bluuebunny/crossref_metadata_2025 huggingface dataset:
Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of
Arabidopsis thaliana
Authors: Wang Zhen , Casas-Mollano Juan Armando , Xu Jianping , Riethoven Jean-Jack M. , Zhang Chi , Cerutti Heriberto
Published: June 2015

Significance

Histone phosphorylation and chromatin reorganization are emerging as critical factors in eukaryotic responses to environmental stimuli. Phosphorylation of histone H3 at Thr 3 is evolutionarily conserved but its role(s) in interphase cells has remained unexplored. In
Arabidopsis
, we found that H3T3ph increases in pericentromeric regions upon drought-like treatments and it might be required for maintaining proper heterochromatin/chromosome structure. In active genes the distribution of H3T3ph appears to be antagonistic to that of H3K4me3, suggesting that H3T3ph may have a repressive function. Interestingly, H3T3 phosphorylation depends on several protein kinase families, including some that are lineage specific. Understanding the dynamics of H3T3 phosphorylation and the kinases involved in its deposition may provide insights into epigenetic aspects of stress responses.
BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase
Authors: Khan Abid , Giri Sumanprava , Wang Yating , Chakraborty Arindam , Ghosh Archit K. , Anantharaman Aparna , Aggarwal Vasudha , Sathyan Kizhakke M. , Ha Taekjip , Prasanth Kannanganattu V. , Prasanth Supriya G.
Published: June 2015

Significance

Transcriptional regulation of the rDNA cluster is a tightly regulated process owing to the cellular demand for ribosomal subunits. Dysregulation of ribosomal biogenesis is associated with genomic instability and tumor progression. Nucleolar-remodeling complex (NoRC) has emerged as a key complex in the maintenance of rDNA repression. However, the mechanisms that regulate the association of NoRC to rDNA gene loci are yet to be understood. We unravel the role for a
B
ANP,
E
5R, and
N
ac1 (BEN) domain-containing transcription repressor, BEND3, in regulating rDNA repression. BEND3 modulates the stability of a NoRC component, TTF-1–interacting protein 5 (Tip5), by controlling the USP21-mediated deubiquitination of Tip5. These results provide crucial insights into the role of a transcription factor in controlling rDNA gene expression by controlling the recruitment and activity of chromatin-modifying complex.
Selective resistance to the PARP inhibitor olaparib in a mouse model for BRCA1-deficient metaplastic breast cancer
Authors: Henneman Linda , van Miltenburg Martine H. , Michalak Ewa M. , Braumuller Tanya M. , Jaspers Janneke E. , Drenth Anne Paulien , de Korte-Grimmerink Renske , Gogola Ewa , Szuhai Karoly , Schlicker Andreas , Bin Ali Rahmen , Pritchard Colin , Huijbers Ivo J. , Berns Anton , Rottenberg Sven , Jonkers Jos
Published: June 2015

Significance

Poly(ADP-ribose) polymerase (PARP) inhibitors hold promise for patients with
breast cancer 1
(
BRCA1
)-associatated cancers but are anticipated to give rise to resistance. We show that mouse mammary tumors resembling BRCA1-associated metaplastic breast carcinoma display intrinsic resistance to the PARP inhibitor olaparib as a result of increased P-glycoprotein drug efflux transporter expression. These findings may have implications for ongoing clinical trials.
Theta–gamma coordination between anterior cingulate and prefrontal cortex indexes correct attention shifts
Authors: Voloh Benjamin , Valiante Taufik A. , Everling Stefan , Womelsdorf Thilo
Published: June 2015

Significance

During flexible goal-directed behavior, our frontal cortex coordinates goal-relevant information from widely distributed neuronal systems to prioritize the relevant over irrelevant information. This coordination may be realized by entraining multiple distributed systems with slow activity oscillation to phase-align their local fast oscillatory activity. We analyzed this spatially distributed oscillatory coupling in macaques during actual attentional stimulus selection. We identified that successful—but not failed—selection of relevant information followed the coupling of slow and fast frequencies at narrow oscillation phases, with interareal anatomical specificity, and based on a reset mechanism for the slow oscillation. These findings suggest a specific functional and mechanistic solution to the fundamental coordination problem in primate brains.
Generating new prions by targeted mutation or segment duplication
Authors: Paul Kacy R. , Hendrich Connor G. , Waechter Aubrey , Harman Madison R. , Ross Eric D.
Published: June 2015

Significance

Prions are self-propagating protein aggregates. We designed rational mutations in four nonprion proteins to examine possible mechanisms for how new prions could evolve. In each case, a small number of mutations were sufficient to cause the proteins to aggregate and, in two cases, to create prion activity. We likewise showed that simply creating tandem repeats of aggregation-prone segments within nonprion proteins can be sufficient to create prion activity, suggesting that such segment duplication may represent a mechanism for generation of new prion domains.
Human population dynamics in Europe over the Last Glacial Maximum
Authors: Tallavaara Miikka , Luoto Miska , Korhonen Natalia , Järvinen Heikki , Seppä Heikki
Published: June 2015

Significance

Despite its importance for understanding genetic, cultural, and linguistic evolution, prehistoric human population history has remained difficult to reconstruct. We show that the dynamics of the human population in Europe from 30,000 to 13,000 y ago can be simulated using ethnographic and paleoclimate data within the climate envelope modeling approach. Correspondence between the population simulation and archaeological data suggests that population dynamics were indeed driven by major climate fluctuations, with population size varying between 130,000 and 410,000 people. Although climate has been an important determinant of human population dynamics, the climatic conditions during the last glacial were not as harsh as is often presented, because even during the coldest phases, the climatically suitable area for humans covered 36% of Europe.
Miniaturized mitogenome of the parasitic plant
Viscum scurruloideum
is extremely divergent and dynamic and has lost all
nad
genes
Authors: Skippington Elizabeth , Barkman Todd J. , Rice Danny W. , Palmer Jeffrey D.
Published: June 2015

Significance

The mitochondrial genomes of flowering plants are characterized by an extreme and often perplexing diversity in size, organization, and mutation rate, but their primary genetic function, in respiration, is extremely well conserved. Here we present the mitochondrial genome of an aerobic parasitic plant, the mistletoe
Viscum scurruloideum
. This genome is miniaturized, shows clear signs of rapid and degenerative evolution, and lacks all genes for complex I of the respiratory electron-transfer chain. To our knowledge, this is the first report of the loss of this key respiratory complex in any multicellular eukaryote. The
Viscum
mitochondrial genome has taken a unique overall tack in evolution that, to some extent, likely reflects the progression of a specialized parasitic lifestyle.
Microneedle-array patches loaded with hypoxia-sensitive vesicles provide fast glucose-responsive insulin delivery
Authors: Yu Jicheng , Zhang Yuqi , Ye Yanqi , DiSanto Rocco , Sun Wujin , Ranson Davis , Ligler Frances S. , Buse John B. , Gu Zhen
Published: June 2015

Significance

For exploiting synthetic glucose-responsive insulin delivery systems, challenges remain to demonstrate a strategy that would combine (
i
) fast responsiveness, (
ii
) ease of administration, and (
iii
) excellent biocompatibility. We have developed a novel glucose-responsive insulin delivery device using a painless microneedle-array patch containing hypoxia-sensitive hyaluronic acid-based vesicles. The vesicles quickly dissociate and release encapsulated insulin under the local hypoxic environment, caused by the enzymatic oxidation of glucose in the hyperglycemic state. This “smart insulin patch” with a new enzyme-based glucose-responsive mechanism can regulate the blood glucose of type 1 diabetic mice to achieve normal levels, with faster responsiveness compared with the commonly used pH-sensitive formulations, and can avoid the risk of hypoglycemia.
A self-lysis pathway that enhances the virulence of a pathogenic bacterium
Authors: McFarland Kirsty A. , Dolben Emily L. , LeRoux Michele , Kambara Tracy K. , Ramsey Kathryn M. , Kirkpatrick Robin L. , Mougous Joseph D. , Hogan Deborah A. , Dove Simon L.
Published: June 2015

Significance

The programmed cell death (PCD) of mammalian cells plays important roles in fighting bacterial infections. Relatively little is known about the adaptive role of PCD in bacteria. Here we report the discovery of a potential PCD pathway in
Pseudomonas aeruginosa
. We show that activation of the system can occur in a subset of cells in response to DNA damage through cleavage of an essential transcription regulator that controls a cell lysis program. Although this is lethal to the individual cell in which it occurs, we find that PCD enhances the ability of the bacterium to cause disease. Our findings suggest that PCD is a strategy used by both host and pathogen to promote survival during an infection.
Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)
Authors: Koch Sandra C. , Kuper Jochen , Gasteiger Karola L. , Simon Nina , Strasser Ralf , Eisen David , Geiger Simon , Schneider Sabine , Kisker Caroline , Carell Thomas
Published: June 2015

Significance

Nucleotide excision repair (NER) is a versatile repair machinery able to protect organisms from DNA damage. Defective NER leads to diseases like xeroderma pigmentosum (XP). XPA is a central NER protein that interacts with DNA in an unknown fashion. Here we present two crystal structures of the yeast homolog of XPA, Rad14, in complex with two NER substrate lesions. Rad14 binds to the damaged DNA from both sides of the lesion. Binding creates a sharp kink of the duplex by 70°. Each protein inserts a hairpin loop into the duplex to induce partial melting around the lesion. The structures provide insight into the mechanism of how XPA binds to kinked and lesion-containing DNA.
Disruption of prostaglandin E2 receptor EP4 impairs urinary concentration via decreasing aquaporin 2 in renal collecting ducts
Authors: Gao Min , Cao Rong , Du Shengnan , Jia Xiao , Zheng Senfeng , Huang Shizheng , Han Qifei , Liu Jia , Zhang Xiaoyan , Miao Yifei , Kang Jihong , Gustafsson Jan-Åke , Guan Youfei
Published: June 2015

Significance

Prostaglandin E2 (PGE2) plays an important role in maintaining water and sodium homeostasis via its four membrane-associated receptors including EP1, EP2, EP3, and EP4. This study uncovers a unique role for the EP4 receptor in controlling urine volume independent of antidiuretic hormone (arginine vasopressin). EP4 activation increases collecting duct aquaporin 2 (AQP2) expression in a cAMP/cAMP-response element binding protein (CREB)-dependent manner and promotes its membrane sorting via the cAMP/protein kinase A and extracellular signal-regulated kinase pathways. The ability of EP4 to increase AQP2 membrane targeting and cellular abundance makes it a potential therapeutic target for the treatment of clinical disorders including acquired and congenital diabetes insipidus.
Single-molecule imaging of Hedgehog pathway protein Smoothened in primary cilia reveals binding events regulated by Patched1
Authors: Milenkovic Ljiljana , Weiss Lucien E. , Yoon Joshua , Roth Theodore L. , Su YouRong S. , Sahl Steffen J. , Scott Matthew P. , Moerner W. E.
Published: June 2015

Significance

In vertebrates, the transmembrane protein Smoothened (Smo) accumulates in the ciliary membrane when cells receive the Hedgehog (Hh) signal. The presence of Smo in primary cilia at baseline conditions has been postulated, but not directly observed. We used highly sensitive single-molecule imaging in live cells to track and analyze the dynamics of individual Smo molecules in cilia, not only after treatment with pathway agonists but also at low, baseline levels. In both conditions, Smo molecules bind at distinct sites at the bases of cilia, but with different dissociation constants. The results provide mechanistic insight into the Hh signal transduction and highlight the distinct compartmentalization of Smo behavior within cilia, which is normally masked by the bulk distribution in ensemble measurements.
Relationship between thermoelectric figure of merit and energy conversion efficiency
Authors: Kim Hee Seok , Liu Weishu , Chen Gang , Chu Ching-Wu , Ren Zhifeng
Published: June 2015

Significance

Thermoelectric materials generate electricity from temperature gradients. The dimensionless figure of merit,
ZT
=
S
2
ρ
−1
κ
−1
T
, is calculated from the Seebeck coefficient (
S
), electrical resistivity (
ρ
), and thermal conductivity (
κ
). The calculated efficiency based on
ZT
using the conventional formula is not reliable in some cases due to the assumption of temperature-independent
S
,
ρ
, and
κ
. We established a new efficiency formula by introducing an engineering figure of merit (
ZT
)

eng

and an engineering power factor (
PF
)

eng

to predict reliably and accurately the efficiency of materials at a large temperature difference between the hot and cold sides, unlike the conventional
ZT
and
PF
providing performance only at specific temperatures. These new formulas will profoundly impact the search for new thermoelectric materials.
DNA polymerase from temperate phage Bam35 is endowed with processive polymerization and abasic sites translesion synthesis capacity
Authors: Berjón-Otero Mónica , Villar Laurentino , de Vega Miguel , Salas Margarita , Redrejo-Rodríguez Modesto
Published: June 2015

Significance

Functional classification of DNA polymerases (DNAPs) usually divides them into replicative faithful replicases and error-prone enzymes devoted to DNA repair and DNA damage tolerance through translesion synthesis (TLS). When we analyzed the biochemical properties of phage Bam35 replicative DNAP, we found it to be a highly faithful DNAP that can couple strand displacement to processive DNA synthesis, suitable for rolling circle amplification of plasmidic DNA. Interestingly, it is also endowed with intrinsic TLS capacity opposite abasic sites and processive primer extension beyond the lesion. These features configure a versatile enzyme for accurate maintenance of viral genomic information over generations and, besides, to deal with DNA lesions, which suggest a possible application of Bam35 DNAP for the amplification of damaged or ancient DNA.
Identity as a dialogic concept
Authors: Weigand Edda
Published: June 2015

Identity has been investigated from different perspectives and there are therefore numerous ways of interpreting this concept. Basically it seems to be a method of categorizing people. We are however not only a slot in a bureaucratic system but social and dialogic human beings. As social individuals we can think about social consequences, and as dialogic individuals we can demonstrate our own supposed identity and evaluate the alleged identity of our fellow human beings in dialogue. ‘The side we are on’ leaves its mark not only on how we evaluate actions and events but also on how we refer to people. In this way identity is constructed and negotiated in dialogue. The paper analyses various authentic texts in order to demonstrate the dialogic nature of the concept.
Dialogic representations of Britishness and Irishness
Authors: Ajtony Zsuzsanna
Published: June 2015

Speakers construct their identities by careful choice of the appropriate linguistic features that will convey the specific social information that identifies them as part of a particular speech community (cf. Riley 2007, Joseph 2004). The social constructionist approach focuses on how social actors use linguistic and other cultural resources in the ongoing construction and re-construction of personal and group identity in interaction. Under such a view, identity (and hence ethnicity) is necessarily dynamic (Schilling-Estes 2004). Recent research on fictional characters and scripted discourse has proved the legitimacy of this scholarly area among language studies (Kozloff 2000, Culpeper 2001, Walshe 2009, Eder et al. 2010, Dynel 2011, Furkó 2013). This paper investigates several possibilities for the dialogic construction of the British and Irish ethnic stereotype. Drawing the distinction between real and fictional characters (Culpeper 2010), the micro-sociolinguistic, pragmalinguistic analysis of my corpora, taken from contemporary cinematographic representations of Britishness and Irishness, aims to compare some of the strategies that interactional partners employ, and which reveal several facets of their identities.
Building identity in humorous media interactions
Authors: Măda Stanca
Published: June 2015

This article presents an analysis of conversational humour (Attardo 1994) occuring in two Romanian television shows with the purpose of demonstrating that journalists use humour to build their own identity in relation to their interlocutors and to their audience. The types of strategic moves identified in media situational humour are two-fold: one directed at a participant in the conversation, having the potential of biting; the other that is directed at an absent other (in this case, the audience), having the potential of bonding (Boxer and Cortes-Conde 1997, 275). A relational identity is developed among participants in conversational joking which can be identified and described in accordance with the communicative norms and expectations that are considered appropriate in the media context in which individuals interact.
Enunciative identity and individual representation of rape
Authors: Batt Martine , Bocerean Christine , Coutelour Marianne , Beckert Thomas , Theiller Ophélie , Trognon Alain
Published: June 2015

A total of 316 cases of forensic psychological assessment for sexual assaults were analyzed for plaintiffs over 15 years of age. The assessments were conducted between 2008 and 2014 in the presence of the same expert psychologist. The analyses clearly highlight the role of others in the act of filing a complaint. Therefore, the enunciations of the complaint were carefully examined in order to clarify the status of others. The Alterity can be observed in the speech of victims. The psychological assessment interview cannot be reduced to a dialoguein praesentia; in fact, another dialogue is brought to light. The latter falls within internal processes which, in turn, distinguish between two main types of plaintiffs: those who present themselves spontaneously to judicial authorities and the others.
‘I’m dying on you’
Authors: Vardi Ruti
Published: June 2015

A specific type of intensification in the domain of love/desire/adoration is conveyed in Hebrew through the use of the idiomatic construction [X PRD al Y] [‘X die/crazy/ill/devastated on Y’] which deviates from the basic patterns of the grammar at both the morphosyntactic and the semantic levels. The present paper examines both the process of emergence and the accessibility of the construction: it explains how pragmatic needs drive a metonymy-based metaphorical mapping between dissociative conceptual domains, and how the mechanisms of negativity bias and embodiment are involved in this mapping. Subsequently the present paper shows how these pragmatic-driven processes are realised within a grammatical construction with a fixed, accessible idiomatic meaning. The paper additionally argues that emotive intensification is not limited to (adverbial) modification, but instead can be expressed by more complex constructions.
Accent-induced coder bias
Authors: Sloos Marjoleine
Published: June 2015

Recent research has shown that speech perception can easily be influenced by the overall accent of the speaker. This paper investigates whether such accentinduced bias also occurs in speech transcription by professional and linguistically trained coders and to what extent such a bias may affect linguistic analyses. We compare the transcriptions of the Bären vowel in Standard German with the acoustic values of these vowels, as well as sociolinguistic analyses based on both of these. The results of the two analyses turn out to be considerably different. Further examination shows that the coders only partly relied on the acoustic values. The residual does not consist of random errors, but correlate with the degree of accentedness of the speakers. We conclude that this accent-induced coder bias led the coders to transcribe the codings according to their expectations about the pronunciation in the local dialect – expectations that were quite different from the acoustic reality.
Visualization and conceptual metaphor as tools for the teaching of abstract motion in German
Authors: De Knop Sabine
Published: June 2015

The case study explores German examples of metaphorical motion events as in (1) einen Text ins Deutsche übersetzen (‘to translate a text into German’) or (2) Er war bei uns über die Feiertage (‘He was with us over (during) the holidays’) in the wider context of verb-framed and satellite-framed languages (Slobin, 1996, 2000; Talmy, 1985). Starting from a general description of the components of motion events (Talmy, 1985) the examples help illustrate the German preferences in the lexicalization of such motion events and also concretize the challenges for the learning tasks of foreign language learners related to the German case-marking. Traditionally, German case-marking constitutes one of the major difficulties for foreign learners, especially in expressions of abstract motion events in which so-called “two-way prepositions” (Smith, 1995) can be used. The learner has to make a decision of whether to use an accusative (for the expression of a dynamic motion event with a path and a goal) or a dative (for the expression of a location) according to the meaning conveyed. The empirical study conducted with intermediate French-speaking students of German shows that the teaching of German motion events with their case-alternation can be facilitated by a methodology which deals with language-specific concepts (Boers & Lindstromberg, 2008), visualization (Paivio, 2001) and metaphor (Littlemore & Low, 2006). The visual support may offer the basis for a potential link with underlying conceptual metaphors (Lakoff & Johnson, 1980), e.g. abstract is concrete or knowing is seeing. Spatial distinctions such as those between containers and surfaces are extended to more abstract areas of experience, especially in the context of situations describing abstract changes. Here one of the main issues for the learner is to find out whether the abstract goal is conceptualized as a container, a surface or still another basic spatial relation.
Información contextual, estructura discursiva y modalidad evidencial en la selección de las locuciones consecutivas del español
Authors: Rodríguez Ramalle Teresa Mª.
Published: June 2015

En trabajos previos se han analizados las locuciones consecutivas a partir de su conexión con la modalidad evidencial (Bermúdez 2005, Rodríguez Ramalle 2014a y b). En este trabajo voy a limitar la extensión de este concepto a aquellas locuciones que tienen carácter ilativo:así que, conque, de manera queyde modo que. Para ello voy a revisar la importancia de la información contextual en la conexión entre oraciones independientes, con el fin de justificar los vínculos que establecen las locuciones mencionadas con los conocimientos previos compartidos por los hablantes.
Por ahí/ni ahí, desde la localización a la modalidad
Authors: Marcovecchio Ana María
Published: June 2015

En el español coloquial de la Argentina se emplean las locucionespor ahíyni ahícomo índices de modalidad. Sin embargo, apenas existen registros lexicográficos depor ahícomo marca de probabilidad y atenuación enunciativa (=a lo mejor) y deni ahícomo refuerzo de la negación (=absolutamente no). Entonces, dentro de un enfoque cognitivo-funcional, intentaré explicar no solo el pasaje de estos giros desde el dominio locativo hasta el de la modalidad, sino también caracterizarlos como índices de modalidad e integrarlos entre los adverbios y formas equivalentes que se deslizan desde el ámbito predicativo hacia una función periférica que repercute sobre elmodusoracional. Esta conversión del dominio locativo al modal supone un proceso de subjetivización, lo que se asocia a una serie de cambios formales por los cuales se redirige el significado referencial literal de las locuciones hacia el ámbito de la enunciación.
Philosophy and ethics of animal use and consumption: from Pythagoras to Bentham.
Authors: Rauw W. M.
Published: June 2015

The human population is projected to rise to 9.15 billion people by 2050, resulting in a projected increase in meat consumption. However, at the same time, the dominant position of meat as the centre of meals is on the decline, resulting in an increasing number of vegetarians and flexitarians in some Western countries. There are several motivations for this trend, including religious, health, moral and environmental considerations. Many of the arguments that are very alive today in the debate follow from those proposed by ancient philosophers and scientists. The aim of this review is to review the ethics of animal use and consumption from the old Greek philosophers (Pythagoras, Heraclitus, Alcmaeon, Anaxagoras, Socrates, Plato, Aristotle, Diogenes, Theophrastus, the Stoics, the Pyrrhonian Skeptics, Plutarch and the Phoenician philosopher Porphyry), the early Christians and the Middle Ages, and the Renaissance, to the seventeenth and eighteenth century (Evelyn, Tryon, Descartes, Malebranche, De La Mettrie, Kant, Spinoza and Bentham).
Resveratrol derivative-rich melinjo (Gnetum gnemon L.) seed extract improves obesity and survival of C57BL/6 mice fed a high-fat diet
Authors: Ikuta Tomoki , Saito Shinichiro , Tani Hiroko , Tatefuji Tomoki , Hashimoto Ken
Published: June 2015

Melinjo (Gnetum gnemon L.) seed extracts (MSEs) are rich in resveratrol dimers (gnemonoside A, C, D, gnetin C), trans-resveratrol, and other resveratrol derivatives. trans-Resveratrol is a widely studied caloric restriction mimetic. In mice fed a high-fat diet (HFD), trans-resveratrol protects against obesity, type 2 diabetes, and premature death. Here, treatment of HFD-fed mice with 2.0% MSE significantly reduced body weight gain (p < 0.001), blood insulin (p < 0.01), and HOMA-IR (p < 0.05) after 8 weeks compared with untreated HFD-fed mice. Additionally, 0.2% MSE treatment of HFD-fed mice significantly improved physiological activity (p < 0.05) at 18 months of age and reduced risk of death due to HFD by 25% (hazard ratio = 0.75, p = 0.036). These data show that MSE can improve several aspects of metabolic syndrome and survival in mice and may have health benefits as a dietary supplement.
Therapeutic targeting of autophagy in neurodegenerative and infectious diseases
Authors: Rubinsztein David C. , Bento Carla F. , Deretic Vojo
Published: June 2015

Autophagy is a conserved process that uses double-membrane vesicles to deliver cytoplasmic contents to lysosomes for degradation. Although autophagy may impact many facets of human biology and disease, in this review we focus on the ability of autophagy to protect against certain neurodegenerative and infectious diseases. Autophagy enhances the clearance of toxic, cytoplasmic, aggregate-prone proteins and infectious agents. The beneficial roles of autophagy can now be extended to supporting cell survival and regulating inflammation. Autophagic control of inflammation is one area where autophagy may have similar benefits for both infectious and neurodegenerative diseases beyond direct removal of the pathogenic agents. Preclinical data supporting the potential therapeutic utility of autophagy modulation in such conditions is accumulating.
Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams
Authors: Kerpedjiev Peter , Hammer Stefan , Hofacker Ivo L.
Published: June 2015

Motivation: The secondary structure of RNA is integral to the variety of functions it carries out in the cell and its depiction allows researchers to develop hypotheses about which nucleotides and base pairs are functionally relevant. Current approaches to visualizing secondary structure provide an adequate platform for the conversion of static text-based representations to 2D images, but are limited in their offer of interactivity as well as their ability to display larger structures, multiple structures and pseudoknotted structures.

Results: In this article, we present forna, a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations. It supports, among other features, the simultaneous visualization of multiple structures, the display of pseudoknotted structures, the interactive editing of the displayed structures, and the automatic generation of secondary structure diagrams from PDB files. It requires no software installation apart from a modern web browser.

Availability and implementation: The web interface of forna is available at http://rna.tbi.univie.ac.at/forna while the source code is available on github at www.github.com/pkerpedjiev/forna.

Contact:  pkerp@tbi.univie.ac.at

Supplementary information:  Supplementary data are available at Bioinformatics online.
Paradigms of forensic science and legal process: a critical diagnosis
Authors: Roberts Paul
Published: June 2015

This article reconsiders the relationship between criminal adjudication and forensic expertise in the light of ‘new paradigms' of forensic practice and recent law reform. It briefly summarizes conventional wisdom on the typical shortcomings of forensic science and other expert evidence, as a springboard for a more searching critical diagnosis of longstanding maladies. The fundamentally jurisdictional nature of law is emphasized, and some implications for expert testimony noted. English law's traditionally adversarial model of criminal procedure is then reassessed, taking account of a proper understanding of its normative structure and modern development, and drawing on comparative legal research and theorizing to obtain a more rounded second opinion. In conclusion, some avenues for intelligent prescription are canvassed, highlighting the importance of promoting and facilitating effective communication between experts, lawyers and courts, and prioritizing modest practical remedies over radical surgery.
The logical foundations of forensic science: towards reliable knowledge
Authors: Evett Ian
Published: June 2015

The generation of observations is a technical process and the advances that have been made in forensic science techniques over the last 50 years have been staggering. But science is about
reasoning
—about making sense from observations. For the forensic scientist, this is the challenge of interpreting a pattern of observations within the context of a legal trial. Here too, there have been major advances over recent years and there is a broad consensus among serious thinkers, both scientific and legal, that the logical framework is furnished by Bayesian inference (Aitken
et al. Fundamentals of Probability and Statistical Evidence in Criminal Proceedings
). This paper shows how the paradigm has matured, centred on the notion of the balanced scientist. Progress through the courts has not been always smooth and difficulties arising from recent judgments are discussed. Nevertheless, the future holds exciting prospects, in particular the opportunities for managing and calibrating the knowledge of the forensic scientists who assign the probabilities that are at the foundation of logical inference in the courtroom.
Is the literature on content analysis of intellectual capital reporting heading towards a dead end?
Authors: Goebel Viktoria
Published: June 2015

Purpose

– The purpose of this paper is to respond to the call by Dumay and Cai (2014) for new ideas to enhance intellectual capital (IC) research. One possibility is to draw conclusions on comparability across the results of prior studies. This study investigates whether the results of prior IC content analyses are comparable despite differences in their IC research frameworks.

Design/methodology/approach

– A content analysis of 428 German management reports is conducted, capturing the IC reporting scores for individual IC items to investigate the role of certain widely used IC items. The relationships of IC scores for different combinations of widely used IC items are further examined in a correlation analysis to indicate comparability of prior results.

Findings

– The findings show that widely used IC items capture the majority of IC reporting and that the IC scores for different combinations of these IC items are highly correlated. These findings indicate that the results of prior IC content analyses are comparable as long as most of the widely used IC items are included in prior IC research frameworks.

Research limitations/implications

– The study contributes to IC reporting research as it shows that conclusions can be drawn across prior studies in meta-analyses because the results of prior studies are comparable in rankings and key findings.

Originality/value

– Although content analyses of IC reporting have been previously criticised, this study seminally questions the comparability of the results of prior studies due to differences in the IC research frameworks.
Exploring intellectual capital disclosure as a mediator for the relationship between IPO firm-specific characteristics and underpricing
Authors: Too Shaw Warn , Wan Yusoff Wan Fadzilah
Published: June 2015

Purpose

– The purpose of this paper is to examine the direct and indirect impact of firm-specific characteristics on the level of underpricing among Malaysian initial public offerings (IPOs).

Design/methodology/approach

– Content analysis of IPO prospectuses was used for 331 firms underwent listing between 2002 and 2008. The extent of disclosure was computed by applying the disclosure index of Bukhet al.(2005).

Findings

– Of the five firm characteristics examined, there is a direct relationship between the firm’s financial performance and the level of foreign activity, and the level of underpricing, instead of being mediated through disclosure. However, some firm characteristics have direct influence on the extent of disclosure but do not have any influence on underpricing.

Research limitations/implications

– This empirical study concentrates on the Malaysian IPOs on a single disclosure mechanism. Other disclosure items can be examined together with the intellectual capital disclosure items.

Practical implications

– As the findings reveal that the extent of disclosure is relatively low in influencing the level of underpricing. Had the disclosure been higher, it may have some influence on underpricing. The accounting governance board need to regulate the disclosures of the intangible resources so that the level of underpricing can be minimized.

Originality/value

– This study provides new insight for the examination of direct and indirect (through disclosure) association between firm-specific characteristics and underpricing. The findings shed some lights to the IPO issuers to enhance disclosure so that the cost of capital can be reduced.
Money laundering in Ukraine
Authors: Stack Graham
Published: June 2015

Purpose

– This paper aims to examine the role in tax evasion and corruption played in Ukraine by money-laundering organisations called “conversion centres”: networks of sham firms and banks implementing “black cash” schemes that facilitate tax evasion by the private sector and embezzlement by the state sector. The paper describes their embedding both in a post-Soviet state as well as in the international political economy.

Design/methodology/approach

– It draws on scholarship, journalist investigations, court records, government agency reports and other open source data and interviews with market participants. It first describes “conversion centres” as an ideal type and then presents three case studies, focusing on international financial flows and the domestic political setting.

Findings

– Ukraine’s conversion centres generate significant international flows of dirty money handled by specialised foreign banks mostly in the Baltic states. Domestically, conversion centres thrive through state capture, resulting from their facilitation of embezzlement by state actors.

Research limitations/implications

– Open source data and investigative methods make it possible to conduct empirical research in crime and corruption in the post-Soviet context. As open sources expand, the scope for such enquiry will increase.

Originality/value

– This is the first empirical description of “black cash” money-laundering platforms in terms of embedding in a post-Soviet state and in the international financial system.
Everyday vulnerabilities – money laundering through cash intensive businesses
Authors: Gilmour Nicholas , Ridley Nick
Published: June 2015

Purpose

– The purpose of this paper is to provide an understanding of the specific techniques through which illicit funds generated by criminals are moved, transferred and laundered in the financial arrangement retained by cash-intensive businesses in the UK and internationally.

Design/methodology/approach

– This paper presents exploratory findings from research conducted between 2011 and 2013 in the UK. The research undertaken sought to identify the process, steps and vulnerabilities behind money laundering via cash-intensive businesses and highlight the explicit facilitators to enable this method of money laundering to take place.

Findings

– Despite significant research into money laundering typologies, the use of cash couriers and cash-intensive businesses has remained largely untouched regardless of the increased implementation of anti-money laundering (AML) policies and procedures seeking to halt the depositing of illicit cash into the global financial system. This paper demonstrates how cash-intensive businesses are extremely vulnerable to money laundering, despite the large-scale AML efforts focused on combating money laundering across a broad range of sectors.

Research limitations/implications

– This paper is of value to government policymakers, regulators and financial institutions considering future preventative measures. It is also of value to financial investigators and law enforcement agencies intent on investigating money laundering. While the paper relies on data from the UK, the overall findings are such that wherever cash-intensive businesses exist, so too does the opportunity for money laundering through the financial arrangement retained by such businesses.

Originality/value

– This paper presents new research on the direct link existing between cash-intensive businesses and money laundering in the UK, despite significant research having previously taken place to identify and develop money laundering typologies.
Identifying money laundering
Authors: Sterling Stephen
Published: June 2015

Purpose

– This study aims to develop a newer, revised model of money laundering of general application, and to apply that updated laundering model to the use of cash in Canada. A wide-ranging analytical tool for identifying money laundering is described, which demands a comparative evaluation of available financial choices against choices made, concentrating on factors which matter most to economic enterprises: speed, cost and security. The model is applied to bulk cash money laundering and the use of cash in the Canadian context, a mature economy where cash is predominantly used for micro-payments. The inference of criminality to be drawn from bulk use of cash is explored, as is any need for continued circulation of large denomination banknotes.

Design/methodology/approach

– Extensive criminal investigative experience is juxtaposed with practices of legitimate commerce. As to patterns of transactional conduct, a review is undertaken of publications from financial institutions including the Bank of Canada.

Findings

– The model may be applied generally. In light of modern banking realities, strong inferences of criminality arise from the bulk use of cash.

Research limitations/implications

– Documented standards of legitimate commerce and proven laundering behaviours provide more reliable evidence than voluntary disclosures from surveys.

Practical implications

– The model promotes an objective analysis of financial conduct either in conjunction with, or independent of extrinsic evidence, and can augment historic lists of laundering indicators and identify new laundering typologies.

Originality/value

– The speed, cost and security model moves towards a renewed paradigm for understanding laundering, beyond traditional cash-based models. This instructive model applies to the full spectrum of laundering, from frauds to cash-based street crimes. By examining the inherent characteristics of financial choices, investigations may proceed without tipping off targets. The model maximizes the investigative value of know-your-customer information.
Differential plasticity of metabolic rate phenotypes in a tropical fish facing environmental change
Authors: Norin Tommy , Malte Hans , Clark Timothy D.
Published: June 2015

Individual differences in metabolic rate have been linked with variations in behaviour and key life‐history traits and can affect ecological patterns within animal populations. Yet, almost nothing is known of the plasticity of the metabolic response under dynamically changing conditions that are representative of the natural environment. This is surprising since the capacity for animals to cope with rapidly changing environments depends on phenotypic variation and plasticity among members of the population.

We measured the standard metabolic rate (SMR), maximum metabolic rate (MMR) and aerobic scope (AS) of 60 juvenile barramundi (Lates calcarifer) under acclimation conditions (35 ppt salinity, 29 °C, normoxia) and when the fish were sequentially faced with low salinity (10 ppt), high temperature (35 °C) and hypoxia (45% air saturation) with each treatment separated by ∼12 days.

The overall degree of interindividual variation in body‐mass‐standardised SMR, MMR and AS changed with environmental conditions, and a metabolic coupling was revealed between SMR and MMR when the fish were faced with the environmental changes. The metabolic response to environmental change differed widely and predictably at an individual level. Individuals that had elevated metabolic attributes under acclimation conditions showed little change in SMR, MMR or AS in response to low salinity and high temperature, but MMR and AS were greatly depressed by hypoxia. In contrast, individuals with low‐metabolic attributes under acclimation conditions displayed a substantial increase in SMR, MMR and AS in response to high temperature and (to a lesser extent) low salinity, but hypoxia had very little effect.

These findings reveal how phenotypic diversity in key physiological traits can create differential plasticity towards environmental change within a population by showing how individual fish can remain metabolically insensitive to one environmental stressor at the cost of being highly sensitive to another.
The crabs that live where hot and cold collide
Authors: Thurber Andrew R.
Published: June 2015

The distribution of Kiwa tyleri with the large male individual in the high‐temperature flow (right hand side – fluid flow indicated by shimmering water) and the mixed sex assemblage (left). Note the heavy coat of epibiotic bacteria (grey colouring) on the individual in the hottest section of the vent, as expected from being closest to the sulphide needed to sustain the epibiotic bacteria that this species harvests for its food. Image courtesy of Dr. L. Marsh (Credit: NERC ChEsSo Consortium).

image

The distribution of Kiwa tyleri with the large male individual in the high‐temperature flow (right hand side – fluid flow indicated by shimmering water) and the mixed sex assemblage (left). Note the heavy coat of epibiotic bacteria (grey colouring) on the individual in the hottest section of the vent, as expected from being closest to the sulphide needed to sustain the epibiotic bacteria that this species harvests for its food. Image courtesy of Dr. L. Marsh (Credit: NERC ChEsSo Consortium).

In Focus: Marsh, L., Copley, J.T., Tyler, P.A. & Thatje, S. (2015) In hot and cold water: differential life‐history traits are key to success in contrasting thermal deep‐sea environments. Journal of Animal Ecology, 84, 898–913.

Southern Ocean hydrothermal vents juxtapose two extremes – intense food‐poor cold and scalding food‐rich oases. At these vents, Marsh et al. (2015) found a community of Kiwa (Yeti) crabs that separated themselves along this gradient with the largest males sitting in hot, food‐rich waters, while smaller males and females co‐occur in an intermediate zone of warmth. However, as their eggs start to develop, females embark away from the vent to the food‐poor yet stable cold of the Southern Ocean. This species has found an intriguing way to balance foraging risk and population persistence at the interface of hot and cold.
Environmentally dependent host–pathogen and vector–pathogen interactions in the Barley yellow dwarf virus pathosystem
Authors: Davis Thomas S. , Bosque‐Pérez Nilsa A. , Foote Nathaniel E. , Magney Troy , Eigenbrode Sanford D.
Published: June 2015

Understanding environmentally dependent variation in interspecific interactions is needed for evaluating how agroecosystems respond to abiotic stressors, including climate change. Both biotic and abiotic conditions shape crop responses to stress events, but interactions between environmental conditions and insect borne plant pathogens remain poorly understood.

We tested the hypothesis that drought stress, as applied by experimental water deprivation, drives conditional outcomes in host–pathogen and host–vector interactions using a cereal–aphid–virus association and greenhouse experiments.

Under conditions of ample water supply, infection of wheat plants with Barley yellow dwarf virus (BYDV) resulted in reduced above‐ground growth, seed set, seed yields and seed germination compared with plants exposed only to non‐infected (non‐viruliferous) aphids or control plants not subjected to aphid infestation. However, when water was chronically limiting, infection with Barley yellow dwarf virus did not significantly affect plant performance.

When wheat was subjected to acute drought stress, plants infected with Barley yellow dwarf virus surpassed both control plants and plants exposed to non‐infected aphids in all measured performance traits.

Feeding experiments with aphid vectors (Rhopalosiphum padi) and subsequent life table analysis revealed that aphid fecundity improved by 47% when feeding on Barley yellow dwarf virus‐infected plants when water inputs were chronically low. However, when plants received ample water, aphid fecundity was enhanced by only 23% from feeding on BYDV‐infected plants.

Synthesis and applications. Collectively, our experiments suggest that wheat– Barley yellow dwarf virus interactions shift along gradients of water stress severity and duration. When Barley yellow dwarf virus infection preceded water deprivation, plant performance was not reduced from virus infection, and infected plants recovered from severe stress events more readily than non‐infected plants. However, vector–pathogen mutualism resulting in enhanced reproduction of aphids on virus‐infected plants is likely to amplify direct plant injury from herbivory in the field. Our findings indicate that during periods of drought, management of Barley yellow dwarf virus infection may not be needed and infection could benefit wheat under conditions of acute water stress.