bluuebunny/crossref_metadata_2025 huggingface dataset:
X-ray grating interferometry with a liquid-metal-jet source
Authors: Thüring T. , Zhou T. , Lundström U. , Burvall A. , Rutishauser S. , David C. , Hertz H. M. , Stampanoni M.
Published: August 2013

A liquid-metal-jet X-ray tube is used in an X-ray phase-contrast microscope based on a Talbot type grating interferometer. With a focal spot size in the range of a few microns and a photon flux of ∼1012 photons/s×sr, the brightness of such a source is approximately one order of magnitude higher than for a conventional microfocus source. For comparison, a standard microfocus source was used with the same grating interferometer, showing significantly increased visibility for the liquid-metal-jet arrangement. Together with the increased flux, this results in improved signal-to-noise ratio.
Efficient demagnetization protocol for the artificial triangular spin ice
Authors: Rodrigues J. H. , Mól L. A. S. , Moura-Melo W. A. , Pereira A. R.
Published: August 2013

In this work, we study demagnetization protocols for an artificial spin ice in a triangular geometry. Our results show that a simple hysteresis-like process is very efficient in driving the system to its ground state, even for a relatively strong disorder in the system, confirming previous expectations. In addition, transitions between the magnetized state and the ground state were observed to be mediated by the creation and propagation of vertices that behave like magnetic monopoles pseudo-particles. This is an important step towards a more detailed experimental study of monopole-like excitations in artificial spin ice systems.
Anion translocation through an Slc26 transporter mediates lumen expansion during tubulogenesis
Authors: Deng Wei , Nies Florian , Feuer Anja , Bočina Ivana , Oliver Dominik , Jiang Di
Published: August 2013

Lumen formation is a critical event in biological tube formation, yet its molecular mechanisms remain poorly understood. Specifically, how lumen expansion is coordinated with other processes of tubulogenesis is not well known, and the role of membrane transporters in tubulogenesis during development has not been adequately addressed. Here we identify a solute carrier 26 (Slc26) family protein as an essential regulator of tubulogenesis using the notochord of the invertebrate chordate
Ciona intestinalis
as a model.
Ci
-Slc26aα is indispensable for lumen formation and expansion, but not for apical/luminal membrane formation and lumen connection.
Ci
-Slc26aα acts as an anion transporter, mediating the electrogenic exchange of sulfate or oxalate for chloride or bicarbonate and electroneutral chloride:bicarbonate exchange. Mutant rescue assays show that this transport activity is essential for
Ci
-Slc26aα’s in vivo function. Our work reveals the consequences and relationships of several key processes in lumen formation, and establishes an in vivo assay for studying the molecular basis of the transport properties of SLC26 family transporters and their related diseases.
US studies may overestimate effect sizes in softer research
Authors: Fanelli Daniele , Ioannidis John P. A.
Published: August 2013

Many biases affect scientific research, causing a waste of resources, posing a threat to human health, and hampering scientific progress. These problems are hypothesized to be worsened by lack of consensus on theories and methods, by selective publication processes, and by career systems too heavily oriented toward productivity, such as those adopted in the United States (US). Here, we extracted 1,174 primary outcomes appearing in 82 meta-analyses published in health-related biological and behavioral research sampled from the Web of Science categories Genetics & Heredity and Psychiatry and measured how individual results deviated from the overall summary effect size within their respective meta-analysis. We found that primary studies whose outcome included behavioral parameters were generally more likely to report extreme effects, and those with a corresponding author based in the US were more likely to deviate in the direction predicted by their experimental hypotheses, particularly when their outcome did not include additional biological parameters. Nonbehavioral studies showed no such “US effect” and were subject mainly to sampling variance and small-study effects, which were stronger for non-US countries. Although this latter finding could be interpreted as a publication bias against non-US authors, the US effect observed in behavioral research is unlikely to be generated by editorial biases. Behavioral studies have lower methodological consensus and higher noise, making US researchers potentially more likely to express an underlying propensity to report strong and significant findings.
Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains
Authors: Sha Fern , Gencer Emel Basak , Georgeon Sandrine , Koide Akiko , Yasui Norihisa , Koide Shohei , Hantschel Oliver
Published: August 2013

Significance

Protein–protein interactions are essential for cellular regulation, but how changes in individual interactions influence cellular physiology or cause disease remains poorly characterized. Although selective and potent inhibitors of protein–protein interactions are powerful tools, developing such reagents is challenging. This is because signaling networks are composed of members of highly conserved protein domain families, with the Src-homology 2 (SH2) domain as an archetype. To address this challenge, we used protein design to successfully generate a set of reagents, termed monobodies, directed to the SH2 domains of SH2 domain-containing phosphatase 2 (SHP2), for which no specific inhibitors had been identified. These monobodies selectively and potently inhibit SHP2 function and demonstrate utility in dissecting the signaling networks of cancer cells.
Integration of responses within and acrossArabidopsisnatural accessions uncovers loci controlling root systems architecture
Authors: Rosas Ulises , Cibrian-Jaramillo Angelica , Ristova Daniela , Banta Joshua A. , Gifford Miriam L. , Fan Angela Huihui , Zhou Royce W. , Kim Grace Jaeyoon , Krouk Gabriel , Birnbaum Kenneth D. , Purugganan Michael D. , Coruzzi Gloria M.
Published: August 2013

Significance

Species display a range of plastic phenotypes that presumably have evolved as a result of adaptation to heterogeneous environments. We asked whether the genetic mechanisms that underlie adaptation across populations also determine the response of an individual plant to environmental cues inArabidopsis. Using an integrative root phenotyping approach, genes that underlie natural variation in root architecture across populations were shown to control plasticity responses within an individual. Together, our results uncover a genetic mechanism underlying the phenotypic plasticity of an individual and phenotypic diversity across natural variants.
Tuning the redox activity of encapsulated metal clusters via the metallic and semiconducting character of carbon nanotubes
Authors: Zhang Fan , Pan Xiulian , Hu Yongfeng , Yu Liang , Chen Xiaoqi , Jiang Peng , Zhang Hongbo , Deng Shibin , Zhang Jin , Bolin Trudy B. , Zhang Shuo , Huang Yuying , Bao Xinhe
Published: August 2013

Significance

The unique property of carbon nanotube channels has triggered wide research interest in different fields. An increasing number of studies show that confinement of metal or metal oxide nanoparticles inside these channels often leads to significantly modified catalytic activity with respect to the same bare metal nanoparticles or those dispersed on the outer walls. We demonstrate here that reactions can be further modulated by the electronic nature (metallic vs. semiconducting character) of nanotubes by taking encapsulated rhenium nanocatalysts as a probe. Particularly, the chemical state of the encapsulated rhenium is tuned due to host–guest electronic interaction. This is of significance for catalytic reactions sensitive to the chemical state of active metals, because it may change the reaction pathways.
Insulin growth factor signaling is regulated by microRNA-486, an underexpressed microRNA in lung cancer
Authors: Peng Yong , Dai Yuntao , Hitchcock Charles , Yang Xiaojuan , Kassis Edmund S. , Liu Lunxu , Luo Zhenghua , Sun Hui-Lung , Cui Ri , Wei Huijun , Kim Taewan , Lee Tae Jin , Jeon Young-Jun , Nuovo Gerard J. , Volinia Stefano , He Qianchuan , Yu Jianhua , Nana-Sinkam Patrick , Croce Carlo M.
Published: August 2013

MicroRNAs (miRNAs) are small 19- to 24-nt noncoding RNAs that have the capacity to regulate fundamental biological processes essential for cancer initiation and progression. In cancer, miRNAs may function as oncogenes or tumor suppressors. Here, we conducted global profiling for miRNAs in a cohort of stage 1 nonsmall cell lung cancers (
n
= 81) and determined that miR-486 was the most down-regulated miRNA in tumors compared with adjacent uninvolved lung tissues, suggesting that miR-486 loss may be important in lung cancer development. We report that miR-486 directly targets components of insulin growth factor (IGF) signaling including insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and phosphoinositide-3-kinase, regulatory subunit 1 (alpha) (PIK3R1, or p85a) and functions as a potent tumor suppressor of lung cancer both in vitro and in vivo. Our findings support the role for miR-486 loss in lung cancer and suggest a potential biological link to p53.
Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins
Authors: Renaud Nicolas , Berlin Yuri A. , Ratner Mark A.
Published: August 2013

Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels.
Cellular capsules as a tool for multicellular spheroid production and for investigating the mechanics of tumor progression in vitro
Authors: Alessandri Kévin , Sarangi Bibhu Ranjan , Gurchenkov Vasily Valérïévitch , Sinha Bidisha , Kießling Tobias Reinhold , Fetler Luc , Rico Felix , Scheuring Simon , Lamaze Christophe , Simon Anthony , Geraldo Sara , Vignjević Danijela , Doméjean Hugo , Rolland Leslie , Funfak Anette , Bibette Jérôme , Bremond Nicolas , Nassoy Pierre
Published: August 2013

Significance

Tumor growth intrinsically generates pressure onto the surrounding tissues, which conversely compress the tumor. These mechanical forces have been suggested to contribute to tumor growth regulation. We developed a microfluidic technique to produce 3D cell-based assays and to interrogate the interplay between tumor growth and mechanics in vitro. Multicellular spheroids are grown in permeable elastic capsules. Capsule deformation provides a direct measure of the exerted pressure. By simultaneously imaging the spheroid by confocal microscopy, we show that confinement induces a drastic cellular reorganization, including increased motility of peripheral cells. We propose that compressive stress has a beneficial impact on slowing down tumor evolution but may have a detrimental effect by triggering cell invasion and metastasis.
Ether lipid generating enzyme AGPS alters the balance of structural and signaling lipids to fuel cancer pathogenicity
Authors: Benjamin Daniel I. , Cozzo Alyssa , Ji Xiaodan , Roberts Lindsay S. , Louie Sharon M. , Mulvihill Melinda M. , Luo Kunxin , Nomura Daniel K.
Published: August 2013

Significance

Ether lipid levels are higher in tumors, but their specific function in cancer has remained unclear. We show here that the metabolic enzyme alkylglyceronephosphate synthase (AGPS), a critical step in the synthesis of ether lipids, is up-regulated across multiple types of aggressive human cancer cells and primary tumors. Inactivation of AGPS leads to significant impairments in cancer pathogenicity through not only lowering the levels of cellular ether lipids, but also by altering fatty acid, eicosanoid, and glycerophospholipid metabolism, resulting in an overall reduction in the levels of several oncogenic signaling lipids.
Burkholderia pseudomallei
suppresses
Caenorhabditis elegans
immunity by specific degradation of a GATA transcription factor
Authors: Lee Song-Hua , Wong Rui-Rui , Chin Chui-Yoke , Lim Tian-Yeh , Eng Su-Anne , Kong Cin , Ijap Nur Afifah , Lau Ming-Seong , Lim Mei-Perng , Gan Yunn-Hwen , He Fang-Lian , Tan Man-Wah , Nathan Sheila
Published: August 2013

Significance

Bacterial pathogens use multiple mechanisms to survive and proliferate within an infected host, including blunting the host’s ability to defend itself from pathogenic assaults. We identified a new immune suppression mechanism by
Burkholderia pseudomallei
, the causative agent of melioidosis, which a life-threatening disease in humans. Analyses of whole-genome transcriptional responses of
Caenorhabditis elegans
to
B. pseudomallei
infection revealed that
B. pseudomallei
, through its type III secretion system, recruits the host ubiquitin–proteasome system to specifically degrade a GATA transcription factor. This GATA factor is critical for host immune defense; thus, its degradation leads to suppression of the host’s ability to mount an effective antimicrobial defense.
GABA
B
autoreceptor-mediated cell type-specific reduction of inhibition in epileptic mice
Authors: Dugladze Tamar , Maziashvili Nino , Börgers Christoph , Gurgenidze Shalva , Häussler Ute , Winkelmann Aline , Haas Carola A. , Meier Jochen C. , Vida Imre , Kopell Nancy J. , Gloveli Tengis
Published: August 2013

Significance

Metabotropic GABA
B
receptors control synaptic transmission and excitability in neuronal circuits of the brain. Although effects of these receptors are predominantly inhibitory at both cellular and network levels, application of the agonist baclofen can promote excitability and induce seizures in patients and animal models of epilepsy. Here we demonstrate that proepileptic effects of baclofen are concentration dependent and result from disinhibition. Although at high doses, baclofen reduces network excitability due to its combined pre- and postsynaptic inhibitory effects in pyramidal cells, at low doses, it leads to an enhanced presynaptic suppression of the synaptic output of a specific set of inhibitory neurons. This disinhibitory effect promotes high-frequency oscillations and the emergence of pathological discharges in the epileptic hippocampal network.
Converting stem cells to dendritic cells by agonist antibodies from unbiased morphogenic selections
Authors: Yea Kyungmoo , Zhang Hongkai , Xie Jia , Jones Teresa M. , Yang Guang , Song Byeong Doo , Lerner Richard A.
Published: August 2013

Significance

In this paper we describe a unique method for selection of agonist antibodies that regulate stem cell fate. Unbiased combinatorial libraries (not preselected by phage panning) were used and, thus, no constraints were placed on the discovery process. Remarkably, we found that a single agonist antibody against the alpha chains of integrins can induce human stem cells to become dendritic cells. These studies are important because they help deconvolute an otherwise complex developmental process. This approach is analogous to forward genetics and should be widely used to identify previously undescribed proteins involved in important cellular pathways.
A relativized probing approach to person encoding in local scenarios
Authors: Georgi Doreen
Published: August 2013

In this paper I discuss three empirical generalizations about local scenarios: (i) four different realization strategies found cross-linguistically, (ii) an asymmetry in the number of arguments encoded on the verb in languages with person hierarchy-effects in non-local scenarios and (iii) the fact that person portmanteaux are particularly prominent in local scenarios. I claim that all three generalizations can be derived if Agree is relativized to target only positively valued person features on a goal. (ii) falls out directly from the Agree mechanism. (i) is a purely morphological phenomenon arising from the speciﬁcation of local person exponents. Person portmanteaux are analyzed as inclusive markers in a derived inclusive context. Such a context can only emerge in local scenarios, which derives (iii). In general, the paper addresses the question how morphological theories that rely on discrete slots can handle portmanteaux by vocabulary insertion, without additional mechanisms like e.g. fusion. Keywords: Agree; relativized probing; person agreement; local scenarios; portmanteau morphemes; hierarchy effects; underspeciﬁcation
Evidence for mass and count in Inuttut
Authors: Gillon Carrie
Published: August 2013

While it is clear that some languages have a grammatical mass/count distinction (e.g. English), in other languages (e.g. Inuktitut) it is not so obvious. In this paper, I show that Inuttut (Labrador Inuktitut) has a subtle grammatical mass/count distinction: while number, numerals, and most quantifiers do not disambiguate between mass and count nouns, in a few places, the morphology or the semantics disambiguates between mass and count. Thus, Inuttut is not a counterexample to Doetjes (1997) or Chierchia (2010), who both argue that all languages distinguish between mass and count. I further argue against Borer (2005) who claims all nouns in all languages are underlyingly neutral, and are assigned mass interpretation by default in the absence of individuation. I show that Inuttut nouns cannot all be underlyingly neutral and/or mass by default. Keywords: mass; count; classifiers; Inuktitut; number; numerals; quantifiers
Effects of harmony on reduction in Kera
Authors: Pearce Mary
Published: August 2013

The reduction of vowels is a popular topic for research, but little has been said about the effects of vowel harmony on vowel reduction. Gendrot and Adda-Decker (2006, 2007) claim that phonetic reduction is linked to the phonetic duration of the vowel so that in short syllables, the vowel converges towards a schwa-like quality. I support this claim in general, but I add the claim that reduction is blocked in vowel harmony domains. Within a harmony domain, even in vowels of short duration, the quality of the vowel retains the quality of the feature which is spreading. This paper demonstrates this with data from Kera, a Chadic language spoken in Chad. I examine fronting, rounding, and height harmony in Kera and confirm the fact that harmony (but not accidental agreement) in some way blocks the reduction. This has implications for the role of harmony and claims concerning privative features. Keywords: phonology; reduction; Kera; vowel harmony; acoustic; formants; duration; blocking; privative
Viral meningitis.
Authors: Irani D. N.
Published: August 2013

This chapter reviews the clinical features, epidemiology, diagnostic approaches, pathophysiology, and management strategies for patients with viral meningitis. Particular emphasis will be placed on the diseases caused by enteroviruses (EVs), which as a group account for the vast majority of all human viral meningitis cases.
Group B Streptococcus meningitis.
Authors: Nizet V. , Doran K. S.
Published: August 2013

This chapter reviews the current understanding of the physiopathology of group B streptococcal (GBS) meningitis, highlighting important bacterial virulence factors and host interactions that promote disease progression. The relationship between bacteraemia and the development of GBS meningitis, and the mechanisms of GBS immune evasion, GBS invasion of the blood-brain barrier (BBB), and GBS activation of the central nervous system's inflammatory response are discussed.
Cross-Accent Intelligibility of Speech in Noise: Long-Term Familiarity and Short-Term Familiarization
Authors: Smith Rachel , Holmes-Elliott Sophie , Pettinato Michèle , Knight Rachael-Anne
Published: August 2013

Listeners must cope with a great deal of variability in the speech signal, and thus theories of speech perception must also account for variability, which comes from a number of sources, including variation between accents. It is well known that there is a processing cost when listening to speech in an accent other than one's own, but recent work has suggested that this cost is reduced when listening to a familiar accent widely represented in the media, and/or when short amounts of exposure to an accent are provided. Little is known, however, about how these factors (long-term familiarity and short-term familiarization with an accent) interact. The current study tested this interaction by playing listeners difficult-to-segment sentences in noise, before and after a familiarization period where the same sentences were heard in the clear, allowing us to manipulate short-term familiarization. Listeners were speakers of either Glasgow English or Standard Southern British English, and they listened to speech in either their own or the other accent, thereby allowing us to manipulate long-term familiarity. Results suggest that both long-term familiarity and short-term familiarization mitigate the perceptual processing costs of listening to an accent that is not one's own, but seem not to compensate for them entirely, even when the accent is widely heard in the media.
The Effects of Facial Adiposity on Attractiveness and Perceived Leadership Ability
Authors: Re Daniel E. , Perrett David I.
Published: August 2013

Facial attractiveness has a positive influence on electoral success both in experimental paradigms and in the real world. One parameter that influences facial attractiveness and social judgements is facial adiposity (a facial correlate to body mass index, BMI). Overweight people have high facial adiposity and are perceived to be less attractive and lower in leadership ability. Here, we used an interactive design in order to assess whether the most attractive level of facial adiposity is also perceived as most leader-like. We found that participants reduced facial adiposity more to maximize attractiveness than to maximize perceived leadership ability. These results indicate that facial appearance impacts leadership judgements beyond the effects of attractiveness. We suggest that the disparity between optimal facial adiposity in attractiveness and leadership judgements stems from social trends that have produced thin ideals for attractiveness, while leadership judgements are associated with perception of physical dominance.
Centrosome repositioning in T cells is biphasic and driven by microtubule end-on capture-shrinkage
Authors: Yi Jason , Wu Xufeng , Chung Andrew H. , Chen James K. , Kapoor Tarun M. , Hammer John A.
Published: August 2013

T cells rapidly reposition their centrosome to the center of the immunological synapse (IS) to drive polarized secretion in the direction of the bound target cell. Using an optical trap for spatial and temporal control over target presentation, we show that centrosome repositioning in Jurkat T cells exhibited kinetically distinct polarization and docking phases and required calcium flux and signaling through both the T cell receptor and integrin to be robust. In “frustrated” conjugates where the centrosome is stuck behind the nucleus, the center of the IS invaginated dramatically to approach the centrosome. Consistently, imaging of microtubules during normal repositioning revealed a microtubule end-on capture-shrinkage mechanism operating at the center of the IS. In agreement with this mechanism, centrosome repositioning was impaired by inhibiting microtubule depolymerization or dynein. We conclude that dynein drives centrosome repositioning in T cells via microtubule end-on capture-shrinkage operating at the center of the IS and not cortical sliding at the IS periphery, as previously thought.
The Nlrp3 inflammasome regulates acute graft-versus-host disease
Authors: Jankovic Dragana , Ganesan Jayanthi , Bscheider Michael , Stickel Natalie , Weber Felix C. , Guarda Greta , Follo Marie , Pfeifer Dietmar , Tardivel Aubry , Ludigs Kristina , Bouazzaoui Abdellatif , Kerl Katrin , Fischer Julius C. , Haas Tobias , Schmitt-Gräff Annette , Manoharan Anand , Müller Leonard , Finke Jürgen , Martin Stefan F. , Gorka Oliver , Peschel Christian , Ruland Jürgen , Idzko Marco , Duyster Justus , Holler Ernst , French Lars E. , Poeck Hendrik , Contassot Emmanuel , Zeiser Robert
Published: August 2013

The success of allogeneic hematopoietic cell transplantation is limited by acute graft-versus-host disease (GvHD), a severe complication accompanied by high mortality rates. Yet, the molecular mechanisms initiating this disease remain poorly defined. In this study, we show that, after conditioning therapy, intestinal commensal bacteria and the damage-associated molecular pattern uric acid contribute to Nlrp3 inflammasome–mediated IL-1β production and that gastrointestinal decontamination and uric acid depletion reduced GvHD severity. Early blockade of IL-1β or genetic deficiency of the IL-1 receptor in dendritic cells (DCs) and T cells improved survival. The Nlrp3 inflammasome components Nlrp3 and Asc, which are required for pro–IL-1β cleavage, were critical for the full manifestation of GvHD. In transplanted mice, IL-1β originated from multiple intestinal cell compartments and exerted its effects on DCs and T cells, the latter being preferentially skewed toward Th17. Compatible with these mouse data, increased levels of active caspase-1 and IL-1β were found in circulating leukocytes and intestinal GvHD lesions of patients. Thus, the identification of a crucial role for the Nlrp3 inflammasome sheds new light on the pathogenesis of GvHD and opens a potential new avenue for the targeted therapy of this severe complication.
Identification of transcription factor binding sites from ChIP-seq data at high resolution
Authors: Bardet Anaïs F. , Steinmann Jonas , Bafna Sangeeta , Knoblich Juergen A. , Zeitlinger Julia , Stark Alexander
Published: August 2013

Motivation: Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-seq) is widely used to study the in vivo binding sites of transcription factors (TFs) and their regulatory targets. Recent improvements to ChIP-seq, such as increased resolution, promise deeper insights into transcriptional regulation, yet require novel computational tools to fully leverage their advantages.

Results: To this aim, we have developed peakzilla, which can identify closely spaced TF binding sites at high resolution (i.e. resolves individual binding sites even if spaced closely), as we demonstrate using semisynthetic datasets, performing ChIP-seq for the TF Twist in Drosophila embryos with different experimental fragment sizes, and analyzing ChIP-exo datasets. We show that the increased resolution reached by peakzilla is highly relevant, as closely spaced Twist binding sites are strongly enriched in transcriptional enhancers, suggesting a signature to discriminate functional from abundant non-functional or neutral TF binding. Peakzilla is easy to use, as it estimates all the necessary parameters from the data and is freely available.

Availability and implementation: The peakzilla program is available from https://github.com/steinmann/peakzilla or http://www.starklab.org/data/peakzilla/.

Contact: stark@starklab.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modelling larval fish navigation: the way forward
Authors: Staaterman Erica , Paris Claire B.
Published: August 2013

Recent advances in high-resolution ocean circulation models, coupled with a greater understanding of larval behaviour, have increased the sophistication of individual-based, biophysical models used to study the dispersal of larvae in the sea. Fish larvae, in particular, have the ability to swim directionally and increasingly fast during ontogeny, indicating that they may not only disperse, but also migrate using environmental signals. How and when larvae use local and large-scale cues remains a mystery. Including three-dimensional swimming schemes into biophysical models is becoming essential to address these questions. Here, we highlight state-of-the-art modelling of vertical and horizontal migrations of fish larvae, as well as current challenges in moving towards more realistic larval movements in response to cues. Improved understanding of causes for orientation will provide insight into the evolutionary drivers of dispersal strategies for fish and marine organisms in general.
Implementing ecosystem-based fisheries management: from single-species to integrated ecosystem assessment and advice for Baltic Sea fish stocks
Authors: Möllmann Christian , Lindegren Martin , Blenckner Thorsten , Bergström Lena , Casini Michele , Diekmann Rabea , Flinkman Juha , Müller-Karulis Bärbel , Neuenfeldt Stefan , Schmidt Jörn O. , Tomczak Maciej , Voss Rüdiger , Gårdmark Anna
Published: August 2013

Theory behind ecosystem-based management (EBM) and ecosystem-based fisheries management (EBFM) is now well developed. However, the implementation of EBFM exemplified by fisheries management in Europe is still largely based on single-species assessments and ignores the wider ecosystem context and impact. The reason for the lack or slow implementation of EBM and specifically EBFM is a lack of a coherent strategy. Such a strategy is offered by recently developed integrated ecosystem assessments (IEAs), a formal synthesis tool to quantitatively analyse information on relevant natural and socio-economic factors, in relation to specified management objectives. Here, we focus on implementing the IEA approach for Baltic Sea fish stocks. We combine both tactical and strategic management aspects into a single strategy that supports the present Baltic Sea fish stock advice, conducted by the International Council for the Exploration of the Sea (ICES). We first review the state of the art in the development of IEA within the current management framework. We then outline and discuss an approach that integrates fish stock advice and IEAs for the Baltic Sea. We intentionally focus on the central Baltic Sea and its three major fish stocks cod (Gadus morhua), herring (Clupea harengus), and sprat (Sprattus sprattus), but emphasize that our approach may be applied to other parts and stocks of the Baltic, as well as other ocean areas.
Cosmological structure formation with augmented Lagrangian perturbation theory
Authors: Kitaura Francisco-Shu , Heß Steffen
Published: August 2013

We present a new fast and efficient approach to model structure formation with augmented Lagrangian perturbation theory (ALPT). Our method is based on splitting the displacement field into a long- and a short-range component. The long-range component is computed by second-order LPT (2LPT). This approximation contains a tidal non-local and non-linear term. Unfortunately, 2LPT fails on small scales due to severe shell crossing and a crude quadratic behaviour in the low-density regime. The spherical collapse (SC) approximation has been recently reported to correct for both effects by adding an ideal collapse truncation. However, this approach fails to reproduce the structures on large scales where it is significantly less correlated with the N-body result than 2LPT or linear LPT (the Zel'dovich approximation). We propose to combine both approximations using for the short-range displacement field the SC solution. A Gaussian filter with a smoothing radius rS is used to separate between both regimes. We use the result of 25 dark-matter-only N-body simulations to benchmark at z = 0 the different approximations: first-, second-, third-order LPT, SC and our novel combined ALPT model. This comparison demonstrates that our method improves previous approximations at all scales showing ∼25 and ∼75 per cent higher correlation than 2LPT with the N-body solution at k = 1 and 2 h Mpc−1, respectively. We conduct a parameter study to determine the optimal range of smoothing radii and find that the maximum correlation is achieved with rS = 4–5 h−1 Mpc. This structure formation approach could be used for various purposes, such as setting-up initial conditions for N-body simulations, generating mock galaxy catalogues, cosmic web analysis or for reconstructions of the primordial density fluctuations.
miR172 Regulates Soybean Nodulation
Authors: Yan Zhe , Hossain Md Shakhawat , Wang Jun , Valdés-López Oswaldo , Liang Yan , Libault Marc , Qiu Lijuan , Stacey Gary
Published: August 2013

Micro-RNAs (miRNAs) play a pivotal role in the control of gene expression and regulate plant developmental processes. miRNA 172 (miR172) is a conserved miRNA in plants reported to control the expression of genes involved in developmental phase transition, floral organ identity, and flowering time. However, the specific role of miR172 in legume nodulation is undefined. Ectopic expression of soybean miR172 resulted in an increase in nodule numbers in transgenic roots and an increase in the expression of both symbiotic leghemoglobin and nonsymbiotic hemoglobin. These nodules showed higher levels of nitrogenase activity. Further analysis revealed a complex regulatory circuit in which miR156 regulates miR172 expression and controls the level of an AP2 transcription factor. The latter, either directly or indirectly, controls the expression of nonsymbiotic hemoglobin, which is essential for regulating the levels of nodulation.
First Report of Tobacco streak virus Infecting Pigeon Pea (Cajanus cajan) in India
Authors: Vemana K. , Goud T. E. Seshadri , Reddy D. L. , Venkateswarlu N. C. , Naik K. S. S. , Kumar D. Sampath , Padma latha Y. , Desai S.
Published: August 2013

Pigeon pea is an important pulse crop grown in diversified cropping systems in India. In the rainy season of August 2011 and September 2012, pigeon pea cv. LRG 30 plants with leaf necrosis having wrinkled margin on one side were observed in Kadiri mandal of the Anantapuram district of Andhra Pradesh (A.P.), India. Symptoms included necrotic spots on young leaves followed by wilting of leaves, petiole and branch/axillary shoot proliferation, with small leaves having mosaic symptoms. Symptomatic leaves were sap-inoculated onto 10 seedlings of cowpea (cv. Pusa Komal) using 0.01 M phosphate buffer (pH 7.0). Localized necrotic lesions developed in all the inoculated plants after 2 days post inoculation. Field symptoms were reproduced on healthy pigeon pea upon back inoculation using single lesions of infected cowpea leaves. In direct antigen coating (DAC)-ELISA, all the infected pigeon pea and cowpea leaf samples were positive to a polyclonal antiserum specific to Tobacco streak virus (TSV) supplied by ICRISAT, India. Total RNA was extracted using infected pigeon pea and healthy leaf samples by TRI Reagent (Sigma). Reverse transcription (RT)-PCR was carried out using primers specific to the coat protein (CP) gene of TSV (1). A product of the 700-bp DNA fragment was obtained in field-infected pigeon pea samples but not in healthy controls. The amplicon was cloned into PTZ57R/T using the Ins TA clone PCR kit (Fermentas). Recombinant clone was sequenced in both directions and the CP gene sequence obtained was deposited in GenBank (KF220492). Sequence analysis of the CP gene of TSV from pigeon pea shared 98 to 100% identity with Indian TSV isolates originating from different hosts including groundnut (FJ355948), mung bean (FJ749259), and sunflower (DQ864448), and 88 to 92% similarity with TSV type isolate (white clover: X00435) both at nucleotide and amino acid levels. TSV belongs to the genus Ilarvirus of family Bromoviride and has a wide host range. TSV is pollen borne, assisted by thrips causing mechanical injury (2). To our knowledge, this is the first report of TSV on pigeon pea in India and was widespread in Anantapuram, Kadapa, Kurnool, and Mahbubnagar districts of A.P. Yield loss depends on the stage of infection as early infection resulted in complete failure of the crop. TSV was prevalent on many legume crops such as black gram, green gram, and groundnut in A.P, Tamil Nadu, Karnataka, and Maharashtra states (3). TSV infection of pigeon pea may pose a serious implication for pulse production.

References: (1). A. I. Bhat et al. Arch. Virol. 147:651, 2002. (2). M. Sharman et al. Australian Plant Dis. 6:54, 2011. (3). K. Vemana and R. K. Jain. Indian J. Virol. 21:117, 2010.
First Report of Potato virus Y in Potato in West Java, Indonesia
Authors: Damayanti T. A. , Alabi O. J. , Hidayat S. H. , Crosslin J. M. , Naidu R. A.
Published: August 2013

Potato (Solanum tuberosum) is an important vegetable crop in Indonesia. A small survey was conducted for virus diseases in November 2011 in Lembang, West Java, as part of assessing the sanitary status of potatoes produced in farmers' fields. Among the six potato fields surveyed, one field had nearly 20% of plants displaying stunted growth with leaves showing mild chlorotic spots and reduced size of lamina. Tubers harvested from symptomatic plants showed no necrosis symptoms. Symptomatic leaves from three representative potato plants were positive for Potato virus Y (PVY) when tested with PVY-specific immunostrips (Agdia Inc., Elkhart, IN). Leaf samples from virus-positive plants were imprinted on FTA Classic Cards (Whatman International Ltd., Maidstone, UK), air dried, and shipped to Washington State University for confirmatory diagnostic tests. Total nucleic acids were eluted from FTA cards (1) and subjected to reverse transcription (RT)-PCR using primers (PVY/Y4A and PVY/Y3S) specific to the coat protein (CP) of PVY (3). Nucleic acid extracts from samples infected with PVY ordinary strain (PVYO), tuber necrosis strain (PVYNTN), tobacco veinal necrosis strains (PVYEU-N and PVYNA-N), and a recombinant strain (PVYN:O) were included as standards to validate RT-PCR assays. The approximately 480-bp DNA fragment, representing a portion of the CP, amplified in RT-PCR was cloned into pCR2.1 (Invitrogen Corp., Carlsbad, CA). DNA isolated from four independent recombinant clones was sequenced from both orientations. Pairwise comparison of these sequences (GenBank Accession Nos. KF261310 to 13) showed 100% identity among themselves and 93 to 100% identity with corresponding sequences of reference strains of PVY available in GenBank (JQ743609 to 21). To our knowledge, this study represents the first confirmed report of PVY in potato in West Java, Indonesia. Studies are in progress to assess the prevalence of PVY in other potato-growing regions of Indonesia and document the presence of different strains of the virus (2). Since the majority of farmers in Indonesia plant seed selected from their previous potato crop, there is an increased risk of primary and secondary spread of PVY through the informal seed supply system, leading to its increased significance to potato production in Indonesia. Therefore, strengthening foundation seed potato and supply chain programs will promote the production of virus-free potatoes in Indonesia.

References: (1) O. J. Alabi et al. Plant Dis. 96:107, 2012. (2) A. Karasev and S. M. Gray. Am. J. Potato Res. 90:7, 2013. (3) R. P. Singh et al. J. Virol. Methods 59:189, 1996.
First Report of Leaf Spot Disease Caused by Epicoccum nigrum on Lablab purpureus in India
Authors: Mahadevakumar S. , Jayaramaiah K. M. , Janardhana G. R.
Published: August 2013

Lablab purpureus (L.) Sweet (Indian bean) is an important pulse crop grown in arid and semi-arid regions of India. It is one of the most widely cultivated legume species and has multiple uses. During a September 2010 survey, we recorded a new leaf spot disease on L. purpureus in and around Mysore district (Karnataka state) with 40 to 80% disease incidence in 130 ha of field crop studied, which accounted for 20 to 35% estimated yield loss. The symptoms appeared as small necrotic spots on the upper leaf surface. The leaf spots were persistent under mild infection throughout the season with production of conidia in clusters on abaxial leaf surface. A Dueteromyceteous fungus was isolated from affected leaf tissues that were surface sterilized with 2% NaOCl2 solution then washed thrice, dried, inoculated on potato dextrose agar (PDA) medium, and incubated at 28 ± 2°C at 12 h alternate light and dark period for 7 days. The fungal colony with aerial mycelia interspersed with dark cushion-shaped sporodochia consists of short, compact conidiophores bearing large isodiametric, solitary, muricate, brown, globular to pear shaped conidia (29.43 to 23.92 μm). Fungal isolate was identified as Epicoccum sp. based on micro-morphological and cultural features (1). Further authenticity of the fungus was confirmed by PCR amplification of the internal transcribed spacer (ITS) region using ITS1/ITS4 universal primer. The amplified PCR product was purified, sequenced directly, and BLASTn search revealed 100% homology to Epicoccum nigrum Link. (DQ093668.1 and JX914480.1). A representative sequence of E. nigrum was deposited in GenBank (Accession No. KC568289.1). The isolated fungus was further tested for its pathogenicity on 30-day-old healthy L. purpureus plants under greenhouse conditions. A conidial suspension (106 conidia/ml) was applied as foliar spray (three replicates of 15 plants each) along with suitable controls. The plants were kept under high humidity (80%) for 5 days and at ambient temperature (28 ± 2°C). The appearance of leaf spot symptoms were observed after 25 days post inoculation. Further, the pathogen was re-isolated and confirmed by micro-morphological characteristics. E. nigrum has been reported to cause post-harvest decay of cantaloupe in Oklahoma (2). It has also been reported as an endophyte (3). Occurrence as a pathogen on lablab bean has not been previously reported. To our knowledge, this is the first report of the occurrence of E. nigrum on L. purpureus in India causing leaf spot disease.

References: (1) H. L. Barnet and B. B. Hunter. Page 150 in: Illustrated Genera of Imperfect Fungi, 1972. (2) B. D. Bruten et al. Plant Dis. 77:1060, 1993. (3) L. C. Fávaro et al. PLoS One 7(6):e36826, 2012.
Evaluation of Urea Reduction Ratio Estimated From the Integrated Value of Urea Concentrations in Spent Dialysate
Authors: Ozaki Masahiro , Hori Jun'ya , Okabayashi Tohru
Published: August 2013

We propose a new apparatus and method to estimate accurate urea reduction ratio without influence of any rebound. For this purpose, we have developed an improved version of a chemiluminescence‐based urea sensor capable of measuring urea concentration in spent dialysate (CD) at 2‐min intervals. The correlation coefficient between the readouts of the sensor and the conventional enzyme‐UV method was 0.97 and the sensor was not affected by 9 mmol/L uric acid, creatinine, or ammonia. Using the urea sensor, CD was measured as a function of dialysis time t during dialysis sessions for various blood flow rates. The urea reduction ratio based on the mass of the urea reduced (mURR) was estimated from the integrated value of CD(t). When in vitro urea concentrations are measured during a dialysis session in model blood (urea solution) at a constant volume (V) in a vessel, the plots of mURR were congruous with theoretical curves of conventional URR calculated based on the one‐pool model, and thus the accuracy of mURR was confirmed. On the other hand, in in vivo measurements of CD(t) during dialysis treatment for two patients, the plots of the mURR were not congruous with the theoretical curves of URR. Such a difference between URR and mURR was explained by the deviation of actual dialysis from the one‐pool model, and it was concluded that mURR might be accurate under any dialysis condition.
Regional Variation in Hip Fracture Incidence Among Japanese Hemodialysis Patients
Authors: Wakasugi Minako , Kazama Junichiro James , Wada Atsushi , Taniguchi Masatomo , Tsubakihara Yoshiharu , Iseki Kunitoshi , Narita Ichiei
Published: August 2013

Hip fracture incidence in Japanese hemodialysis patients is five‐fold higher than in the general population, although the mechanisms underlying this difference are not fully understood. Substantial regional variation exists in hip fracture incidence in the general Japanese population, despite a uniform health care and insurance system and lack of ethnic and racial variation. In this study, we determined whether the regional variation seen in the general population also applies to hemodialysis patients in Japan. Standardized incidence ratios were calculated for each regional district, and regional variations of hip fracture incidence among hemodialysis patients were evaluated using data obtained from the Japanese Society for Dialysis Therapy registry (data collected from December 2007 to December 2008). Standardized hip fracture incidence ratios across the districts ranged from 0.71 to 1.29 for male and 0.49 to 1.36 for female hemodialysis patients. Incidence ratios tended to be higher in western Japan and lower in eastern Japan, suggesting that regional variation also exists among hemodialysis patients. Our findings suggest that common risk factors for hip fracture may be shared among the general population and hemodialysis patients. Further research aimed at identifying factors, including those associated with regional variation, may help decrease hip fracture incidence in both the general population and hemodialysis patients in Japan.
A Strategy to Design Efficient Fermentation Processes for Traditional Beverages Production: Prickly Pear Wine
Authors: Navarrete‐Bolaños J.L. , Fato‐Aldeco E. , Gutiérrez‐Moreno K. , Botello‐Álvarez J.E. , Jiménez‐Islas H. , Rico‐Martínez R.
Published: August 2013

This paper describes a methodology to establish an optimal process design for prickly pear wine production that preserves the peculiar and unique traits of traditional products, generating at the same time, technical information for appropriate design of both bioreactor and overall process. The strategy includes alcoholic fermentation optimization by the mixed native culture composed by Pichia fermentans and Saccharomyces cerevisiae, followed by malolactic fermentation optimization by Oenococcus oeni. The optimization criteria were based on multiple output functions: alcohol content, volatile compounds profile, organic acids profile, and compound contents related to color, which were analyzed by spectroscopy–chromatography methods and sensory analysis. The results showed that the mixed culture inoculated into a bioreactor containing prickly pear juice with 20 °Bx of fermentable sugars concentration, processed at a constant temperature of 20 °C for 240 h, leads to a fermented product with 9.93% (v/v) total alcohol content, and significant abundance of volatile compounds, which provide fruity and ethereal aromatic notes, complemented by a lively but not unpleasant acidity. This young wine was further subjected to malolactic fermentation at constant temperature (16 °C) for 192 h, decreasing malic acid, and balancing volatile compounds contents, thus resulting in a product with better aroma and flavor perception, and a velvety feeling of long aftertaste. Repeated assays showed that the process is stable, predictable, controllable, and reproducible. These results were used for process design and spreadsheet construction in order to simulate the process, and properly select and size the equipment required for such process.