bluuebunny/crossref_metadata_2025 huggingface dataset:
ERK signaling couples nutrient status to antiviral defense in the insect gut
Authors: Xu Jie , Hopkins Kaycie , Sabin Leah , Yasunaga Ari , Subramanian Harry , Lamborn Ian , Gordesky-Gold Beth , Cherry Sara
Published: August 2013

Significance

A unique facet of arthropod-borne virus infection is that the pathogens are orally acquired by insects during the taking of a blood meal. Hence, there is a direct link between nutrient acquisition and pathogen challenge. We found that the classic nutrient-responsive ERK pathway is a molecular determinant of this “midgut barrier”; ERK signaling is essential for antiviral defense in the insect intestinal epithelial cells. Surprisingly, we also found vertebrate insulin, which activates ERK signaling during a blood meal, both restricts viral infection in insect cells and protects against viral invasion of the gut epithelium. ERK signaling in the insect intestines restricts viral infection, suggesting that insects may take advantage of cross-species signals in the meal to preemptively activate antiviral immunity.
Magnetotactic bacteria form magnetite from a phosphate-rich ferric hydroxide via nanometric ferric (oxyhydr)oxide intermediates
Authors: Baumgartner Jens , Morin Guillaume , Menguy Nicolas , Perez Gonzalez Teresa , Widdrat Marc , Cosmidis Julie , Faivre Damien
Published: August 2013

The iron oxide mineral magnetite (Fe
3
O
4
) is produced by various organisms to exploit magnetic and mechanical properties. Magnetotactic bacteria have become one of the best model organisms for studying magnetite biomineralization, as their genomes are sequenced and tools are available for their genetic manipulation. However, the chemical route by which magnetite is formed intracellularly within the so-called magnetosomes has remained a matter of debate. Here we used X-ray absorption spectroscopy at cryogenic temperatures and transmission electron microscopic imaging techniques to chemically characterize and spatially resolve the mechanism of biomineralization in those microorganisms. We show that magnetite forms through phase transformation from a highly disordered phosphate-rich ferric hydroxide phase, consistent with prokaryotic ferritins, via transient nanometric ferric (oxyhydr)oxide intermediates within the magnetosome organelle. This pathway remarkably resembles recent results on synthetic magnetite formation and bears a high similarity to suggested mineralization mechanisms in higher organisms.
Quantitative basis for neuroimaging of cortical laminae with calibrated functional MRI
Authors: Herman Peter , Sanganahalli Basavaraju G. , Blumenfeld Hal , Rothman Douglas L. , Hyder Fahmeed
Published: August 2013

Significance

This work challenges the notion that conventional functional magnetic resonance imaging (fMRI), that is, blood oxygenation level-dependent signal alone, can accurately reflect laminar neural activity. Instead, we show that calibrated fMRI methods for metabolic and hemodynamic measurements can better reflect laminar neuronal activities.
An unusual CsrA family member operates in series with RsmA to amplify posttranscriptional responses inPseudomonas aeruginosa
Authors: Marden Jeremiah N. , Diaz Manisha R. , Walton William G. , Gode Cindy J. , Betts Laurie , Urbanowski Mark L. , Redinbo Matthew R. , Yahr Timothy L. , Wolfgang Matthew C.
Published: August 2013

Members of the CsrA family of prokaryotic mRNA-binding proteins alter the translation and/or stability of transcripts needed for numerous global physiological processes. The previously described CsrA family member inPseudomonas aeruginosa(RsmA) plays a central role in determining infection modality by reciprocally regulating processes associated with acute (type III secretion and motility) and chronic (type VI secretion and biofilm formation) infection. Here we describe a second, structurally distinct RsmA homolog inP. aeruginosa(RsmF) that has an overlapping yet unique regulatory role. RsmF deviates from the canonical 5 β-strand and carboxyl-terminal α-helix topology of all other CsrA proteins by having the α-helix internally positioned. Despite striking changes in topology, RsmF adopts a tertiary structure similar to other CsrA family members and binds a subset of RsmA mRNA targets, suggesting that RsmF activity is mediated through a conserved mechanism of RNA recognition. Whereas deletion ofrsmFalone had little effect on RsmA-regulated processes, strains lacking bothrsmAandrsmFexhibited enhanced RsmA phenotypes for markers of both type III and type VI secretion systems. In addition, simultaneous deletion ofrsmAandrsmFresulted in superior biofilm formation relative to the wild-type orrsmAstrains. We show that RsmF translation is derepressed in anrsmAmutant and demonstrate that RsmA specifically binds torsmFmRNA in vitro, creating a global hierarchical regulatory cascade that operates at the posttranscriptional level.
Emphasis of spatial cues in the temporal fine structure during the rising segments of amplitude-modulated sounds
Authors: Dietz Mathias , Marquardt Torsten , Salminen Nelli H. , McAlpine David
Published: August 2013

Significance

Sound localization in rooms is challenging, especially for hearing-impaired listeners or technical devices. Reflections from walls and ceilings make it difficult to distinguish sounds arriving direct from a source from the mixture of potentially confounding sounds arriving a few milliseconds later. Nevertheless, normal-hearing listeners show remarkable localization abilities under such challenging listening conditions. The current study investigates the underlying mechanisms responsible for accurate localization performance. Stimuli we named amplitude modulated binaural beats are introduced. These stimuli allow for a more controlled testing than speech stimuli. Results from two experimental procedures (psychoacoustics and the brain-imaging technique magnetoencephalography) reveal that listeners appear to “glimpse” reliable spatial information during the early, rising portions of modulated sounds, ignoring later-arriving, potentially conflicting, spatial cues.
Natalisin, a tachykinin-like signaling system, regulates sexual activity and fecundity in insects
Authors: Jiang Hongbo , Lkhagva Ankhbayar , Daubnerová Ivana , Chae Hyo-Seok , Šimo Ladislav , Jung Sung-Hwan , Yoon Yeu-Kyung , Lee Na-Rae , Seong Jae Young , Žitňan Dušan , Park Yoonseong , Kim Young-Joon
Published: August 2013

Significance

Successful courtship and reproduction, which are at the center of evolutionary processes, involve complex interactions between neural and endocrine systems. In this study, we describe a group of neuropeptides that we have named “natalisin” (from the Latin
natalis
for “birth”) because of their function in promoting reproduction in arthropods. Three holometabolous insects,
Drosophila melanogaster
,
Bombyx mori
, and
Tribolium castaneum
were examined to understand the patterns of natalisin expression and to assess the phenotype of natalisin RNAi, and revealed the functions in courtship behavior and egg production. The natalisin receptor identified here warrants expanded study to elucidate the mechanisms of natalisin in arthropod reproduction.
Spin-dependent electron transmission through bacteriorhodopsin embedded in purple membrane
Authors: Mishra Debabrata , Markus Tal Z. , Naaman Ron , Kettner Matthias , Göhler Benjamin , Zacharias Helmut , Friedman Noga , Sheves Mordechai , Fontanesi Claudio
Published: August 2013

Significance

The role of the electron spin in chemistry and biology has been receiving much attention because of a plausible relation to electromagnetic field effects on living organisms. Part of the difficulty in studying the subject arises from the lack of a physical model that can rationalize these phenomena. Recently the chiral-induced spin selectivity effect was observed in electron transmission through organic molecules. The question is to what extent the effect takes place in proteins. In the present study, we probed bacteriorhodopsin embedded in its native membrane environment. We observed clear evidence for spin-dependent electron transmission through this system. The results point to the possibility that the effect may play a role in electron transfer in biological systems.
Immunotherapy of chronic hepatitis C virus infection with antibodies against programmed cell death-1 (PD-1)
Authors: Fuller Michael J. , Callendret Benoit , Zhu Baogong , Freeman Gordon J. , Hasselschwert Dana L. , Satterfield William , Sharpe Arlene H. , Dustin Lynn B. , Rice Charles M. , Grakoui Arash , Ahmed Rafi , Walker Christopher M.
Published: August 2013

Hepatitis C virus (HCV) persistence is facilitated by exhaustion of CD8+ T cells that express the inhibitory receptor programmed cell death 1 (PD-1). Blockade of PD-1 signaling improves in vitro proliferation of HCV-specific T lymphocytes, but whether antiviral function can be restored in infected individuals is unknown. To address this question, chimpanzees with persistent HCV infection were treated with anti–PD-1 antibodies. A significant reduction in HCV viremia was observed in one of three treated animals without apparent hepatocellular injury. Viremia rebounded in the responder animal when antibody treatment was discontinued. Control of HCV replication was associated with restoration of intrahepatic CD4+ and CD8+ T-cell immunity against multiple HCV proteins. The responder animal had a history of broader T-cell immunity to multiple HCV proteins than the two chimpanzees that did not respond to PD-1 therapy. The results suggest that successful PD-1 blockade likely requires a critical threshold of preexisting virus-specific T cells in liver and warrants consideration of therapeutic vaccination strategies in combination with PD-1 blockade to broaden narrow responses. Anti–PD-1 immunotherapy may also facilitate control of other persistent viruses, notably the hepatitis B virus where options for long-term control of virus replication are limited.
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
Authors: He Yi , Mozolewska Magdalena A. , Krupa Paweł , Sieradzan Adam K. , Wirecki Tomasz K. , Liwo Adam , Kachlishvili Khatuna , Rackovsky Shalom , Jagieła Dawid , Ślusarz Rafał , Czaplewski Cezary R. , Ołdziej Stanisław , Scheraga Harold A.
Published: August 2013

Significance

With the example of the coarse-grained United Residue model of polypeptide chains, this paper demonstrates that the physics-based approach for protein-structure prediction can lead to exceptionally good results when correct domain packing is an issue, even for a highly homologous target. The reason for this is probably that emphasis is placed on energetically favorable residue–residue interactions, including those with residues in relatively flexible linker regions; these regions are usually very different in the target compared with those of proteins in the databases used for template-based modeling. The results suggest that a combination of bioinformatics and a physics-based approach could result in a major increase in the prediction capacity of existing approaches.
Superpriming of synaptic vesicles after their recruitment to the readily releasable pool
Authors: Lee Jae Sung , Ho Won-Kyung , Neher Erwin , Lee Suk-Ho
Published: August 2013

Significance

During sustained nerve activity, synapses must continuously recycle vesicles. We used the unique opportunities for quantitative analysis offered by the calyx of Held synapse to study late stages in the process that renders vesicles release-ready. We dissect two sequential steps with distinct pharmacology and kinetics, the characterization of which is essential for an understanding of molecular mechanisms of transmitter release and short-term plasticity.
Definition of a thirdVLRgene in hagfish
Authors: Li Jianxu , Das Sabyasachi , Herrin Brantley R. , Hirano Masayuki , Cooper Max D.
Published: August 2013

Significance

The jawless vertebrates (hagfish and lampreys) possess an alternative adaptive immune system in which variable lymphocyte receptors (VLRs) constructed of leucine-rich repeats are used to recognize foreign antigens. ThreeVLRgenes have been identified in lampreys (VLRA,VLRB, andVLRC), but only two (VLRAandVLRB) have been found in hagfish. Here, we identified and characterized a third hagfishVLRgene. Our analysis indicates that the third hagfishVLRis the ortholog of lampreyVLRA, while the previously identified hagfish “VLRA” is the counterpart of lampreyVLRC. The demonstration of three orthologousVLRgenes in hagfish and lampreys suggests that this anticipatory receptor system evolved in a common ancestor of the two jawless vertebrate lineages ∼480 Mya.
Coherent delta-band oscillations between cortical areas correlate with decision making
Authors: Nácher Verónica , Ledberg Anders , Deco Gustavo , Romo Ranulfo
Published: August 2013

Significance

Delta oscillations have been largely associated with slow-wave sleep and anesthesia, when no conscious functions take place during these states. However, our study demonstrates that coherent delta-band oscillations reflect the linkage between distant parietal and frontal cortical circuits during decision making. Thus, these findings open an avenue for investigating whether the activity between distant cortical circuits oscillates in the delta frequency range during other cognitive functions.
The influence of community on language structure
Authors: Meir Irit , Israel Assaf , Sandler Wendy , Padden Carol A. , Aronoff Mark
Published: August 2013

By comparing two sign languages of approximately the same age but which arose and developed under different social circumstances, we are able to identify possible relationships between social factors and language structure. We argue that two structural properties of these languages are related to the size and the heterogeneity versus homogeneity of their respective communities: use of space in grammatical structure and degree of lexical and sublexical variability. A third characteristic, the tendency toward single-argument clauses appears to be a function of a different social factor: language age. Our study supports the view that language is not just a structure in the brain, nor is it strictly the domain of the individual. It is very much a socio-cultural artifact. Keywords: community and language structure; sign languages; ISL; ABSL; variation; space; argument structure
Anatomy of the meninges: structural and functional aspects.
Authors: Weller R. O.
Published: August 2013

This chapter deals with the structure and functional aspects of the human meninges. It is shown that, although grouped together under the general heading of meninges, the dura mater and the leptomeninges, consisting of the arachnoid and pia mater, have distinctly different structures and functions. There are 4 major fluid compartments in the central nervous system: blood, cerebrospinal fluid (CSF), interstitial (extracellular) fluid, and intracellular fluid. This chapter focuses mainly on blood, CSF and interstitial fluid, and the interrelations between these 3 fluids.
Pathogenesis of cerebrospinal meningitis caused by Neisseria meningitidis.
Authors: Coureuil M. , Miller F. , Join-Lambert O. , Lécuyer H. , Bourdoulous S. , Marullo S. , Nassif X.
Published: August 2013

This chapter describes the pathogenesis of Neisseria meningitidis-related cerebrospinal meningitis, and examines the 2 main obstacles that N. meningitidis has to overcome before reaching the meninges: the bloodstream and the blood-brain barrier (BBB). The mechanisms and consequences of N. meningitidis-endothelial cell interactions on meningeal invasion are explored.
Haemophilus influenzae meningitis.
Authors: Hill D. J. , Christodoulides M.
Published: August 2013

This chapter reviews the pathogenesis of Haemophilus influenzae type b (Hib) meningitis, a multistep process that begins with: (i) colonization of the nasopharynx; (ii) subsequent invasion into the blood, which leads to haematogenous dissemination; (iii) bacterial penetration of the blood-cerebrospinal fluid barrier/blood-brain barrier and entry into the subarachnoid space; which leads to (iv) a compartmentalized host inflammatory response. A newborn rat model for Hib meningitis is proposed, which is based on current knowledge of bacterial virulence factors and host cell receptor recognition of these ligands.
Chronic meningitis.
Authors: Schmutzhard E. , Helbok R.
Published: August 2013

This chapter deals exclusively with common infectious causes of chronic meningitis in the immunocompetent patient, citing particular examples of bacterial, fungal and helminthic causes. The following types of infectious meningitis are described in terms of symptoms, diagnosis and treatment: tuberculous meningitis, cryptococcal meningitis, Coccidioides immitis meningitis, Treponema pallidum meningitis, and Taenia solium meningitis,.
Streptococcus suis meningitis.
Authors: Gottschalk M. , Fittipaldi N. , Segura M.
Published: August 2013

This chapter first reviews the epidemiology of Streptococcus suis infections in humans and pigs, then describes the pathogenesis and clinical course of S. suis meningitis in humans, the role of bacteraemia in S. suis invasion of the central nervous system, and the inflammatory processes involved in S. suis meningitis.
Inflammation in the subarachnoid space.
Authors: Christodoulides M.
Published: August 2013

Classical pyogenic leptomeningitis is an acute, compartmentalized intracranial inflammatory response induced in the cerebrospinal fluid (CSF)-filled spaces of the subarachnoid space (SAS) and is characterized by the upregulated accumulation of a wide variety of host response factors and the production of 'pus'. This chapter describes the proinflammatory cytokines, chemokines, reactive oxygen species, nitric oxide, matrix metalloproteinases, and the other molecules that are produced in the SAS in response to invading bacteria.
The ‘turn to the victim’ in Italian culture: victim-centred narratives of theanni di piombo
Authors: Glynn Ruth
Published: August 2013

This article considers the emergence of a corpus of victim centred-narratives addressing the experience of political violence during theanni di piomboin the period surrounding the establishment of the ‘Day of Memory for the Victims of Terrorism’. Bringing a critical victim-studies approach to bear, it explores how the victim of terrorism is portrayed in the corpus of victim-centred narratives and asks what is claimed, effected and achieved by the corpus in cultural terms. It further explores how the perspective of survivors of terrorist attacks and of relatives of the victims reshapes the cultural imaginary of theanni di piomboin the new millennium.
Sandro Penna and anti-Oedipalimpegno
Authors: Champagne John
Published: August 2013

A number of Italianists have recently argued the need to reconsider the termimpegnoin the light of feminist and queer critiques. Such critiques do not simply highlight the way in whichimpegnohas usually been construed as a masculine, heterosexual domain. They also note that its employment often presupposes a gendered, heteronormative account of politics itself. Complicating this sense of politics via a reading of recent work in queer theory which insists that desire and need are intertwined, this essay argues for a reconsideration of the work of Italian poet Sandro Penna – someone whose oeuvre has regularly been construed by literary critics as apolitical – as an example ofimpegno. Bringing together psychoanalysis, the work of Michel Foucault, and historical materialism, the essay argues that, in their historical context, Penna's poems staged a resistance to what Freud termed the genital organisation of the libido and are thus ‘anti-Oedipal’.
Weekday and weekend physical activity patterns of French and Spanish adolescents
Authors: Aibar Alberto , Bois Julien E. , Zaragoza Casterad Javier , Generelo Eduardo , Paillard Thierry , Fairclough Stuart
Published: August 2013

Adolescents' objectively assessed physical activity (PA) patterns during specific segments of the day remain unclear. In order to develop a clearer understanding this study examined country and gender differences in moderate to vigorous physical activity (MVPA) levels during specific segments of weekdays and weekend days, and explored the contribution of each segment to PA guidelines. Morpho‐demographic, socio‐economic and PA data were collected from a sample of 829 French and Spanish adolescents (45.0% Spanish; 55.2% females; 14.33±.73 years). Actigraph GT3X accelerometers were worn for seven days to assess adolescents' MVPA for three segments of weekdays (school‐travel‐time, school‐time, and non‐school‐time), and weekend days (morning‐time, afternoon‐time and night‐time). Data were analysed using multilevel modelling. The most active segments were non‐school‐time (29.2±17.5 min) and school‐time (25.8±14.2 min) during weekdays, and morning‐time (28.2±25.8 min) on weekend days. Except for school‐time, Spanish adolescents were more significantly active than French adolescents during all segments. Significant gender differences were found in all segments. Country differences highlight the need to recognise cultural contexts that influence adolescents' PA. Common European‐wide strategies may be insufficient to increase MVPA levels if cultural variability is not considered. Spanish and French PA intervention programmes should target girls and low‐active boys during non‐school‐time and weekends.
Raven's Matrices and Working Memory: A Dual-Task Approach
Authors: Rao K. Venkata , Baddeley Alan
Published: August 2013

Raven's Matrices Test was developed as a “pure” measure of Spearman's concept of general intelligence, g. Subsequent research has attempted to specify the processes underpinning performance, some relating it to the concept of working memory and proposing a crucial role for the central executive, with the nature of other components currently unclear. Up to this point, virtually all work has been based on correlational analysis of number of correct solutions, sometimes related to possible strategies. We explore the application to this problem of the concurrent task methodology used widely in developing the concept of multicomponent working memory. Participants attempted to solve problems from the matrices under baseline conditions, or accompanied by backward counting or verbal repetition tasks, assumed to disrupt the central executive and phonological loop components of working memory, respectively. As in other uses of this method, number of items correct showed little effect, while solution time measures gave very clear evidence of an important role for the central executive, but no evidence for phonological loop involvement. We conclude that this and related concurrent task techniques hold considerable promise for the analysis of Raven's matrices and potentially for other established psychometric tests.
JNK-mediated phosphorylation of DLK suppresses its ubiquitination to promote neuronal apoptosis
Authors: Huntwork-Rodriguez Sarah , Wang Bei , Watkins Trent , Ghosh Arundhati Sengupta , Pozniak Christine D. , Bustos Daisy , Newton Kim , Kirkpatrick Donald S. , Lewcock Joseph W.
Published: August 2013

Neurons are highly polarized cells that often project axons a considerable distance. To respond to axonal damage, neurons must transmit a retrograde signal to the nucleus to enable a transcriptional stress response. Here we describe a mechanism by which this signal is propagated through injury-induced stabilization of dual leucine zipper-bearing kinase (DLK/MAP3K12). After neuronal insult, specific sites throughout the length of DLK underwent phosphorylation by c-Jun N-terminal kinases (JNKs), which have been shown to be downstream targets of DLK pathway activity. These phosphorylation events resulted in increased DLK abundance via reduction of DLK ubiquitination, which was mediated by the E3 ubiquitin ligase PHR1 and the de-ubiquitinating enzyme USP9X. Abundance of DLK in turn controlled the levels of downstream JNK signaling and apoptosis. Through this feedback mechanism, the ubiquitin–proteasome system is able to provide an additional layer of regulation of retrograde stress signaling to generate a global cellular response to localized external insults.
Spindle assembly checkpoint proteins are positioned close to core microtubule attachment sites at kinetochores
Authors: Varma Dileep , Wan Xiaohu , Cheerambathur Dhanya , Gassmann Reto , Suzuki Aussie , Lawrimore Josh , Desai Arshad , Salmon E.D.
Published: August 2013

Spindle assembly checkpoint proteins have been thought to reside in the peripheral corona region of the kinetochore, distal to microtubule attachment sites at the outer plate. However, recent biochemical evidence indicates that checkpoint proteins are closely linked to the core kinetochore microtubule attachment site comprised of the Knl1–Mis12–Ndc80 (KMN) complexes/KMN network. In this paper, we show that the Knl1–Zwint1 complex is required to recruit the Rod–Zwilch–Zw10 (RZZ) and Mad1–Mad2 complexes to the outer kinetochore. Consistent with this, nanometer-scale mapping indicates that RZZ, Mad1–Mad2, and the C terminus of the dynein recruitment factor Spindly are closely juxtaposed with the KMN network in metaphase cells when their dissociation is blocked and the checkpoint is active. In contrast, the N terminus of Spindly is ∼75 nm outside the calponin homology domain of the Ndc80 complex. These results reveal how checkpoint proteins are integrated within the substructure of the kinetochore and will aid in understanding the coordination of microtubule attachment and checkpoint signaling during chromosome segregation.
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples
Authors: Behr Jonas , Kahles André , Zhong Yi , Sreedharan Vipin T. , Drewe Philipp , Rätsch Gunnar
Published: August 2013

Motivation: High-throughput sequencing of mRNA (RNA-Seq) has led to tremendous improvements in the detection of expressed genes and reconstruction of RNA transcripts. However, the extensive dynamic range of gene expression, technical limitations and biases, as well as the observed complexity of the transcriptional landscape, pose profound computational challenges for transcriptome reconstruction.

Results: We present the novel framework MITIE (Mixed Integer Transcript IdEntification) for simultaneous transcript reconstruction and quantification. We define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data and show how to find the optimal solution using Mixed Integer Programming. MITIE can (i) take advantage of known transcripts, (ii) reconstruct and quantify transcripts simultaneously in multiple samples, and (iii) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction. We present an extensive study based on realistic simulated RNA-Seq data. When compared with state-of-the-art approaches, MITIE proves to be significantly more sensitive and overall more accurate. Moreover, MITIE yields substantial performance gains when used with multiple samples. We applied our system to 38 Drosophila melanogaster modENCODE RNA-Seq libraries and estimated the sensitivity of reconstructing omitted transcript annotations and the specificity with respect to annotated transcripts. Our results corroborate that a well-motivated objective paired with appropriate optimization techniques lead to significant improvements over the state-of-the-art in transcriptome reconstruction.

Availability: MITIE is implemented in C++ and is available from http://bioweb.me/mitie under the GPL license.

Contact:  Jonas_Behr@web.de and raetsch@cbio.mskcc.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Analysis of Ferulic and p‐Coumaric Acids in Japanese Rice for Sake Brewing
Authors: Hashizume Katsumi , Ito Toshihiko , Nakayama Airi , Okuda Masaki
Published: August 2013

Ferulic and p‐coumaric acids were analyzed in 50 rice (Oryza sativa L.) samples from 32 cultivars harvested in Japan. In brown rice, ferulic and p‐coumaric acid levels ranged from 309 to 607 mg/kg and from 49 to 100 mg/kg, respectively. In 70% polished rice, ferulic and p‐coumaric acid levels ranged from 27 to 103 mg/kg and from 0.4 to 3.5 mg/kg, respectively. Ratios of average phenolic acid levels in the 70% polished rice to the brown rice were 13.9% for ferulic acid and 1.9% for p‐coumaric acid. The ferulic acid level was highly correlated between brown and 70% polished rice (R = 0.815; P < 0.01), but there was no clear correlation for p‐coumaric acid. Phenolic acid levels in the 70% polished rice did not show any clear correlations between the analytical index measurements for sake brewing suitability (weight of 1,000 grains, water absorption, digestibility, crude protein, and potassium content). Phenolic acid levels in the 70% polished rice directly affected levels in the rice koji enzyme digest. The results indicated that phenolic acid levels in sake were affected by the levels in ingredient rice grains, which may then influence the sensory quality of sake.
Effects of Crop Management Practices on Current-Season Spread of Potato virus Y
Authors: MacKenzie Tyler D. B. , Fageria Manphool S. , Nie Xianzhou , Singh Mathuresh
Published: August 2013

The current-season spread of Potato virus Y (PVY) was monitored in 19 fields under various management practices in New Brunswick, Canada, through the 2011 and 2012 growing seasons. The focus of this study was to evaluate the role of seedborne PVY inoculum, aphid vector abundance, and the numbers, timing, and types of insecticide and mineral oil sprays, and to confirm the reliability and forecasting capacity of midseason PVY testing. In each field, 100 to 110 virus-free plants were identified shortly after emergence and were assessed four times from early July to early September (after top-kill) with enzyme-linked immunosorbent assay (ELISA) and reverse-transcription polymerase chain reaction (RT-PCR) to track PVY spread. In addition, tubers harvested during development in August and after top-kill were grown-out in the greenhouse for ELISA testing. PVY spread to selected virus-free plants varied widely, ranging from 0 to 76.2% across all studied fields. Of the 19 fields over two seasons, 10 fields were planted with no detectable seedborne PVY, and they showed 0 to 8.7% (mean 2.9%) PVY spread by harvest. The remaining nine study fields with 0.9 to 5.8% seedborne PVY showed 1 to 76.2% (mean 15.2%) PVY spread by harvest. PVY spread was detected in most fields during midseason testing with ELISA and RT-PCR; all tests correlated well with final PVY rates after top-kill, though RT-PCR detection in developing tubers was most sensitive and correlated. Logistic regression modeling was used to identify major factors in PVY spread, including seedborne PVY, early-season aphid abundance, and the numbers of insecticide and mineral oil sprays. The best-fitting model, constructed using these factors as well as a measurement of July PVY incidence (ELISAJuly), strongly explained PVY spread by harvest, with the most significant management factor being the number of mineral oil sprays supplemented with insecticide used during the growing season. A similar model fitted without the ELISAJuly did not adequately predict ultimate PVY spread. The analysis suggests that mineral oil alone was effective at lowering PVY spread, and more effective when combined with insecticide, particularly when used early in the season. No evidence was found for differences in PVY spread across the eight cultivars used or across the range of mineral oil application rates, whereas some evidence was found for differences in the effectiveness of different insecticide types.
Quantification of Yield Loss Caused by Triticum mosaic virus and Wheat streak mosaic virus in Winter Wheat Under Field Conditions
Authors: Byamukama E. , Wegulo S. N. , Tatineni S. , Hein G. L. , Graybosch R. A. , Baenziger P. S. , French R.
Published: August 2013

Triticum mosaic virus (TriMV) and Wheat streak mosaic virus (WSMV) infect winter wheat (Triticum aestivum) in the Great Plains region of the United States. The two viruses are transmitted by wheat curl mites (Aceria tosichella), which also transmit High Plains virus. In a field study conducted in 2011 and 2012, winter wheat cultivars Millennium (WSMV-susceptible) and Mace (WSMV-resistant) were mechanically inoculated with TriMV, WSMV, TriMV+WSMV, or sterile water at the two-leaf growth stage. Chlorophyll meter (soil plant analysis development [SPAD]) readings, area under the SPAD progress curve (AUSPC), grain yield (=yield), yield components (spikes/m2, kernels/spike, 1,000-kernel weight), and aerial dry matter were determined. In Millennium, all measured variables were significantly reduced by single or double virus inoculation, with the greatest reductions occurring in the double-inoculated treatment. Among the yield components, the greatest reductions occurred in spikes/m2. In Mace, only AUSPC was significantly reduced by the TriMV+WSMV treatment in 2012. There was a significant (P ≤ 0.05), negative linear relationship between SPAD readings and day of year in all inoculation treatments in Millennium and in the TriMV+WSMV treatment in Mace. There were significant (P ≤ 0.05), positive linear relationships between yield and SPAD readings and between yield and aerial dry matter in Millennium but not in Mace. The results from this study indicate that under field conditions, (i) Mace, a WSMV-resistant cultivar, is also resistant to TriMV, and (ii) double inoculation of winter wheat by TriMV and WSMV exacerbates symptom expression and yield loss in a susceptible cultivar.
Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification
Authors: Laverock B. , Kitidis V. , Tait K. , Gilbert J. A. , Osborn A. M. , Widdicombe S.
Published: August 2013

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO
2
) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp
Upogebia deltaura
. Seawater was acidified to one of four target pH values (pH
T
7.90, 7.70, 7.35 and 6.80) in comparison with a control (pH
T
8.10). At pH
T
8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79–97%;
p
< 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pH
T
declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (
amoA
) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms.
Effects of forest successional status on microenvironmental conditions, diversity, and distribution of filmy fern species in a temperate rainforest
Authors: Saldaña Alfredo , Parra Maria J. , Flores‐Bavestrello Alejandra , Corcuera Luis J. , Bravo León A.
Published: August 2013

The vertical distribution of Hymenophyllaceae species has been related to microenvironmental variations around host trees. We addressed the questions: Do the vertical microenvironmental conditions within forest stands of differing successional statuses vary significantly? Does the diversity of Hymenophyllaceae species differ between forest successional statuses? Are the vertical distribution and diversity of Hymenophyllaceae species related more to humidity or light availability? Are there any interspecific differences in the desiccation tolerance of these species which can be related to their vertical distribution? We characterized the microhabitat conditions (vapor pressure deficit [VPD], air relative humidity [RH], and light availability [PAR]) and the vertical distribution of Hymenophyllaceae species in host trees, in both a secondary forest and an old‐growth temperate rainforest in Chile. Chlorophyll fluorescence was used to monitor the integrity of the photosynthetic apparatus during desiccation experiments. The stand basal area, tree height, and leaf area index were all significantly greater in the old‐growth forest stands, but VPD, RH, and PAR showed no significant differences between the two forests. Both successional statuses showed the same amount of filmy fern species in terms of both abundance and diversity. In both successional statuses VPD and RH decreased while PAR increased with the height of the hosts. Regardless of the forest's age, abundance and diversity of filmy ferns were greater in microsites of greater humidity and less light availability. Desiccation tolerance differed significantly among Hymenophyllaceae species. The distribution pattern could be better explained by the specific microenvironmental requirements and desiccation tolerance rather than the forest's successional status.
Impacts of Recombinant Human Erythropoietin Treatment During Predialysis Periods on the Progression of Chronic Kidney Disease in a Large‐Scale Cohort Study (Co‐JET study)
Authors: Akizawa Tadao , Saito Akira , Gejyo Fumitake , Suzuki Masashi , Nishizawa Yoshiki , Tomino Yasuhiko , Tsubakihara Yoshiharu , Akiba Takashi , Hirakata Hideki , Watanabe Yuzo , Kawanishi Hideki , Bessho Masami , Udagawa Yukio , Aoki Kotonari , Uemura Yukari , Ohashi Yasuo ,   Co‐JET Study Group
Published: August 2013

The effect of recombinant human erythropoietin (rHuEPO) treatment on the progression of chronic kidney disease (CKD) has not been fully evaluated in Japan. We therefore retrospectively evaluated this in a sub‐cohort of a prospective multicenter study to investigate optimal hemoglobin (Hb) level of CKD patients on hemodialysis (HD) treated with rHuEPO; Japan Erythropoietin Treatment Study for Target Hb and Survival (JET study). Effect of rHuEPO treatment during predialysis period to delay initiation of HD was retrospectively assessed in 2434 patients from the JET study comparing groups with and without rHuEPO treatment. The assessment was done by Cox proportional hazards regression analysis and inverse probability‐weighted (IPW) analysis to adjust for time‐dependent confounders. The weights used in the IPW analysis were calculated using a logistic model that included baseline confounders and time‐dependent variables. During the predialysis period, 71.7% (1746 patients) were treated with rHuEPO (mean Hb level of 8.7 g/dL at initiation of rHuEPO treatment). Covariates significantly associated with initiation of rHuEPO treatment were Hb level, serum creatinine level, age, diabetes, cardiac insufficiency, and hypertension. The adjusted hazard ratio for time until HD initiation under rHuEPO treatment was 0.272 (95% CI, 0.223–0.331; P < 0.001) in the Cox analysis and 0.63 (95% CI, 0.53–0.76; P < 0.0001) in the IPW analysis. This retrospective study suggests that rHuEPO treatment during the predialysis period has preventive effects on the progression of CKD although further prospective investigation on the efficacy is needed.
Randomized Controlled Trial of Bixalomer Versus Sevelamer Hydrochloride in Hemodialysis Patients With Hyperphosphatemia
Authors: Akizawa Tadao , Origasa Hideki , Kameoka Chisato , Kaneko Yuichiro , Kawasaki Shigenori ,   Bixalomer Study Group
Published: August 2013

Hyperphosphatemia is a prognostic factor for morbidity and mortality in chronic kidney disease. Bixalomer is a nonabsorbable polymer that decreases serum phosphate levels by binding phosphate in the gastrointestinal tract. This study compared the efficacy and safety of bixalomer versus sevelamer hydrochloride for controlling hyperphosphatemia in hemodialysis patients. This was a multicenter, randomized open‐label, non‐inferiority study. The primary endpoint was serum phosphate on completion of treatment. Administration of bixalomer was started at 1.5 g/day and adjusted to a maximum of 7.5 g/day depending on the serum phosphate level. Sevelamer hydrochloride was started at 3.0 or 6.0 g/day and adjusted to a maximum of 9.0 g/day. Treatment was continued for 12 weeks. Fifty‐five patients were randomized to each treatment group. After 12 weeks, the baseline adjusted mean serum phosphate level was 5.87 mg/dL in the bixalomer group and 5.55 mg/dL in the sevelamer group, with a difference of 0.31 mg/dL and 95% confidence interval (CI) of [−0.13 to 0.76]. The upper limit of the 95%CI for the difference of the mean serum phosphate level between the two groups was <1.0 mg/dL, which was the non‐inferiority margin in this study. Thus, non‐inferiority of bixalomer to sevelamer was confirmed. The incidence of adverse events was lower in the bixalomer group, and bixalomer did not promote acidosis. Bixalomer achieved a similar reduction of serum phosphate to sevelamer, while causing fewer adverse reactions. Consequently, the usefulness of bixalomer for treating hyperphosphatemia was confirmed.
Lack of mitochondrial DNA structure in Balkan donkey is consistent with a quick spread of the species after domestication
Authors: Pérez‐Pardal L. , Grizelj J. , Traoré A. , Cubric‐Curik V. , Arsenos G. , Dovenski T. , Marković B. , Fernández I. , Cuervo M. , Álvarez I. , Beja‐Pereira A. , Curik I. , Goyache F.
Published: August 2013

A total of 132 mtDNA sequences from 10 Balkan donkey populations were analysed to ascertain their regional genetic structure and to contribute to the knowledge of the spreading of the species after domestication. The Balkan donkey sequences were compared with those from 40 Burkina Faso donkeys as an African outgroup to account for possible local Balkan scenarios. The 172 sequences gave 62 different haplotypes (55 in Balkan donkey). Virtually all the analysed populations had haplotypes assigned to either Clade 1 or Clade 2 even though the relative proportion of Clade 1 or 2 haplotypes differed across populations. Geographical maps constructed using factors computed via principal component analysis showed that the Balkan donkey populations are not spatially structured. AMOVA confirmed a lack of genetic structure in Balkan donkey mtDNA. Balkan populations were poorly differentiated (ΦST = 0.071). Differentiation between the Balkan donkey and the African outgroup also was low. The lack of correspondence between geographical areas and maternal genetic structure is consistent with the hypothesis suggesting a very quick spread of the species after domestication. The current research illustrates the difficulties to trace routes of expansion in donkey, as the species has no geographical structure.
Accuracy of visual prediction of pathology of colorectal polyps: how accurate are we?
Authors: Sharma Prashant , Frye John , Frizelle Frank
Published: August 2013

Background

Small and diminutive polyps seen at colonoscopy could be left unresected because of a balance of risks between perceived low malignant potential and complications of removing the polyp. This relies on a high accuracy in prediction of the pathology of the polyp. This study was undertaken to determine if experienced endoscopists could determine the histological types of polyps found at colonoscopy.

Methods

We performed a prospective study at Christchurch Hospital from December 2010 to December 2012. Gastroenterologists and surgeons were asked to fill out a questionnaire at time of colonic polypectomy, predicting pathology of polyp excised. Data were collected on indication for colonoscopy, location, size of polyp and use of narrow band imaging. Predictive accuracy was then calculated.

Results

A total of 527 polyps were excised from 258 patients. Ninety‐one per cent were less than 1 cm. Predictive accuracy of hyperplastic polyps was 47%. Of the 53% wrong predictions, 82% were adenomas. Predictive accuracy of adenoma was 42%, with 66% of incorrect predictions being hyperplastic polyps. Accuracy was lowest in the right colon, with only 25% of predicted hyperplastic polyps actually being hyperplastic. A patient's age, sex, polyp size and site did not affect prediction accuracy. Overall accuracy of visual prediction of pathology of all colorectal polyps was 45%. Narrow band imaging was used too infrequently to determine how useful it was.

Conclusion

Pathology of colorectal polyps cannot be accurately predicted visually alone. All polyps visualized at colonoscopy should be excised for ex vivo histology, regardless of size, location or predicted pathology.
Comparison of Hemolysis Between CentriMag and RotaFlow Rotary Blood Pumps During Extracorporeal Membrane Oxygenation
Authors: Palanzo David A. , El‐Banayosy Aly , Stephenson Edward , Brehm Christoph , Kunselman Allen , Pae Walter E.
Published: August 2013

The purpose of this investigation was to compare the hemolysis levels for patients on extracorporeal membrane oxygenation (ECMO) incorporating two different rotary blood pumps (CentriMag [CMAG] and RotaFlow [RF]) in identical circuits otherwise. The difference between the two pumps is the cost. One is 20–30 times less expensive than the other. A retrospective analysis of all patients placed on ECMO from June 2008 through May 2012 was done to evaluate hemolysis. Daily plasma hemoglobin (pHb), lactate dehydrogenase (LDH), and lactate levels were collected on all patients. Values were compared between those patients who received a CMAG and those who received an RF. Patients had to be on ECMO for more than 2 days to be included in the study. Linear mixed effects models were fit to the data to assess differences over time for each continuous outcome. Forty patients were placed on ECMO incorporating CMAG, whereas 40 patients received an RF. There were no significant statistical differences between CMAG and RF groups when comparing days on support (8.7 ± 5.0; 8.4 ± 5.7), age (44.8 ± 18.3; 46.1 ± 16.0), body surface area (2.03 ± 0.36; 1.96 ± 0.31), gender (male: 58%, female: 42%; male: 55%, female: 45%), etiology, type of support (veno‐arterial [VA)]: 78%, veno‐venous [VV)]: 22%; VA: 82%, VV: 18%) and pre‐ECMO LDH levels (4004.0 ± 3583.2; 3603.7 ± 3354.1). There were also no significant differences between the CMAG and RF groups when comparing the mean values for daily pHb levels (5.7 ± 3.6; 5.7 ± 4.2), lactate levels (2.8 ± 1.9; 3.0 ± 2.1), and LDH levels (2656.3 ± 1606.8; 2688.6 ± 1726.1) or daily lactate, LDH, and pHb levels for the first 10 days of support. From our investigation, there is no difference between the CMAG and the RF blood pumps in regard to the creation of hemolysis during ECMO. The difference in cost of the devices does not correlate with the performance and outcomes.