STATE-AND-TRANSITION MODELING AND ADAPTIVE MANAGEMENT: TOOLS FOR FUTURE CO-DEVELOPMENT OF MADAGASCAR’S NATURAL RESOURCES AND PEOPLE

Madagascar’s terrestrial and aquatic ecosystems have long supported a unique set of ecological communities, many of whom are endemic to the tropical island. Those same ecosystems have been a source of valuable natural resources to some of the poorest people in the world. Nevertheless, with pride, ingenuity and resourcefulness, the Malagasy people of the southwest coast, being of Vezo identity, subsist with low development fishing techniques aimed at an increasingly threatened host of aquatic seascapes. Mangroves, sea grass bed, and coral reefs of the region are under increased pressure from the general populace for both food provisions and support of economic opportunity. Besides purveyors and extractors, the coastal waters are also subject to a number of natural stressors, including cyclones and invasive, predator species of both flora and fauna. In addition, the aquatic ecosystems of the region are undergoing increased nutrient and sediment runoff due, in part, to Madagascar’s heavy reliance on land for agricultural purposes (Scales, 2011). Moreover, its coastal waters, like so many throughout the world, have been proven to be warming at an alarming rate over the past few decades. In recognizing the intimate interconnectedness of the both the social and ecological systems, conservation organizations have invoked a host of complimentary conservation and social development efforts with the dual aim of preserving or restoring the health of both the coastal ecosystems and the people of the region. This paper provides a way of thinking more holistically about the social-ecological system within a resiliency frame of understanding. Secondly, it applies a platform known as state-and-transition modeling to give form to the process. State-and-transition modeling is an iterative investigation into the physical makeup of a system of study as well as the boundaries and influences on that state, and has been used in restorative ecology for more than a decade. Lastly, that model is sited within an adaptive management scheme that provides a structured, cyclical, objective-oriented process for testing stakeholders cognitive understanding of the ecosystem through a pragmatic implementation and monitoring a host of small-scale interventions developed as part of the adaptive management process. Throughout, evidence of the application of the theories and frameworks are offered, with every effort made to retool conservation-minded development practitioners with a comprehensive strategy for addressing the increasingly fragile social-ecological systems of southwest Madagascar. It is offered, in conclusion, that the seascapes of the region would be an excellent case study worthy of future application of state-and-transition modeling and adaptive management as frameworks for conservation-minded development practitioners whose multiple projects, each with its own objective, have been implemented with a single goal in mind: preserve and protect the state of the supporting environment while providing for the basic needs of the local Malagasy people.

A Missense Mutation in the SERPINH1 Gene in Dachshunds with Osteogenesis Imperfecta

Osteogenesis imperfecta (OI) is a hereditary disease occurring in humans and dogs. It is characterized by extremely fragile bones and teeth. Most human and some canine OI cases are caused by mutations in the COL1A1 and COL1A2 genes encoding the subunits of collagen I. Recently, mutations in the CRTAP and LEPRE1 genes were found to cause some rare forms of human OI. Many OI cases exist where the causative mutation has not yet been found. We investigated Dachshunds with an autosomal recessive form of OI. Genotyping only five affected dogs on the 50 k canine SNP chip allowed us to localize the causative mutation to a 5.82 Mb interval on chromosome 21 by homozygosity mapping. Haplotype analysis of five additional carriers narrowed the interval further down to 4.74 Mb. The SERPINH1 gene is located within this interval and encodes an essential chaperone involved in the correct folding of the collagen triple helix. Therefore, we considered SERPINH1 a positional and functional candidate gene and performed mutation analysis in affected and control Dachshunds. A missense mutation (c.977C>T, p.L326P) located in an evolutionary conserved domain was perfectly associated with the OI phenotype. We thus have identified a candidate causative mutation for OI in Dachshunds and identified a fifth OI gene.

The impact of new technologies on distance learning students

This is a European Commission Leonardo da Vinci Reference Material project on the impact of new technology on distance learning students. It is known that all the Ministries of Education of the 27 European Union countries pay millions of Euros annually in the provision of educational technology for their schools, colleges and universities. A review of the literature of the impact of technology, however, showed that the research in this field was unacceptably fragile. What research there was focused on the impact of technology on children in American schools. The project set out, therefore, to measure the impact of technology on adult education, lifelong learning and distance education, with a particular focus on adult distance learning.

Neighborhood Disadvantage and Birth Weight: The Role of Perceived Danger and Substance Abuse

In this analysis we connect structural neighborhood conditions to birth outcomes through their intermediate effects on mothers’ perceptions of neighborhood danger and their tendency to abuse substances during pregnancy. We hypothesize that neighborhood poverty and racial/ethnic concentration combine to produce environments that mothers perceive as unsafe, thereby increasing the likelihood of negative coping behaviors (substance abuse). We expect these behaviors, in turn, to produce lower birth weights. Using data from the Fragile Families and Child Wellbeing Study, a survey of a cohort mothers and children born between 1998 and 2000 in large cities in the United States, we find little evidence to suggest that neighborhood circumstances have strong, direct effects on birth weight. Living in a neighborhood with more foreigners had a positive effect on birth weight. To the extent that neighborhood conditions influence birth weight, the effect mainly occurs through an association with perceived neighborhood danger and subsequent negative coping behaviors. Poverty and racial/ethnic concentration increase a mother’s sense that her neighborhood is unsafe. The perception of an unsafe neighborhood, in turn, associates with a greater likelihood of smoking cigarettes and using illegal drugs, and these behaviors have strong and significant effects in reducing birth weight. However, demographic characteristics, rather than perceived danger or substance abuse, mediate the influence of neighborhood characteristics on birth weight.

'Balance of Terror' -- Rival Militias and Vigilantes in Nigeria

Militias and vigilantes that assume public authority by fighting crime reject the laws of the state, yet they have no other set of rules to regulate their activities. Many of them claim to be accountable to their ethnic or religious community on whose behalf they operate. But their communities have found no means to institutionalise control over them. Moreover, there are no institutions to settle conflicts between different militias and vigilantes. On a local level, rival groups have reached informal arrangements. However, these compromises are unstable, as they reflect fragile alliances and shifting balances of power. Leaders of militias and other 'self-determination groups' have suggested organising a conference of all ethnic nationalities in Nigeria in order to design a new constitution that would give militias and vigilantes a legal role and define their authority. But the groups compared in this article – Oodua People's Congress, Sharia Vigilantes, Bakassi Boys, MASSOB, and Niger Delta militias – pursue very divergent interests, and they are far from reaching a consensus on how to contain violence between them.

Dynamics of supercooled water in highly compacted clays studied by neutron scattering

The freezing behavior of water confined in compacted charged and uncharged clays (montmorillonite in Na-and Ca-forms, illite in Na-and Ca-forms, kaolinite and pyrophyllite) was investigated by neutron scattering. Firstly, the amount of frozen (immobile) water was measured as a function of temperature at the IN16 backscattering spectrometer, Institute Laue-Langevin (ILL). Water in uncharged, partly hydrophobic (kaolinite) and fully hydrophobic (pyrophyllite) clays exhibited a similar freezing and melting behavior to that of bulk water. In contrast, water in charged clays which are hydrophilic could be significantly supercooled. To observe the water dynamics in these clays, further experiments were performed using quasielastic neutron scattering. At temperatures of 250, 260 and 270 K the diffusive motion of water could still be observed, but with a strong reduction in the water mobility as compared with the values obtained above 273 K. The diffusion coefficients followed a non-Arrhenius temperature dependence well described by the Vogel-Fulcher-Tammann and the fractional power relations. The fits revealed that Na-and Ca-montmorillonite and Ca-illite have similar Vogel-Fulcher-Tammann temperatures (T-VFT, often referred to as the glass transition temperature) of similar to 120 K and similar temperatures at which the water undergoes the 'strong-fragile' transition, T-s similar to 210 K. On the other hand, Na-illite had significantly larger values of T-VFT similar to 180 K and T-s similar to 240 K. Surprisingly, Ca-illite has a similar freezing behavior of water to that of montmorillonites, even though it has a rather different structure. We attribute this to the stronger hydration of Ca ions as compared with the Na ions occurring in the illite clays.

Carbon sequestration in community forests: trade-offs, multiple outcomes and institutional diversity in the Bolivian Amazon

Carbon sequestration in community forests presents a major challenge for the Reducing Emissions from Deforestation and Forest Degradation (REDD+) programme. This article uses a comparative analysis of the agricultural and forestry practices of indigenous peoples and settlers in the Bolivian Amazon to show how community-level institutions regulate the trade-offs between community livelihoods, forest species diversity, and carbon sequestration. The authors argue that REDD+ implementation in such areas runs the risk of: 1) reinforcing economic inequalities based on previous and potential land use impacts on ecosystems (baseline), depending on the socio-cultural groups targeted; 2) increasing pressure on land used for food production, possibly reducing food security and redirecting labour towards scarce off-farm income opportunities; 3) increasing dependence on external funding and carbon market fluctuations instead of local production strategies; and 4) further incentivising the privatization and commodification of land to avoid transaction costs associated with collective property rights. The article also advises against taking a strictly economic, market-based approach to carbon sequestration, arguing that such an approach could endanger fragile socio-ecological systems. REDD+ schemes should directly support existing efforts towards forest sustainability rather than simply compensating local land users for avoiding deforestation and forest degradation

Raw as Archival Still Image Format: A Consideration

Source materials like fine art, over-sized, fragile maps, and delicate artifacts have traditionally been digitally converted through the use of controlled lighting and high resolution scanners and camera backs. In addition the capture of items such as general and special collections bound monographs has recently grown both through consortial efforts like the Internet Archive's Open Content Alliance and locally at the individual institution level. These projects, in turn, have introduced increasingly higher resolution consumer-grade digital single lens reflex cameras or "DSLRs" as a significant part of the general cultural heritage digital conversion workflow. Central to the authors' discussion is the fact that both camera backs and DSLRs commonly share the ability to capture native raw file formats. Because these formats include such advantages as access to an image's raw mosaic sensor data within their architecture, many institutions choose raw for initial capture due to its high bit-level and unprocessed nature. However to date these same raw formats, so important to many at the point of capture, have yet to be considered "archival" within most published still imaging standards, if they are considered at all. Throughout many workflows raw files are deleted and thrown away after more traditionally "archival" uncompressed TIFF or JPEG 2000 files have been derived downstream from their raw source formats [1][2]. As a result, the authors examine the nature of raw anew and consider the basic questions, Should raw files be retained? What might their role be? Might they in fact form a new archival format space? Included in the discussion is a survey of assorted raw file types and their attributes. Also addressed are various sustainability issues as they pertain to archival formats with a special emphasis on both raw's positive and negative characteristics as they apply to archival practices. Current common archival workflows versus possible raw-based ones are investigated as well. These comparisons are noted in the context of each approach's differing levels of usable captured image data, various preservation virtues, and the divergent ideas of strictly fixed renditions versus the potential for improved renditions over time. Special attention is given to the DNG raw format through a detailed inspection of a number of its various structural components and the roles that they play in the format's latest specification. Finally an evaluation is drawn of both proprietary raw formats in general and DNG in particular as possible alternative archival formats for still imaging.

Genetic Engineering of Induced Pluripotent Stem Cells and Reprogramming to Motor Neurons to Elucidate Selective Motor Neuron Death in Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease, fatal within 1 to 5 years after onset of symptoms. About 3 out of 100’000 persons are diagnosed with ALS and there is still no cure available [1, 2]. 95% of all cases occur sporadically and the aetiology remains largely unknown [XXXX]. However, up to now 16 genes were identified to play a role in the development of familial ALS. One of these genes is FUS that encodes for the protein fused in sarcoma/translocated in liposarcoma (FUS/TLS). Mutations in this gene are responsible for some cases of sporadic as well as of inherited ALS [3]. FUS belongs to the family of heterogeneous nuclear ribonucleoproteins and is predicted to be involved in several cellular functions like transcription regulation [4], RNA splicing [5, 6], mRNA transport in neurons [7] and microRNA processing [8]. Aberrant accumulation of mutated FUS has been found in the cytoplasm of motor neurons from ALS patients [9]. The mislocalization of FUS is based on a mutation in the nuclear localization signal of FUS [10]. However, it is still unclear if the cytoplasmic localization of FUS leads to a toxic gain of cytoplasmic function and/or a loss of nuclear function that might be crucial in the course of ALS. The goal of this project is to characterize the impact of ALS-associated FUS mutations on in vitro differentiated motor neurons. To this end, we edit the genome of induced pluripotent stem cells (iPSC) using transcription activator-like effector nucleases (TALENs) [11,12] to create three isogenic cell lines, each carrying an ALS-associated FUS mutation (G156E, R244C and P525L). These iPSC’s will then be differentiated to motor neurons according to a recently establishe protocol (Ref Wichterle) and serve to study alterations in the transcriptome, proteome and metabolome upon the expression of ALS-associated FUS. With this approach, we hope to unravel the molecular mechanism leading to FUS-associated ALS and to provide new insight into the emerging connection between misregulation of RNA metabolism and neurodegeneration, a connection that is currently implied in a variety of additional neurological diseases, including spinocerebellar ataxia 2 (SCA-2), spinal muscular atrophy (SMA), fragile X syndrome, and myotonic dystrophy.

Genetic Engineering of Induced Pluripotent Stem Cells and Reprogramming to Motor Neurons to Elucidate Selective Motor Neuron Death in Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease, fatal within 1 to 5 years after onset of symptoms. About 3 out of 100’000 persons are diagnosed with ALS and there is still no cure available [1, 2]. 95% of all cases occur sporadically and the aetiology remains largely unknown [3]. However, up to now 16 genes were identified to play a role in the development of familial ALS. One of these genes is FUS that encodes for the protein fused in sarcoma (FUS). Mutations in this gene are responsible for some cases of sporadic as well as of inherited ALS [4]. FUS belongs to the family of heterogeneous nuclear ribonucleoproteins and is predicted to be involved in several cellular functions like transcription regulation, RNA splicing, mRNA transport in neurons and microRNA processing [5] Aberrant accumulation of mutated FUS has been found in the cytoplasm of motor neurons from ALS patients [6]. The mislocalization of FUS is based on a mutation in the nuclear localization signal of FUS [7]. However, it is still unclear if the cytoplasmic localization of FUS leads to a toxic gain of cytoplasmic function and/or a loss of nuclear function that might be crucial in the course of ALS. The goal of this project is to characterize the impact of ALS-associated FUS mutations on in vitro differentiated motor neurons. To this end, we edit the genome of induced pluripotent stem cells (iPSC) using transcription activator-like effector nucleases (TALENs) [8,9] to create three isogenic cell lines, each carrying an ALS-associated FUS mutation (G156E, R244C and P525L). These iPSC’s will then be differentiated to motor neurons according to a recently established protocol [10] and serve to study alterations in the transcriptome, proteome and metabolome upon the expression of ALS-associated FUS. With this approach, we hope to unravel the molecular mechanism leading to FUS-associated ALS and to provide new insight into the emerging connection between misregulation of RNA metabolism and neurodegeneration, a connection that is currently implied in a variety of additional neurological diseases, including spinocerebellar ataxia 2 (SCA-2), spinal muscular atrophy (SMA), fragile X syndrome, and myotonic dystrophy. [1] Cleveland, D.W. et al. (2001) Nat Rev Neurosci 2(11): 806-819 [2] Sathasivam, S. (2010) Singapore Med J 51(5): 367-372 [3] Schymick, J.C. et al. (2007) Hum Mol Genet Vol 16: 233-242 [4] Pratt, A.J. et al. (2012). Degener Neurol Neuromuscul Dis 2012(2): 1-14 [5] Lagier-Tourenne, C. Hum Mol Genet, 2010. 19(R1): p. R46-64 [6] Mochizuki, Y. et al. (2012) J Neurol Sci 323(1-2): 85-92 [7] Dormann, D. et al. (2010) EMBO J 29(16): 2841-2857 [8] Hockemeyer, D. et al. (2011) Nat Biotech 29(8): 731-734 [9] Joung, J.K. and J.D. Sander (2013) Nat Rev Mol Cell Biol 14(1): 49-55 [10]Amoroso, M.W. et al. (2013) J Neurosci 33(2): 574-586.

Can eye movements bias memory recall?

A large body of research suggests that when we retrieve visual information from memory, we look back to the location where we encoded these objects. It has been proposed that the oculomotor trace we act out during encoding is stored in long-term memory, along other contents of the episodic representation. If memory recall triggers the eyes to revisit the location where the stimulus was encoded, is there also an effect in the reverse direction? Can eye movements trigger memory recall? In Experiment 1 participants encoded two faces at two different locations on the computer screen. Then, the average face (morph) of these two faces appeared in either of the two encoding locations and participants had to indicate whether it resembles more the first or second face. In Experiment 2 the morph appeared in a new location, but participants had to repeat one of the oculomotor traces that was used during encoding. Participants’ morph perception was influenced both by the location and the eye-movement it was presented with. Our results suggest that eye-movements can bias memory recall, but only in a short-lasting and rather fragile way.

Bounded Seas: Island Parsing Without Shipwrecks

Imprecise manipulation of source code (semi-parsing) is useful for tasks such as robust parsing, error recovery, lexical analysis, and rapid development of parsers for data extraction. An island grammar precisely defines only a subset of a language syntax (islands), while the rest of the syntax (water) is defined imprecisely. Usually, water is defined as the negation of islands. Albeit simple, such a definition of water is naive and impedes composition of islands. When developing an island grammar, sooner or later a programmer has to create water tailored to each individual island. Such an approach is fragile, however, because water can change with any change of a grammar. It is time-consuming, because water is defined manually by a programmer and not automatically. Finally, an island surrounded by water cannot be reused because water has to be defined for every grammar individually. In this paper we propose a new technique of island parsing - bounded seas. Bounded seas are composable, robust, reusable and easy to use because island-specific water is created automatically. We integrated bounded seas into a parser combinator framework as a demonstration of their composability and reusability.

Probing the effect of minor groove interactions on the catalytic efficiency of DNAzymes 8–17 and 10–23

DNAzymes (Dz) 8–17 and 10–23 are two widely studied and well-characterized RNA-cleaving DNA catalysts. In an effort to further improve the understanding of the fragile interactions and dynamics of the enzymatic mechanism, this study examines the catalytic efficiency of minimally modified DNAzymes. Five single mutants of Dz8–17 and Dz10–23 were prepared by replacing the adenine residues in the corresponding catalytic cores with 3-deazaadenine units. Kinetic assays were used to assess the effect on the catalytic activity and thereby identify the importance of hydrogen bonding that arises from the N3 atoms. The results suggest that modifications at A15 and A15.0 of Dz8–17 have a significant influence and show a reduction in catalytic activity. Modification at each location in Dz10–23 results in a decrease of the observed rate constants, with A12 appearing to be the most affected with a reduction of ∼80% of kobs and ∼25% of the maximal cleavage rate compared to the wild-type DNAzyme. On the other hand, modification of A12 in Dz8–17 showed an ∼130% increase in kobs, thus unraveling a new potential site for the introduction of chemical modifications. A pH-profile analysis showed that the chemical cleavage step is rate-determining, regardless of the presence and/or location of the mutation. These findings point towards the importance of the N3-nitrogens of certain adenine nucleotides located within the catalytic cores of the DNAzymes for efficient catalytic activity and further suggest that they might directly partake in maintaining the appropriate tertiary structure. Therefore, it appears that minor groove interactions constitute an important feature of DNAzymes as well as ribozymes.

A Transatlantic Trade and Investment Partnership Agreement: Implications for Swiss Agriculture

To say that regionalism is gaining momentum has become an understatement. To mourn the lack of progress in multilateral trade rule-making is a commonplace in the discourse of politicians regretting the WTO negotiation standstill, and of “know-what-to-do” academics. The real problem is the uneven level-playing field resulting from increasing differences of rules and obligations. The Transatlantic Trade and Investment Partnership Agreement (TTIP) is a very ambitious project. WTI studies in 2014 have shown that the implications for Switzerland could be enormous. But even the combined market power of the two TTIP participants – the EU and the USA – will not level the playing field impairing the regulatory framework, and the market access barriers for trade in agriculture. Such differences will remain in three areas which, incidentally, are also vital for a global response to the food security challenge to feed 9 billion people before the year 2050: market access, non-tariff barriers, and trade-distorting domestic support programmes. This means that without multilateral progress the TTIP and other so-called mega-regionals, if successfully concluded, will exacerbate rather than lessen trade distortions. While this makes farmers in rich countries safer from competition, competitive production in all countries will be hampered. Consequently, and notwithstanding the many affirmations to the contrary, farm policies worldwide will continue to only address farmer security without increasing global food security. What are the implications of the TTIP for Swiss agriculture? This article, commissioned by Waseda University in Tokyo, finds that the failure to achieve further reforms – including a number of areas where earlier reforms have been reversed – is presenting Switzerland and Swiss agriculture with a terrible dilemma in the eventuality of a successful conclusion of the TTIP. If Swiss farm production is to survive for more than another generation, continuous reform efforts are required, and over-reliance on the traditional instruments of border protection and product support is to be avoided. Without a substantial TTIP obliging Switzerland to follow suit, autonomous reforms will remain extremely fragile.