bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenomenal Experiences, First-Person Methods, and the Artificiality of Experimental Data
Authors: Feest Uljana
Published: November 2014

While philosophical discussions of first-person methods often turn on the veridicality of first-person reports, I argue that more attention should be paid to the circumstances and aims of their experimental production in the science of perception. After pointing to the ‘constructedness’ of first-person reports, I raise questions about the criteria by which to judge whether they illuminate something about the nature of perception. I illustrate this point with a historical debate between Gestalt psychologists and atomists, both of whom used first-person methods to investigate perception, but who disagreed deeply over the epistemic value of their respective first-person data.
The Brain at Rest: What It Is Doing and Why That Matters
Authors: Klein Colin
Published: November 2014

Neuroimaging studies of the resting state continue to gather philosophical and scientific attention. Most discussions assume an identification between resting-state activity and activity in the so-called default mode network. I argue we should resist this identification, structuring my discussion around a dilemma first posed by Morcom and Fletcher. I offer an alternative view of rest as a state dominated by long-term processes and show how interaction effects might thereby let rest shed light on short-term changes in activation.
The Overlooked Role of Cases in Causal Attribution in Medicine
Authors: Ankeny Rachel A.
Published: November 2014

Although cases are central to the epistemic practices utilized within clinical medicine, they appear to be limited in their ability to provide evidence about causal relations because they provide detailed accounts of particular patients without explicit filtering of those attributes most likely to be relevant for explaining the phenomena observed. This paper uses a series of recent case reports to explore the role of cases in causal attribution in medical diagnosis. It is argued that cases are brought together by practitioners to generate causal attributions and testable predictions using a manipulability view of causation.
Explaining Financial Markets in Terms of Complex Systems
Authors: Kuhlmann Meinard
Published: November 2014

Large changes of financial market prices without exogenous causes deviate significantly from the Gaussian behavior of random variables. This indicates that financial markets should be treated as complex systems, for which nonlinear interactions of its subunits/agents are crucial. I focus on how the complex systems perspective impacts the notion of explanations in economics. The mechanistic model seems to fit the bill, but problems surface on closer scrutiny. One characteristic of complex systems is that their behavior is surprisingly independent from microscopic details. Thus, mechanistic explanations in the microreductionist manner seem unavailable. Despite these conflicts, I defend a modified structural mechanistic approach.
Testing Bottom-Up Models of Complex Citation Networks
Authors: Bedau Mark A.
Published: November 2014

The robust behavior of the patent citation network is a complex target of recent bottom-up models in science. This paper investigates the purpose and testing of three especially simple bottom-up models of the citation count distribution observed in the patent citation network. The complex causal webs in the models generate weakly emergent patterns of behavior, and this explains both the need for empirical observation of computer simulations of the models and the epistemic harmlessness of the resulting epistemic opacity.
Psychophysical Methods and the Evasion of Introspection
Authors: Chirimuuta M.
Published: November 2014

In this paper I argue that certain methodological conventions within psychophysics reflect a continued uncertainty over the reliability of subjects’ introspective judgements. Firstly, different psychophysical methods do not rely equally on the introspective capabilities of experimental subjects. I contrast “minimally introspective” tasks with “introspection-reliant” ones. It is only in the latter that introspection can be said to have a nontrivial role in the subjects’ performance. Secondly, my distinction maps onto a number of important methodological divisions in vision science. The introspection-reliant categorization captures many of the tasks typically considered less able to yield useful information regarding the processes underlying visual sensation.
Psychological Experiments and Phenomenal Experience in Size and Shape Constancy
Authors: Hatfield Gary
Published: November 2014

Some experiments in perceptual psychology measure perceivers’ phenomenal experiences of objects versus their cognitive assessments of object properties. Analyzing such experiments, this article responds to Pizlo’s claim that much work on shape constancy before 1985 confused problems of shape ambiguity with problems of shape constancy. Pizlo fails to grasp the logic of experimental designs directed toward phenomenal aspects of shape constancy. In the domain of size perception, Granrud’s studies of size constancy in children and adults distinguish phenomenal from cognitive factors.
What Is a Singularity in Geometrized Newtonian Gravitation?
Authors: Weatherall James Owen
Published: November 2014

I discuss singular space-times in the context of the geometrized formulation of Newtonian gravitation. I argue first that geodesic incompleteness is a natural criterion for when a model of geometrized Newtonian gravitation is singular, and then I show that singularities in this sense arise naturally in classical physics by stating and proving a classical version of the Raychaudhuri-Komar singularity theorem.
Rule-Following and the Evolution of Basic Concepts
Authors: Barrett Jeffrey A.
Published: November 2014

This article concerns how rule-following behavior might evolve, how an old evolved rule might come to be appropriated to a new context, and how simple concepts might coevolve with rule-following behavior. In particular, we consider how the transitive inferential rule-following behavior exhibited by pinyon and scrub jays might evolve in the context of a variety of the Skyrms-Lewis signaling game, then how such a rule might come to be appropriated to carry out inferences regarding stimuli different from those involved in the original evolution of the rule, and how this appropriation involves a step toward the evolution of basic ordinal concepts.
Experimental Modeling in Biology: In Vivo Representation and Stand-Ins as Modeling Strategies
Authors: Weber Marcel
Published: November 2014

Experimental modeling in biology involves the use of living organisms (not necessarily so-called model organisms) in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call “in vivo representations,” where one kind of causal process is used to stand in for a physically different kind of process. I discuss the advantages of this approach in the context of evolutionary biology.
A Functional Account of Causation; or, A Defense of the Legitimacy of Causal Thinking by Reference to the Only Standard That Matters—Usefulness (as Opposed to Metaphysics or Agreement with Intuitive Judgment)
Authors: Woodward James
Published: November 2014

This essay advocates a “functional” approach to causation and causal reasoning: these are to be understood in terms of the goals and purposes of causal thinking. This approach is distinguished from accounts based on metaphysical considerations or on reconstruction of “intuitions.”
Dietary change in Cape gannets reflects distributional and demographic shifts in two South African commercial fish stocks
Authors: Green David B. , Klages Norbert T. W. , Crawford Robert J. M. , Coetzee Janet C. , Dyer Bruce M. , Rishworth Gavin M. , Pistorius Pierre A.
Published: November 2014

Seabirds are upper trophic level predators, and are often highly sensitive to changes in the availability of their prey. Altered prey assemblages resulting from fluctuations in oceanographic conditions may be mirrored by shifts in seabird diet. Long-term studies of dietary change in seabirds therefore provide valuable insight into the nature of environmental shifts within the systems in which they forage. In recent decades, the Agulhas region in South Africa has undergone significant oceanographic change related to warming and intensification of the Agulhas current. Concurrent with this change, the population of Cape gannets Morus capensis at Bird Island, Algoa Bay, has grown rapidly, probably as a result of an increased availability of its dominant prey items, sardine Sardinops sagax and anchovy Engraulis encrasicolus. Using one of the longest and most complete time-series available on diet of a seabird (spanning 34 years), we tested for changes in composition and the abundance of dominant prey species of this population. These observed changes were also compared with acoustic survey estimates of their biomass, and annual catch data. Since 1979, the prey composition has remained similar, but the dietary contribution of sardine and anchovy, which fluctuated inversely to each other, increased over the study period. These shifts seem to be reflective of fluctuations in the stock size of sardine and anchovy. Conversely, a third species, saury Scomberesox saurus, dominant in the non-breeding diet of the 1980s, decreased significantly in dietary abundance over the following two decades. It is likely that dietary shifts of Cape gannets at Bird Island were related to climate-mediated oceanographic change. The implications of such changes are discussed.
Effect of Glutamate Accumulation During Sourdough Fermentation with Lactobacillus reuteri on the Taste of Bread and Sodium‐Reduced Bread
Authors: Zhao Cindy J. , Kinner Mathias , Wismer Wendy , Gänzle Michael G.
Published: November 2014

NaCl is an important contributor to the taste and texture of bread; therefore, it is challenging to reduce NaCl in bread without compromising quality. This study investigated sensory properties of bread with sourdough fermented with Lactobacillus reuteri accumulating glutamate or γ‐aminobutyrate (GABA). Sourdough was fermented with the GABA‐producing L. reuteri 100‐23 and LTH5448 as well as the glutamate‐accumulating L. reuteri 100‐23ΔgadB and TMW1.106. A consumer panel detected significant differences in the taste of bread with 6% addition of sourdough fermented with glutamate‐ or GABA‐producing L. reuteri. Remarkably, this difference was also detected when GABA‐producing L. reuteri 100‐23 was compared with its glutamate‐producing isogenic mutant L. reuteri 100‐23ΔgadB. The intensity of the salty taste of sourdough bread produced with 1% (flour basis) salt was equivalent to the intensity of the salty taste of reference bread produced with 1.5% salt. A trained panel found that sourdough breads (1 or 2% NaCl flour base) had a higher sour and umami taste intensity when compared with reference bread with the same salt content. Bread produced with sourdough fermented with L. reuteri 100‐23ΔgadB consistently had a higher umami taste intensity when compared with other sourdough breads. Neither sourdough addition nor NaCl level influenced bread volume or texture. In conclusion, the use of sourdough fermented with glutamate‐accumulating lactobacilli allowed reduction of NaCl without adverse effects on the taste or other quality attributes of bread.
Characterization of the Coronatine-Like Phytotoxins Produced by the Common Scab Pathogen Streptomyces scabies
Authors: Fyans Joanna K. , Altowairish Mead S. , Li Yuting , Bignell Dawn R. D.
Published: November 2014

Streptomyces scabies is an important causative agent of common scab disease of potato tubers and other root crops. The primary virulence factor produced by this pathogen is a phytotoxic secondary metabolite called thaxtomin A, which is essential for disease development. In addition, the genome of S. scabies harbors a virulence-associated biosynthetic gene cluster called the coronafacic acid (CFA)-like gene cluster, which was previously predicted to produce metabolites that resemble the Pseudomonas syringae coronatine (COR) phytotoxin. COR consists of CFA linked to an ethylcyclopropyl amino acid called coronamic acid, which is derived from L-allo-isoleucine. Using a combination of genetic and chemical analyses, we show that the S. scabies CFA-like gene cluster is responsible for producing CFA-L-isoleucine as the major product as well as other minor COR-like metabolites. Production of the metabolites was shown to require the cfl gene, which is located within the CFA-like gene cluster and encodes an enzyme involved in ligating CFA to its amino acid partner. CFA-L-isoleucine purified from S. scabies cultures was shown to exhibit bioactivity similar to that of COR, though it was found to be less toxic than COR. This is the first report demonstrating the production of coronafacoyl phytotoxins by S. scabies, which is the most prevalent scab-causing pathogen in North America.
Hydroxycinnamic Acid Degradation, a Broadly Conserved Trait, ProtectsRalstonia solanacearumfrom Chemical Plant Defenses and Contributes to Root Colonization and Virulence
Authors: Lowe Tiffany M. , Ailloud Florent , Allen Caitilyn
Published: November 2014

Plants produce hydroxycinnamic acid (HCA) defense compounds to combat pathogens, such as the bacterium Ralstonia solanacearum. We showed that an HCA degradation pathway is genetically and functionally conserved across diverse R. solanacearum strains. Further, a feruloyl-CoA synthetase (Δfcs) mutant that cannot degrade HCA was less virulent on tomato plants. To understand the role of HCA degradation in bacterial wilt disease, we tested the following hypotheses: HCA degradation helps the pathogen i) grow, as a carbon source; ii) spread, by reducing HCA-derived physical barriers; and iii) survive plant antimicrobial compounds. Although HCA degradation enabled R. solanacearum growth on HCA in vitro, HCA degradation was dispensable for growth in xylem sap and root exudate, suggesting that HCA are not significant carbon sources in planta. Acetyl-bromide quantification of lignin demonstrated that R. solanacearum infections did not affect the gross quantity or distribution of stem lignin. However, the Δfcs mutant was significantly more susceptible to inhibition by two HCA, namely, caffeate and p-coumarate. Finally, plant colonization assays suggested that HCA degradation facilitates early stages of infection and root colonization. Together, these results indicated that ability to degrade HCA contributes to bacterial wilt virulence by facilitating root entry and by protecting the pathogen from HCA toxicity.
Detached-Leaflet Evaluation of Tomato Germplasm for Late Blight Resistance and Its Correspondence to Field and Greenhouse Screenings
Authors: Foolad Majid R. , Sullenberger Matthew T. , Ashrafi Hamid
Published: November 2014

Breeding for disease resistance requires efficient techniques for screening large plant populations. Late blight (LB), caused by the oomycete Phytophthora infestans, is one of the most devastating diseases of tomato (Solanum lycopersicum) worldwide, and there is a great interest in developing cultivars with resistance to this pathogen. Screening for LB resistance is commonly conducted under field or greenhouse conditions using whole plants. In a previous study, we demonstrated correspondence between field and greenhouse screening of tomato for LB resistance. Here, we report the use of a detached-leaflet assay for such screening. Seventy-two genotypes from two tomato species, varying in degree of resistance and susceptibility to LB, were evaluated in two replicated experiments for response to LB in a detached-leaflet assay, and the results were compared with those previously obtained from field and greenhouse screening of the same genotypes. There were significant (P < 0.001) positive correlations between replications (average r = 0.75) and experiments (average r = 0.72), suggesting that the detached-leaflet experiments were consistent. Further, there were significant (P < 0.001) positive correlations between responses in the detached-leaflet assay and those from field (r = 0.82) and greenhouse screenings (r = 0.84), suggesting reliability of the detached-leaflet assay. The results indicate the utility of the detached-leaflet assay for evaluating tomato for LB resistance, which may facilitate screening of large breeding populations.
Identification and Molecular Characterization of Nuclear Citrus leprosis virus, a Member of the Proposed Dichorhavirus Genus Infecting Multiple Citrus Species in Mexico
Authors: Roy Avijit , Stone Andrew L. , Shao Jonathan , Otero-Colina Gabriel , Wei Gang , Choudhary Nandlal , Achor Diann , Levy Laurene , Nakhla Mark K. , Hartung John S. , Schneider William L. , Brlansky Ronald H.
Published: November 2014

Citrus leprosis is one of the most destructive diseases of Citrus spp. and is associated with two unrelated virus groups that produce particles primarily in either the cytoplasm or nucleus of infected plant cells. Symptoms of leprosis, including chlorotic spots surrounded by yellow haloes on leaves and necrotic spots on twigs and fruit, were observed on leprosis-affected mandarin and navel sweet orange trees in the state of Querétaro, Mexico. Serological and molecular assays showed that the cytoplasmic types of Citrus leprosis virus (CiLV-C) often associated with leprosis symptomatic tissues were absent. However, using transmission electron microscopy, bullet-shaped rhabdovirus-like virions were observed in the nuclei and cytoplasm of the citrus leprosis-infected leaf tissues. An analysis of small RNA populations from symptomatic tissue was carried out to determine the genome sequence of the rhabdovirus-like particles observed in the citrus leprosis samples. The complete genome sequence showed that the nuclear type of CiLV (CiLV-N) present in the samples consisted of two negative-sense RNAs: 6,268-nucleotide (nt)-long RNA1 and 5,847-nt-long RNA2, excluding the poly(A) tails. CiLV-N had a genome organization identical to that of Orchid fleck virus (OFV), with the exception of shorter 5′ untranslated regions in RNA1 (53 versus 205 nt) and RNA2 (34 versus 182 nt). Phylogenetic trees constructed with the amino acid sequences of the nucleocapsid (N) and glycoproteins (G) and the RNA polymerase (L protein) showed that CiLV-N clusters with OFV. Furthermore, phylogenetic analyses of N protein established CiLV-N as a member of the proposed genus Dichorhavirus. Reverse-transcription polymerase chain reaction primers for the detection of CiLV-N were designed based on the sequence of the N gene and the assay was optimized and tested to detect the presence of CiLV-N in both diseased and symptom-free plants.
A One-Two Punch: Hydralazine-Induced Liver Injury in a Recovering Ischemic Hepatitis
Authors: Alansari Ahmed , Quiel Luis , Boma Noella
Published: November 2014

A 77-year-old woman presented to the emergency department with a 2-day history of nausea and vomiting. Her medical history included diabetes mellitus, hypertension, atrial fibrillation, dilated cardiomyopathy, and coronary artery disease. Her home medications included aspirin, clopidogrel, warfarin, digoxin, metoprolol, losartan, simvastatin, isosorbide dinitrate, furosemide, and spironolactone. Initial physical examination showed blood pressure of 170/80 mm Hg with a heart rate of 69 beats per minute, otherwise unremarkable. Initial laboratory workup was significant for INR of 3.6, with slightly elevated troponin I and creatinine of 0.06 ng/mL and 1.4 mg/dL, respectively. The patient was admitted to the medicine floor. However, a few hours later, her atrial fibrillation went into rapid ventricular response, associated with hypotension. Cardiac enzymes began to trend up along with worsening of her renal function tests and hepatic enzymes. Her INR remained supratherapeutic despite holding coumadin and giving vitamin K. The patient was transferred to the medical intensive care unit for closer monitoring. During day 1 of the medical intensive care unit stay, losartan, simvastatin, and diuretics were held, whereas aspirin, clopidogrel, and isosorbide dinitrate were continued. In the following 2 days, there was worsening of tissue perfusion, and laboratory workup showed AST 514 IU/L, ALT 391 IU/L, INR >9, creatinine 3.8 mg/dL, and troponin I 0.19 ng/mL; therefore, digoxin was also held. Once the patient achieved hemodynamic stability, she was started on hydralazine. On day 4, renal function, cardiac, and hepatic enzymes improved significantly. However, 24 hours later, transaminases began to trend up again reaching a maximum of AST and ALT of 359 and 525 IU/L, respectively. Other possible causes were ruled out because her viral hepatitis markers, antihistone antibody, antinuclear antibody, and anti–double-stranded DNA were all negative. After thorough review of all medications, hydralazine was held with subsequent improvement in transaminases. The patient was seen a month later after her discharge, and all her laboratory workup improved to baseline.
Multiple solutions in supersymmetry and the Higgs
Authors: Allanach Ben C.
Published: November 2014

Weak-scale supersymmetry is a well-motivated, if speculative, theory beyond the Standard Model of particle physics. It solves the thorny issue of the Higgs mass, namely: how can it be stable to quantum corrections, when they are expected to be 10
15
times bigger than its mass? The experimental signal of the theory is the production and measurement of supersymmetric particles in the Large Hadron Collider (LHC) experiments. No such particles have been seen to date, but hopes are high for the impending run in 2015. Searches for supersymmetric particles can be difficult to interpret. Here, we shall discuss the fact that, even given a well-defined model of supersymmetry breaking with few parameters, there can be multiple solutions. These multiple solutions are physically different and could potentially mean that points in parameter space have been ruled out by interpretations of LHC data when they should not have been. We shall review the multiple solutions and illustrate their existence in a universal model of supersymmetry breaking.
The Higgs boson and cosmology
Authors: Shaposhnikov Mikhail
Published: November 2014

I will discuss how the Higgs field of the Standard Model may have played an important role in cosmology, leading to the homogeneity, isotropy and flatness of the Universe; producing the quantum fluctuations that seed structure formation; triggering the radiation-dominated era of the hot Big Bang; and contributing to the processes of baryogenesis and dark matter production.
Beyond the standard Higgs after the 125 GeV Higgs discovery
Authors: Grojean C.
Published: November 2014

An elementary, weakly coupled and solitary Higgs boson allows one to extend the validity of the Standard Model up to very high energy, maybe as high as the Planck scale. Nonetheless, this scenario fails to fill the universe with dark matter and does not explain the matter–antimatter asymmetry. However, amending the Standard Model tends to destabilize the weak scale by large quantum corrections to the Higgs potential. New degrees of freedom, new forces, new organizing principles are required to provide a consistent and natural description of physics beyond the standard Higgs.
The upgraded ATLAS and CMS detectors and their physics capabilities
Authors: Wells Pippa S.
Published: November 2014

The update of the European Strategy for Particle Physics from 2013 states that Europe's top priority should be the exploitation of the full potential of the LHC, including the high-luminosity upgrade of the machine and detectors with a view to collecting 10 times more data than in the initial design. The plans for upgrading the ATLAS and CMS detectors so as to maintain their performance and meet the challenges of increasing luminosity are presented here. A cornerstone of the physics programme is to measure the properties of the 125 GeV Higgs boson with the highest possible precision, to test its consistency with the Standard Model. The high-luminosity data will allow precise measurements of the dominant production and decay modes, and offer the possibility of observing rare modes including Higgs boson pair production. Direct and indirect searches for additional Higgs bosons beyond the Standard Model will also continue.
The discovery and measurements of a Higgs boson
Authors: Gianotti F. , Virdee T. S.
Published: November 2014

In July 2012, the ATLAS and CMS collaborations at CERN's Large Hadron Collider announced the discovery of a Higgs-like boson, a new heavy particle at a mass more than 130 times the mass of a proton. Since then, further data have revealed its properties to be strikingly similar to those of the Standard Model Higgs boson, a particle expected from the mechanism introduced almost 50 years ago by six theoreticians including British physicists Peter Higgs from Edinburgh University and Tom Kibble from Imperial College London. The discovery is the culmination of a truly remarkable scientific journey and undoubtedly the most significant scientific discovery of the twenty-first century so far. Its experimental confirmation turned out to be a monumental task requiring the creation of an accelerator and experiments of unprecedented capability and complexity, designed to discern the signatures that correspond to the Higgs boson. Thousands of scientists and engineers, in each of the ATLAS and CMS teams, came together from all four corners of the world to make this massive discovery possible.
Regime shifts in exploited marine food webs: detecting mechanisms underlying alternative stable states using size-structured community dynamics theory
Authors: Gårdmark Anna , Casini Michele , Huss Magnus , van Leeuwen Anieke , Hjelm Joakim , Persson Lennart , de Roos André M.
Published: November 2014

Many marine ecosystems have undergone ‘regime shifts’, i.e. abrupt reorganizations across trophic levels. Establishing whether these constitute shifts between alternative stable states is of key importance for the prospects of ecosystem recovery and for management. We show how mechanisms underlying alternative stable states caused by predator–prey interactions can be revealed in field data, using analyses guided by theory on size-structured community dynamics. This is done by combining data on individual performance (such as growth and fecundity) with information on population size and prey availability. We use Atlantic cod (
Gadus morhua
) and their prey in the Baltic Sea as an example to discuss and distinguish two types of mechanisms, ‘cultivation-depensation’ and ‘overcompensation’, that can cause alternative stable states preventing the recovery of overexploited piscivorous fish populations. Importantly, the type of mechanism can be inferred already from changes in the predators' body growth in different life stages. Our approach can thus be readily applied to monitored stocks of piscivorous fish species, for which this information often can be assembled. Using this tool can help resolve the causes of catastrophic collapses in marine predatory–prey systems and guide fisheries managers on how to successfully restore collapsed piscivorous fish stocks.
Resilience indicators: prospects and limitations for early warnings of regime shifts
Authors: Dakos Vasilis , Carpenter Stephen R. , van Nes Egbert H. , Scheffer Marten
Published: November 2014

In the vicinity of tipping points—or more precisely bifurcation points—ecosystems recover slowly from small perturbations. Such slowness may be interpreted as a sign of low resilience in the sense that the ecosystem could easily be tipped through a critical transition into a contrasting state. Indicators of this phenomenon of ‘critical slowing down (CSD)’ include a rise in temporal correlation and variance. Such indicators of CSD can provide an early warning signal of a nearby tipping point. Or, they may offer a possibility to rank reefs, lakes or other ecosystems according to their resilience. The fact that CSD may happen across a wide range of complex ecosystems close to tipping points implies a powerful generality. However, indicators of CSD are not manifested in all cases where regime shifts occur. This is because not all regime shifts are associated with tipping points. Here, we review the exploding literature about this issue to provide guidance on what to expect and what not to expect when it comes to the CSD-based early warning signals for critical transitions.
Theoretical basis for predicting climate-induced abrupt shifts in the oceans
Authors: Beaugrand Gregory
Published: November 2014

Among the responses of marine species and their ecosystems to climate change, abrupt community shifts (ACSs), also called regime shifts, have often been observed. However, despite their effects for ecosystem functioning and both provisioning and regulating services, our understanding of the underlying mechanisms involved remains elusive. This paper proposes a theory showing that some ACSs originate from the interaction between climate-induced environmental changes and the species ecological niche. The theory predicts that a substantial stepwise shift in the thermal regime of a marine ecosystem leads indubitably to an ACS and explains why some species do not change during the phenomenon. It also explicates why the timing of ACSs may differ or why some studies may detect or not detect a shift in the same ecosystem, independently of the statistical method of detection and simply because they focus on different species or taxonomic groups. The present theory offers a way to predict future climate-induced community shifts and their potential associated trophic cascades and amplifications.
Evaluating trophic cascades as drivers of regime shifts in different ocean ecosystems
Authors: Pershing Andrew J. , Mills Katherine E. , Record Nicholas R. , Stamieszkin Karen , Wurtzell Katharine V. , Byron Carrie J. , Fitzpatrick Dominic , Golet Walter J. , Koob Elise
Published: November 2014

In ecosystems that are strongly structured by predation, reducing top predator abundance can alter several lower trophic levels—a process known as a trophic cascade. A persistent trophic cascade also fits the definition of a regime shift. Such ‘trophic cascade regime shifts' have been reported in a few pelagic marine systems—notably the Black Sea, Baltic Sea and eastern Scotian Shelf—raising the question of how common this phenomenon is in the marine environment. We provide a general methodology for distinguishing top-down and bottom-up effects and apply this methodology to time series from these three ecosystems. We found evidence for top-down forcing in the Black Sea due primarily to gelatinous zooplankton. Changes in the Baltic Sea are primarily bottom-up, strongly structured by salinity, but top-down forcing related to changes in cod abundance also shapes the ecosystem. Changes in the eastern Scotian Shelf that were originally attributed to declines in groundfish are better explained by changes in stratification. Our review suggests that trophic cascade regime shifts are rare in open ocean ecosystems and that their likelihood increases as the residence time of water in the system increases. Our work challenges the assumption that negative correlation between consecutive trophic levels implies top-down forcing.
Synergistic impacts of global warming on the resilience of coral reefs
Authors: Bozec Yves-Marie , Mumby Peter J.
Published: November 2014

Recent epizootics have removed important functional species from Caribbean coral reefs and left communities vulnerable to alternative attractors. Global warming will impact reefs further through two mechanisms. A chronic mechanism reduces coral calcification, which can result in depressed somatic growth. An acute mechanism, coral bleaching, causes extreme mortality when sea temperatures become anomalously high. We ask how these two mechanisms interact in driving future reef state (coral cover) and resilience (the probability of a reef remaining within a coral attractor). We find that acute mechanisms have the greatest impact overall, but the nature of the interaction with chronic stress depends on the metric considered. Chronic and acute stress act additively on reef state but form a strong synergy when influencing resilience by intensifying a regime shift. Chronic stress increases the size of the algal basin of attraction (at the expense of the coral basin), whereas coral bleaching pushes the system closer to the algal attractor. Resilience can change faster—and earlier—than a change in reef state. Therefore, we caution against basing management solely on measures of reef state because a loss of resilience can go unnoticed for many years and then become disproportionately more difficult to restore.
The importance of within-system spatial variation in drivers of marine ecosystem regime shifts
Authors: Fisher J. A. D. , Casini M. , Frank K. T. , Möllmann C. , Leggett W. C. , Daskalov G.
Published: November 2014

Comparative analyses of the dynamics of exploited marine ecosystems have led to differing hypotheses regarding the primary causes of observed regime shifts, while many ecosystems have apparently not undergone regime shifts. These varied responses may be partly explained by the decade-old recognition that within-system spatial heterogeneity in key climate and anthropogenic drivers may be important, as recent theoretical examinations have concluded that spatial heterogeneity in environmental characteristics may diminish the tendency for regime shifts. Here, we synthesize recent, empirical within-system spatio-temporal analyses of some temperate and subarctic large marine ecosystems in which regime shifts have (and have not) occurred. Examples from the Baltic Sea, Black Sea, Bengula Current, North Sea, Barents Sea and Eastern Scotian Shelf reveal the largely neglected importance of considering spatial variability in key biotic and abiotic influences and species movements in the context of evaluating and predicting regime shifts. We highlight both the importance of understanding the scale-dependent spatial dynamics of climate influences and key predator–prey interactions to unravel the dynamics of regime shifts, and the utility of spatial downscaling of proposed mechanisms (as evident in the North Sea and Barents Sea) as a means of evaluating hypotheses originally derived from among-system comparisons.
Shifts in fisheries management: adapting to regime shifts
Authors: King Jacquelynne R. , McFarlane Gordon A. , Punt André E.
Published: November 2014

For many years, fisheries management was based on optimizing yield and maintaining a target biomass, with little regard given to low-frequency environmental forcing. However, this policy was often unsuccessful. In the last two to three decades, fisheries science and management have undergone a shift towards balancing sustainable yield with conservation, with the goal of including ecosystem considerations in decision-making frameworks. Scientific understanding of low-frequency climate–ocean variability, which is manifested as ecosystem regime shifts and states, has led to attempts to incorporate these shifts and states into fisheries assessment and management. To date, operationalizing these attempts to provide tactical advice has met with limited success. We review efforts to incorporate regime shifts and states into the assessment and management of fisheries resources, propose directions for future investigation and outline a potential framework to include regime shifts and changes in ecosystem states into fisheries management.
Globalization, marine regime shifts and the Soviet Union
Authors: Österblom Henrik , Folke Carl
Published: November 2014

Regime shifts have been observed in marine ecosystems around the world, with climate and fishing suggested as major drivers of such shifts. The global and regional dynamics of the climate system have been studied in this context, and efforts to develop an analogous understanding of fishing activities are developing. Here, we investigate the timing of pelagic marine regime shifts in relation to the emergence of regional and global fishing activities of the Soviet Union. Our investigation of official catch statistics reflects that the Soviet Union was a major fishing actor in all large marine ecosystems where regime shifts have been documented, including in ecosystems where overfishing has been established as a key driver of these changes (in the Baltic and Black Seas and the Scotian Shelf). Globalization of Soviet Union fishing activities pushed exploitation to radically new levels and triggered regional and global governance responses for improved management. Since then, exploitation levels have remained and increased with new actors involved. Based on our exploratory work, we propose that a deeper understanding of the role of global fishing actors is central for improved management of marine ecosystems.
A holistic view of marine regime shifts
Authors: Conversi Alessandra , Dakos Vasilis , Gårdmark Anna , Ling Scott , Folke Carl , Mumby Peter J. , Greene Charles , Edwards Martin , Blenckner Thorsten , Casini Michele , Pershing Andrew , Möllmann Christian
Published: November 2014

Understanding marine regime shifts is important not only for ecology but also for developing marine management that assures the provision of ecosystem services to humanity. While regime shift theory is well developed, there is still no common understanding on drivers, mechanisms and characteristic of abrupt changes in real marine ecosystems. Based on contributions to the present theme issue, we highlight some general issues that need to be overcome for developing a more comprehensive understanding of marine ecosystem regime shifts. We find a great divide between benthic reef and pelagic ocean systems in how regime shift theory is linked to observed abrupt changes. Furthermore, we suggest that the long-lasting discussion on the prevalence of top-down trophic or bottom-up physical drivers in inducing regime shifts may be overcome by taking into consideration the synergistic interactions of multiple stressors, and the special characteristics of different ecosystem types. We present a framework for the holistic investigation of marine regime shifts that considers multiple exogenous drivers that interact with endogenous mechanisms to cause abrupt, catastrophic change. This framework takes into account the time-delayed synergies of these stressors, which erode the resilience of the ecosystem and eventually enable the crossing of ecological thresholds. Finally, considering that increased pressures in the marine environment are predicted by the current climate change assessments, in order to avoid major losses of ecosystem services, we suggest that marine management approaches should incorporate knowledge on environmental thresholds and develop tools that consider regime shift dynamics and characteristics. This grand challenge can only be achieved through a holistic view of marine ecosystem dynamics as evidenced by this theme issue.
The synthesis, crystal structure and magnetic properties of a one-dimensional terbium(III)–octacyanidomolybdate(V) assembly
Authors: Shen Hong
Published: November 2014

A one-dimensional cyanide-bridged coordination polymer, poly[[aquadi-μ-cyanido-κ4C:N-hexacyanido-κ6C-(dimethylformamide-κO)bis(3,4,7,8-tetramethyl-1,10-phenanthroline-κ2N,N′)terbium(III)molybdate(V)] 4.5-hydrate], [MoTb(CN)8(C16H16N2)2(C3H7NO)(H2O)]·4.5H2O}n, has been prepared and characterized through IR spectroscopy, elemental analysis and single-crystal X-ray diffraction. The compound consists of one-dimensional chains in which cationic [Tb(tmphen)2(DMF)(H2O)]3+(tmphen is 3,4,7,8-tetramethyl-1,10-phenanthroline) and anionic [MoV(CN)8]3−units are linked in an alternating fashion through bridging cyanide ligands. Neighbouring chains are connected by three types of hydrogen bonds (O—H...O, O—H...N and C—H...O) and by π–π interactions to form a three-dimensional supramolecular structure. In addition, magnetic investigations show that ferromagnetic interactions exist in the compound.
Lichen planus pigmentosus‐inversus: Report of three Chinese cases and review of the published work
Authors: Chen Shumin , Sun Wenqi , Zhou Guizhi , Chen Shengli , Lu Xuanmei
Published: November 2014

Lichen planus pigmentosus‐inversus is a rare variant of lichen planus. So far, only 24 cases from 12 reports have been documented in the published work. The prominent characteristics of the disease are dark‐brown macules and patches confined to the non‐sun exposed, flexural areas and skin folds with lichenoid pathological changes and prominent melanin incontinence. We report three female Chinese patients with typical clinical and pathological manifestations and a miniature review of the published work.
‘Trophic whales’ as biotic buffers: weak interactions stabilize ecosystems against nutrient enrichment
Authors: Schwarzmüller Florian , Eisenhauer Nico , Brose Ulrich
Published: November 2014

Human activities may compromise biodiversity if external stressors such as nutrient enrichment endanger overall network stability by inducing unstable dynamics. However, some ecosystems maintain relatively high diversity levels despite experiencing continuing disturbances.

This indicates that some intrinsic properties prevent unstable dynamics and resulting extinctions. Identifying these ‘ecosystem buffers’ is crucial for our understanding of the stability of ecosystems and an important tool for environmental and conservation biologists. In this vein, weak interactions have been suggested as stabilizing elements of complex systems, but their relevance has rarely been tested experimentally.

Here, using network and allometric theory, we present a novel concept for a priori identification of species that buffer against externally induced instability of increased population oscillations via weak interactions. We tested our model in a microcosm experiment using a soil food‐web motif.

Our results show that large‐bodied species feeding at the food web's base, so called ‘trophic whales’, can buffer ecosystems against unstable dynamics induced by nutrient enrichment. Similar to the functionality of chemical or mechanical buffers, they serve as ‘biotic buffers’ that take up stressor effects and thus protect fragile systems from instability.

We discuss trophic whales as common functional building blocks across ecosystems. Considering increasing stressor effects under anthropogenic global change, conservation of these network‐intrinsic biotic buffers may help maintain the stability and diversity of natural ecosystems.
β‐asarone and levodopa co‐administration protects against 6‐hydroxydopamine‐induced damage in parkinsonian rat mesencephalon by regulating autophagy: down‐expression Beclin‐1 and light chain 3B and up‐expression P62
Authors: Huang Li‐Ping , Deng Min‐Zhen , He Yu‐Ping , Fang Yong‐Qi
Published: November 2014

In this study, we investigated Beclin‐1, light chain (LC)3B, and p62 expression in 6‐hydroxydopamine (6‐OHDA)‐induced parkinsonian rats after β‐asarone and levodopa (l‐dopa) co‐administration. Unilateral 6‐OHDA injection into the medial forebrain bundle was used to create the models, except in sham‐operated rats. Rats were divided into eight groups: sham‐operated group; 6‐OHDA model group; madopar group (75 mg/kg, per os (p.o.)); l‐dopa group (60 mg/kg, p.o.); β‐asarone group (15 mg/kg, p.o.); β‐asarone + l‐dopa co‐administered group (15 mg/kg + 60 mg/kg, p.o.); 3‐methyladenine group (500 nmol, intraperitoneal injection); and rapamycin group (1 mg/kg, intraperitoneal injection). Then, Beclin‐1, LC3B, and p62 expression in the mesencephalon were detected. The mesencephalon was also observed by transmission electron microscope. The results showed that Beclin‐1 and LC3B expression decreased and that p62 expression increased significantly in the madopar, l‐dopa, β‐asarone, and co‐administered groups when compared with the 6‐OHDA model. Beclin‐1 and LC3B expression in the β‐asarone and co‐administered groups were less than in the madopar or l‐dopa groups, whereas p62 expression in the β‐asarone and co‐administered groups was higher than in the madopar or l‐dopa groups. In addition, a significant decrease in autophagosome was exhibited in the β‐asarone and co‐administered groups when compared with the 6‐OHDA group. Our findings indicate that Beclin‐1 and LC3B expression decreased, whereas p62 expression increased after co‐administration treatment. In sum, all data suggest that the co‐administration of β‐asarone and l‐dopa may contribute to the treatment of 6‐OHDA‐induced damage in rats by inhibiting autophagy activity.
Carvedilol promotes neurological function, reduces bone loss and attenuates cell damage after acute spinal cord injury in rats
Authors: Liu Da , Huang Ying , Li Bin , Jia Changqing , Liang Feng , Fu Qin
Published: November 2014

Acute spinal cord injury (SCI) leads to permanent functional deficits via mechanical injury and secondary mechanisms, but the therapeutic strategy for SCI is limited. Carvedilol has been shown to possess multiple biological and pharmacological properties. The of the present study was to investigate the possible protective effect of carvedilol in SCI rats. An acute SCI rat model was established and neurological function was tested. After carvedilol (10 mg/kg, oral gavage) treatment for 21 days, the status of osteoporosis, neuron damage, astrocyte activation, inflammation, oxidative stress and apoptosis were evaluated in rats. Carvedilol significantly improved locomotor activity that was decreased by SCI. In addition, carvedilol promoted bone growth by regulating the expression of nuclear factor‐κB ligand (receptor activator of nuclear factor‐κB ligand; RANKL) and osteoprotegerin (OPG), inactivating osteoclasts and thereby increasing bone mineral density in tibias. In addition, carvedilol reduced SCI‐induced neural damage, increased neuron number and reduced astrocyte activation in the spinal cord. Furthermore, the production and mRNA expression of tumour necrosis factor‐α, interleukin (IL)‐1β and IL‐6 were significantly reduced, reduced glutathione content and superoxide dismutase activity were markedly increased and malondialdehyde content was markedly decreased in the spinal cords of carvedilol‐treated rats. These results indicate that carvedilol exhibits anti‐inflammatory and anti‐oxidative effects in SCI rats. In addition, the expression of Fas and Fas ligand was reduced by carvedilol treatment, which, in turn, reduced cleaved caspase 3 expression and finally decreased the number of apoptotic cells in the spinal cord. In conclusion, carvedilol promotes neurological function, reduces bone loss and attenuates cell damage after acute SCI in rats.