bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential nutritional strategies for the amelioration or prevention of high rigor temperature in cattle – a review
Authors: DiGiacomo Kristy , Leury Brian J. , Dunshea Frank R.
Published: February 2014

Environmental conditions influence animal production from an animal performance perspective and at the carcass level post-slaughter. High rigor temperature occurs when the animal is hyperthermic pre-slaughter, and this leads to tougher meat. Hyperthermia can result from increased environmental temperature, exercise, stress or a combination of these factors. Consumer satisfaction with beef meat is influenced by the visual and sensory traits of the product when raw and cooked, with beef consumers commonly selecting tenderness of the product as the most important quality trait. High rigor temperature leads to a reduction in carcass and eating quality. This review examines some possible metabolic causes of hyperthermia, with focus on the importance of adipose tissue metabolism and the roles of insulin and leptin. Potential strategies for the amelioration or prevention of high rigor temperature are offered, including the use of dietary supplements such as betaine and chromium, anti-diabetic agents such as thiazolidinediones, vitamin D, and magnesium (Mg) to provide stress relief.
Does artificial light influence the activity of vertebrates beneath rural buildings?
Authors: Borchard Philip , Eldridge David J.
Published: February 2014

Interactions between humans and wildlife have increased dramatically over the past century as human populations increase and occupy areas formerly dominated by native animals. In Australia, increases in land clearing and farming close to riparian areas has brought humans into contact with the common wombat (Vombatus ursinus), a relatively large-bodied, semifossorial marsupial. The common wombat is regarded as a pest in some agricultural areas due to its habit of burrowing beneath buildings, destroying fences and destabilising stream banks. We examined the effectiveness of artificial lighting to deter wombats from using the subfloor cavity under an historic cottage at ‘Bundanon’ in southern New South Wales, Australia. The response of wombats to artificial light (10 weeks on followed by 10 weeks off) was assessed using heat- and motion-sensing cameras continuously over a period of 58 weeks. While the main focus was on light effects on wombats, the study also allowed us to record non-nuisance animals using the subfloor cavity. Of the total of 1086 animal detections over the 58-week period (2.67 detections day–1), 965 (89%) were of mammals, 106 birds and 15 reptiles. Wombats (622; 57%) and kangaroos (228; 22%) made up 79% of all detections. Nocturnal activity of wombats remained unchanged in response to lighting (on: 266; off: 268), but there were significantly more diurnal detections when the lights were on (58) than off (30). For kangaroos, there were more nocturnal detections when lights were off, but more diurnal detections when lights were on. More antechinus were detected at night (night: 107; day: 8), and with the lights off (99 cf. 8), and insectivorous birds were detected almost entirely during the day, mostly with the lights on (66 cf. 39). Our study showed that, overall, the lighting regime we used was ineffective at reducing wombat activity under the building.
Physical contact influences how much people pay at celebrity auctions
Authors: Newman George E. , Bloom Paul
Published: February 2014

Significance

Contagion is a form of magical thinking in which people believe that a person's immaterial qualities or essence can be transferred to an object through physical contact. Our paper provides unique evidence for the influence of contagion beliefs in an actual market context. We analyze several high-profile celebrity auctions and demonstrate that the degree of perceived physical contact that a celebrity has with an item influences the amount of money that collectors are willing to pay for it at auction. This effect does not appear to be accounted for in preauction estimates. Therefore, our paper is unique in suggesting the existence of contagion effects outside of the laboratory using consequential purchase decisions.
Habenular kisspeptin modulates fear in the zebrafish
Authors: Ogawa Satoshi , Nathan Fatima M. , Parhar Ishwar S.
Published: February 2014

Significance

Kisspeptin, a hypothalamic neuropeptide, plays a key role in vertebrate reproduction. In the zebrafish, kisspeptin and its receptor are predominantly expressed in the habenula, a highly evolutionarily conserved brain region mediating behavioral responses to stressful conditions. However, the physiological significance of kisspeptin expressed in the habenula remains unknown. Here we demonstrate a unique role for the kisspeptin system in inhibiting fear response in the zebrafish that extends beyond the control of reproduction.
Point-of-care diagnostics for noncommunicable diseases using synthetic urinary biomarkers and paper microfluidics
Authors: Warren Andrew D. , Kwong Gabriel A. , Wood David K. , Lin Kevin Y. , Bhatia Sangeeta N.
Published: February 2014

Significance

Noncommunicable diseases, including cardiovascular disease and cancer, are growing worldwide but are challenging to diagnose because biomarkers that can accurately detect them in patients are lacking. Here, we designed nanoscale agents that are administered to reveal the presence of diseased tissues by producing a biomarker in the urine that can be detected using paper strips similar to a home pregnancy test. Using mouse models, we show that we can detect diseases as diverse as solid cancer and blood clots using only a single injection of our diagnostic followed by urine analysis on paper. This platform does not require expensive instruments, invasive procedures, or trained medical personnel, and may allow low-cost diagnosis of diseases at the point of care in resource-limited settings.
MURC/Cavin-4 facilitates recruitment of ERK to caveolae and concentric cardiac hypertrophy induced by α1-adrenergic receptors
Authors: Ogata Takehiro , Naito Daisuke , Nakanishi Naohiko , Hayashi Yukiko K. , Taniguchi Takuya , Miyagawa Kotaro , Hamaoka Tetsuro , Maruyama Naoki , Matoba Satoaki , Ikeda Koji , Yamada Hiroyuki , Oh Hidemasa , Ueyama Tomomi
Published: February 2014

Significance

Caveolae are recognized as a platform for preassembled complexes of receptors, signal components, and their targets, facilitating efficient and specific cellular responses at the plasma membrane. ERK is activated at the plasma membrane and an important molecule that has been well studied for its integral role in signal transduction events during physiological adaptation and pathological manifestation. Here we show that although muscle-restricted coiled-coil protein (MURC)/Cavin-4, a muscle-specific caveola component, is dispensable for caveolar formation in cardiomyocytes, MURC/Cavin-4 serves as an ERK-recruiting protein in the caveolae within cardiomyocytes. The recruiting function of MURC/Cavin-4 is necessary to elicit efficient signaling of the α1-adrenergic receptor–ERK cascade in concentric cardiac hypertrophy. Our findings provide unique insight into the molecular mechanisms underlying caveola-mediated signaling in cardiac hypertrophy.
Mycobacterium abscessus
cording prevents phagocytosis and promotes abscess formation
Authors: Bernut Audrey , Herrmann Jean-Louis , Kissa Karima , Dubremetz Jean-François , Gaillard Jean-Louis , Lutfalla Georges , Kremer Laurent
Published: February 2014

Significance

Mycobacterium abscessus
is the most frequently isolated rapidly growing mycobacterium in human disease and recently has emerged as responsible for severe pulmonary infections in cystic fibrosis patients. However, little is known about the virulence mechanisms of this human pathogen. We adapted the zebrafish embryo as a tractable infection model to study, at a spatiotemporal level, the physiopathology of
M. abscessus
infection. We describe the high propensity of virulent rough variant
M. abscessus
to produce serpentine cords in vivo
,
which are not observed with the less virulent smooth variant. We demonstrate that extracellular cording allows the bacterium to withstand phagocytosis, leading to uncontrolled growth and establishment of an acute and lethal infection, thus constituting a determinant of virulence.
Pilus hijacking by a bacterial coaggregation factor critical for oral biofilm development
Authors: Reardon-Robinson Melissa E. , Wu Chenggang , Mishra Arunima , Chang Chungyu , Bier Naomi , Das Asis , Ton-That Hung
Published: February 2014

Significance

The development of dental plaque biofilm requires specific and sequential molecular interactions between oral bacteria-colonizing host surfaces. Coaggregation between early colonizers is crucial to establish an environment suitable for late colonizers. Here, we describe that a surface protein in a Gram-positive bacterium that is not genetically linked to the fimbrial gene clusters hijacks a specific fimbrial polymerization apparatus to be displayed on the fimbrial tip. This tip-localized protein not only functions as the bona fide cell-to-cell adhesion factor for mediating coaggregation between the early colonizersActinomyces orisandStreptococcus oralisbut also serves as an initiator of fimbrial assembly.
Crystal structures of human soluble adenylyl cyclase reveal mechanisms of catalysis and of its activation through bicarbonate
Authors: Kleinboelting Silke , Diaz Ana , Moniot Sebastien , van den Heuvel Joop , Weyand Michael , Levin Lonny R. , Buck Jochen , Steegborn Clemens
Published: February 2014

Significance

Soluble adenylyl cyclase (sAC) generates the ubiquitous signaling molecule cAMP in response to bicarbonate. In physiological systems, bicarbonate is in nearly instantaneous equilibrium with carbon dioxide and pH; therefore, sAC, and its evolutionarily related cyclases, serve as nature’s carbon dioxide/bicarbonate/pH sensors. In particular, bicarbonate regulation of mammalian sAC mediates numerous cellular processes, from sperm activation to pH homeostasis and mitochondrial ATP synthesis. We solved crystal structures of sAC’s catalytic domains in complex with substrate, products, and regulators. The structures reveal insights into sAC catalysis, how bicarbonate binds to and activates sAC, and how sAC can be inhibited by a drug. Our results reveal mechanisms that will facilitate the development of drugs targeting this signaling system.
Autoantibodies to IgG/HLA class II complexes are associated with rheumatoid arthritis susceptibility
Authors: Jin Hui , Arase Noriko , Hirayasu Kouyuki , Kohyama Masako , Suenaga Tadahiro , Saito Fumiji , Tanimura Kenji , Matsuoka Sumiko , Ebina Kosuke , Shi Kenrin , Toyama-Sorimachi Noriko , Yasuda Shinsuke , Horita Tetsuya , Hiwa Ryosuke , Takasugi Kiyoshi , Ohmura Koichiro , Yoshikawa Hideki , Saito Takashi , Atsumi Tatsuya , Sasazuki Takehiko , Katayama Ichiro , Lanier Lewis L. , Arase Hisashi
Published: February 2014

Significance

Cellular misfolded proteins are transported to the cell surface by MHC class II molecules via association with the peptide-binding groove without processing to peptides. We found that IgG heavy chain is transported to the cell surface by MHC class II molecules. Furthermore, IgG heavy chain associated with MHC class II molecules is recognized by autoantibodies in rheumatoid arthritis patients. Autoantibody binding to IgG heavy chain complexed with different MHC class II alleles was strongly associated with rheumatoid arthritis susceptibility conferred by certain MHC class II alleles. These findings suggest that misfolded proteins complexed with MHC class II molecules could be targets for autoantibodies in autoimmune diseases, which might be involved in autoimmune disease susceptibility.
Eukaryotic algal phytochromes span the visible spectrum
Authors: Rockwell Nathan C. , Duanmu Deqiang , Martin Shelley S. , Bachy Charles , Price Dana C. , Bhattacharya Debashish , Worden Alexandra Z. , Lagarias J. Clark
Published: February 2014

Significance

Photosynthetic organisms exploit photosensory proteins to respond to changing light conditions. In land plants, phytochromes use the ratio of red to far-red light to detect shading by neighboring plants, leading to changes in growth and development. Light conditions can be more variable for algae because of the wavelength-dependent attenuation of light by water and because of ocean mixing. We studied phytochromes from taxonomically diverse eukaryotic algae from groups considered important for coastal ecosystems and the global carbon cycle. These proteins detect light throughout the visible spectrum (blue, green, orange, red, and far-red). Extensive spectral tuning has evolved within these algae, presumably reflecting aquatic light environments. These studies should ultimately facilitate engineering of crop plant species for diverse light environments.
The discursive dynamics of neo-liberal consensus
Authors: Phelan Sean
Published: February 2014

The stock market floatation of Telecom Eireann (the soon to be renamed Eircom) in July 1999 was, and remains, “the biggest privatization in the history of the Irish state”. Through the application of a critical discourse analysis framework (Chouliaraki and Fairclough 1999; Fairclough 2003), this article examines editorial discourse both before and after the company’s initially ‘successful’ floatation in six Irish broadsheet newspapers. The different editorial stances are analyzed in terms of the authority of three key neo-liberal assumptions: that the full privatization of the company is desirable; that the notion of direct state involvement in a modern Telecoms market is archaic; and that public participation in the stock market should be encouraged. The article suggests that while the evidence illustrates a context of neo-liberal hegemony, the ideological authority of neo-liberalism should not be understood in undifferentiated, monolithic terms, as the evidence points to a plurality of neo-liberal discourses and styles, which can be partly understood in terms of the ‘media field’ identity of the different newspapers.
Language, ideology and neoliberalism
Authors: Holborow Marnie
Published: February 2014

When the ideas of capitalist globalisation appear to speak as one across the world, it is timely to re-examine the interconnections between language and ideology. The global market and its dominant neoliberal ideology, increasingly expressed in English, have led some to hold that the language itself constructs the hegemonic order of global capitalism. Others have focussed on language not only as the bearer of ideology but as part of theimmaterial productionof capitalism. This paper discusses the way in which language and ideology interconnect but argues that the ideology of neoliberalism cannot be adequately described as adiscourse. Instead, it is an ideology with specific historical roots and which, as a dominant ideology, makes itself felt in language, although not without contradictions. Two aspects of language and neoliberal ideology are examined here: firstly the way in which the customer metaphor has been adopted in different and unexpected settings and, secondly, how models of listening and speaking in call centres are framed around neoliberal assumptions. Both processes aim to impose a kind of ‘corporate speak’ to reinforce neoliberal ideas ascommon sense, but both also contain tensions because language is neither a straitjacket nor a settled ideological product. This paper argues that language and ideology are not the same and that it is in the dynamic of their interconnection that world views are both made and contested.
Language as a political category
Authors: Pelinka Anton
Published: February 2014

The article is based on an understanding that everything in society — including language — is political, at least potentially. For that reason, language must be seen (and analyzed) as a political phenomenon. Language is one of the decisive ‘nation building’ factors among others — sometimes cross-cutting other potentially defining factors. In its identity-building capacity, language is inclusive and exclusive at the very same time. Language has to be seen as one of the most important social (and: therefore political) cleavages. As more and more societies are confronted with ‘multiculturalism’ expressed in a multi-linguistic reality, politics have to come to terms with diversity in different ways.
Bill Clinton’s “new partnership” anecdote
Authors: Edwards Jason A. , Valenzano III Joseph M.
Published: February 2014

This essay explores the composition of United States post-Cold War foreign policy rhetoric under President Bill Clinton. We contend that Bill Clinton offered a coherent and comprehensive foreign policy narrative for the direction of U.S. foreign policy discourse in the post-Cold War world. Specifically, we analyze the “new partnership” narrative that Clinton articulated in his 1998 trip to Africa as a representative anecdote for the larger body of his foreign policy discourse. This “new partnership” narrative was structured by three narrative themes: (1) America’s role as world leader; (2) reconstituting the threat environment; (3) democracy promotion as the strategy for American foreign policy. These three themes can be found throughout Clinton’s foreign policy rhetoric and serve as the basis for a foreign policy narrative used by Clinton, and perhaps, future administrations.
The political potential of multi-accentuality in the exhibition title ‘gastarbajteri’
Authors: Böse Martina , Busch Brigitta
Published: February 2014

This article explores the multi-accentuality of the sign ‘gastarbajteri’, used as title word in an exhibition on labour migration that took place in Vienna, Austria, in 2004. Based on an ethnographic study of the exhibition, it addresses a variety of readings of this word, both at the level of production and reception. The analysis of texts shows, firstly, the divergent rationales of the two agents who cooperated as exhibition producers, the minority NGO who wished to signal self-empowerment of migrants on the hand and the city museum who aimed at selling the exhibition to a mainstream audience on the other hand. Secondly, it juxtaposes them with the plurality of readings by its recipients, which range from the recognition of an appeal to migrants via the mis-reading as ‘guestworker’ and its upvaluation through to an insider-perspective based on the knowledge of the word’s connotations in the former Yugoslavia.
Negatives and positives in the language of politics
Authors: Chen Lily
Published: February 2014

An analytic model based on MAK Halliday’s System of Transitivity provides a powerful tool for decoding a journalist’s attitude to the events or individuals being written about. Chen (2005) showed how in the UK Times use of certain verbal processes rather than others to introduce direct or indirect speech could be an indicator that the journalist’s attitude towards the person being quoted was either negative or positive.

In this study, using a model for the linguistic comparison of the British and Chinese press developed by Chen (2004), verbal process use in the UK Times and the English-language China Daily is contrasted for evidence of differences in the attitude of British and Chinese journalists towards political figures.

The evidence is clear. Times journalists frequently use ‘negative’ verbal processes which indicate doubt or scepticism towards the person being quoted. China Daily journalists, meanwhile, more often use ‘positive’ verbal processes which enhance the authority of the speaker.
The Rise of the Safavids According to their Old Veterans: Amini Haravi's Futuhat-e Shahi
Authors: Anooshahr Ali
Published: February 2014

This article studies an early Safavid chronicle, Futuhat-e Shahi by Amini Haravi. In 1521, the founder of the Safavid state, Shah Isma‘il, provided Haravi with a number of veterans from the early days of the Safavid uprising as informants. Their narrative presents an alternative view on the early career of the shah that differs from the dominant version current in modern scholarship. From the perspective of the Futuhat, the rise of the Safavids did not occur as a wild apocalyptic explosion, but was a carefully planned and cautious campaign run by experienced commanders who kept a tight rein on the teenage Shah Isma‘il.
Arp5 is a key regulator of myocardin in smooth muscle cells
Authors: Morita Tsuyoshi , Hayashi Ken’ichiro
Published: February 2014

Myocardin (Myocd) and Myocd-related transcription factors (MRTFs) are robust coactivators of serum response factor (SRF). RPEL motifs are monomeric globular actin (G-actin) binding elements that regulate MRTF localization and activity. However, the function of the RPEL motif in Myocd is largely unknown because of its low affinity for G-actin. Here, we demonstrated that the Myocd RPEL motif bound to actin-related protein 5 (Arp5) instead of conventional actin, resulting in a significant suppression of Myocd activity. In addition, Arp5 bound to a DNA binding domain of SRF via its C-terminal sequence and prevented the association of the Myocd–SRF complex with the promoter regions of smooth muscle genes. Well-differentiated smooth muscle cells mainly expressed a specific splicing variant of arp5; therefore, the protein level of Arp5 was markedly reduced by partial messenger RNA decay and translational suppression. In dedifferentiated smooth muscle cells, Arp5 knockdown restored the differentiated phenotype via Myocd activation. Thus, Arp5 is a key regulator of Myocd activity.
Fission of SNX-BAR–coated endosomal retrograde transport carriers is promoted by the dynamin-related protein Vps1
Authors: Chi Richard J. , Liu Jingxuan , West Matthew , Wang Jing , Odorizzi Greg , Burd Christopher G.
Published: February 2014

Retromer is an endosomal sorting device that orchestrates capture and packaging of cargo into transport carriers coated with sorting nexin BAR domain proteins (SNX-BARs). We report that fission of retromer SNX-BAR–coated tubules from yeast endosomes is promoted by Vps1, a dynamin-related protein that localizes to endosomes decorated by retromer SNX-BARs and Mvp1, a SNX-BAR that is homologous to human SNX8. Mvp1 exhibits potent membrane remodeling activity in vitro, and it promotes association of Vps1 with the endosome in vivo. Retrograde transport carriers bud from the endosome coated by retromer and Mvp1, and cargo export is deficient in mvp1- and vps1-null cells, but with distinct endpoints; cargo export is delayed in mvp1-null cells, but cargo export completely fails in vps1-null cells. The results indicate that Mvp1 promotes Vps1-mediated fission of retromer- and Mvp1-coated tubules that bud from the endosome, revealing a functional link between the endosomal sorting and fission machineries to produce retrograde transport carriers.
A Bub1–Mad1 interaction targets the Mad1–Mad2 complex to unattached kinetochores to initiate the spindle checkpoint
Authors: Moyle Mark W. , Kim Taekyung , Hattersley Neil , Espeut Julien , Cheerambathur Dhanya K. , Oegema Karen , Desai Arshad
Published: February 2014

Recruitment of Mad1–Mad2 complexes to unattached kinetochores is a central event in spindle checkpoint signaling. Despite its importance, the mechanism that recruits Mad1–Mad2 to kinetochores is unclear. In this paper, we show that MAD-1 interacts with BUB-1 in Caenorhabditis elegans. Mutagenesis identified specific residues in a segment of the MAD-1 coiled coil that mediate the BUB-1 interaction. In addition to unattached kinetochores, MAD-1 localized between separating meiotic chromosomes and to the nuclear periphery. Mutations in the MAD-1 coiled coil that selectively disrupt interaction with BUB-1 eliminated MAD-1 localization to unattached kinetochores and between meiotic chromosomes, both of which require BUB-1, and abrogated checkpoint signaling. The identified MAD-1 coiled-coil segment interacted with a C-terminal region of BUB-1 that contains its kinase domain, and mutations in this region prevented MAD-1 kinetochore targeting independently of kinase activity. These results delineate an interaction between BUB-1 and MAD-1 that targets MAD-1–MAD-2 complexes to kinetochores and is essential for spindle checkpoint signaling.
Mdm2 pulls the plug on glycolysis
Authors: Short Ben
Published: February 2014

The ubiquitin ligase induces senescence by promoting degradation of the glycolytic enzyme phosphoglycerate mutase.
Real-time immune cell interactions in target tissue during autoimmune-induced damage and graft tolerance
Authors: Miska Jason , Abdulreda Midhat H. , Devarajan Priyadharshini , Lui Jen Bon , Suzuki Jun , Pileggi Antonello , Berggren Per-Olof , Chen Zhibin
Published: February 2014

Real-time imaging studies are reshaping immunological paradigms, but a visual framework is lacking for self-antigen-specific T cells at the effector phase in target tissues. To address this issue, we conducted intravital, longitudinal imaging analyses of cellular behavior in nonlymphoid target tissues to illustrate some key aspects of T cell biology. We used mouse models of T cell–mediated damage and protection of pancreatic islet grafts. Both CD4+ and CD8+ effector T (Teff) lymphocytes directly engaged target cells. Strikingly, juxtaposed β cells lacking specific antigens were not subject to bystander destruction but grew substantially in days, likely by replication. In target tissue, Foxp3+ regulatory T (Treg) cells persistently contacted Teff cells with or without involvement of CD11c+ dendritic cells, an observation conciliating with the in vitro “trademark” of Treg function, contact-dependent suppression. This study illustrates tolerance induction by contact-based immune cell interaction in target tissues and highlights potentials of tissue regeneration under antigenic incognito in inflammatory settings.
Asymmetry in skeletal distribution of mouse hematopoietic stem cell clones and their equilibration by mobilizing cytokines
Authors: Verovskaya Evgenia , Broekhuis Mathilde J.C. , Zwart Erik , Weersing Ellen , Ritsema Martha , Bosman Lisette J. , van Poele Theo , de Haan Gerald , Bystrykh Leonid V.
Published: February 2014

Hematopoietic stem cells (HSCs) are able to migrate through the blood stream and engraft bone marrow (BM) niches. These features are key factors for successful stem cell transplantations that are used in cancer patients and in gene therapy protocols. It is unknown to what extent transplanted HSCs distribute throughout different anatomical niches in the BM and whether this changes with age. Here we determine the degree of hematopoietic migration at a clonal level by transplanting individual young and aged mouse HSCs labeled with barcoded viral vector, followed by assessing the skeletal distribution of hundreds of HSC clones. We detected highly skewed representation of individual clones in different bones at least 11 mo after transplantation. Importantly, a single challenge with the clinically relevant mobilizing agent granulocyte colony-stimulating factor (G-CSF) caused rapid redistribution of HSCs across the skeletal compartments. Old and young HSC clones showed a similar level of migratory behavior. Clonal make-up of blood of secondary recipients recapitulates the barcode composition of HSCs in the bone of origin. These data demonstrate a previously unanticipated high skeletal disequilibrium of the clonal composition of HSC pool long-term after transplantation. Our findings have important implications for experimental and clinical and stem cell transplantation protocols.
Responsive Justice?
Authors: Nelson Michael J.
Published: February 2014

Do elected judges and prosecutors change their behavior to reflect public opinion after they receive information about constituent preferences? In this article I use a unique measure of public opinion—votes on an initiative to legalize marijuana—to examine the responsiveness of prosecutors and trial court judges to a strong, issue-specific, constituency-level opinion signal. I find that, at least in recent drug cases in Colorado, both prosecutors and judges changed their sentencing behavior after receiving that signal. Prosecutors responded only to local-level opinion, while judges responded to both local and statewide opinion.
Judges and Their Allies
Authors: Trochev Alexei , Ellett Rachel
Published: February 2014

The social construction of judicial power is a complicated process, especially in hybrid political regimes. We argue that off-bench resistance against blatant interference supported by vibrant social networks is an important manifestation of judicial autonomy. By drawing on evidence from field research, media coverage, and the existing scholarly literature, we clarify the logic of off-bench judicial resistance against external interference, outline a taxonomy of five strategies of resistance in hybrid regimes, and explain the political implications of off-bench judicial behavior.
A note on the cohomology of the Langlands group
Authors: Fan Edward
Published: February 2014

We begin with a comparison of various cohomology theories for topological groups. Using the continuity result for Moore cohomology, we establish a Hochschild-Serre spectral sequence for a slightly larger class of groups. We use these properties to compute the cohomology of the Langlands group of a totally imaginary field. The appendix answers a question raised by Flach concerning the cohomological dimension of the group

R

\mathbb {R}

.
iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array
Authors: Zhou Jin , Tantoso Erwin , Wong Lai-Ping , Ong Rick Twee-Hee , Bei Jin-Xin , Li Yi , Liu Jianjun , Khor Chiea-Chuen , Teo Yik-Ying
Published: February 2014

Motivation: Next-generation genotyping microarrays have been designed with insights from 1000 Genomes Project and whole-exome sequencing studies. These arrays additionally include variants that are typically present at lower frequencies. Determining the genotypes of these variants from hybridization intensities is challenging because there is less support to locate the presence of the minor alleles when the allele counts are low. Existing algorithms are mainly designed for calling common variants and are notorious for failing to generate accurate calls for low-frequency and rare variants. Here, we introduce a new calling algorithm, iCall, to call genotypes for variants across the whole spectrum of allele frequencies.

Results: We benchmarked iCall against four of the most commonly used algorithms, GenCall, optiCall, illuminus and GenoSNP, as well as a post-processing caller zCall that adopted a two-stage calling design. Normalized hybridization intensities for 12 370 individuals genotyped on the Illumina HumanExome BeadChip were considered, of which 81 individuals were also whole-genome sequenced. The sequence calls were used to benchmark the accuracy of the genotype calling, and our comparisons indicated that iCall outperforms all four single-stage calling algorithms in terms of call rates and concordance, particularly in the calling accuracy of minor alleles, which is the principal concern for rare and low-frequency variants. The application of zCall to post-process the output from iCall also produced marginally improved performance to the combination of zCall and GenCall.

Availability and implementation: iCall is implemented in C++ for use on Linux operating systems and is available for download at http://www.statgen.nus.edu.sg/∼software/icall.html.

Contact:  statyy@nus.edu.sg, zhoujin@nus.edu.sg
Evaluation of a fishing captain's ability to predict species composition, sizes, and quantities of tunas associated with drifting fish-aggregating devices in the eastern Pacific Ocean
Authors: Fuller Daniel W. , Schaefer Kurt M.
Published: February 2014

Experiments were conducted to evaluate a fishing captain's ability to predict species composition, sizes, and quantities of tunas associated with drifting fish-aggregating devices (FADs), before encirclement with a purse-seine net. Operating in the equatorial eastern Pacific Ocean, during 11 May–23 July 2011, Captain Ricardo Diaz detected small quantities of bigeye (Thunnus obesus) and yellowfin (Thunnus albacares) tunas within large FAD-associated aggregations dominated by skipjack tuna (Katsuwonus pelamis). The captain's predictions were significantly related to the actual total catch and catch by species, but not to size categories by species. His predictions of species composition were most accurate when estimates of bigeye and yellowfin tuna were combined. If purse-seine captains are able to make accurate predictions of the proportion of bigeye and yellowfin tunas present in mixed-species aggregations associated with FADs, managers may wish to consider incentives to fishers to reduce the fishing mortality on those species.
Determination of the masses of the components of the HDE 226868/Cyg X-1 binary system
Authors: Ziółkowski J.
Published: February 2014

A recent determination of the distance to the HDE 226868/Cyg X-1 binary system and a more precise determination of the effective temperature of HDE 226868 allow for a more accurate estimate of the masses of both components. Using up-to-date evolutionary models, I obtain a mass range of between 25 and 35 M⊙ for the mass of the supergiant and between 13 and 23 M⊙ for the mass of the black hole. By accepting more liberal estimates of uncertainties in both the distance and the effective temperature, it is possible to extend these ranges to 21–35 and 10–23 M⊙ for both masses, respectively. The most likely values within these ranges are 27 and 16 M⊙, respectively. The mass obtained for the black hole agrees with the value of 15 ± 1 M⊙ suggested by Orosz et al. However, their value of 19 ± 2 M⊙ suggested for the mass of the supergiant should not be used because such a star violates the mass–luminosity relation for the massive core hydrogen-burning stars. This consideration was not incorporated into the iterative process of Orosz et al. To resolve this violation, I consider the possibility that the hydrogen content of HDE 226868 might be lowered as a result of the mass transfer and the induced fast rotation of the mass gainer. I have analysed the evolutionary effects of such a situation and have found that, while important, these do not invalidate the conclusions listed above. If, as a result of the rotation-induced mixing, the present hydrogen content of HDE 226868 is equal to about 0.6 (as suggested by some observational data), then its present mass might be lower: ∼24 M⊙ rather than ∼27 M⊙.
Single-photon imaging in complementary metal oxide semiconductor processes
Authors: Charbon E.
Published: February 2014

This paper describes the basics of single-photon counting in complementary metal oxide semiconductors, through single-photon avalanche diodes (SPADs), and the making of miniaturized pixels with photon-counting capability based on SPADs. Some applications, which may take advantage of SPAD image sensors, are outlined, such as fluorescence-based microscopy, three-dimensional time-of-flight imaging and biomedical imaging, to name just a few. The paper focuses on architectures that are best suited to those applications and the trade-offs they generate. In this context, architectures are described that efficiently collect the output of single pixels when designed in large arrays. Off-chip readout circuit requirements are described for a variety of applications in physics, medicine and the life sciences. Owing to the dynamic nature of SPADs, designs featuring a large number of SPADs require careful analysis of the target application for an optimal use of silicon real estate and of limited readout bandwidth. The paper also describes the main trade-offs involved in architecting such chips and the solutions adopted with focus on scalability and miniaturization.
Analog synthetic biology
Authors: Sarpeshkar R.
Published: February 2014

We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog–digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA–protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in
Escherichia coli
using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.
trans-Chloridobis(ethane-1,2-diamine-κ2N,N′)(thiocyanato-κN)cobalt(III) diamminetetrakis(thiocyanato-κN)cromate(III)
Authors: Rusanova Julia A. , Semenaka Valentyna V. , Zubatyuk Roman I.
Published: February 2014

The title ionic complex [CoCl(NCS)(C2H8N2)2][Cr(NCS)4(NH3)2], which crystallizes as a non-merohedral twin, is build up of a complex cation [CoCl(NCS)(en)2]+(en is ethane-1,2-diamine) and the Reinecke's salt anion [Cr(NCS)4(NH3)2]−as complex counter-ion. A network of N—H...S and N—H...Cl hydrogen bonds, as well as short S...S contacts [3.538 (2) and 3.489 (3) Å], between the NCS groups of the complex anions link the molecules into a three-dimentional supramolecular network. Intensity statistic indicated twinning by non-merohedry with refined weighs of twin components are 0.5662:0.4338.
5,6-Dimethyl-2-(pyridin-2-yl)-1-[(pyridin-2-yl)methyl]-1H-benzimidazole
Authors: Geiger David K. , DeStefano Matthew R.
Published: February 2014

The title compound, C20H18N4, was obtainedviathe condensation of 4,5-dimethylbenzene-1,2-diamine with pyridine-2-carbaldehyde. The plane of the 2-(pyridin-2-yl) substitutent is canted by 2.75 (11)° from the plane of the benzimidazole system. The molecule exhibits anS(6) C—H...N intramolecular hydrogen-bond motif. In the crystal, C—H...N hydrogen bonds link pairs of molecules related by a crystallographic inversion center, formingR22(20) rings. Additional weak C—H...N hydrogen bonds result inC(9) chains parallel to [001].
3-(2,3-Dioxoindolin-1-yl)propanenitrile
Authors: Qachchachi Fatima-Zahrae , Kandri Rodi Youssef , Essassi El Mokhtar , Bodensteiner Michael , El Ammari Lahcen
Published: February 2014

The asymmetric unit of the title compound, C11H8N2O2, contains two independent molecules (AandB). Each molecule is build up from fused five- and six-membered rings with the former linked to a cyanoethyl group. The indoline ring and two carbonyl O atoms of each molecule are nearly coplanar, with the largest deviations from the mean planes being 0.0198 (9) (moleculeA) and 0.0902 (9) Å (moleculeB), each by a carbonyl O atom. The fused ring system is nearly perpendicular to the mean plane passing through the cyanoethyl chains, as indicated by the dihedral angles between them of 69.72 (9) (moleculeA) and 69.15 (9)° (moleculeB). In the crystal, molecules are linked by C—H...O and π–π [intercentroid distance between inversion-related indoline (A) rings = 3.6804 (7) Å] interactions into a double layer that stacks along thea-axis direction.
Linking functional traits and demographic rates in a subtropical tree community: the importance of size dependency
Authors: Iida Yoshiko , Kohyama Takashi S. , Swenson Nathan G. , Su Sheng‐Hsin , Chen Chien‐Teh , Chiang Jyh‐Min , Sun I‐Fang
Published: February 2014

An important goal in plant community ecology is to understand how species traits determine demographic performance. Several functional traits have been shown to correlate with growth and mortality rates in trees, but less is known about how the relationships between functional traits and demographic rates change with tree size.

We examined the associations of functional traits with growth and mortality across 43 tree species in the Fushan 25‐ha subtropical rain forest plot in northern Taiwan. We estimated the 95th percentile maximum stem diameter, wood density and six leaf functional traits (leaf area, specific leaf area, thickness, succulence, and mass‐based nitrogen and phosphorus contents) obtained from leaves on juvenile and adult individuals of each species.

To quantify size‐dependent changes in growth and mortality, relative growth rate (RGR) and mortality were estimated as a function of stem diameter using hierarchical Bayesian models. These rate estimates were then correlated with functional traits at a range of stem diameter classes.

Relationships between functional traits and demographic rates varied with tree size. Maximum size was positively correlated with RGR across a wide range of tree sizes. Wood density was negatively correlated with RGR and mortality for small‐sized trees. Leaf traits such as leaf area and specific leaf area at juvenile and adult stages were associated more strongly with demographic rates for corresponding sizes than from other sizes.

Synthesis. The observed size‐dependent changes in the trait–demography relationships are possibly due to the effects of developmental and environmental changes with increasing tree size. The underlying effects of functional traits on demographic performance vary with tree size, and this should influence dynamics in a tree community.
Variability in seed cone production and functional response of seed predators to seed cone availability: support for the predator satiation hypothesis
Authors: Linhart Yan B. , Moreira Xoaquín , Snyder Marc A. , Mooney Kailen A.
Published: February 2014

Mast seeding is a reproductive strategy in some perennial plants defined as synchronous production of large seed crops at irregular intervals. One widely accepted theory to explain this behaviour is the predator satiation hypothesis, which states that the synchronous and variable production of seeds within a population will maximize the probability of seed survival through satiation of seed predators.

Although some short‐term studies have documented the influence of variable and synchronized production of seeds on herbivore attack rate during one or few mast years, long‐term data including multiple mast seeding years and patterns of cone production and herbivore attack on individual trees are needed to assess (i) how cone production, variability and synchrony affect individual plant fitness and (ii) the functional responses of seed predators to mast seeding events.

We tested these objectives, collecting long‐term (29 years) data on female seed cone production and rates of seed predator attack from 217 individual contiguous trees within aPinus ponderosapopulation.

Our results support the predator satiation hypothesis. First, we found high interannual synchrony and variability in seed cone production and a typeIIfunctional response of seed predators to available cones. Secondly, years with high cone production (mast years) had markedly lower rates of seed predator attack than years of low production (i.e. a population‐level satiation effect). Thirdly, within mast years, individuals with high cone production had markedly lower rates of attack than individuals with low cone production (i.e. an individual‐level satiation effect). Finally, individual trees with greater synchrony and more variable cone production suffered lower rates of attack.

Synthesis: Our long‐term data on individual trees lend strong support to the hypothesis that mast seeding inPinus ponderosahas evolved in response to natural selection from insect seed predators.
Climate drivers, host identity and fungal endophyte infection determine virus prevalence in a grassland ecosystem
Authors: Rúa Megan A. , McCulley Rebecca L. , Mitchell Charles E.
Published: February 2014

Under climate change, alterations to precipitation and temperature regimes are expected to impact ecosystem structure and function. These impacts may in part be determined by feedbacks between plants and associated microbes, including both endophytic fungal symbionts and viral pathogens.

To test potential key components of these feedbacks in a grassland system, we conducted a field experiment that factorially manipulated temperature regime, precipitation regime and endophyte infection of a dominant species, Schedonorus arundinaceus. After one growing season, we evaluated the four most frequently occurring grass species for infection by three species of barley and cereal yellow dwarf viruses (B/CYDVs). For S. arundinaceus, we also tracked changes in viral prevalence over an additional two growing seasons, for a total of three growing seasons.

Plant species identity played a strong role in determining virus prevalence; Poa pratensis and Paspalum dilatatum were more frequently infected than either S. arundinaceus (endophyte infected or endophyte free) or Eleusine indica. Both elevated temperature and elevated precipitation impacted virus prevalence, but effects varied among years and interacted with fungal endophyte symbiosis for S. arundinaceus.

In the final year of data collection, elevated precipitation increased virus prevalence in endophyte‐infected, but not endophyte‐free, S. arundinaceus. In the same year, but regardless of endophyte infection, elevated temperature by itself increased virus prevalence for S. arundinaceus. This effect of temperature on virus prevalence may have been driven by vector abundance because the viruses are obligately aphid‐transmitted, and aphids were found more frequently in heated plots.

Synthesis. Overall, our investigation experimentally demonstrates strong combined impacts of biotic and abiotic factors on disease dynamics in a grassland system. Impacts of climate change on virus prevalence in grasslands may depend on the responses of aphid vectors and the presence of endophytic fungal symbionts.