Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.

Analysis of educational materials and destruction/opt-out initiatives for storage and use of residual newborn screening samples.

In recent years, the storage and use of residual newborn screening (NBS) samples has gained attention. To inform ongoing policy discussions, this article provides an update of previous work on new policies, educational materials, and parental options regarding the storage and use of residual NBS samples. A review of state NBS Web sites was conducted for information related to the storage and use of residual NBS samples in January 2010. In addition, a review of current statutes and bills introduced between 2005 and 2009 regarding storage and/or use of residual NBS samples was conducted. Fourteen states currently provide information about the storage and/or use of residual NBS samples. Nine states provide parents the option to request destruction of the residual NBS sample after the required storage period or the option to exclude the sample for research uses. In the coming years, it is anticipated that more states will consider policies to address parental concerns about the storage and use of residual NBS samples. Development of new policies regarding storage and use of residual NBS samples will require careful consideration of impact on NBS programs, parent and provider educational materials, and respect for parents among other issues.

Caregivers of people with neurodegenerative diseases: profile and unmet needs from a population-based survey in South Australia.

INTRODUCTION: Neurodegenerative diseases (NDD) are characterized by progressive decline and loss of function, requiring considerable third-party care. NDD carers report low quality of life and high caregiver burden. Despite this, little information is available about the unmet needs of NDD caregivers. METHODS: Data from a cross-sectional, whole of population study conducted in South Australia were analyzed to determine the profile and unmet care needs of people who identify as having provided care for a person who died an expected death from NDDs including motor neurone disease and multiple sclerosis. Bivariate analyses using chi(2) were complemented with a regression analysis. RESULTS: Two hundred and thirty respondents had a person close to them die from an NDD in the 5 years before responding. NDD caregivers were more likely to have provided care for more than 2 years and were more able to move on after the death than caregivers of people with other disorders such as cancer. The NDD caregivers accessed palliative care services at the same rate as other caregivers at the end of life, however people with an NDD were almost twice as likely to die in the community (odds ratio [OR] 1.97; 95% confidence interval [CI] 1.30 to 3.01) controlling for relevant caregiver factors. NDD caregivers reported significantly more unmet needs in emotional, spiritual, and bereavement support. CONCLUSION: This study is the first step in better understanding across the whole population the consequences of an expected death from an NDD. Assessments need to occur while in the role of caregiver and in the subsequent bereavement phase.

Toward the development of national telehealth services: the role of Veterans Health Administration and future directions for research.

The Veterans Health Administration (VHA) in the Department of Veteran Affairs (VA) has emerged as a national and international leader in the delivery and research of telehealth-based treatment. Several unique characteristics of care in VA settings intersect to create an ideal environment for telehealth modalities and research. However, the value of telehealth experience and initiatives in VA settings is limited if telehealth strategies cannot be widely exported to other public or private systems. Whereas a hierarchical organization, such as VA, can innovate and fund change relatively quickly based on provider and patient preferences and a growing knowledge base, other health provider organizations and third-party payers may likely require replicable scientific findings over time before incremental investments will be made to create infrastructure, reform regulatory barriers, and amend laws to accommodate expansion of telehealth modalities. Accordingly, large-scale scientifically rigorous telehealth research in VHA settings is essential not only to investigate the efficacy of existing and future telehealth practices in VHA, but also to hasten the development of telehealth infrastructure in private and other public health settings. We propose an expanded partnership between the VA, NIH, and other funding agencies to investigate creative and pragmatic uses of telehealth technology. To this end, we identify six specific areas of research we believe to be particularly relevant to the efficient development of telehealth modalities in civilian and military contexts outside VHA.

Automatic verification of linear controller software

© 2015 IEEE.We consider the problem of verification of software implementations of linear time-invariant controllers. Commonly, different implementations use different representations of the controller's state, for example due to optimizations in a third-party code generator. To accommodate this variation, we exploit input-output controller specification captured by the controller's transfer function and show how to automatically verify correctness of C code controller implementations using a Frama-C/Why3/Z3 toolchain. Scalability of the approach is evaluated using randomly generated controller specifications of realistic size.

Social Decision-Making in Bonobos and Chimpanzees

Humans are natural politicians. We obsessively collect social information that is both observable (e.g., about third-party relationships) and unobservable (e.g., about others’ psychological states), and we strategically employ that information to manage our cooperative and competitive relationships. To what extent are these abilities unique to our species, and how did they evolve? The present dissertation seeks to contribute to these two questions. To do so, I take a comparative perspective, investigating social decision-making in humans’ closest living relatives, bonobos and chimpanzees. In Chapter 1, I review existing literature on theory of mind—or the ability to understand others’ psychological states—in these species. I also present a theoretical framework to guide further investigation of social cognition in bonobos and chimpanzees based on hypotheses about the proximate and ultimate origins of their species differences. In Chapter 2, I experimentally investigate differences in the prosocial behavior of bonobos and chimpanzees, revealing species-specific prosocial motivations that appear to be less flexible than those exhibited by humans. In Chapter 3, I explore through decision-making experiments bonobos’ ability to evaluate others based on their prosocial or antisocial behavior during third-party interactions. Bonobos do track the interactions of third-parties and evaluate actors based on these interactions. However, they do not exhibit the human preference for those who are prosocial towards others, instead consistently favoring an antisocial individual. The motivation to prefer those who demonstrate a prosocial disposition may be a unique feature of human psychology that contributes to our ultra-cooperative nature. In Chapter 4, I investigate the adaptive value of social cognition in wild primates. I show that the recruitment behavior of wild chimpanzees at Gombe National Park, Tanzania is consistent with the use of third-party knowledge, and that those who appear to use third-party knowledge receive immediate proximate benefits. They escape further aggression from their opponents. These findings directly support the social intelligence hypothesis that social cognition has evolved in response to the demands of competing with one’s own group-mates. Thus, the studies presented here help to better characterize the features of social decision-making that are unique to humans, and how these abilities evolved.

Institutions, Innovation, and Grassroots Change: Alternatives to Transnational Governance in the Global South

Transnational governance has been advanced as a viable option for regulating commodities produced in emerging economies—where incapable or unwilling states may undersupply institutions requisite for overseeing supply chains consistent with the quality, safety, environmental, or social standards demanded by the global marketplace. Producers from these jurisdictions, otherwise left with few venues for securing market access and price premiums, ostensibly benefit from whatever pathways transnational actors offer to minimize barriers to entry—including voluntary certification for compliance with a panoply of public and private rules, such as those promulgated by NGOs like the Fair Trade Federation or multinational retailers like Wal-Mart. Yet, such transnational “sustainability” governance may neither be effective nor desirable. Regulatory schemes, like third-party certification, often privilege the interests of primary architects and beneficiaries—private business associations, governments, NGOs, and consumers in the global North—over regulatory targets—producers in the global South. Rather than engaging with the international marketplace via imported and externally-driven schemes, some producer groups are instead challenging existing rules and innovating homegrown institutions. These alternatives to commercialization adopt some institutional characteristics of their transnational counterparts yet deliver benefits in a manner more aligned with the needs of producers. Drawing on original empirical cases from Nicaragua and Mexico, this dissertation examines the role of domestic institutional alternatives to transnational governance in enhancing market access, environmental quality and rural livelihoods within producer communities. Unlike the more technocratic and expert-driven approaches characteristic of mainstream governance efforts, these local regulatory institutions build upon the social capital, indigenous identity, “ancestral” knowledge, and human assets of producer communities as new sources of power and legitimacy in governing agricultural commodities.

Essays in Empirical Operations Management: Bayesian Learning of Service Quality and Structural Estimation of Complementary Product Pricing and Inventory Management

This dissertation contributes to the rapidly growing empirical research area in the field of operations management. It contains two essays, tackling two different sets of operations management questions which are motivated by and built on field data sets from two very different industries --- air cargo logistics and retailing.

The first essay, based on the data set obtained from a world leading third-party logistics company, develops a novel and general Bayesian hierarchical learning framework for estimating customers' spillover learning, that is, customers' learning about the quality of a service (or product) from their previous experiences with similar yet not identical services. We then apply our model to the data set to study how customers' experiences from shipping on a particular route affect their future decisions about shipping not only on that route, but also on other routes serviced by the same logistics company. We find that customers indeed borrow experiences from similar but different services to update their quality beliefs that determine future purchase decisions. Also, service quality beliefs have a significant impact on their future purchasing decisions. Moreover, customers are risk averse; they are averse to not only experience variability but also belief uncertainty (i.e., customer's uncertainty about their beliefs). Finally, belief uncertainty affects customers' utilities more compared to experience variability.

The second essay is based on a data set obtained from a large Chinese supermarket chain, which contains sales as well as both wholesale and retail prices of un-packaged perishable vegetables. Recognizing the special characteristics of this particularly product category, we develop a structural estimation model in a discrete-continuous choice model framework. Building on this framework, we then study an optimization model for joint pricing and inventory management strategies of multiple products, which aims at improving the company's profit from direct sales and at the same time reducing food waste and thus improving social welfare.

Collectively, the studies in this dissertation provide useful modeling ideas, decision tools, insights, and guidance for firms to utilize vast sales and operations data to devise more effective business strategies.

Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques.

HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4+ T cells. Although broadly neutralizing antibodies (bnAbs) are the type of HIV-1 antibodies that are most likely protective, they are not induced with current vaccine candidates. In contrast, antibodies that do not neutralize primary HIV-1 strains in the TZM-bl infection assay are readily induced by current vaccine candidates and have also been implicated as secondary correlates of decreased HIV-1 risk in the RV144 vaccine efficacy trial. Here, we have studied the capacity of anti-Env monoclonal antibodies (mAbs) against either the immunodominant region of gp41 (7B2 IgG1), the first constant region of gp120 (A32 IgG1), or the third variable loop (V3) of gp120 (CH22 IgG1) to modulate in vivo rectal mucosal transmission of a high-dose simian-human immunodeficiency virus (SHIV-BaL) in rhesus macaques. 7B2 IgG1 or A32 IgG1, each containing mutations to enhance Fc function, was administered passively to rhesus macaques but afforded no protection against productive clinical infection while the positive control antibody CH22 IgG1 prevented infection in 4 of 6 animals. Enumeration of transmitted/founder (T/F) viruses revealed that passive infusion of each of the three antibodies significantly reduced the number of T/F genomes. Thus, some antibodies that bind HIV-1 Env but fail to neutralize virus in traditional neutralization assays may limit the number of T/F viruses involved in transmission without leading to enhancement of viral infection. For one of these mAbs, gp41 mAb 7B2, we provide the first co-crystal structure in complex with a common cyclical loop motif demonstrated to be critical for infection by other retroviruses.