bluuebunny/crossref_metadata_2025 huggingface dataset:
Depolymerization of Poly(2,6-dimethyl-1,4-phenylene oxide) in Green Solvents: Water and Ionic Liquid
Authors: Nanayakkara Sepa , Patti Antonio F. , Saito Kei
Published: October 2012

The depolymerization of poly(2,6-dimethyl-1,4-phenyleneoxide) (PPO) was accomplished by employing 4-tert-butyl-2,6-dimethylphenol (TBDMP) and 2,6-dimethylphenol (DMP) under oxidative conditions in green solvents: water and ionic liquid. PPO depolymerized to oligomeric products in a faster process within 5 min with TBDMP and within 1 min with DMP in water. In addition to water, an ionic liquid mixture containing the 1-ethyl-3-methylimidazolium cation [C2mim] and a mixture of alkylbenzenesulfonate with xylene sulfonate anion [ABS] was used for the depolymerization of PPO. Depolymerization was successfully achieved in [C2mim][ABS] with TBDMP in a slower process within 3 h.
Predicting continuous variation in forest fuel load using biophysical models: a case study in south-eastern Australia
Authors: Duff Thomas J. , Bell Tina L. , York Alan
Published: October 2012

The increasing potential for wildfires in Mediterranean-type landscapes has resulted in pressure to mitigate fire threats. This is typically achieved by strategic reduction of fuel. To prioritise fuel management, it is necessary to understand vegetation dynamics and the relationships between plants and fuel. As the direct measurement of fuel in the field is labour intensive, mapped vegetation classes are typically used as to estimate fuel load. As vegetation properties vary continuously, the error in such estimates can be high. Remotely sensed and biophysical data are commonly used for vegetation classification, but rarely for estimating fuel load. This study investigated how fuel load varied with vegetation composition in an Australian woodland and assessed the potential for using biophysical models to create continuous estimates. Fuel was found to be influenced by species abundance, with some species having a greater contribution to load than others. Fuel was found to be somewhat predictable, with quantities related to fire history and several other biophysical variables. Models were applied to create continuous maps of fuel load; these provided a more precise representation of fuel variation than using discrete classes. Improved maps have the potential to facilitate improved prediction of fire behaviour and assist targeted fuel management.
Tibet is one of the centers of domestication of cultivated barley
Authors: Dai Fei , Nevo Eviatar , Wu Dezhi , Comadran Jordi , Zhou Meixue , Qiu Long , Chen Zhonghua , Beiles Avigdor , Chen Guoxiong , Zhang Guoping
Published: October 2012

The Near East Fertile Crescent is well recognized as a primary center of barley origin, diversity, and domestication. A large number of wild barleys have been collected from the Tibetan Plateau, which is characterized by an extreme environment. We used genome-wide diversity array technology markers to analyze the genotypic division between wild barley from the Near East and Tibet. Our results confirmed the existence of Tibetan wild barley and suggested that the split between the wild barleys in the Near East and those in Tibet occurred around 2.76 million years ago (Mya). To test the concept of polyphyletic domestication of barley, we characterized a set of worldwide cultivated barley. Some Chinese hulless and six-rowed barleys showed a close relationship with Tibetan wild barley but showed no common ancestor with other cultivated barley. Our data support the concept of polyphyletic domestication of cultivated barley and indicate that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. The current results may be highly significant in exploring the elite germplasm for barley breeding, especially against cold and drought stresses.
Phosphorylation of CRTC3 by the salt-inducible kinases controls the interconversion of classically activated and regulatory macrophages
Authors: Clark Kristopher , MacKenzie Kirsty F. , Petkevicius Kasparas , Kristariyanto Yosua , Zhang Jiazhen , Choi Hwan Geun , Peggie Mark , Plater Lorna , Pedrioli Patrick G. A. , McIver Ed , Gray Nathanael S. , Arthur J. Simon C. , Cohen Philip
Published: October 2012

Macrophages acquire strikingly different properties that enable them to play key roles during the initiation, propagation, and resolution of inflammation. Classically activated (M1) macrophages produce proinflammatory mediators to combat invading pathogens and respond to tissue damage in the host, whereas regulatory macrophages (M2b) produce high levels of anti-inflammatory molecules, such as IL-10, and low levels of proinflammatory cytokines, like IL-12, and are important for the resolution of inflammatory responses. A central problem in this area is to understand how the formation of regulatory macrophages can be promoted at sites of inflammation to prevent and/or alleviate chronic inflammatory and autoimmune diseases. Here, we demonstrate that the salt-inducible kinases (SIKs) restrict the formation of regulatory macrophages and that their inhibition induces striking increases in many of the characteristic markers of regulatory macrophages, greatly stimulating the production of IL-10 and other anti-inflammatory molecules. We show that SIK inhibitors elevate IL-10 production by inducing the dephosphorylation of cAMP response element-binding protein (CREB)-regulated transcriptional coactivator (CRTC) 3, its dissociation from 14-3-3 proteins and its translocation to the nucleus where it enhances a gene transcription program controlled by CREB. Importantly, the effects of SIK inhibitors on IL-10 production are lost in macrophages that express a drug-resistant mutant of SIK2. These findings identify SIKs as a key molecular switch whose inhibition reprograms macrophages to an anti-inflammatory phenotype. The remarkable effects of SIK inhibitors on macrophage function suggest that drugs that target these protein kinases may have therapeutic potential for the treatment of inflammatory and autoimmune diseases.
From discourse to grammar
Authors: Rodríguez Rosique Susana
Published: October 2012

This article deals with discourse functions of the Spanish scalar particle incluso in interaction with a si conditional. It will be shown that scalar properties of incluso require paying attention not only to its focus and scope, but also to its argumentative function and discourse structure. Thus, three main discourse functions are proposed for incluso when it appears with a si construction: co-argumentation, co-argumentation with a concessive sense, and counter-argumentation. Among these values, the latter constitutes a scalar concessive conditional. More generally, this article may shed light to understand how concessive conditionals work, and it may provide evidence for some controversial questions about the category.
Analyse syntaxique à l’aide des tables du Lexique-Grammaire du français
Authors: Tolone Elsa
Published: October 2012

Lexicon-Grammar tables, whose development was initiated by Gross (1975), are a very rich syntactic lexicon for the French language. They cover various lexical categories such as verbs, nouns, adjectives and adverbs. This linguistic database is nevertheless not directly usable by computer programs, as it is incomplete and lacks consistency.

Tables are defined on the basis of features which are not explicitly recorded in the lexicon. These features are only described in literature. To use these tables, we must make explicit the essential features appearing in each one of them. In addition, many features must be renamed for consistency sake.

Our aim is to adapt the tables, so as to make them usable in various Natural Language Processing (NLP) applications, in particular parsing. We describe the problems we encountered and the approaches we followed to enable their integration into a parser.

LGExtract
LGLex

fff
Lexique des Formes Fléchies du Français

fff
Produire des Annotations Syntaxiques à Grande Échelle
et al
fff
The cognitive basis of translation universals
Authors: Halverson Sandra L.
Published: October 2012

At present, there are few attempts to provide external explanations for the patterns subsumed under the heading of “translation universal”. In this paper, I discuss the possible cognitive basis for the patterns/processes that have been variously referred to as simplification/generalization, normalization, standardization, sanitization, and exaggeration of target language features. The framework that I adopt is that of cognitive grammar, and my claim is that all of the above arise from the existence of asymmetries in the cognitive organization of semantic information. I also propose that the converse case is true: cases involving a lack of conspicuous cognitive asymmetries will demonstrate the opposite effect in translated text. In closing, I place the argument in a larger perspective by adopting Croft’s (1990) scalar notion of generalization in a discussion of explanation in translation studies.
Deixis as an interactive feature in literary translations from Romanian into English
Authors: Mason Ian , Şerban Adriana
Published: October 2012

This study aims to investigate the use of deixis in a corpus of translations from twentieth century Romanian literature (novels and short stories) into English. Viewing deixis as an interactive feature of texts, it endeavours to find whether there are significant differences between the use of deixis in source texts and translations, and to see how systematic shifts as well as single occurrences can contribute to the shaping of a translated text which positions the reader in a different way from the source texts. It also explores ways in which the translators position themselves with respect to the text. The study finds that the main tendency is one of distancing, whereby proximal deictics tend to become distals, with the effect that readers will be presented with a translation which elicits less involvement on their part than the original text did in its context.
Changes in word order in two Hebrew translations of an Ibsen play
Authors: Muchnik Malka
Published: October 2012

This study examines differences in word order between two translations of Ibsen’s play An enemy of the people into Hebrew. Both versions were translated by Rivka Meshulach, with approximately 25 years between them. In the first version word order conforms to the norms of Classical Hebrew. In the second version, however, the translator changed word order so that the language would be closer to contemporary spoken Hebrew. This is illustrated through examples related to various syntactic constituents, including subject–predicate, predicate complements, parentheme and address forms. The reasoning behind this tendency focuses on the change in the norms of written language. As opposed to the normative restrictions which were widely accepted in written Hebrew just a generation ago, the current trend is for features of contemporary spoken language to be used in literature and theater.
Homogeneous matchbox manifolds
Authors: Clark Alex , Hurder Steven
Published: October 2012

We prove that a homogeneous matchbox manifold is homeomorphic to a McCord solenoid, thereby proving a strong version of a conjecture of Fokkink and Oversteegen, which is a general form of a conjecture of Bing. A key step in the proof shows that if the foliation of a matchbox manifold has equicontinuous dynamics, then it is minimal. Moreover, we then show that a matchbox manifold with equicontinuous dynamics is homeomorphic to a weak solenoid. A result of Effros is used to conclude that a homogeneous matchbox manifold has equicontinuous dynamics, and the main theorem is a consequence. The proofs of these results combine techniques from the theory of foliations and pseudogroups, along with methods from topological dynamics and coding theory for pseudogroup actions. These techniques and results provide a framework for the study of matchbox manifolds in general, and exceptional minimal sets of smooth foliations.
NMI mediates transcription-independent ARF regulation in response to cellular stresses
Authors: Li Zengpeng , Hou Jingjing , Sun Li , Wen Taoyong , Wang Liqin , Zhao Xinmeng , Xie Qingqing , Zhang Si Qing
Published: October 2012

The ARF tumor suppressor is a product of the INK4a/ARF locus, which is frequently mutated in human cancer. The expression of ARF is up-regulated in response to certain types of DNA damage, oncogene activation, and interferon stimuli. Through interaction with the p53 negative regulator MDM2, ARF controls a well-described p53/MDM2-dependent checkpoint. However, the mechanism of ARF induction is poorly understood. Using a yeast two-hybrid screen, we identify a novel ARF-interacting protein, N-Myc and STATs interactor (NMI). Previously, NMI was known to be a c-Myc–interacting protein. Here we demonstrate that through competitive binding to the ARF ubiquitin E3 ligase (ubiquitin ligase for ARF [ULF]), NMI protects ARF from ULF-mediated ubiquitin degradation. In response to cellular stresses, NMI is induced, and a fraction of NMI is translocated to the nucleus to stabilize ARF. Thus our work reveals a novel NMI-mediated, transcription-independent ARF induction pathway in response to cellular stresses.
Information-theoretic lower bound on energy cost of stochastic computation
Authors: Wiesner Karoline , Gu Mile , Rieper Elisabeth , Vedral Vlatko
Published: October 2012

Physical systems are often simulated using a stochastic computation where different final states result from identical initial states. Here, we derive the minimum energy cost of simulating a data sequence of a general physical system by stochastic computation. We show that the cost is proportional to the difference between two information-theoretic measures of complexity of the data—the
statistical complexity
and the
predictive information
. We derive the difference as the amount of information erased during the computation. Finally, we illustrate the physics of information by implementing the stochastic computation as a Gedanken experiment with a Szilard-type engine. The results create a new link between thermodynamics, information theory and complexity.
The spectrum of filament entanglement complexity and an entanglement phase transition
Authors: Buck Gregory , Simon Jonathan
Published: October 2012

DNA, hair, shoelaces, vortex lines, rope, proteins, integral curves, thread, magnetic flux tubes, cosmic strings and extension cords; filaments come in all sizes and with diverse qualities. Filaments tangle, with profound results: DNA replication is halted, field energy is stored, polymer materials acquire their remarkable properties, textiles are created and shoes stay on feet. We classify entanglement patterns by the rate with which entanglement complexity grows with the length of the filament. We show which rates are possible and which are expected in arbitrary circumstances. We identify a fundamental phase transition between linear and nonlinear entanglement rates. We also find (perhaps surprising) relationships between total curvature, bending energy and entanglement.
The life-history trade-off between fertility and child survival
Authors: Lawson David W. , Alvergne Alexandra , Gibson Mhairi A.
Published: October 2012

Evolutionary models of human reproduction argue that variation in fertility can be understood as the local optimization of a life-history trade-off between offspring quantity and ‘quality’. Child survival is a fundamental dimension of quality in these models as early-life mortality represents a crucial selective bottleneck in human evolution. This perspective is well-rehearsed, but current literature presents mixed evidence for a trade-off between fertility and child survival, and little empirical ground to evaluate how socioecological and individual characteristics influence the benefits of fertility limitation. By compiling demographic survey data, we demonstrate robust negative relationships between fertility and child survival across 27 sub-Saharan African countries. Our analyses suggest this relationship is primarily accounted for by offspring competition for parental investment, rather than by reverse causal mechanisms. We also find that the trade-off increases in relative magnitude as national mortality declines and maternal somatic (height) and extrasomatic (education) capital increase. This supports the idea that socioeconomic development, and associated reductions in extrinsic child mortality, favour reduced fertility by increasing the relative returns to parental investment. Observed fertility, however, falls considerably short of predicted optima for maximizing total offspring survivorship, strongly suggesting that additional unmeasured costs of reproduction ultimately constrain the evolution of human family size.
Unprecedented ichneumonid parasitoid wasp diversity in tropical forests
Authors: Veijalainen Anu , Wahlberg Niklas , Broad Gavin R. , Erwin Terry L. , Longino John T. , Sääksjärvi Ilari E.
Published: October 2012

The megadiverse parasitoid wasp family Ichneumonidae (Hymenoptera) is classically considered an exception to the extensively studied latitudinal diversity gradient: the majority of ichneumonid species are described from temperate regions. The gradient has been hypothesized to be dependent on the biology of the wasps, but recently questions of sampling and description biases have been raised. Here, we show with primary data that the species richness of Ichneumonidae is markedly underestimated in tropical areas and that latitudinal diversity patterns in the family remain uncharacterized. We discovered a startling 177 likely undescribed orthocentrine species with relatively low sampling effort in the forests of Central America and Amazonian Ecuador, over three times the previously known orthocentrine diversity in the world's tropics. Species accumulation curves reveal that we are just beginning to unveil the true extent of tropical orthocentrine diversity. We also found evidence for cryptic species; our DNA analysis revealed additional species not easily distinguishable using morphological characteristics. The difficulty in establishing species richness patterns of Ichneumonidae probably follows from the relative lack of taxonomic expertise and the low density of ichneumonid species throughout the landscape.
Cost of autotomy drives ontogenetic switching of anti-predator mechanisms under developmental constraints in a land snail
Authors: Hoso Masaki
Published: October 2012

Autotomy of body parts offers various prey animals immediate benefits of survival in compensation for considerable costs. I found that a land snailSatsuma caliginosaof populations coexisting with a snail-eating snakePareas iwasakiisurvived the snake predation by autotomizing its foot, whereas those out of the snake range rarely survived. Regeneration of a lost foot completed in a few weeks but imposed a delay of shell growth. Imprints of autotomy were found in greater than 10 per cent ofS. caliginosain the snake range but in only less than 1 per cent out of it, simultaneously demonstrating intense predation by the snakes and high efficiency of autotomy for surviving snake predation in the wild. However, in experiments, matureS. caliginosaperformed autotomy less frequently. Instead of the costly autotomy, they can use defensive denticles on the inside of their shell apertures. Owing to the constraints from the additive growth of shells, most pulmonate snails can produce these denticles only when they have fully grown up. Thus, this developmental constraint limits the availability of the modified aperture, resulting in ontogenetic switching of the alternative defences. This study illustrates how costs of adaptation operate in the evolution of life-history strategies under developmental constraints
A Comparative Study of Iron Uptake Mechanisms in Marine Microalgae: Iron Binding at the Cell Surface Is a Critical Step
Authors: Sutak Robert , Botebol Hugo , Blaiseau Pierre-Louis , Léger Thibaut , Bouget François-Yves , Camadro Jean-Michel , Lesuisse Emmanuel
Published: October 2012

We investigated iron uptake mechanisms in five marine microalgae from different ecologically important phyla: the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana, the prasinophyceae Ostreococcus tauri and Micromonas pusilla, and the coccolithophore Emiliania huxleyi. Among these species, only the two diatoms were clearly able to reduce iron, via an inducible (P. tricornutum) or constitutive (T. pseudonana) ferrireductase system displaying characteristics similar to the yeast (Saccharomyces cerevisiae) flavohemoproteins proteins. Iron uptake mechanisms probably involve very different components according to the species, but the species we studied shared common features. Regardless of the presence and/or induction of a ferrireductase system, all the species were able to take up both ferric and ferrous iron, and iron reduction was not a prerequisite for uptake. Iron uptake decreased with increasing the affinity constants of iron-ligand complexes and with increasing ligand-iron ratios. Therefore, at least one step of the iron uptake mechanism involves a thermodynamically controlled process. Another step escapes to simple thermodynamic rules and involves specific and strong binding of ferric as well as ferrous iron at the cell surface before uptake of iron. Binding was paradoxically increased in iron-rich conditions, whereas uptake per se was induced in all species only after prolonged iron deprivation. We sought cell proteins loaded with iron following iron uptake. One such protein in O. tauri may be ferritin, and in P. tricornutum, Isip1 may be involved. We conclude that the species we studied have uptake systems for both ferric and ferrous iron, both involving specific iron binding at the cell surface.
Bladder interstitial cells: an updated review of current knowledge
Authors: McCloskey K. D.
Published: October 2012

The field of bladder research has been energized by the study of novel interstitial cells (IC) over the last decade. Several subgroups of IC are located within the bladder wall and make structural interactions with nerves and smooth muscle, indicating integration with intercellular communication and key physiological functions. Significant progress has been made in the study of bladder ICs' cellular markers, ion channels and receptor expression, electrical and calcium signalling, yet their specific functions in normal bladder filling and emptying remain elusive. There is increasing evidence that the distribution of IC is altered in bladder pathophysiologies suggesting that changes in IC may be linked with the development of bladder dysfunction. This article summarizes the current state of the art of our knowledge of IC in normal bladder and reviews the literature on IC in dysfunctional bladder.
Autonomic nervous control of the urinary bladder
Authors: Ochodnicky P. , Uvelius B. , Andersson K.‐E. , Michel M. C.
Published: October 2012

The autonomic nervous system plays an important role in the regulation of the urinary bladder function. Under physiological circumstances, noradrenaline, acting mainly on β3‐adrenoceptors in the detrusor and on α1A‐adrenoceptors in the bladder outflow tract, promotes urine storage, whereas neuronally released acetylcholine acting mainly on M3 receptors promotes bladder emptying. Under pathophysiological conditions, however, this system may change in several ways. Firstly, there may be plasticity at the levels of innervation and receptor expression and function. Secondly, non‐neuronal acetylcholine synthesis and release from the urothelium may occur during the storage phase, leading to a concomitant exposure of detrusor smooth muscle, urothelium and afferent nerves to acetylcholine and noradrenaline. This can cause interactions between the adrenergic and cholinergic system, which have been studied mostly at the post‐junctional smooth muscle level until now. The implications of such plasticity are being discussed.
Organization of the neural switching circuitry underlying reflex micturition
Authors: de Groat W. C. , Wickens C.
Published: October 2012

The functions of the lower urinary tract to store and periodically eliminate urine are regulated by a complex neural control system in the brain and spinal cord that coordinates the activity of the bladder and urethral outlet. Experimental studies in animals indicate that urine storage is modulated by reflex mechanisms in the spinal cord, whereas voiding is mediated by a spinobulbospinal pathway passing through a coordination centre in the rostral brain stem. Many of the neural circuits controlling micturition exhibit switch‐like patterns of activity that turn on and off in an all‐or‐none manner. This study summarizes the anatomy and physiology of the spinal and supraspinal micturition switching circuitry and describes a computer model of these circuits that mimics the switching functions of the bladder and urethra at the onset of micturition.
Different mechanisms causing loss of mismatched human leukocyte antigens in relapsing t(6;11)(q27;q23) acute myeloid leukemia after haploidentical transplantation
Authors: Tamaki Hiroya , Fujioka Tatsuya , Ikegame Kazuhiro , Yoshihara Satoshi , Kaida Katsuji , Taniguchi Kyoko , Kato Ruri , Tokugawa Taduko , Nakata Jun , Inoue Takayuki , Yano Aya , Eguchi Ryoji , Okada Masaya , Maruya Etsuko , Saji Hiroh , Ogawa Hiroyasu
Published: October 2012

Mismatched human leukocyte antigens (HLAs) on leukemic cells can be targeted by donor T cells in HLA‐mismatched/haploidentical stem cell transplantation. In two cases of acute myeloid leukemia with t(6;11)(q27;q23) abnormality presented here, flow cytometry analysis showed a lack of HLA‐A unshared between recipients and donors in relapsing leukemic cells after HLA‐haploidentical transplantation. However, high‐resolution HLA genotyping showed that one case lacked a corresponding HLA haplotype, whereas the other preserved it. These cases suggest that leukemic cells, which lacked mismatched HLA expression, might have an advantage in selective expansion under donor T‐cell immune surveillance after HLA‐haploidentical transplantation. Most importantly, down‐regulation of unshared HLA expression potentially occurs by genetic alterations other than loss of HLA alleles.
Hypocupremia associated cytopenia and myelopathy: a national retrospective review
Authors: Gabreyes Alemayehu A. , Abbasi Hina Naz , Forbes Kirsten P. , McQuaker Grant , Duncan Andrew , Morrison Ian
Published: October 2012

Copper is an essential trace element that is involved in a number of important enzymatic processes throughout the body. Recent single case reports and small studies have shown that deficiency of copper can cause reversible haematological changes and irreversible neurological injury. We chose to undertake a national study, looking at all cases of copper deficiency in Scotland over a 5‐yr period using information from a national reference laboratory. From 16 identified patients, we determined that 86% had both haematological and neurological features of copper deficiency, while 18% had haematological features only at presentation. Twelve of the sixteen patients had high serum zinc concentrations (>18 μm/L) nine patients were using zinc‐containing dental fixatives at time of diagnosis. 94% of patients had haematological features as an initial manifestation of copper deficiency, which included anaemia, thrombocytopenia and neutropenia. Patients who underwent later bone marrow testing had appearances in keeping with refractory cytopenia with multilineage dysplasia, refractory anaemia with excess of blasts, unclassified marrow dysplasia or probable myelodysplasia (MDS). 75% of patients had neurological symptoms or signs, including progressive walking difficulties and paraesthesia, or gait difficulties without sensory signs. Clinical examination was in keeping with spastic paraparesis (either with or without sensory neuropathy). Magnetic resonance imaging (MRI) showed multifocal T2 hyper intense foci in the subcortical white matter, and atrophy of the cerebrum and cerebellum was also seen on computerised tomography (CT). MRI of the spinal cord showed signal change in the dorsal columns in either the cervical or thoracic cord. 93% of cytopenias responded to copper replacement and addressing the original cause of the copper deficiency, but only 25% of patients had improvement in their neurological function, while 33% deteriorated and 42% remained unchanged. Our study demonstrates that copper deficiency is an under‐recognised cause of several types of cytopenia, which are reversible but can progress to significant neurological injury if left untreated. We illustrate the importance of identifying these patients early to prevent irreversible neurological injury.
Programmed cell death pathways in cancer: a review of apoptosis, autophagy and programmed necrosis
Authors: Ouyang L. , Shi Z. , Zhao S. , Wang F.‐T. , Zhou T.‐T. , Liu B. , Bao J.‐K.
Published: October 2012

Programmed cell death (PCD), referring to apoptosis, autophagy and programmed necrosis, is proposed to be death of a cell in any pathological format, when mediated by an intracellular program. These three forms of PCD may jointly decide the fate of cells of malignant neoplasms; apoptosis and programmed necrosis invariably contribute to cell death, whereas autophagy can play either pro‐survival or pro‐death roles. Recent bulk of accumulating evidence has contributed to a wealth of knowledge facilitating better understanding of cancer initiation and progression with the three distinctive types of cell death. To be able to decipher PCD signalling pathways may aid development of new targeted anti‐cancer therapeutic strategies. Thus in this review, we present a brief outline of apoptosis, autophagy and programmed necrosis pathways and apoptosis‐related microRNA regulation, in cancer. Taken together, understanding PCD and the complex interplay between apoptosis, autophagy and programmed necrosis may ultimately allow scientists and clinicians to harness the three types of PCD for discovery of further novel drug targets, in the future cancer treatment.
Exploring the role of environmental variables in shaping patterns of seabed biodiversity composition in regional‐scale ecosystems
Authors: Roland Pitcher C. , Lawton Peter , Ellis Nick , Smith Stephen J. , Incze Lewis S. , Wei Chih‐Lin , Greenlaw Michelle E. , Wolff Nicholas H. , Sameoto Jessica A. , Snelgrove Paul V. R.
Published: October 2012

1. Environmental variables are often used as indirect surrogates for mapping biodiversity because species survey data are scant at regional scales, especially in the marine realm. However, environmental variables are measured on arbitrary scales unlikely to have simple, direct relationships with biological patterns. Instead, biodiversity may respond nonlinearly and to interactions between environmental variables.

2. To investigate the role of the environment in driving patterns of biodiversity composition in large marine regions, we collated multiple biological survey and environmental data sets from tropical NE Australia, the deep Gulf of Mexico and the temperate Gulf of Maine. We then quantified the shape and magnitude of multispecies responses along >30 environmental gradients and the extent to which these variables predicted regional distributions. To do this, we applied a new statistical approach, Gradient Forest, an extension of Random Forest, capable of modelling nonlinear and threshold responses.

3. The regional‐scale environmental variables predicted an average of 13–35% (up to 50–85% for individual species) of the variation in species abundance distributions. Important predictors differed among regions and biota and included depth, salinity, temperature, sediment composition and current stress. The shapes of responses along gradients also differed and were nonlinear, often with thresholds indicative of step changes in composition. These differing regional responses were partly due to differing environmental indicators of bioregional boundaries and, given the results to date, may indicate limited scope for extrapolating bio‐physical relationships beyond the region of source data sets.

4. Synthesis and applications. Gradient Forest offers a new capability for exploring relationships between biodiversity and environmental gradients, generating new information on multispecies responses at a detail not available previously. Importantly, given the scarcity of data, Gradient Forest enables the combined use of information from disparate data sets. The gradient response curves provide biologically informed transformations of environmental layers to predict and map expected patterns of biodiversity composition that represent sampled composition better than uninformed variables. The approach can be applied to support marine spatial planning and management and has similar applicability in terrestrial realms.
Aerial surveys of seabirds: the advent of digital methods
Authors: Buckland Stephen T. , Burt M. Louise , Rexstad Eric A. , Mellor Matt , Williams Adrian E. , Woodward Rebecca
Published: October 2012

1. Aerial seabird surveys are often conducted so that changes in abundance may be monitored. For example, large‐scale offshore wind farms are proposed for UK waters, and surveys are currently being conducted to quantify numbers and distribution ahead of construction.

2. Technological advances mean that strip transect surveys may now be conducted, using digital methods. We address survey design and data analysis issues for such digital surveys, contrasting them with visual aerial line transect surveys.

3. We also explore the relative performances of the methods for estimating the size of a large aggregation of common scoters in Carmarthen Bay, Wales. We found that abundance estimates from two digital methods were closely comparable, while estimates from visual aerial surveys were appreciably lower.

4. Synthesis and applications. Efficient survey methods to quantify abundance and distribution of seabirds are needed, to assess change arising from climate change, or developments such as the construction of large‐scale offshore wind farms. The traditional survey methods are visual surveys conducted along transects from ships or aircraft. Digital video and stills surveys can be conducted from aircraft flying sufficiently high to avoid disturbance, while still being able to detect and identify seabirds. Given the rapid technological developments, we expect digital surveys largely to replace visual surveys for seabirds in offshore regions.
Twenty‐five years of sagebrush steppe plant community development following seed addition
Authors: Hoelzle Timothy B. , Jonas Jayne L. , Paschke Mark W.
Published: October 2012

1. Plant community succession has been a major area of study over the past century with recent research focusing on the importance of initial colonisers following disturbance. Seed addition can accelerate ecosystem regeneration and is a method commonly used by land managers to restore disturbed lands. However, few studies have examined the effects of seeding treatments on long‐term community composition.

2. A study was established in 1984 in the Piceance Basin of northwest Colorado to examine how various revegetation seed mixes affect plant community development following disturbance. The site was surveyed again in 2008 and 2009 to assess long‐term community development.

3. Initial seed mix resulted in significant differences in plant community composition after 25 years. Seeding with native and exotic early‐seral species resulted in a community with significantly more exotic species and mid‐seral shrubs, while seeding with native late‐seral species resulted in a community dominated by perennial grasses. Additionally, an unseeded control resulted in a vegetation community dominated by both perennial grasses and mid‐seral shrubs, but community composition at the species level was considerably different from that of the seeded treatments. However, the plant community composition of each of the three treatments was significantly different from an adjacent undisturbed reference area, which was dominated by the late‐seral shrub, Artemisia tridentata, and perennial grasses.

4. Synthesis and applications. Our results illustrate how initial colonisers (seed mix) can strongly affect subsequent community assemblage after 25 years of development. Restoration ecologists should give considerable thought to the species used in a restoration seed mix to ensure the success of restoration designs and to create the desired community assembly and associated ecosystem services.
Comparing large‐scale bioregions and fine‐scale community‐level biodiversity predictions from subtidal rocky reefs across south‐eastern Australia
Authors: Leaper Rebecca , Dunstan Piers K. , Foster Scott D. , Barrett Neville J. , Edgar Graham J.
Published: October 2012

1. In the absence of knowledge of the large‐scale structure and distribution of marine biota, bioregionalisations, that is, spatial classifications of data on a range of environmental and/or biological attributes, are often viewed as one of the most appropriate frameworks within which to develop networks of marine protected areas (MPAs). However, despite their potential usefulness, few studies have assessed whether bioregionalisations can be used for management of species other than those it was derived from or whether bioregionalisations capture fully fine‐scale community‐level biodiversity patterns.

2. We investigated the large‐scale structure and distribution of demersal fishes and macroinvertebrates in south‐eastern Australia, using rank abundance distributions (RADs). We used a recently developed community modelling method that allows their multivariate distribution to vary according to environmental gradients, assessing the congruency of mapped biogeographic patterns between the different taxa, and in the light of the Interim Marine and Coastal Regionalisation for Australia (IMCRA).

3. A clear pattern in our analysis based on RADs showed a large difference in assemblage structure (i.e. in abundance, richness and evenness) between South Australia, where assemblages were generally more species rich and even, and Victoria and Tasmania, where assemblages were generally more species poor and uneven. The strong longitudinal pattern in species richness and evenness was generally congruent for both demersal fishes and macroinvertebrates and related to regional differences in oceanography.

4. We found that the regions of highest species richness were found in the ‘core’ bioregions rather than ‘transition’ bioregions as defined in the IMCRA and for both taxa. Moreover, we found that not all assemblage structures were equally alike and that South Australia had the greatest range of unique assemblage structures.

5. Synthesis and applications. While bioregionalisations are typically based on data from a single taxon, our findings highlight that they can be used as a surrogate for biological patterns seen in other taxa. Bioregionalisations, however, may not capture fully fine‐scale community‐level biodiversity patterns, and this may compromise the ability of protected area networks to protect the full variability in assemblage types. We suggest that it may be necessary to validate existing regionalisations with additional data and analyses such as the RAD analyses conducted here.
Disentangling the effects of multiple anthropogenic drivers on the decline of two tropical dry forest trees
Authors: Ticktin Tamara , Ganesan Rengaian , Paramesha Mallegowda , Setty Siddappa
Published: October 2012

1. Tropical plant populations are often subject to multiple types of anthropogenic disturbance. Effective management requires disentangling the effects of these disturbances and prioritizing interventions for the driver(s) most responsible for population decline. However, the effects of multiple drivers on plant population dynamics are rarely examined.

2. We assessed the independent and combined effects of common anthropogenic disturbances on the transient and long‐term population dynamics of two economically important, declining tree species in an Indian dry forest. Specifically, we drew on 10 years of demographic monitoring to assess the effects of non‐timber forest product (NTFP) harvest and two invasive species (an understorey shrub Lantana camara and a mistletoe Taxillus tomentosus) on amla (Phyllanthus emblica and Phyllanthus indofischeri) populations.

3. Although fruit harvest has been blamed for declining amla populations, the current policy and management strategies implemented to restrict it have little effect on long‐term stochastic growth rates (λs) of amla both with and without invasive species. In contrast, mistletoes significantly decreased λs of both species.

4. Lantana had both direct and indirect effects on P. emblica, causing a regeneration bottleneck. Lantana had a direct negative effect on seeding and sapling growth, whereas populations without lantana experienced higher levels of grazing by wild animals. Over 10 years, P. emblica populations dropped to 16% of their original size in areas with invasive species.

5. Synthesis and applications. Our results illustrate that mistletoe and lantana, not fruit harvest, are the main drivers of amla decline, and these species are likely to be driving the decline of other Indian dry forest tree species. Management directed only at limiting fruit harvest will be ineffective. Instead, control of both invasive species combined with temporary protection from grazing is urgently needed. The ban on fruit harvest in Indian protected areas is not an effective conservation policy for these species. Harvest is not necessarily the main cause of decline for NTFP species. Management plans for NTFP and other at‐risk species must consider the relative effects of different drivers of decline, including direct and indirect effects of invasive species.
Landscape‐scale responses of birds to agri‐environment management: a test of the English Environmental Stewardship scheme
Authors: Baker David J. , Freeman Stephen N. , Grice Phil V. , Siriwardena Gavin M.
Published: October 2012

1. Agri‐environment schemes (AES) are used extensively across Europe to address biodiversity declines in farmland. In England, Environmental Stewardship (ES) was introduced in 2005 to address the shortcomings of previous schemes, but as for schemes in other countries, assessments to date have revealed little evidence for national‐scale biodiversity benefits.

2. Here, we assess the efficacy of ES in driving changes in national farmland bird populations over the period 2002–2010, using BTO/JNCC/RSPB Breeding Bird Survey data. We tested for associations between ES management options, grouped into categories reflecting intended biological effects (e.g. stubble), and species’ population growth rates, wherever benefits of management might be expected to occur.

3. We found strong evidence for positive effects of management that provides winter food resources (i.e. ES stubble and wild bird seed [WBS] crops) on population growth rates across multiple granivorous species, at three landscape scales. The results for management aiming to provide breeding season benefits (i.e. grassland, field margin and boundary [hedge, ditch] management) showed mixed patterns of positive and negative associations.

4. The results for stubble and WBS provide the first evidence for landscape‐scale responses of biodiversity to AES management. The negative relationships identified may also show the importance of management context driving unforeseen predation or competition effects.

5. Synthesis and Applications. This study demonstrates that agri‐environment scheme management has the potential to have national‐scale effects on avian population growth rates, although our results suggest that some components of the scheme have had little effect on bird populations. Therefore, whilst this study provides the first proof‐of‐concept for broad‐and‐shallow scheme impacts on biodiversity, our results underline the importance of targeting towards population‐limiting factors, here winter food resources. A combination of low uptake of key in‐field options that provide winter seed and a failure to cover the late‐winter period effectively explains the lack of national population responses. Such issues need to be addressed before schemes like Environmental Stewardship will achieve their goals. This study shows the value of feedback from monitoring for informing scheme design, through identifying problems and testing solutions.
Macroinvertebrate responses along broad stressor gradients of deposited fine sediment and dissolved nutrients: a stream mesocosm experiment
Authors: Wagenhoff Annika , Townsend Colin R. , Matthaei Christoph D.
Published: October 2012

1. Degradation of freshwater ecosystems is a major concern worldwide. Agriculture introduces multiple stressors to streams, presenting a challenge for freshwater managers who must understand the relative strengths of individual stressor effects and their combined multiple‐stressor effects.

2. Using a replicated regression design, we manipulated levels of fine sediment and nutrients to create a broad eight‐point gradient for each stressor across 128 stream mesocosms to determine the shapes of macroinvertebrate responses after 21 days of exposure.

3. Subsidy–stress response patterns occurred along both stressor gradients. Sediment addition provided an initial subsidy for some pollution‐tolerant taxa and total macroinvertebrate density, but produced consistently negative effects for other taxa, total taxon richness and the density and richness of pollution‐sensitive Ephemeroptera, Plecoptera, Trichoptera (EPT) taxa. Nutrient enrichment provided an initial subsidy for densities of two common EPT taxa, total EPT density, macroinvertebrate and EPT taxon richness.

4. Few macroinvertebrate variables were affected by a single stressor (always fine sediment). The majority of responses were additive multiple‐stressor patterns, although Chironomidae density and EPT taxon richness followed complex synergistic patterns.

5. Fine sediment was a much more pervasive stressor than augmented nutrient concentrations. Overall, macroinvertebrate traits responded to stressors as strongly as community variables or individual taxa.

6. Synthesis and applications. Managing both fine sediment and nutrient inputs from agriculture is crucial to achieve good stream condition but priority should be given to minimizing fine sediment, which should be maintained below a threshold of 5% cover and 0·5‐mm depth. Managers also need to be wary of interactive multiple‐stressor effects because ecological outcomes of an increase in stressor load may be worse than predicted based on the knowledge of single‐stressor effects.