Global value chains and agrifood standards: challenges and possibilities for smallholders in developing countries.

The rise of private food standards has brought forth an ongoing debate about whether they work as a barrier for smallholders and hinder poverty reduction in developing countries. This paper uses a global value chain approach to explain the relationship between value chain structure and agrifood safety and quality standards and to discuss the challenges and possibilities this entails for the upgrading of smallholders. It maps four potential value chain scenarios depending on the degree of concentration in the markets for agrifood supply (farmers and manufacturers) and demand (supermarkets and other food retailers) and discusses the impact of lead firms and key intermediaries on smallholders in different chain situations. Each scenario is illustrated with case examples. Theoretical and policy issues are discussed, along with proposals for future research in terms of industry structure, private governance, and sustainable value chains.

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

Alternative splicing in multiple sclerosis and other autoimmune diseases.

Alternative splicing is a general mechanism for regulating gene expression that affects the RNA products of more than 90% of human genes. Not surprisingly, alternative splicing is observed among gene products of metazoan immune systems, which have evolved to efficiently recognize pathogens and discriminate between "self" and "non-self", and thus need to be both diverse and flexible. In this review we focus on the specific interface between alternative splicing and autoimmune diseases, which result from a malfunctioning of the immune system and are characterized by the inappropriate reaction to self-antigens. Despite the widespread recognition of alternative splicing as one of the major regulators of gene expression, the connections between alternative splicing and autoimmunity have not been apparent. We summarize recent findings connecting splicing and autoimmune disease, and attempt to find common patterns of splicing regulation that may advance our understanding of autoimmune diseases and open new avenues for therapy.

Informatic Opacity: Biometric Facial Recognition and the Aesthetics and Politics of Defacement

Confronting the rapidly increasing, worldwide reliance on biometric technologies to surveil, manage, and police human beings, my dissertation Informatic Opacity: Biometric Facial Recognition and the Aesthetics and Politics of Defacement charts a series of queer, feminist, and anti-racist concepts and artworks that favor opacity as a means of political struggle against surveillance and capture technologies in the 21st century. Utilizing biometric facial recognition as a paradigmatic example, I argue that today's surveillance requires persons to be informatically visible in order to control them, and such visibility relies upon the production of technical standardizations of identification to operate globally, which most vehemently impact non- normative, minoritarian populations. Thus, as biometric technologies turn exposures of the face into sites of governance, activists and artists strive to make the face biometrically illegible and refuse the political recognition biometrics promises through acts of masking, escape, and imperceptibility. Although I specifically describe tactics of making the face unrecognizable as "defacement," I broadly theorize refusals to visually cohere to digital surveillance and capture technologies' gaze as "informatic opacity," an aesthetic-political theory and practice of anti- normativity at a global, technical scale whose goal is maintaining the autonomous determination of alterity and difference by evading the quantification, standardization, and regulation of identity imposed by biometrics and the state. My dissertation also features two artworks: Facial Weaponization Suite, a series of masks and public actions, and Face Cages, a critical, dystopic installation that investigates the abstract violence of biometric facial diagramming and analysis. I develop an interdisciplinary, practice-based method that pulls from contemporary art and aesthetic theory, media theory and surveillance studies, political and continental philosophy, queer and feminist theory, transgender studies, postcolonial theory, and critical race studies.

PARTAKE survey of public knowledge and perceptions of clinical research in India.

BACKGROUND: A public that is an informed partner in clinical research is important for ethical, methodological, and operational reasons. There are indications that the public is unaware or misinformed, and not sufficiently engaged in clinical research but studies on the topic are lacking. PARTAKE - Public Awareness of Research for Therapeutic Advancements through Knowledge and Empowerment is a program aimed at increasing public awareness and partnership in clinical research. The PARTAKE Survey is a component of the program. OBJECTIVE: To study public knowledge and perceptions of clinical research. METHODS: A 40-item questionnaire combining multiple-choice and open-ended questions was administered to 175 English- or Hindi-speaking individuals in 8 public locations representing various socioeconomic strata in New Delhi, India. RESULTS: Interviewees were 18-84 old (mean: 39.6, SD ± 16.6), 23.6% female, 68.6% employed, 7.3% illiterate, 26.3% had heard of research, 2.9% had participated and 58.9% expressed willingness to participate in clinical research. The following perceptions were reported (% true/% false/% not aware): 'research benefits society' (94.1%/3.5%/2.3%), 'the government protects against unethical clinical research' (56.7%/26.3%/16.9%), 'research hospitals provide better care' (67.2%/8.7%/23.9%), 'confidentiality is adequately protected' (54.1%/12.3%/33.5%), 'participation in research is voluntary' (85.3%/5.8%/8.7%); 'participants treated like 'guinea pigs'' (20.7%/53.2%/26.0%), and 'compensation for participation is adequate' (24.7%/12.9%/62.3%). CONCLUSIONS: Results suggest the Indian public is aware of some key features of clinical research (e.g., purpose, value, voluntary nature of participation), and supports clinical research in general but is unaware of other key features (e.g., compensation, confidentiality, protection of human participants) and exhibits some distrust in the conduct and reporting of clinical trials. Larger, cross-cultural surveys are required to inform educational programs addressing these issues.

Dispersal and Integration in Female Chimpanzees

In chimpanzees, most females disperse from the community in which they were born to reproduce in a new community, thereby eliminating the risk of inbreeding with close kin. However, across sites, some females breed in their natal community, raising questions about the flexibility of dispersal, the costs and benefits of different strategies and the mitigation of costs associated with dispersal and integration. In this dissertation I address these questions by combining long-term behavioral data and recent field observations on maturing and young adult females in Gombe National Park with an experimental manipulation of relationship formation in captive apes in the Congo.

To assess the risk of inbreeding for females who do and do not disperse, 129 chimpanzees were genotyped and relatedness between each dyad was calculated. Natal females were more closely related to adult community males than were immigrant females. By examining the parentage of 58 surviving offspring, I found that natal females were not more related to the sires of their offspring than were immigrant females, despite three instances of close inbreeding. The sires of all offspring were less related to the mothers than non-sires regardless of the mother’s residence status. These results suggest that chimpanzees are capable of detecting relatedness and that, even when remaining natal, females can largely avoid, though not eliminate, inbreeding.

Next, I examined whether dispersal was associated with energetic, social, physiological and/or reproductive costs by comparing immigrant (n=10) and natal (n=9) females of similar age using 2358 hours of observational data. Natal and immigrant females did not differ in any energetic metric. Immigrant females received aggression from resident females more frequently than natal females. Immigrants spent less time in social grooming and more time self-grooming than natal females. Immigrant females primarily associated with resident males, had more social partners and lacked close social allies. There was no difference in levels of fecal glucocorticoid metabolites in immigrant and natal females. Immigrant females gave birth 2.5 years later than natal females, though the survival of their first offspring did not differ. These results indicate that immigrant females in Gombe National Park do not face energetic deficits upon transfer, but they do enter a hostile social environment and have a delayed first birth.

Next, I examined whether chimpanzees use condition- and phenotype-dependent cues in making dispersal decisions. I examined the effect of social and environmental conditions present at the time females of known age matured (n=25) on the females’ dispersal decisions. Females were more likely to disperse if they had more male maternal relatives and thus, a high risk of inbreeding. Females with a high ranking mother and multiple maternal female kin tended to disperse less frequently, suggesting that a strong female kin network provides benefits to the maturing daughter. Females were also somewhat less likely to disperse when fewer unrelated males were present in the group. Habitat quality and intrasexual competition did not affect dispersal decisions. Using a larger sample of 62 females observed as adults in Gombe, I also detected an effect of phenotypic differences in personality on the female’s dispersal decisions; extraverted, agreeable and open females were less likely to disperse.

Natural observations show that apes use grooming and play as social currency, but no experimental manipulations have been carried out to measure the effects of these behaviors on relationship formation, an essential component of integration. Thirty chimpanzees and 25 bonobos were given a choice between an unfamiliar human who had recently groomed or played with them over one who did not. Both species showed a preference for the human that had interacted with them, though the effect was driven by males. These results support the idea that grooming and play act as social currency in great apes that can rapidly shape social relationships between unfamiliar individuals. Further investigation is needed to elucidate the use of social currency in female apes.

I conclude that dispersal in female chimpanzees is flexible and the balance of costs and benefits varies for each individual. Females likely take into account social cues present at maturity and their own phenotype in choosing a settlement path and are especially sensitive to the presence of maternal male kin. The primary cost associated with philopatry is inbreeding risk and the primary cost associated with dispersal is delay in the age at first birth, presumably resulting from intense social competition. Finally, apes may strategically make use of affiliative behavior in pursuing particular relationships, something that should be useful in the integration process.

The paradox of openness revisited: Collaborative innovation and patenting by UK innovators

© 2016 The Authors.We revisit the "paradox of openness" in the literature which consists of two conflicting views on the link between patenting and open innovation-the spillover prevention and the organizational openness views. We use the data from the Survey of Innovation and Patent Use and the Community Innovation Survey (CIS6) in the UK to assess the empirical support for the distinct predictions of these theories. We argue that both patenting and external sourcing (openness) are jointly-determined decisions made by firms. Their relationship is contingent upon whether the firms are technically superior to their rivals and lead in the market or not. Leading firms are more vulnerable to unintended knowledge spillovers during collaboration as compared to followers, and consequently, the increase in patenting due to openness is higher for leaders than for followers. We develop a simple framework that allows us to formally derive the empirical implications of this hypothesis and test it by estimating whether the reduced form relationship between patenting and collaboration is stronger for leaders than for followers.

High-Resolution In Situ Oxygen-Argon Studies of Surface Biological and Physical Processes in the Polar Oceans

The Arctic Ocean and Western Antarctic Peninsula (WAP) are the fastest warming regions on the planet and are undergoing rapid climate and ecosystem changes. Until we can fully resolve the coupling between biological and physical processes we cannot predict how warming will influence carbon cycling and ecosystem function and structure in these sensitive and climactically important regions. My dissertation centers on the use of high-resolution measurements of surface dissolved gases, primarily O2 and Ar, as tracers or physical and biological functioning that we measure underway using an optode and Equilibrator Inlet Mass Spectrometry (EIMS). Total O2 measurements are common throughout the historical and autonomous record but are influenced by biological (net metabolic balance) and physical (temperature, salinity, pressure changes, ice melt/freeze, mixing, bubbles and diffusive gas exchange) processes. We use Ar, an inert gas with similar solubility properties to O2, to devolve distinct records of biological (O2/Ar) and physical (Ar) oxygen. These high-resolution measurements that expose intersystem coupling and submesoscale variability were central to studies in the Arctic Ocean, WAP and open Southern Ocean that make up this dissertation.

Key findings of this work include the documentation of under ice and ice-edge blooms and basin scale net sea ice freeze/melt processes in the Arctic Ocean. In the WAP O2 and pCO2 are both biologically driven and net community production (NCP) variability is controlled by Fe and light availability tied to glacial and sea ice meltwater input. Further, we present a feasibility study that shows the ability to use modeled Ar to derive NCP from total O2 records. This approach has the potential to unlock critical carbon flux estimates from historical and autonomous O2 measurements in the global oceans.

Introducing molaR: a New R Package for Quantitative Topographic Analysis of Teeth (and Other Topographic Surfaces)

© 2016 Springer Science+Business Media New YorkResearchers studying mammalian dentitions from functional and adaptive perspectives increasingly have moved towards using dental topography measures that can be estimated from 3D surface scans, which do not require identification of specific homologous landmarks. Here we present molaR, a new R package designed to assist researchers in calculating four commonly used topographic measures: Dirichlet Normal Energy (DNE), Relief Index (RFI), Orientation Patch Count (OPC), and Orientation Patch Count Rotated (OPCR) from surface scans of teeth, enabling a unified application of these informative new metrics. In addition to providing topographic measuring tools, molaR has complimentary plotting functions enabling highly customizable visualization of results. This article gives a detailed description of the DNE measure, walks researchers through installing, operating, and troubleshooting molaR and its functions, and gives an example of a simple comparison that measured teeth of the primates Alouatta and Pithecia in molaR and other available software packages. molaR is a free and open source software extension, which can be found at the doi:10.13140/RG.2.1.3563.4961(molaR v. 2.0) as well as on the Internet repository CRAN, which stores R packages.

A New Method for Modeling Free Surface Flows and Fluid-structure Interaction with Ocean Applications

The computational modeling of ocean waves and ocean-faring devices poses numerous challenges. Among these are the need to stably and accurately represent both the fluid-fluid interface between water and air as well as the fluid-structure interfaces arising between solid devices and one or more fluids. As techniques are developed to stably and accurately balance the interactions between fluid and structural solvers at these boundaries, a similarly pressing challenge is the development of algorithms that are massively scalable and capable of performing large-scale three-dimensional simulations on reasonable time scales. This dissertation introduces two separate methods for approaching this problem, with the first focusing on the development of sophisticated fluid-fluid interface representations and the second focusing primarily on scalability and extensibility to higher-order methods.

We begin by introducing the narrow-band gradient-augmented level set method (GALSM) for incompressible multiphase Navier-Stokes flow. This is the first use of the high-order GALSM for a fluid flow application, and its reliability and accuracy in modeling ocean environments is tested extensively. The method demonstrates numerous advantages over the traditional level set method, among these a heightened conservation of fluid volume and the representation of subgrid structures.

Next, we present a finite-volume algorithm for solving the incompressible Euler equations in two and three dimensions in the presence of a flow-driven free surface and a dynamic rigid body. In this development, the chief concerns are efficiency, scalability, and extensibility (to higher-order and truly conservative methods). These priorities informed a number of important choices: The air phase is substituted by a pressure boundary condition in order to greatly reduce the size of the computational domain, a cut-cell finite-volume approach is chosen in order to minimize fluid volume loss and open the door to higher-order methods, and adaptive mesh refinement (AMR) is employed to focus computational effort and make large-scale 3D simulations possible. This algorithm is shown to produce robust and accurate results that are well-suited for the study of ocean waves and the development of wave energy conversion (WEC) devices.

Advanced Aerogel Composites for Oil Remediation and Recovery

Oil spills in marine environments often damage marine and coastal life if not remediated rapidly and efficiently. In spite of the strict enforcement of environmental legislations (i.e., Oil Pollution Act 1990) following the Exxon Valdez oil spill (June 1989; the second biggest oil spill in U.S. history), the Macondo well blowout disaster (April 2010) released 18 times more oil. Strikingly, the response methods used to contain and capture spilled oil after both accidents were nearly identical, note that more than two decades separate Exxon Valdez (1989) and Macondo well (2010) accidents.

The goal of this dissertation was to investigate new advanced materials (mechanically strong aerogel composite blankets-Cabot® Thermal Wrap™ (TW) and Aspen Aerogels® Spaceloft® (SL)), and their applications for oil capture and recovery to overcome the current material limitations in oil spill response methods. First, uptake of different solvents and oils were studied to answer the following question: do these blanket aerogel composites have competitive oil uptake compared to state-of-the-art oil sorbents (i.e., polyurethane foam-PUF)? In addition to their competitive mechanical strength (766, 380, 92 kPa for Spaceloft, Thermal Wrap, and PUF, respectively), our results showed that aerogel composites have three critical advantages over PUF: rapid (3-5 min.) and high (more than two times of PUF’s uptake) oil uptake, reusability (over 10 cycles), and oil recoverability (up to 60%) via mechanical extraction. Chemical-specific sorption experiments showed that the dominant uptake mechanism of aerogels is adsorption to the internal surface, with some contribution of absorption into the pore space.

Second, we investigated the potential environmental impacts (energy and chemical burdens) associated with manufacturing, use, and disposal of SL aerogel and PUF to remove the oil (i.e., 1 m3 oil) from a location (i.e., Macondo well). Different use (single and multiple use) and end of life (landfill, incinerator, and waste-to-energy) scenarios were assessed, and our results demonstrated that multiple use, and waste-to-energy choices minimize the energy and material use of SL aerogel. Nevertheless, using SL once and disposing via landfill still offers environmental and cost savings benefits relative to PUF, and so these benefits are preserved irrespective of the oil-spill-response operator choices.

To inform future aerogel manufacture, we investigated the different laboratory-scale aerogel fabrication technologies (rapid supercritical extraction (RSCE), CO2 supercritical extraction (CSCE), alcohol supercritical extraction (ASCE)). Our results from anticipatory LCA for laboratory-scaled aerogel fabrication demonstrated that RSCE method offers lower cumulative energy and ecotoxicity impacts compared to conventional aerogel fabrication methods (CSCE and ASCE).

The final objective of this study was to investigate different surface coating techniques to enhance oil recovery by modifying the existing aerogel surface chemistries to develop chemically responsive materials (switchable hydrophobicity in response to a CO2 stimulus). Our results showed that studied surface coating methods (drop casting, dip coating, and physical vapor deposition) were partially successful to modify surface with CO2 switchable chemical (tributylpentanamidine), likely because of the heterogeneous fiber structure of the aerogel blankets. A possible solution to these non-uniform coatings would be to include switchable chemical as a precursor during the gel preparation to chemically attach the switchable chemical to the pores of the aerogel.

Taken as a whole, the implications of this work are that mechanical deployment and recovery of aerogel composite blankets is a viable oil spill response strategy that can be deployed today. This will ultimately enable better oil uptake without the uptake of water, potential reuse of the collected oil, reduced material and energy burdens compared to competitive sorbents (e.g., PUF), and reduced occupational exposure to oiled sorbents. In addition, sorbent blankets and booms could be deployed in coastal and open-ocean settings, respectively, which was previously impossible.