Fisheries and Coastal Resources Co-management in Asia: Selected Results from a Regional Research Project

Coastal fisheries, Fishery management, Resource management

Clustering by soft-constraint affinity propagation: Applications to gene-expression data

Motivation: Similarity-measure based clustering is a crucial problem appearing throughout scientific data analysis. Recently, a powerful new algorithm called Affinity Propagation (AP) based on message-passing techniques was proposed by Frey and Dueck \cite{Frey07}. In AP, each cluster is identified by a common exemplar all other data points of the same cluster refer to, and exemplars have to refer to themselves. Albeit its proved power, AP in its present form suffers from a number of drawbacks. The hard constraint of having exactly one exemplar per cluster restricts AP to classes of regularly shaped clusters, and leads to suboptimal performance, {\it e.g.}, in analyzing gene expression data. Results: This limitation can be overcome by relaxing the AP hard constraints. A new parameter controls the importance of the constraints compared to the aim of maximizing the overall similarity, and allows to interpolate between the simple case where each data point selects its closest neighbor as an exemplar and the original AP. The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering. Even though a new {\it a priori} free-parameter is introduced, the overall dependence of the algorithm on external tuning is reduced, as robustness is increased and an optimal strategy for parameter selection emerges more naturally. SCAP is tested on biological benchmark data, including in particular microarray data related to various cancer types. We show that the algorithm efficiently unveils the hierarchical cluster structure present in the data sets. Further on, it allows to extract sparse gene expression signatures for each cluster.Comment: 11 pages, supplementary material: http://isiosf.isi.it/~weigt/scap_supplement.pd

Using the TIDieR checklist to standardize the description of a functional strength training intervention for the upper limb after stroke

Background and Purpose: Published reports of intervention in randomized controlled trials are often poorly described. The Template for Intervention Description and Replication (TIDieR) checklist has been recently developed to improve the reporting of interventions. The aim of this article is to describe a therapy intervention used in the stroke rehabilitation trial, "Clinical Efficacy of Functional Strength Training for Upper Limb Motor Recovery Early After Stroke: Neural Correlates and Prognostic Indicators" (FAST-INdICATE), using TIDieR. Methods: The functional strength training intervention used in the FAST-INdICATE trial was described using TIDieR so that intervention can be replicated by both clinicians, who may implement it in practice, and researchers, who may deliver it in future research. The usefulness of TIDieR in the context of a complex stroke rehabilitation intervention was then discussed. Results and Discussion: The TIDieR checklist provided a systematic way of describing a treatment intervention used in a clinical trial of stroke rehabilitation. Clarification is needed regarding several aspects of the TIDieR checklist, including in which section to report about the development of the intervention in pilot studies, results of feasibility studies; overlap between training and procedures for assessing fidelity; and where to publish supplementary material so that it remains in the public domain. Summary: TIDieR is a systematic way of reporting the intervention delivered in a clinical trial of a complex intervention such as stroke rehabilitation. This approach may also have value for standardizing intervention in clinical practice. Video abstract is available for more insights from the authors (see Supplemental Digital Content 1, http://links.lww.com/JNPT/A131)

The Characterization and Reactivity of Tris(4-methylpyrazolyl)methane and its Tungsten and Molybdenum Metal Complexes

The scorpionate ligand tris(pyrazolyl)borate (Tp) has contributed to the understanding of coordination and organometallic chemistry and has proven to be useful in the synthesis of metalloprotein models. Studies focusing on the similar ligand, tris(pyrazolyl)methane (Tpm), have recently been made possible with improved synthetic techniques. Characterization of the Tpm ligand and its metal derivatives, [TpmW(CO)3L]+ and [TpmMo(CO)3L]+, unveiled unexpected activity in the 1H NMR chemical shift of the methane hydrogen after the coordination of a seventh ligand. The more electronegative the seventh ligand was, the more downfield the chemical shift appeared. Various analogs of Tpm have since been synthesized that substitute methyl groups on different positions of the pyrazolyl rings and the effect of these substitutions on the methane hydrogen was examined. This work successfully synthesized an analog of Tpm(4-methyl) and its metal complexes of Tpm(4-methyl)W(CO)3 and Tpm(4-methyl)Mo(CO)3. The reactivity of Tpm(4-methyl)M(CO)3 (M = W or Mo) was observed and FTIR, 1H NMR, and 13C NMR were used for the characterization of [Tpm(4-methyl)M(CO)3L]+[X]- (L = H, I, or Br; X = counterion). The chemical shift of the methane hydrogen was further examined and determined to follow the same trend seen in the previously reported Tpm metal complexes

Bioeconomics of the Philippine small pelagics fishery

Time series analysis of catch and effort data in the Philippines small pelagics fishery resulted in a level of biological and economic overexploitation. Open-access equilibrium has been reached at 410,000 hp representing a catch level of 465,000 tonnes. Present levels of effort would have to be reduced by 40% to attain maximum economic yield. An analysis of producer surplus showed that municipal aand commercial fishers were sustaining pure losses amounting to P9.4 billion indicating misallocation of labor and capital in an already overexploited fishery. Solutions to fisheries management problems are shown to emanate not just from the fishery, but more importantly, from the broader macroeconomic environment.Pelagic fisheries, Bioeconomics, Fishery economics, Fishery management, Philippines,

Observed Effects of a Changing Step-Edge Density on Thin-Film Growth Dynamics

We grew SrTiO3 on SrTiO3 [001] by pulsed laser deposition, while observing x-ray diffraction at the (0 0 .5) position. The drop dI in the x-ray intensity following a laser pulse contains information about plume-surface interactions. Kinematic theory predicts dI/I = -4sigma(1-sigma), so that dI/I depends only on the amount of deposited material sigma. In contrast, we observed experimentally that |dI/I| < 4sigma(1-sigma), and that dI/I depends on the phase of x-ray growth oscillations. The combined results suggest a fast smoothing mechanism that depends on surface step-edge density.Comment: 4 figure

Afghanistan Legal Lessons Learned: Army Rule of Law Operations

One of the most crucial components of the 2002 National Security Strategy which will impact virtually all other components is the world-wide implementation of the rule of law. In furtherance of the Strategy, National Security Presidential Directive 44 was issued in late 2005 and states that it is U.S. policy to work with other countries towards effective implementation of the rule of law. The Directive tasks the Secretaries of State and Defense with coordinating rule of law efforts and with integrating them into military contingency plans. Consequently, by direction of the President, the military has a key role to play in implementing the rule of law and Judge Advocates must be prepared to lead these efforts. Commanders look to Judge Advocates with the expectation that they will be competent and innovative in implementing the unit\u27s rule of law mission. This is clearly demonstrated by the Center for Law and Military Operations\u27 publication of the Rule of Law Handbook: A Practitioner\u27s Guide for Judge Advocates, where a constantly re-occurring theme is that the command naturally turns to the legal expert within the task force to plan, execute, coordinate, and evaluate rule of law efforts. Over six years of operations in Afghanistan, commanders have relied on JAs in their rule of law operations. These operations have created a number of lessons learned; this paper will highlight three: 1) Rule of law operations must be totally integrated into all phases and aspects of military operations and the unit mission; 2) U.S. Army Rule of Law efforts must be completely coordinated and synchronized with other rule of law efforts, especially those of the host nation, and must recognize what role the military is organizationally qualified to fill; 3) Military rule of law operations must be effects-based

A review of the ecological effectiveness of subtidal marine reserves in Central California, Part I: Synopsis of scientific investigations

Marine reserves, often referred to as no-take MPAs, are defined as areas within which human activities that can result in the removal or alteration of biotic and abiotic components of an ecosystem are prohibited or greatly restricted (NRC 2001). Activities typically curtailed within a marine reserve are extraction of organisms (e.g., commercial and recreational fishing, kelp harvesting, commercial collecting), mariculture, and those activities that can alter oceanographic or geologic attributes of the habitat (e.g., mining, shore-based industrial-related intake and discharges of seawater and effluent). Usually, marine reserves are established to conserve biodiversity or enhance nearby fishery resources. Thus, goals and objectives of marine reserves can be inferred, even if they are not specifically articulated at the time of reserve formation. In this report, we review information about the effectiveness of the three marine reserves in the Monterey Bay National Marine Sanctuary (Hopkins Marine Life Refuge, Point Lobos Ecological Reserve, Big Creek Ecological Reserve), and the one in the Channel Islands National Marine Sanctuary (the natural area on the north side of East Anacapa Island). Our efforts to objectively evaluate reserves in Central California relative to reserve theory were greatly hampered for four primary reasons; (1) few of the existing marine reserves were created with clearly articulated goals or objectives, (2) relatively few studies of the ecological consequences of existing reserves have been conducted, (3) no studies to date encompass the spatial and temporal scope needed to identify ecosystem-wide effects of reserve protection, and (4) there are almost no studies that describe the social and economic consequences of existing reserves. To overcome these obstacles, we used several methods to evaluate the effectiveness of subtidal marine reserves in Central California. We first conducted a literature review to find out what research has been conducted in all marine reserves in Central California (Appendix 1). We then reviewed the scientific literature that relates to marine reserve theory to help define criteria to use as benchmarks for evaluation. A recent National Research Council (2001) report summarized expected reserve benefits and provided the criteria we used for evaluation of effectiveness. The next step was to identify the research projects in this region that collected information in a way that enabled us to evaluate reserve theory relative to marine reserves in Central California. Chapters 1-4 in this report provide summaries of those research projects. Contained within these chapters are evaluations of reserve effectiveness for meeting specific objectives. As few studies exist that pertain to reserve theory in Central California, we reviewed studies of marine reserves in other temperate and tropical ecosystems to determine if there were lessons to be learned from other parts of the world (Chapter 5). We also included a discussion of social and economic considerations germane to the public policy decision-making processes associated with marine reserves (Chapter 6). After reviewing all of these resources, we provided a summary of the ecological benefits that could be expected from existing reserves in Central California. The summary is presented in Part II of this report. (PDF contains 133 pages.

On the importance of sublimation to an alpine snow mass balance in the Canadian Rocky Mountains

A modelling study was undertaken to evaluate the contribution of sublimation to an alpine snow mass balance in the Canadian Rocky Mountains. Snow redistribution and sublimation by wind, snowpack sublimation and snowmelt were simulated for two winters over an alpine ridge transect located in the Canada Rocky Mountains. The resulting snowcover regimes were compared to those from manual snow surveys. Simulations were performed using physically based blowing snow (PBSM) and snowpack ablation (SNOBAL) models. A hydrological response unit (HRU)-based spatial discretization was used rather than a more computationally expensive fully-distributed one. The HRUs were set up to follow an aerodynamic sequence, whereby eroded snow was transported from windswept, upwind HRUs to drift accumulating, downwind HRUs. That snow redistribution by wind can be adequately simulated in computationally efficient HRUs over this ridge has important implications for representing snow transport in large-scale hydrology models and land surface schemes. Alpine snow sublimation losses, in particular blowing snow sublimation losses, were significant. Snow mass losses to sublimation as a percentage of cumulative snowfall were estimated to be 20–32% with the blowing snow sublimation loss amounting to 17–19% of cumulative snowfall. This estimate is considered to be a conservative estimate of the blowing snow sublimation loss in the Canadian Rocky Mountains because the study transect is located in the low alpine zone where the topography is more moderate than the high alpine zone and windflow separation was not observed. An examination of the suitability of PBSM's sublimation estimates in this environment and of the importance of estimating blowing snow sublimation on the simulated snow accumulation regime was conducted by omitting sublimation calculations. Snow accumulation in HRUs was overestimated by 30% when neglecting blowing snow sublimation calculations