bluuebunny/crossref_metadata_2025 huggingface dataset:
A Raman-based endoscopic strategy for multiplexed molecular imaging
Authors: Zavaleta Cristina L. , Garai Ellis , Liu Jonathan T. C. , Sensarn Steven , Mandella Michael J. , Van de Sompel Dominique , Friedland Shai , Van Dam Jacques , Contag Christopher H. , Gambhir Sanjiv S.
Published: May 2013

Endoscopic imaging is an invaluable diagnostic tool allowing minimally invasive access to tissues deep within the body. It has played a key role in screening colon cancer and is credited with preventing deaths through the detection and removal of precancerous polyps. However, conventional white-light endoscopy offers physicians structural information without the biochemical information that would be advantageous for early detection and is essential for molecular typing. To address this unmet need, we have developed a unique accessory, noncontact, fiber optic-based Raman spectroscopy device that has the potential to provide real-time, multiplexed functional information during routine endoscopy. This device is ideally suited for detection of functionalized surface-enhanced Raman scattering (SERS) nanoparticles as molecular imaging contrast agents. This device was designed for insertion through a clinical endoscope and has the potential to detect and quantify the presence of a multiplexed panel of tumor-targeting SERS nanoparticles. Characterization of the Raman instrument was performed with SERS particles on excised human tissue samples, and it has shown unsurpassed sensitivity and multiplexing capabilities, detecting 326-fM concentrations of SERS nanoparticles and unmixing 10 variations of colocalized SERS nanoparticles. Another unique feature of our noncontact Raman endoscope is that it has been designed for efficient use over a wide range of working distances from 1 to 10 mm. This is necessary to accommodate for imperfect centering during endoscopy and the nonuniform surface topology of human tissue. Using this endoscope as a key part of a multiplexed detection approach could allow endoscopists to distinguish between normal and precancerous tissues rapidly and to identify flat lesions that are otherwise missed.
Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism
Authors: Cohen Samuel I. A. , Linse Sara , Luheshi Leila M. , Hellstrand Erik , White Duncan A. , Rajah Luke , Otzen Daniel E. , Vendruscolo Michele , Dobson Christopher M. , Knowles Tuomas P. J.
Published: May 2013

The generation of toxic oligomers during the aggregation of the amyloid-β (Aβ) peptide Aβ42 into amyloid fibrils and plaques has emerged as a central feature of the onset and progression of Alzheimer’s disease, but the molecular pathways that control pathological aggregation have proved challenging to identify. Here, we use a combination of kinetic studies, selective radiolabeling experiments, and cell viability assays to detect directly the rates of formation of both fibrils and oligomers and the resulting cytotoxic effects. Our results show that once a small but critical concentration of amyloid fibrils has accumulated, the toxic oligomeric species are predominantly formed from monomeric peptide molecules through a fibril-catalyzed secondary nucleation reaction, rather than through a classical mechanism of homogeneous primary nucleation. This catalytic mechanism couples together the growth of insoluble amyloid fibrils and the generation of diffusible oligomeric aggregates that are implicated as neurotoxic agents in Alzheimer’s disease. These results reveal that the aggregation of Aβ42 is promoted by a positive feedback loop that originates from the interactions between the monomeric and fibrillar forms of this peptide. Our findings bring together the main molecular species implicated in the Aβ aggregation cascade and suggest that perturbation of the secondary nucleation pathway identified in this study could be an effective strategy to control the proliferation of neurotoxic Aβ42 oligomers.
Present and future global distributions of the marine CyanobacteriaProchlorococcusandSynechococcus
Authors: Flombaum Pedro , Gallegos José L. , Gordillo Rodolfo A. , Rincón José , Zabala Lina L. , Jiao Nianzhi , Karl David M. , Li William K. W. , Lomas Michael W. , Veneziano Daniele , Vera Carolina S. , Vrugt Jasper A. , Martiny Adam C.
Published: May 2013

The CyanobacteriaProchlorococcusandSynechococcusaccount for a substantial fraction of marine primary production. Here, we present quantitative niche models for these lineages that assess present and future global abundances and distributions. These niche models are the result of neural network, nonparametric, and parametric analyses, and they rely on >35,000 discrete observations from all major ocean regions. The models assess cell abundance based on temperature and photosynthetically active radiation, but the individual responses to these environmental variables differ for each lineage. The models estimate global biogeographic patterns and seasonal variability of cell abundance, with maxima in the warm oligotrophic gyres of the Indian and the western Pacific Oceans and minima at higher latitudes. The annual mean global abundances ofProchlorococcusandSynechococcusare 2.9 ± 0.1 × 1027and 7.0 ± 0.3 × 1026cells, respectively. Using projections of sea surface temperature as a result of increased concentration of greenhouse gases at the end of the 21st century, our niche models projected increases in cell numbers of 29% and 14% forProchlorococcusandSynechococcus, respectively. The changes are geographically uneven but include an increase in area. Thus, our global niche models suggest that oceanic microbial communities will experience complex changes as a result of projected future climate conditions. Because of the high abundances and contributions to primary production ofProchlorococcusandSynechococcus, these changes may have large impacts on ocean ecosystems and biogeochemical cycles.
Migratory Movements of American Shad in the James River Fall Zone, Virginia
Authors: Aunins Aaron W. , Brown Bonnie L. , Balazik Matt , Garman Greg C.
Published: May 2013

The installation of Bosher's Dam fishway and notches or breaches to all dams downstream in the James River, Virginia, were completed during 1989–1999 to help restore the river's alosine populations by providing access to over 400 river kilometers (rkm) of historical spawning habitat that had been blocked for about 175 years. We used stationary radiotelemetry receivers in April–July 2009 to assess the passage of tagged adult American Shad Alosa sapidissima through the fall zone and Bosher's Dam fishway. Three receivers encompassed 25 rkm from below head of tide to 3 rkm above Bosher's Dam. Ninety-four American Shad were radio-tagged over 30 d, either at the head of tide (n = 64) or upstream below the Bosher's Dam fishway (n = 30). No American Shad tagged at the head of tide were detected at the base of Bosher's Dam, and none were detected above Bosher's Dam fishway. However, several tagged fish released at the base of Bosher's Dam remained there for days ( = 4.0 d, SD = 5.9 d) without negotiating the fishway. These results suggest that passage at Bosher's Dam and through other fall zone dams needs improvement and that American Shad access to historical spawning habitat remains thwarted.

Received April 18, 2012; accepted January 10, 2013
Angler Characteristics and Management Implications in a Large, Multistock, Spatially Structured Recreational Fishery
Authors: Ward Hillary G. M. , Quinn Michael S. , Post John R.
Published: May 2013

Management of recreational fisheries involves understanding how anglers interact with the fishery resource. Managers must understand the source (spatial distribution), efficiency, and behavior of angler effort in order to develop optimal management strategies in a social–ecological framework. We interviewed anglers (n = 1,956) and assessed fish populations in 21 lakes that are part of a multistock, spatially structured fishery for Rainbow Trout Oncorhynchus mykiss in the interior of British Columbia, Canada. Our objective was to assess the spatial behavior, harvest behavior, and catch efficiency of anglers and to understand the strengths of interactions between anglers and fish populations in three regions within this large fishery. Our results suggest a diverse angler population that varied in its behavior and its impact on the fishery. Using a hierarchical cluster analysis, we identified four distinct angler groups based on three variables that directly described how anglers interacted with the fishery (spatial distribution, catchability, and harvest behavior). Angler characteristics varied between groups, and the relative proportions of the four discrete angler groups varied among management regions. Substantial variation in angler characteristics across groups and variation in the relative distribution of the groups across regions imply that a “one size fits all” management approach is not optimal for this fishery. Instead, strategies that are attuned to angler characteristics would constitute a better approach for managing this large, spatially structured fishery.

Received April 18, 2012; accepted March 10, 2013
An Individual-Based Model for Population Viability Analysis of Humpback Chub in Grand Canyon
Authors: Pine William E. , Healy Brian , Smith Emily Omana , Trammell Melissa , Speas Dave , Valdez Rich , Yard Mike , Walters Carl , Ahrens Rob , Vanhaverbeke Randy , Stone Dennis , Wilson Wade
Published: May 2013

We developed an individual-based population viability analysis model (females only) for evaluating risk to populations from catastrophic events or conservation and research actions. This model tracks attributes (size, weight, viability, etc.) for individual fish through time and then compiles this information to assess the extinction risk of the population across large numbers of simulation trials. Using a case history for the Little Colorado River population of Humpback Chub Gila cypha in Grand Canyon, Arizona, we assessed extinction risk and resiliency to a catastrophic event for this population and then assessed a series of conservation actions related to removing specific numbers of Humpback Chub at different sizes for conservation purposes, such as translocating individuals to establish other spawning populations or hatchery refuge development. Our results suggested that the Little Colorado River population is generally resilient to a single catastrophic event and also to removals of larvae and juveniles for conservation purposes, including translocations to establish new populations. Our results also suggested that translocation success is dependent on similar survival rates in receiving and donor streams and low emigration rates from recipient streams. In addition, translocating either large numbers of larvae or small numbers of large juveniles has generally an equal likelihood of successful population establishment at similar extinction risk levels to the Little Colorado River donor population. Our model created a transparent platform to consider extinction risk to populations from catastrophe or conservation actions and should prove useful to managers assessing these risks for endangered species such as Humpback Chub.

Received August 28, 2012; accepted March 13, 2013
Predictors of Criminal Justice Outcomes Among Mental Health Courts Participants: The Role of Perceived Coercion and Subjective Mental Health Recovery
Authors: Pratt Christina , Koerner Joshua , Alexander MaryJane , Yanos PhilipT. , Kopelovich SarahL.
Published: May 2013

Internationally, one effort to reduce the number of people with serious mental illness (SMI) in jails and prisons is the development of Mental Health Courts (MHC). Research on MHCs to date has been disproportionately focused on the study of recidivism and re-incarceration over the potential of these problem-solving courts to facilitate mental health recovery and affect the slope or gradient of opportunity for recovery. Despite the strong conceptual links between the MHC approach and the recovery-orientation in mental health, the capacity for MHCs to facilitate recovery has not been explored. This user-informed mental health and criminal justice (MH/CJ) community-based participatory (CBPR) study assesses the extent to which MHC practices align with recovery-oriented principles and may subsequently affect criminal justice outcomes. We report on the experiences and perceptions of 51 MHC participants across four metropolitan Mental Health Courts. Specifically, the current study assesses: (1) how defendants’ perceptions of court practices, particularly with regard to procedural justice and coercion, relate to perceptions of mental health recovery and psychiatric symptoms, and, (2) how perceptions of procedural justice and mental health recovery relate to subsequent criminal justice outcomes. The authors hypothesized that perceived coercion and mental health recovery would be inversely related, that perceived coercion would be associated with worse criminal justice outcomes, and perceptions of mental health recovery would be associated with better criminal justice outcomes. Results suggest that perceived coercion in the MHC experience was negatively associated with perceptions of recovery among MHC participants. Perceptions of “negative pressures,” a component of coercion, were important predictors of criminal justice involvement in the 12-month period following MHC admission, even when controlling for other factors that were related to criminal justice outcomes, and that an increase in procedural justice was associated with a decrease in symptoms but curiously not to an increase in attitudes toward recovery. Implications and future directions are discussed.
Uniform hyperbolic approximations of measures with non-zero Lyapunov exponents
Authors: Luzzatto Stefano , Sánchez-Salas Fernando
Published: May 2013

We show that for any

C

1
+
α

C^{1+\alpha }

diffeomorphism of a compact Riemannian manifold, every non-atomic, ergodic, invariant probability measure with non-zero Lyapunov exponents is approximated by uniformly hyperbolic sets in the sense that there exists a sequence

Ω

n

\Omega _{n}

of compact, topologically transitive, locally maximal, uniformly hyperbolic sets such that for any sequence

{

μ

n

}

\{\mu _{n}\}

of

f
f

-invariant ergodic probability measures with

s
u
p
p
(

μ

n

)
⊆

Ω

n

supp (\mu _{n}) \subseteq \Omega _{n}

we have

μ

n

→
μ

\mu _{n}\to \mu

in the weak-

∗
*

topology.
Sharp local lower 𝐿^{𝑝}-bounds for Dyadic-like maximal operators
Authors: Melas Antonios , Nikolidakis Eleftherios , Stavropoulos Theodoros
Published: May 2013

We provide sharp lower

L

p

L^{p}

-bounds for the localized dyadic maximal operator on

R

n

\mathbb {R}^{n}

when the local

L

1

L^{1}

and the local

L

p

L^{p}

norm of the function are given. We actually do that in the more general context of homogeneous trees in probability spaces. For this we use an effective linearization for such maximal operators on an adequate set of functions.
miRTCat: a comprehensive map of human and mouse microRNA target sites including non-canonical nucleation bulges
Authors: Kim Ka-Kyung , Ham Juyoung , Chi Sung Wook
Published: May 2013

Summary: MicroRNAs (miRNAs) regulate various biological functions by binding hundreds of transcripts to impart post-transcriptional repression. Recently, by applying a transcriptome-wide experimental method for identifying miRNA target sites (Ago HITS-CLIP), a novel non-canonical target site, named ‘nucleation bulge’, was discovered as widespread, functional and evolutionally conserved. Although such non-canonical nucleation bulges have been proven to be predictive by using ‘pivot pairing rule’ and sequence conservation, this approach has not been applied yet. To facilitate the functional studies of non-canonical miRNA targets, we implement miRTCat: a comprehensive searchable map of miRNA target sites, including non-canonical nucleation bulges, not only mapped in experimentally verified miRNA-bound regions but also predicted in all 3′-untranslated regions (3′-UTRs) derived from human and mouse (∼15.6% as expected false-positive results).

Availability:  http://ion.skku.edu/mirtcat.

Contact:  swchi@skku.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Iron deficiency is a key determinant of health‐related quality of life in patients with chronic heart failure regardless of anaemia status
Authors: Comín‐Colet Josep , Enjuanes Cristina , González Gina , Torrens Ainhoa , Cladellas Mercè , Meroño Oona , Ribas Nuria , Ruiz Sonia , Gómez Miquel , Verdú José Maria , Bruguera Jordi
Published: May 2013

Aims

To evaluate the effect of iron deficiency (ID) and/or anaemia on health‐related quality of life (HRQoL) in patients with chronic heart failure (CHF).

Methods and results

We undertook a post‐hoc analysis of a cohort of CHF patients in a single‐centre study evaluating cognitive function. At recruitment, patients provided baseline information and completed the Minnesota Living with Heart Failure questionnaire (MLHFQ) for HRQoL (higher scores reflect worse HRQoL). At the same time, blood samples were taken for serological evaluation. ID was defined as serum ferritin levels <100 ng/mL or serum ferritin <800 ng/mL with transferrin saturation <20%. Anaemia was defined as haemoglobin ≤12 g/dL. A total of 552 CHF patients were eligible for inclusion, with an average age of 72 years and 40% in NYHA class III or IV. The MLHFQ overall summary scores were 41.0 ± 24.7 among those with ID, vs. 34.4 ± 26.4 for non‐ID patients (P = 0.003), indicating worse HRQoL. When adjusted for other factors associated with HRQoL, ID was significantly associated with worse MLHFQ overall summary (P = 0.008) and physical dimension scores (P = 0.002), whereas anaemia was not (both P > 0.05). Increased levels of soluble transferrin receptor were also associated with impaired HRQoL (P ≤ 0.001). Adjusting for haemoglobin and C‐reactive protein, ID was more pronounced in patients with anaemia compared with those without (P < 0.001).

Conclusion

In patients with CHF, ID but not anaemia was associated with reduced HRQoL, mostly due to physical factors.
Spectral microvolt T‐wave alternans testing has no prognostic value in patients recently hospitalized with decompensated heart failure
Authors: Jackson Colette E. , Myles Rachel C. , Tsorlalis Ioannis K. , Dalzell Jonathan R. , Rocchiccioli J. Paul , Rodgers John R. , Spooner Richard J. , Greenlaw Nicola , Ford Ian , Gardner Roy S. , Cobbe Stuart M. , Petrie Mark C. , McMurray John J.V.
Published: May 2013

Aims

Microvolt T‐wave alternans (MTWA) testing identifies beat‐to‐beat fluctuations in T‐wave morphology, which have been linked to ventricular arrhythmias. However, clinical studies have produced conflicting results and data in heart failure (HF) have been limited. The aim of this study was to determine the prevalence and incremental prognostic value of spectral MTWA testing in an unselected cohort of patients recently hospitalized with HF.

Methods and results

Consecutive admissions with confirmed HF were recruited, and survivors were invited to attend 1 month post‐discharge for MTWA testing. A total of 648 of 1003 enrolled patients returned for MTWA testing (58% male, mean age 71 years). Forty‐nine per cent were ineligible due to AF, pacemaker dependency, or inability to exercise. Of the 330 MTWA test results, 30% were positive, 24% negative, and 46% indeterminate. Overall, 268 deaths occurred during a median follow‐up of 3.1 (interquartile range 1.9–3.9) years. Of the ineligible patients, 48% died vs. 35% of eligible patients (P < 0.001). Of those patients with positive, negative, and indeterminate tests, 27, 35, and 40%, respectively, died (P = 0.12). Even when analysed as non‐negative (positive/indeterminate) vs. negative, there was still no between‐group difference in mortality (P = 0.95). MTWA results categorized as positive, negative, or indeterminate showed no incremental prognostic value in a multivariable model, which included BNP. Paradoxically, when compared in a binary fashion with a non‐negative result, a negative test was an independent predictor of death, as was ineligibility for MTWA testing.

Conclusion

Spectral MTWA testing was not widely applicable and failed to predict mortality, and so cannot be endorsed as a risk stratification tool in HF.
Economic value of biological attributes of artificial coral reefs
Authors: Polak Omer , Shashar Nadav
Published: May 2013

Polak, O., and Shashar, N. 2013. Economic value of biological attributes of artificial coral reefs – ICES Journal of Marine Science, 70: 904–912. Visitor appreciation of natural scenes such as coral reefs is well documented. However, what part the value of the biological component in these scenes plays in fostering people's enjoyment is unclear. Using the contingent valuation method (CVM), we examined divers' willingness to pay for changes in the fish and coral attributes over an artificial reef. Using image manipulations, different levels of community descriptors, such as richness, abundance, and biodiversity of corals and fish, were isolated, and the willingness to pay for proposed factors was examined. The results showed that divers were willing to contribute towards all increases in reef community attributes, and were partially able to discriminate between them. Biodiversity was the most valued index, while fish abundance was the least favoured. These results, which demonstrate that visitors understand the fundamentals that constitute a coral reef community and value its diversity, may help direct conservation efforts undertaken in the design of marine reserves and pre-planned artificial reefs.
Evidence for substock dynamics within whiting (Merlangius merlangus) management regions
Authors: de Castro Carlos , Wright Peter J. , Millar Colin P. , Holmes Steven J.
Published: May 2013

de Castro, C., Wright, P. J., Millar, C. P., and Holmes, S. J. 2013. Evidence for substock dynamics within whiting (Merlangius merlangus) management regions. – ICES Journal of Marine Science, 70: 1118–1127. Whiting in the North Sea and Eastern Channel is currently assessed as a single management unit. However, several studies suggest that this stock may be comprised of more than one subpopulation within a larger metapopulation. A key characteristic of metapopulations is asynchrony in the dynamics of component subpopulations. In this study, indices of recruitment and spawning–stock biomass (SSB) were developed to test for asynchrony across putative subpopulations in the North Sea and west of Scotland. Differences in SSB and recruitment trends were detected, consistent with expectations from metapopulation dynamics. At least three different subpopulation components (southern and northern North Sea, and west of Scotland) were indicated on the basis of differing trends. Analysis of spatial distribution suggested that the boundary between the northern and southern North Sea subpopulations was associated with the change in bathymetry that extended from the coast of Norfolk in England to the southern tip of Norway. The current management system for whiting in the North Sea assumes a unit stock, which is contrary to current sources of biological evidence and seems inappropriate. Consideration of a north–south split along the boundary detected should be beneficial for both assessment and management of the resource.
Rapid growth of wahoo (Acanthocybium solandri) in the Coral Sea, based on length-at-age estimates using annual and daily increments on sagittal otoliths
Authors: Zischke Mitchell T. , Griffiths Shane P. , Tibbetts Ian R.
Published: May 2013

Zischke, M. T., Griffiths, S. P., and Tibbetts, I. R. 2013. Rapid growth of wahoo (Acanthocybium solandri) in the Coral Sea, based on length-at-age estimates using annual and daily increments on sagittal otoliths. – ICES Journal of Marine Science, 70: 1128–1139. The wahoo (Acanthocybium solandri) is an economically important species incidentally caught in oceanic fisheries targeting tuna and coastal fisheries targeting mackerels. The age and growth of wahoo was examined using whole and sectioned otoliths from 395 fish (790–1770 mm LF) sampled from the Coral Sea. Growth increments were more reliably assigned on whole otoliths than sectioned otoliths. Edge analyses revealed that growth increments were deposited annually, primarily between October and February. Furthermore, analysis of presumed daily microincrements showed that ∼90% of fish had deposited the first “annual” growth increment by the 365th day, thereby indirectly validating annual increment formation. Wahoo were aged at between 108 d and 7 years, with 76% of fish being <2-year old. The specialized von Bertalanffy growth function provided the best fit to length-at-age data, with parameter estimates (sexes combined) of L∞ = 1499 mm LF, K = 1.58 year−1, and t0 = −0.17 years. The growth performance index for wahoo in the Coral Sea (φ′ = 4.55) was one of the highest of all pelagic fish, with their growth and maximum size most similar to dolphinfish. This study suggests that wahoo are one of the fastest growing teleosts and provides growth parameter estimates that may facilitate future stock assessments and guide fisheries management.
Identifying and characterizing demersal fish biodiversity hotspots in the Benguela Current Large Marine Ecosystem: relevance in the light of global changes
Authors: Kirkman Stephen P. , Yemane Dawit , Kathena John , Mafwila Samuel K. , Nsiangango Silvi E. , Samaai Toufiek , Axelsen Bjorn , Singh Larvika
Published: May 2013

Kirkman, S. P., Yemane, D., Kathena, J., Mafwila, S. K., Nsiangango, S. E., Samaai, T., Axelsen, B., and Singh, L. 2013. Identifying and characterizing demersal fish biodiversity hotspots in the Benguela Current Large Marine Ecosystem: relevance in the light of global changes. – ICES Journal of Marine Science, 70: 943–954. This study made use of distribution and abundance data of demersal fish and cephalopod species targeted during trawl surveys off Angola, Namibia and the west coast of South Africa, to determine species richness patterns including the location of diversity hotspots in the Benguela Current Large Marine Ecosystem. The reliability of alternative techniques for determining species richness patterns over the study domain, including geostatistical and non-geostatistical interpolation methods and regression type modelling, was tested using a cross-validation method. Generalized additive models were found to be the most effective method and were used to generate horizontal maps of species richness for different periods in each country. Despite changes in community structure that have been documented during the study period and which may be associated with climatic changes, this study showed the presence of consistently predictable hotspot areas over a 20–30-year study period (depending on country). The relationship between species richness and physical/environmental variables was inconsistent between countries, but generally hotspots of species richness were associated with greater depths and cooler bottom temperatures. Range shifts of species associated, for example, with warming of temperatures could conceivably affect the spatio-temporal persistence of hotspots in the long term.
Killer whale (Orcinus orca) depredation effects on catch rates of six groundfish species: implications for commercial longline fisheries in Alaska
Authors: Peterson Megan J. , Mueter Franz , Hanselman Dana , Lunsford Chris , Matkin Craig , Fearnbach Holly
Published: May 2013

Peterson, M. J., Mueter, F., Hanselman, D., Lunsford, C., Matkin, C., and Fearnbach, H. 2013. Killer whale (Orcinus orca) depredation effects on catch rates of six groundfish species: implications for commercial longline fisheries in Alaska. – ICES Journal of Marine Science, 70: 1220–1232. Killer whale (Orcinus orca) depredation occurs when whales damage or remove fish caught on longline gear. This study uses National Marine Fisheries Service longline survey data from 1998–2011 to explore spatial and temporal trends in killer whale depredation and to quantify the effect of killer whale depredation on catches of six groundfish species within three management areas in Alaska: the Bering Sea, Aleutian Islands and Western Gulf of Alaska. When killer whales were present during survey gear retrieval, whales removed an estimated 54–72% of sablefish (Anoplopoma fimbria), 41–84% of arrowtooth flounder (Atheresthes stomias) and 73% (Bering Sea only) of Greenland turbot (Reinhardtius hippoglossoides). Effects on Pacific halibut (Hippoglossus stenolepis) and Pacific cod (Gadus macrocephalus) were significant in the Western Gulf only with 51% and 46% reductions, respectively. Overall catches (depredated and non-depredated sets) for all groundfish species significantly impacted by killer whale depredation were lower by 9–28% (p < 0.05). Effects on shortspine thornyhead (Sebastolobus alascanus) catches were not significant in any management area (p > 0.05). These results provide insight into the potential impacts of killer whale depredation on fish stock abundance indices and commercially important fisheries in Alaska and will inform future research on apex predator–fisheries interactions.
Effects of General Anesthetics on Substance P Release and c-Fos Expression in the Spinal Dorsal Horn
Authors: Takasusuki Toshifumi , Yamaguchi Shigeki , Hamaguchi Shinsuke , Yaksh Tony L.
Published: May 2013

Background:

The authors examined in vivo the effects of general anesthetics on evoked substance P release (primary afferent excitability) and c-Fos expression (neuronal activation) in superficial dorsal horn.

Methods:

Rats received saline, propofol (100 mg/kg), pentobarbital (50 mg/kg), isoflurane (2 minimum alveolar concentration), nitrous oxide (66%), or fentanyl (30 μg/kg). During anesthesia, rats received intraplantar 5% formalin (50 μl) to left hind paw. Ten minutes later, rats underwent transcardial perfusion with 4% paraformaldehyde. Substance P release from small primary afferents was assessed by incidence of neurokinin 1 receptor internalization in the superficial dorsal horn. In separate studies, rats were sacrificed after 2 h and c-Fos expression measured.

Results:

Intraplantar formalin-induced robust neurokinin 1 receptor internalization in ipsilateral dorsal horn (ipsilateral: 54 ± 6% [mean ± SEM], contralateral: 12 ± 2%; P < 0.05; n = 4). Fentanyl, but not propofol, pentobarbital, isoflurane, nor nitrous oxide alone inhibited neurokinin 1 receptor internalization. However, 2 minimum alveolar concentration isoflurane + nitrous oxide reduced neurokinin 1 receptor internalization (27 ± 3%; P < 0.05; n = 5). All agents reduced c-Fos expression (control: 34 ± 4, fentanyl: 8 ± 2, isoflurane: 12 ± 3, nitrous oxide: 11 ± 2, isoflurane + nitrous oxide: 12 ± 1, pentobarbital: 11 ± 2, propofol: 13 ± 3; P < 0.05; n = 3).

Conclusion:

General anesthetics at anesthetic concentrations block spinal neuron activation through a mechanism that is independent of an effect on small primary afferent peptide release. The effect of fentanyl alone and the synergistic effect of isoflurane and nitrous oxide on substance P release suggest a correlative rationale for the therapeutic use of these anesthetic protocols by blocking nociceptive afferent transmitter release and preventing the initiation of cascade, which is immediately postsynaptic to the primary afferent.
PYR/RCAR Receptors Contribute to Ozone-, Reduced Air Humidity-, Darkness-, and CO2-Induced Stomatal Regulation
Authors: Merilo Ebe , Laanemets Kristiina , Hu Honghong , Xue Shaowu , Jakobson Liina , Tulva Ingmar , Gonzalez-Guzman Miguel , Rodriguez Pedro L. , Schroeder Julian I. , Broschè Mikael , Kollist Hannes
Published: May 2013

Rapid stomatal closure induced by changes in the environment, such as elevation of CO2, reduction of air humidity, darkness, and pulses of the air pollutant ozone (O3), involves the SLOW ANION CHANNEL1 (SLAC1). SLAC1 is activated by OPEN STOMATA1 (OST1) and Ca2+-dependent protein kinases. OST1 activation is controlled through abscisic acid (ABA)-induced inhibition of type 2 protein phosphatases (PP2C) by PYRABACTIN RESISTANCE/REGULATORY COMPONENTS OF ABA RECEPTOR (PYR/RCAR) receptor proteins. To address the role of signaling through PYR/RCARs for whole-plant steady-state stomatal conductance and stomatal closure induced by environmental factors, we used a set of Arabidopsis (Arabidopsis thaliana) mutants defective in ABA metabolism/signaling. The stomatal conductance values varied severalfold among the studied mutants, indicating that basal ABA signaling through PYR/RCAR receptors plays a fundamental role in controlling whole-plant water loss through stomata. PYR/RCAR-dependent inhibition of PP2Cs was clearly required for rapid stomatal regulation in response to darkness, reduced air humidity, and O3. Furthermore, PYR/RCAR proteins seem to function in a dose-dependent manner, and there is a functional diversity among them. Although a rapid stomatal response to elevated CO2 was evident in all but slac1 and ost1 mutants, the bicarbonate-induced activation of S-type anion channels was reduced in the dominant active PP2C mutants abi1-1 and abi2-1. Further experiments with a wider range of CO2 concentrations and analyses of stomatal response kinetics suggested that the ABA signalosome partially affects the CO2-induced stomatal response. Thus, we show that PYR/RCAR receptors play an important role for the whole-plant stomatal adjustments and responses to low humidity, darkness, and O3 and are involved in responses to elevated CO2.
MIXTA-Like Transcription Factors and WAX INDUCER1/SHINE1 Coordinately Regulate Cuticle Development inArabidopsisandTorenia fournieri
Authors: Oshima Yoshimi , Shikata Masahito , Koyama Tomotsugu , Ohtsubo Norihiro , Mitsuda Nobutaka , Ohme-Takagi Masaru
Published: May 2013

The waxy plant cuticle protects cells from dehydration, repels pathogen attack, and prevents organ fusion during development. The transcription factor WAX INDUCER1/SHINE1 (WIN1/SHN1) regulates the biosynthesis of waxy substances in Arabidopsis thaliana. Here, we show that the MIXTA-like MYB transcription factors MYB106 and MYB16, which regulate epidermal cell morphology, also regulate cuticle development coordinately with WIN1/SHN1 in Arabidopsis and Torenia fournieri. Expression of a MYB106 chimeric repressor fusion (35S:MYB106-SRDX) and knockout/down of MYB106 and MYB16 induced cuticle deficiencies characterized by organ adhesion and reduction of epicuticular wax crystals and cutin nanoridges. A similar organ fusion phenotype was produced by expression of a WIN1/SHN1 chimeric repressor. Conversely, the dominant active form of MYB106 (35S:MYB106-VP16) induced ectopic production of cutin nanoridges and increased expression of WIN1/SHN1 and wax biosynthetic genes. Microarray experiments revealed that MYB106 and WIN1/SHN1 regulate similar sets of genes, predominantly those involved in wax and cutin biosynthesis. Furthermore, WIN1/SHN1 expression was induced by MYB106-VP16 and repressed by MYB106-SRDX. These results indicate that the regulatory cascade of MIXTA-like proteins and WIN1/SHN1 coordinately regulate cutin biosynthesis and wax accumulation. This study reveals an additional key aspect of MIXTA-like protein function and suggests a unique relationship between cuticle development and epidermal cell differentiation.
Adaptive Enumeration of Implicit Surfaces with Affine Arithmetic
Authors: de Figueiredo Luiz Henrique , Stolfi Jorge
Published: May 2013

We discuss adaptive enumeration and rendering methods for implicit surfaces, using octrees computed with affine arithmetic, a new tool for range analysis. Affine arithmetic is similar to standard interval arithmetic, but takes into account correlations between operands and sub‐formulas, generally providing much tighter bounds for the computed quantities. The resulting octrees are accordingly much smaller, and the rendering faster.
Efficient Hierarchical Refinement and Clustering for Radiosity in Complex Environments
Authors: Gibson S. , Hubbold R.J.
Published: May 2013

Generating accurate radiosity solutions of very complex environments is a time‐consuming problem. We present a rapid hierarchical algorithm that enables such solutions to be computed quickly and efficiently. Firstly, a new technique for bounding the error in the transfer of radiosity between surfaces is discussed, incorporating bounds on form factors, visibility, irradiance, and reflectance over textured surfaces. This technique is then applied to the problem of bounding radiosity transfer between clusters of surfaces, leading to a fast, practical clustering algorithm that builds on the previous work of Sillion1. Volumes are used to represent clusters of small surfaces, but unlike previous algorithms, the orientations of surfaces inside each cluster are accounted for in both the error bound and radiosity transfer. This enables an accurate solution to be generated very efficiently, and results are presented demonstrating the performance of the algorithm on a variety of complex models, one containing almost a quarter of a million initial surfaces.
The Production of Volume Data from Triangular Meshes Using Voxelisation
Authors: Jones Mark W.
Published: May 2013

Voxelisation is the term given to the process of converting data from one source type into a three dimensional volume of data values. The techniques known collectively as volume visualisation can then be applied to the data in order to produce a graphical representation of the object. This paper gives a practical approach to the voxelisation of data in the form of triangular meshes, and demonstrates the use of the method on various datasets. Visualisation is achieved by a method also described in the paper.
Approximate Conversion of Parametric to Implicit Surfaces
Authors: Velho Luiz , Gomes Jonas
Published: May 2013

In this paper we present a framework for the approximate conversion of parametric to implicit surfaces. It takes as input a parametric description and generates a piecewise analytic implicit representation. The conversion process consists of three steps: 1) the parametric surface is rasterized into a volumetric characteristic function. 2) this binary function is converted into a volume array corresponding to samples of a smooth implicit function. 3) this volumetric representation is converted into a multiscale B‐spline model. This method is based on wavelet analysis and synthesis techniques and is very general. It can convert to implicit form any geometric object that is suitable for discretization into a characteristic function.
The ‘Graying’ of ‘Green’ Zones: Spatial Governance and Irregular Settlement in Xochimilco, Mexico City
Authors: Wigle Jill
Published: May 2013

This article details the evolving social and spatial dynamics of a planning approach that is now being used to regulate irregular or informal settlements in the conservation zone of Xochimilco in the Federal District of Mexico City. As part of the elaboration of ‘normative’ planning policies and practices, this approach counts, maps and then classifies irregular settlements into different categories with distinct land‐use regularization possibilities. These spatial calculations establish a continuum of ‘gray’ spaces, placing many settlements in a kind of planning limbo on so‐called ‘green’ conservation land. The research suggests that these spatial calculations are now an important part of enacting land‐use planning and presenting a useful ‘technical’ veneer through which the state negotiates competing claims to space. Based on a case study of an irregular settlement, the article examines how the state is implicated in the production and regulation of irregularity as part of a larger strategy of spatial governance. The research explores how planning ‘knowledges’ and ‘techniques’ help to create fragmented but ‘governable’ spaces that force communities to compete for land‐use regularization. The analysis raises questions about the conception of informality as something that, among other things, simply takes place outside of the formal planning system.
Urbanizing Refuge: Interrogating Spaces of Displacement
Authors: Sanyal Romola
Published: May 2013

Refugee spaces are emerging as quintessential geographies of the modern, yet their intimate and everyday spatialities remain under‐explored. Rendered largely through geopolitical discourses, they are seen as biopolitical spaces where the sovereign can reduce the subject to bare life. In conceptualizing refugee spaces some scholars have argued that, although many camps grow and develop over time, they evolve their own unique form of urbanism that is still un‐urban. This article challenges this idea of the camp as space of pure biopolitics and explores the politics of space in the refugee camp using urban debates. Using case studies from the Middle East and South Asia, it looks at how the refugee spaces developed and became informalized, and how people recovered their agency through ‘producing spaces’ both physically and politically. In doing so, it draws connections between refugee camps and other spaces of urban marginality, and suggests that refugee spaces can be seen as important sites for articulating new politics.
Wing geometric morphometrics and molecular assessment of members in the Albitarsis Complex from Colombia
Authors: Gómez G. , Jaramillo L. , Correa M. M.
Published: May 2013

Malaria parasites are transmitted to humans by female mosquitoes of the genus Anopheles. The Albitarsis Complex harbours at least eight species not readily differentiable by morphology. This complicates the determination of those species involved in malaria transmission and the implementation of targeted and effective vector control strategies. In Colombia, there is little information about the identity and distribution of the Albitarsis Complex members. In this work, COI DNA barcoding was used to assign specimens Anopheles albitarsis s.l. to any of the previously designated species of the Albitarsis Complex. Two molecular operational taxonomic units (MOTUs), differentially distributed in Colombia, were detected, A. albitarsis I in the NW and NE, and A. albitarsis F, E and NE Colombia. In contrast, nuclear white gene and ITS2 sequence analyses did not allow differentiating between the MOTUs. Wing landmark‐based geometric morphometrics applied to explore intertaxa phenotypic heterogeneity showed a subtle but significant difference in size, while shape did not allow the separation of the MOTUs. In general, the multiple marker analysis was not supportive of the existence in Colombia of more than one species of the Albitarsis Complex.
Inferring dispersal dynamics from local population demographic modelling: the case of the slender‐billed gull inFrance
Authors: Doxa A. , Besnard A. , Bechet A. , Pin C. , Lebreton J.‐D. , Sadoul N.
Published: May 2013

Although it is today accepted that population viability analyses are needed at a meta‐population level for most species, usually only single populations are monitored in the context of management and conservation programmes. This paper outlines a fairly general and easy‐to‐implement approach based on counts and capture–recapture data that allow the dynamics of single populations to be assessed even when they are highly connected to other populations. This approach was motivated by a study of the French population of the slender‐billed gullLarus genei, which experienced a sharp population increase in the 1980s and 1990s, suggesting that the species was not at risk of extinction. However, several recently raised concerns indicate that the observed population increase is unlikely to have been achieved uniquely by an intrinsic growth rate. We estimated local adult survival probability at 0.81 (0.79–0.83), which is considerably lower than that of other gull species of comparable size. Moreover, local fecundity observed in slender‐billed gulls [0.66 (0.47–0.85)] is lower than that observed in similar species. Massive reproduction failures and the low demographic parameters observed could be caused by chick exposure to aerial and terrestrial predation, leading to permanent emigration. Unrealistically high demographic parameter values would be needed to generate the observed local population increase. The results of our study indicate that connections with other neighbouring populations are responsible for the local population dynamics, and that about 10% of the individuals may be immigrants into this local population annually. However, our results suggest that the population of the slender‐billed gull may be stable at the west Mediterranean scale. The high annual fluctuations of population size observed at a larger scale also highlight the necessity for coordinated international action to protect a maximum of potential breeding sites in order to protect the species.
Injectable extended‐release naltrexone (XR‐NTX) for opioid dependence: long‐term safety and effectiveness
Authors: Krupitsky Evgeny , Nunes Edward V. , Ling Walter , Gastfriend David R. , Memisoglu Asli , Silverman Bernard L.
Published: May 2013

Aims

To describe drug use and safety with intramuscular injectable extended‐release naltrexone (XR‐NTX) in opioid dependence during a 1‐year open‐label extension phase.

Design

Following 6 months of randomized, double‐blind, placebo (PBO)‐controlled injections given every 28 days, patients receiving XR‐NTX 380 mg continued and PBO patients were switched to open‐label XR‐NTX, with monthly individual drug counseling, for a further year.

Setting

Thirteen clinical sites in Russia.

Participants

Adult opioid‐dependent outpatients.

Measurements

Monthly urine samples; reports of craving and functioning; adverse events.

Findings

For the open‐label extension (n = 114), 67 continued on XR‐NTX and 47 switched from PBO during the double‐blind phase to XR‐NTX during the open‐label phase. Overall, 62.3% (95% CI: 52.7%, 71.2%) completed the extension. Discontinuation occurred most commonly because of withdrawal of consent (18.4%) and loss to follow‐up (11.4%); two patients discontinued as a result of lack of efficacy and one because of adverse events. Urine testing revealed that 50.9% (41.5%, 60.4%) were abstinent from opioids at all assessments during the 1‐year open‐label phase. Adverse events reported by 21.1% of patients were judged to be study drug‐related. Injection site reactions were infrequent (6.1%) and the majority were mild. Elevations in liver function tests occurred for 16.7% of patients, but none of these elevations was judged to be clinically significant. No patients died, overdosed or discontinued as a result of severe adverse events.

Conclusions

During a 1‐year open‐label extension phase of injectable XR‐NTX for the prevention of relapse in opioid dependence, 62.3% of patients completed the phase and 50.9% were abstinent from opioids. No new safety concerns were evident.
Weather index insurance for agricultural development: introduction and overview
Authors: Sarris Alexander
Published: May 2013

This introductory paper highlights the key attributes of weather index insurance, and summarizes the major points and conclusions of the three subsequent papers included in the special issue.