institutional Repository for the University of Pittsburgh, D-Scholarship. In addition, these records were used to share documents in PubMed Central, many of which are accessible today. When the University Library System began to work with Plum Analytics on an altmetrics project, all items in the Institutional Repository were imported into PlumX in order to gather metrics about their use. As expected, Dr. Starzl's work had large amounts of citations (over 800 each on two individual articles, for example), but because the bulk of his work was done between 1963 and 1999, there was not much evidence of social attention (including social media) surrounding Dr. Starzl's work. The profile lay dormant for several years as the service was refined and implemented for active scholars. When Dr. Starzl passed away on March 4, 2017, at the age of 90, staff at the University Library System noticed an increase of media attention surrounding his work that was captured in PlumX. Analysis of the PlumX profile for Dr. Starzl (plu.mx/pitt/u/pitt-tes11) revealed that his social media mentions had increased in the past two years surrounding not only his death, but another incident where scholars had used his work to refute a controversial argument in popular news outlets. In the following sections, we detail the role of Dr. Starzl's research papers in these two situations. ControversyAfter examining the PlumX profile for Dr. Starzl, it became evident that one his papers receives occasional attention on Twitter and other social media outlets in response to an argument surrounding organ transplants. One side of the argument says that race is a factor when performing organ transplants, and this viewpoint is repeated occasionally in news stories (see, for example, "Black and Asian people wait YEAR longer for kidney transplant because of ethnic minority donor shortage", March 12, 2014, in The Daily Mirror www.mirror.co.uk/lifestyle/health/organ-donors-black-asian-people-3235968) as well as on the website for the organization Association for Multicultural Affairs in Transplantation (AMAT) (www.amat1.org/about-amat/closing-the-donation-gap/). This argument is also often repeated on social media outlets in discussions about the nature of race.Whenever this argument resurfaces, whether started by an individual or an organization, the 1990 paper "Effect of race upon organ donation and recipient survival in liver transplantation" \cite{Pillay_1990}, co-authored by Dr. Starzl,  is frequently cited on social media to disprove the idea that race factors into organ transplantation. By investigating the PlumX profile of Dr. Starzl and specifically this article (see plu.mx/pitt/a/-KmvbhDSWlrlZJ2IRqdTyXCnWnLg2PsBjssfaLmH5QQ/), we discovered a spike in social media mentions surrounding the publication and sharing of the 2014 article in the Daily Mirror, as well as a scattering of other tweets after individuals discover the mission statement of AMAT. PlumX revealed several of those conversations; although some of the argumentative tweets had been deleted and were no longer visible, the nature and tone of the argument is still evident based on one half of the conversation. One conversation survives in whole; this interaction occurred on Twitter where this paper was used to back up an argument about race and transplants on Twitter. These interactions show how a paper from more than a decade ago can be introduced into modern conversations. 

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Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape, and energy minimization. Users can import, create, and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization. In addition to a number of pre-built databases of popular compound libraries, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session. The easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design. Pharmit is available under a dual BSD/GPL open-source license.

Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here we introduce and evaluate Fragment Oriented Molecular Shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of _shape constraints_, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search.

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry.

When the measurements from the FCC-ee become available, an improved determination of the standard-model “input” parameters will be needed to fully exploit the new precision data towards either constraining or fitting the parameters of beyond-the-standard-model theories. Among these input parameters is the electromagnetic coupling constant estimated at the Z mass scale, $(m^2_{\rm Z})$. The measurement of the muon forward-backward asymmetry at the FCC-ee, just below and just above the Z pole, can be used to make a direct determination of $(m^2_{\rm Z})$ with an accuracy deemed adequate for an optimal use of the FCC-ee precision data.