bluuebunny/crossref_metadata_2025 huggingface dataset:
Pasture intake and milk production of dairy cows grazing annual ryegrass with or without corn silage supplementation
Authors: Miguel Marcolino Frederico , Ribeiro-Filho Henrique Mendonça Nunes , Américo de Andrade Ederson , Genro Teresa Cristina Moraes , Delagarde Rémy
Published: December 2014

The use of corn silage to supplement grazing dairy cows can improve milk production and nutrient intake when the substitution rate is low. This enhancement occurs by increasing the total DM intake. The hypothesis tested in this study was that increasing corn silage supplementation level of dairy cows grazing annual ryegrass at medium pasture allowance could increase substitution rate and decrease milk production response. Three supplementation levels (0, 4 and 8 kg DM/day) were compared for dairy cows strip-grazing annual ryegrass (Lolium multiflorum cv. Common). The study was arranged as a 3 × 3 Latin square design, repeated three times using nine Holstein lactating cows. The supplement was a 7 : 1 mixture based on the DM of corn silage and soybean meal and was offered individually twice daily after the morning and afternoon milkings. Each treatment group of cows grazed separately at a common daily pasture allowance of 35 kg DM/cow to ground level. Each experimental period was 12 days, with an 8-day adaptation and a 4-day measurement period. The individual pasture intake was measured from Day 9 to Day 12 using the n-alkane technique. The daily pattern of grazing and ruminating times were measured by visual observations. The supplement DM intake was lower than expected, averaging 3.0 and 4.3 kg DM/day for cows receiving 4 and 8 kg DM/day, respectively. Pasture and supplement energy value were 7.0 and 6.3 MJ of NEL/kg DM, respectively. The substitution rate averaged 0.2 and was unaffected by the supplementation level. The pasture intake was similar for all treatments (14.0 kg of DM/day), and total DM intake and milk production (+0.5 kg of milk/kg DM of supplement) increased linearly with increasing supplementation level. The daily grazing time was shorter by 111 min/day for the supplemented cows than for the unsupplemented cows. Cows grazing the annual ryegrass at medium pasture allowance improved their total DM intake and individual performance when supplemented with corn silage.
Using partial records to identify productive older ewes to retain in the breeding flock to increase the flock net reproduction rate
Authors: Lee G. J. , Sladek M. A. , Hatcher S. , Richards J. S.
Published: December 2014

The reproductive performance of 7286 ewes from three Merino genetic resource flocks maintained in the central-western region of New South Wales was used to compare the use of fertility and fecundity information and net reproduction information whether recorded early (at 2 and 3 years of age) or later in life (at 4 and 5 years of age) with lifetime performance (at 2–6 years of age) as alternative selection criteria to identify productive older ewes to retain in the breeding flock. While the lifetime net reproduction rate is the best indicator of a ewe’s reproductive performance in later life, producers basing their selection decisions on pregnancy scanning data, which provides information on both fertility and fecundity, can improve the net reproduction rate of their flock by 2% regardless of the base reproduction rate. Despite little difference in likely flock reproduction rates between using early or later life scanning information as the selection criteria, early life performance is the best choice for commercial producers because it provides scope for eliminating twice-dry ewes from the breeding flock early in life, especially when combined with udder examination at marking.
Drives and limits to feed intake in ruminants
Authors: Allen Michael S.
Published: December 2014

The control of energy intake is complex, including mechanisms that act independently (e.g. distention, osmotic effects, fuel-sensing) as well as interacting factors that are likely to affect feeding via their effects on hepatic oxidation. Effects of ruminant diets on feed intake vary greatly because of variation in their filling effects, as well as the type and temporal absorption of fuels. Effects of nutrients on endocrine response and gene expression affect energy partitioning, which in turn affects feeding behaviour by altering clearance of fuels from the blood. Dominant mechanisms controlling feed intake change with physiological state, which is highly variable among ruminants, especially through the lactation cycle. Ruminal distention might dominate control of feed intake when ruminants consume low-energy diets or when energy requirements are high, but fuel-sensing by tissues is likely to dominate control of feed intake when fuel supply is in excess of that required. The liver is likely to be a primary sensor of energy status because it is supplied by fuels from the portal drained viscera as well as the general circulation, it metabolises a variety of fuels derived from both the diet and tissues, and a signal related to hepatic oxidation of fuels is conveyed to feeding centres in the brain by hepatic vagal afferents stimulating or inhibiting feeding, depending on its energy status. The effects of somatotropin on export of fuels by milk secretion, effects of insulin on gluconeogenesis, and both on mobilisation and repletion of tissues, determine fuel availability and feed intake over the lactation cycle. Control of feed intake by hepatic energy status, affected by oxidation of fuels, is an appealing conceptual model because it integrates effects of various fuels and physiological states on feeding behaviour.
Livestock water productivity: feed resourcing, feeding and coupled feed-water resource data bases
Authors: Blümmel Michael , Haileslassie Amare , Samireddypalle Anandan , Vadez Vincent , Notenbaert An
Published: December 2014

While water requirement for livestock is widely perceived as daily drinking water consumption, ~100 times more water is required for daily feed production than for drinking water. Increasing livestock water productivity can be achieved through increasing the water-use efficiency (WUE) of feed production and utilisation. The current paper briefly reviews water requirements for meat and milk production and the extent of, and reason for, variations therein. Life-cycle analysis (LCA) can reveal these variations in WUE but LCA are not tools that can be employed routinely in designing and implementing water-use-efficient feed resourcing and feeding strategies. This can be achieved by (1) choosing agricultural by-products and crop residues where water applications are partitioned over several products for example grain and straw (or food and fodder) contrary to planted forage production where water and land have to be exclusively allocated to fodder production, (2) select and breed WUE crops and forages and exploit cultivar variations, (3) increase crop productivity by closing yield gaps; and (4) increase per animal productivity to reduce the proportion of feed (and therefore water) allocated for maintenance requirement rather than productive purposes. Feed-mediated WUE of dairy buffalo production on almost completely (94%) by-product-based feeding systems could be reduced from 2350 to 548 L of water per kg of milk by the combined effect of increasing basal ration quality in a total mixed ration, which resulted in increased milk yield of ~30%, and by increasing crop productivity from 1 t (actual crop yield) to 3 t (potential crop yield). Exemplary, multi-dimensional sorghum improvement using staygreen quantitative trait loci (QTL) introgression for concomitant improvement of WUE of grain and stover production and stover fodder quality showed opportunities for further linked improvement in WUE of crop and livestock production. Metabolisable energy (ME) yield under water stress conditions measured in lysimeters, (which measure crop water transpired) ranged QTL dependent from 16.47 to 23.93 MJ ME per m3 H2O. This can be extrapolated to 8.23–11.97 MJ ME per m3 H2O evapotranspired under field conditions. To mainstream improvement in WUE of feed resourcing and feeding, the paper suggests the combination of feed resource databases with crop–soil–meteorological data to calculate how much water is required to produce the feed at the available smallest spatial scale of crop–soil–meteorological data available. A framework is presented of how such a tool can be constructed from secondary datasets on land use, cropping patterns and spatially explicit crop–soil–meteorological datasets.
FeIIaq–FeIIIoxide electron transfer and Fe exchange: effect of organic carbon
Authors: Pasakarnis Timothy , McCormick Michael L. , Parkin Gene F. , Thompson Aaron , Scherer Michelle M.
Published: December 2014

Environmental context Concerns about carbon-driven climate change make it critical to better understand how carbon interacts with soils. We examined whether carbon compounds commonly found in soils affect the behaviour of soil iron minerals, and found that iron minerals remain dynamic and mix with the surrounding water, despite the presence of carbon in the water. Our findings suggest that both carbon and trace elements in the minerals may be more mobile and less stable than we previously thought. Abstract The close association of organic carbon and Fe oxides has been recognised for decades and recently interest in the role of Fe oxides in organic C sequestration has increased. Here we explore the effect of natural organic C on electron transfer and exchange of aqueous FeII and Fe in the bulk structure of goethite and magnetite. Using 57Fe isotope experiments coupled with 57Fe Mössbauer spectroscopy it is found that electron transfer occurs between aqueous FeII and structural FeIII in both goethite and magnetite in the presence of most organic C compounds, including natural organic matter (NOM), extracellular polysaccharides (EPS), and cell materials. Only a long-chain (39-C) phospholipid containing organic C significantly inhibited electron transfer. Despite evidence for FeII–FeIIIoxide electron transfer in the presence of NOM, exchange of Fe between the aqueous phase and bulk Fe was less than observed in the absence of NOM. Our findings suggest that electron transfer between aqueous FeII and bulk structural Fe in goethite and magnetite is a robust process likely to occur in a variety of organic-rich biogeochemical environments but that Fe exchange may be inhibited by the presence of some C compounds.
Effect of slope on spread of a linear flame front over a pine needle fuel bed: experiments and modelling
Authors: Liu Naian , Wu Jinmo , Chen Haixiang , Xie Xiaodong , Zhang Linhe , Yao Bin , Zhu Jiping , Shan Yanlong
Published: December 2014

This paper experimentally evaluates the effect of slope on spread of a linear flame front over a pine needle fuel bed in still air. The slope angle of the fuel bed varied from 0 to 32°. The fuel mass consumption in flaming fire spread, temperature over the fuel bed, velocities of the flow around the flame front and heat fluxes (total and radiant) near the end of the fuel bed were measured. The mass loss rate and rate of fire spread both increased with increasing slope, whereas the fuel consumption efficiency varied in the opposite way. It was shown that a weak reverse inflow and an upslope wind (induced by the flame itself) exist respectively ahead of and behind the flame front, and their significant difference in velocity (causing a pressure difference) plays an essential role in the forward tilting of the flame front. This mechanism promotes burning, especially on higher slopes. Natural convective cooling has a remarkable effect on the fuel pre-heating in the spread of linear flame fronts under slope conditions. A fire spread model for a linear flame front was developed to consider the natural convective cooling and the fuel consumption efficiency. The model agrees well with the experimental data on fire spread rate. Its reliability, especially for higher slopes, was verified by comparison with other models.
Literary Translation in Modern Iran
Authors: Haddadian-Moghaddam Esmaeil
Published: December 2014

Literary Translation in Modern Iran: A sociological study is the first comprehensive study of literary translation in modern Iran, covering the period from the late 19th century up to the present day. By drawing on Pierre Bourdieu's sociology of culture, this work investigates the people behind the selection, translation, and production of novels from English into Persian. The choice of novels such as Morier's The Adventures of Hajji Baba of Ispahan, Austen's Pride and Prejudice, and Vargas Llosa's The War of the End of the World provides insights into who decides upon titles for translation, motivations of translators and publishers, and the context in which such decisions are made.The author suggests that literary translation in Iran is not a straightforward activity. As part of the field of cultural production, literary translation has remained a lively game not only to examine and observe, but also often a challenging one to play. By adopting hide-and-seek strategies and with attention to the dynamic of the field of publishing, Iranian translators and publishers have continued to play the game against all odds.
The book is not only a contribution to the growing scholarship informed by sociological approaches to translation, but an essential reading for scholars and students of Translation Studies, Iranian Studies, and Middle Eastern Studies.
‘A badge of Europeanness’
Authors: Zappettini Franco
Published: December 2014

This paper contributes to the advancement of the established body of literature on language and identity by ascertaining how discursive representations of multilingualism at an institutional level have interplayed with the construction and the definition of European identities. Using the Discourse Historical Approach (Wodak 2001), the analysis focuses on a corpus of official speeches given by the European Commissioner for Multilingualism to identify discursive strategies and linguistic devices and link them to wider socio-political and historic dynamics. Findings suggest that the institutional construction of Europeanness has primarily occurred through macro discourses predicated on cultural, civic and economic dimensions of multilingualism with some inherent tensions in contrasting representations of ‘diverse’ and multilingual EU-rope. It is suggested that through heterogeneous representations of multilingualism torn between identity politics and commodification, European identities emerge as hybrid and fragmented constructs in between national, post national and global dimensions.
The “Illegal alien” as a category of analysis
Authors: Ackerman Edwin F.
Published: December 2014

“Illegal alien,” as a category of analysis, should be understood primarily as a discursive formation, yet the emergence and spread of the category in public debate cannot be explained by its discursive qualities. Failing to see this has analytical consequences: it results in a constant sidetracking of the question of why illegality itself came to be a central issue, and in a reification of the category. This paper is intended as a methodological intervention aimed at solving these issues. The first part illustrates the absence of a strict legalistic basis for the category, and reviews key works that fail to incorporate this into their conceptual design. The second part, contrasts two periods of time in U.S. political debate – the mid-2000s when the category was dominant, and the 1930s when the category, albeit pushed by elites, failed to become central- suggesting the need for a discursive analysis that goes beyond discourse.
Form, function and particularities of discursive practices in one-on-one supervision in Germany
Authors: Aksu Yasmin
Published: December 2014

One-on-one supervision in Germany is not always the counselling of a professional in the helping professions by a supervisor from a similar field. It can also be – due to its adaptation to modern work contexts – a counselling format for a professional in a managerial position, not unlike business coaching. In some cases, these two aspects converge. In this article I will – based on two excerpts from a transcript – describe how two of the ubiquitous communicative tasks in one-on-one supervision (‘establishing the need for counseling, establishing the counselor as authority’ and ‘presenting the problem’) are tackled in light of this convergence and show that supervision is a conversation between experts who create a specific supervisor-supervisee relationship.
What lies behind dative/accusative alternations in Romance
Authors: Pineda Anna
Published: December 2014

This paper accounts for dative/accusative alternations in several Romance languages with verbs with one complement of person, such as Catalan telefonar [DAT a la Roser]/telefonar [ACC la Roser] ‘to phone Roser’. Although the paper focuses on Catalan and Spanish, reference is also made to Italian Southern dialects and Asturian. Regardless of their case-marking, these complements are always Goals of unergative verbs: if dative-marked, they behave as expected; if accusative-marked, they instantiate what we call Differential Indirect Object Marking (following Bilous 2011). The two options of case-assignment are due to two different sorts of Low Applicatives, one Romance-like (the dative-assigning one) and the other English-like (the accusative-assigning one). The postulation of an Applicative Head with our apparently unergative verbs follows from analysing them as hidden transitive verbs (light verb + cognate noun).
(Pseudo-)Inflected infinitives and Control as Agree
Authors: Gonçalves Anabela , Santos Ana Lúcia , Duarte Inês
Published: December 2014

This paper discusses the distribution of inflected infinitives in standard and non-standard European Portuguese. In the standard variety, inflected infinitives are generally available in non-obligatory control contexts, but can only occur in obligatory control contexts when the temporal orientation of the complement is not specified by the matrix verb. An explanation for this fact is offered along the lines of an Agree theory of control. This analysis also accounts for the possibility of controlled inflected infinitives, which bear morphological inflection but which cannot license nominative, occurring in non-standard varieties of European Portuguese: they are considered the result of the spell out of the Agree operation that takes place in control contexts.
Pedagogical Grammar
Authors: Keck Casey , Kim YouJin
Published: December 2014

This book provides a comprehensive overview of pedagogical grammar research and explores its implications for the teaching of grammar in second language classrooms. Drawing on several research domains (e.g., corpus linguistics, task-based language teaching) and a number of theoretical orientations (e.g., cognitive, sociocultural), the book proposes a framework for pedagogical grammar which brings together three major areas of inquiry: (1) descriptions of grammar in use, (2) descriptions of grammar acquisition processes, and (3) investigations of the relative effectiveness of different approaches to L2 grammar instruction. The book balances research and theory with practical discussions of the decisions that teachers must make on a daily basis, offering guidance in such areas as materials development, data-driven learning, task design, and classroom assessment.
Getting a Head in the Renaissance: Mementos of Lost Love in Boccaccio and Beyond*
Authors: Ruggiero Guido
Published: December 2014

This essay offers a historian’s reading of Boccaccio’s tale of Lisabetta da Messina (4:5), rethinking it in terms of fourteenth-century ways of understandingvirtùand identity. In analyzing the tale in the context of theDecameron,while reading it against archival material from the period, the deeper context of its discussion of love suggests a reading that makes the tale central to the tragic stories of the fourth day and highlights a lesson about the dangers of passion that make it fit powerfully as the day’s central tale. In the end, love offers many things in theDecameron,but Boccaccio’sbrigataof storytellers and his readers could appreciate a danger more difficult to see today — that the powerful passions associated with lost love and mourning without the support of the groups that surrounded and sustained one’s sense of identity also threatened in the most profound way the negation of self: death.
The Rhetoric of Providence: Thomas Middleton’s A Game at Chess (1624) and Seventeenth-Century Political Engraving*
Authors: Carlson Christina Marie
Published: December 2014

This essay compares the rhetoric of providentialism in Samuel Ward’s 1621 engraving To God, In Memorye of his Double Deliveraunce from ye Invincible Navie and ye Unmatcheable Powder Treason with that in Thomas Middleton’s 1624 play A Game at Chess. Both satirize the negotiations over the Spanish Match by using providentialist discourse to modulate and veil their more satirical, and polemical, intentions. Ward and Middleton employ a technique of historical retrospection, referring to past events in order to present a simultaneously diachronic and synchronic world view.
CCEM Key comparison CCEM.RF-K25.W. RF power from 33 GHz to 50 GHz in waveguide. Final report of the pilot laboratory
Authors: Judaschke Rolf
Published: December 2014

This report summarizes the results of the Key Comparison CCEM.RF-K25.W on high frequency power which has been performed between December 2010 and May 2013.

In this comparison, the effective efficiency and calibration factor of two waveguide thermistor power sensors were determined by nine National Metrology Institutions (NMIs) in the frequency range 33 GHz to 50 GHz.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Global analysis of the generalised Helfrich flow of closed curves immersed in ℝⁿ
Authors: Wheeler Glen
Published: December 2014

In this paper we consider the evolution of regular closed elastic curves

γ
\gamma

immersed in

R

n

\mathbb {R}^n

. Equipping the ambient Euclidean space with a vector field

c

:

R

n

→

R

n

\mathbb {c}:\mathbb {R}^n\rightarrow \mathbb {R}^n

and a function

f
:

R

n

→

R

f:\mathbb {R}^n\rightarrow \mathbb {R}

, we assume the energy of

γ
\gamma

is smallest when the curvature

κ
→

\vec {\kappa }

of

γ
\gamma

is parallel to

c
→

0

=
(

c

∘
γ
)
+
(
f
∘
γ
)
τ

\vec {c}_0 = (\mathbb {c}\circ \gamma ) + (f\circ \gamma )\tau

, where

τ
\tau

is the unit vector field spanning the tangent bundle of

γ
\gamma

. This leads us to consider a generalisation of the Helfrich functional

H

λ

c
→

0

\mathcal {H}^{\vec {c}_0}_{\lambda }

, defined as the sum of the integral of

|

κ
→

−

c
→

0

|

2

|\vec {\kappa }-\vec {c}_0|^2

and

λ
\lambda

-weighted length. We primarily consider the case where

f
:

R

n

→

R

f:\mathbb {R}^n\rightarrow \mathbb {R}

is uniformly bounded in

C
∞

(

R

n

)

C^\infty (\mathbb {R}^n)

and

c

:

R

n

→

R

n

\mathbb {c}:\mathbb {R}^n\rightarrow \mathbb {R}^n

is an affine transformation. Our first theorem is that the steepest descent

L
2

L^2

-gradient flow of

H

λ

c
→

0

\mathcal {H}^{\vec {c}_0}_{\lambda }

with smooth initial data exists for all time and subconverges to a smooth solution of the Euler-Lagrange equation for a limiting functional

H

λ

c
→

∞

\mathcal {H}^{\vec {c}_\infty }_{\lambda }

. We additionally perform some asymptotic analysis. In the broad class of gradient flows for which we obtain global existence and subconvergence, there exist many examples for which full convergence of the flow does not hold. This may manifest in its simplest form as solutions translating or spiralling off to infinity. We prove that if either

c

\mathbb {c}

and

f
f

are constant, the derivative of

c

\mathbb {c}

is invertible and non-vanishing, or

(
f
,

γ
0

)

(f,\gamma _0)

satisfy a ‘properness’ condition, then one obtains full convergence of the flow and uniqueness of the limit. This last result strengthens a well-known theorem of Kuwert, Schätzle and Dziuk on the elastic flow of closed curves in

R

n

\mathbb {R}^n

where

f
f

is constant and

c

\mathbb {c}

vanishes.
Characterization of a genomic island in Stenotrophomonas maltophilia that carries a novel floR gene variant
Authors: He Tao , Shen Jianzhong , Schwarz Stefan , Wu Congming , Wang Yang
Published: December 2014

Objectives

To characterize the chromosomally encoded novel floR gene variant floRv from Stenotrophomonas maltophilia of porcine origin and elucidate the gene order and content of the floRv-flanking regions in an MDR genomic island (GI).

Methods

Whole genome sequencing was used to identify the unknown florfenicol resistance gene in S. maltophilia strain GZP-Sm1. The candidate gene was cloned into pMD19-T and Escherichia coli transformants carrying this vector were tested for phenicol MICs. Flanking sequences of the florfenicol resistance gene were identified by a de novo assembly and a primer walking strategy.

Results

GZP-Sm1 carried a floR gene variant, designated floRv. E. coli clones carrying this gene were resistant to chloramphenicol and florfenicol. The deduced 404 amino acid FloRv protein showed 84.1%–91.8% amino acid identity to various FloR proteins. The gene floRv was located in an MDR region within a 40 226 bp GI region. Six resistance genes, including floRv (phenicol resistance), tetR-tetA(A) (tetracycline resistance), strA/strB (streptomycin resistance), sul1 (sulphonamide resistance) and aadA2 (streptomycin/spectinomycin resistance), were located in this MDR region. PCR analysis revealed that the GI was not stable and could be excised from the chromosome as a circular intermediate.

Conclusions

The floRv gene was identified in a porcine S. maltophilia isolate. Six resistance genes including floRv were located in a novel GI. As an opportunistic pathogen in animals and humans, S. maltophilia might act as a resistance gene reservoir in farm environments. Its contribution to the spread of resistance genes to other pathogens should be monitored.
GABAergic Inhibition Regulated Pain Sensitization through STEP61 Signaling in Spinal Dorsal Horn of Mice
Authors: Li Lu , Shi Lei , Xu Ying-Ming , Yang Xian , Suo Zhan-Wei , Hu Xiao-Dong
Published: December 2014

AbstractAbstract

STEP61 is expressed in spinal cord dorsal horn neurons. γ-Aminobutyric acid type A receptors work through STEP61 to regulate extracellular signal–regulated kinase and Src-family protein tyrosine kinases member Fyn. STEP61 dysfunction augments glutamate receptor function.

Background:

The reduction of γ-aminobutyric acid (GABA) type A receptor–mediated inhibition has long been implicated in spinal sensitization of nociceptive responses. However, it is largely unknown which signaling cascades in spinal dorsal horn neurons are initiated by the reduced inhibition to trigger pain hypersensitivity.

Methods:

GABAergic inhibition was manipulated by intrathecal application of GABA type A receptor antagonist bicuculline in intact mice or by GABA type A receptor agonist muscimol in complete Freund’s adjuvant–injected mice. Immunoblotting, coimmunoprecipitation, immunohistochemistry, and behavioral tests were used to explore the signaling pathways downstream of the altered GABAergic tone.

Results:

The study data revealed that the 61-kD isoform of striatal-enriched protein phosphatase (STEP61) was a key molecule that relayed the signals from GABAergic neurotransmission. The authors found that STEP61 was highly expressed in dorsal horn neurons. Under physiological conditions, STEP61 tonically interacted with and negatively controlled the activities of extracellular signal–regulated kinase and Src-family protein tyrosine kinases member Fyn, two critical kinases involved in spinal sensitization. Once GABAergic inhibition was impaired, STEP61 interaction with its substrates was substantially disturbed, allowing for activation of extracellular signal–regulated kinase and Fyn (n = 4 to 6). The hyperactivities of extracellular signal–regulated kinase and Fyn, along with STEP61 dysregulation, caused the tyrosine phosphorylation and synaptic accumulation of GluN2B subunit-containing N-methyl-d-aspartate subtype of glutamate receptors (n = 6), leading to GluN2B receptor-dependent pain hypersensitivity. Overexpression of wild-type STEP61 to resume its enzymatic activity significantly blocked the mechanical allodynia evoked by bicuculline and more importantly, alleviated chronic inflammatory pain (n = 6 in each group).

Conclusion:

These data identified STEP61 as a key intermediary for GABAergic inhibition to regulate pain sensitization.
When to use Quantile Normalization?
Authors: Hicks Stephanie C. , Irizarry Rafael A.
Published: December 2014

Normalization and preprocessing are essential steps for the analysis of high-throughput data including next-generation sequencing and microarrays. Multi-sample global normalization methods, such as quantile normalization, have been successfully used to remove technical variation from noisy data. These methods rely on the assumption that observed global changes across samples are due to unwanted technical variability. Transforming the data to remove these differences has the potential to remove interesting biologically driven global variation and therefore may not be appropriate depending on the type and source of variation. Currently, it is up to the subject matter experts, for example biologists, to determine if the stated assumptions are appropriate or not. Here, we propose a data-driven method to test for the assumptions of global normalization methods. We demonstrate the utility of our method (quantro), by applying it to multiple gene expression and DNA methylation and show examples of when global normalization methods are not appropriate. We also perform a Monte Carlo simulation study to illustrate how our method generally outperforms the current approach. An R-package implementing our method is available on Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/quantro.html).
MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron
Authors: Cowieson Nathan Philip , Aragao David , Clift Mark , Ericsson Daniel J. , Gee Christine , Harrop Stephen J. , Mudie Nathan , Panjikar Santosh , Price Jason R. , Riboldi-Tunnicliffe Alan , Williamson Rachel , Caradoc-Davies Tom
Published: December 2014

MX1 is a bending-magnet crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range from 8 to 18 keV to a focal spot at the sample position of 120 µm FWHM. The beamline endstation and ancillary equipment facilitate local and remote access for both chemical and biological macromolecular crystallography. Here, the design of the beamline and endstation are discussed. The beamline has enjoyed a full user program for the last seven years and scientific highlights from the user program are also presented.
The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment –Olex2dissected
Authors: Bourhis Luc J. , Dolomanov Oleg V. , Gildea Richard J. , Howard Judith A. K. , Puschmann Horst
Published: December 2014

This paper describes the mathematical basis forolex2.refine, the new refinement engine which is integrated within theOlex2program. Precise and clear equations are provided for every computation performed by this engine, including structure factors and their derivatives, constraints, restraints and twinning; a general overview is also given of the different components of the engine and their relation to each other. A framework for adding multiple general constraints with dependencies on common physical parameters is described. Several new restraints on atomic displacement parameters are also presented.
Crystal structure of 5,5-bis(4-methylbenzyl)pyrimidine-2,4,6(1H,3H,5H)-trione monohydrate
Authors: Ravi Kiran Bhaskarachar , Suchetan Parameshwar Adimule , Amar Hosamani , Vijayakumar Giriyapura R
Published: December 2014

The asymmetric unit of the title compound, C20H20N2O3·H2O, contains two independent molecules (AandB), with similar conformations and two independent water molecules. In the crystal, N—H...O and Owater—H...O hydrogen bonds link all moieties into two crystallographically independent kinds of sheets parallel to theacplane. These independent sheets, each containing eitherAorBmolecules, are further alternately stacked along thebaxis and interconnectedviaC—H...πarylinteractions.
Crystal structure of (Z)-3-(4-methoxybenzylidene)-2,3-dihydrobenzo[b][1,4]thiazepin-4(5H)-one
Authors: Vinayagam V. , Mohan Raj J. , Murugavel S. , Selvakumar R. , Bakthadoss M.
Published: December 2014

In the title compound, C17H15NO2S, the two C atoms linking the S and carbonyl C atoms of the seven-membered thiazepine ring are disordered over two sites, with occupancies of 0.511 (4) and 0.489 (4); both disorder components adopt distorted twist-boat conformations. In the crystal, N—H...O and C—H...O hydrogen bonds link inverted-related molecules into dimers, incorporatingR12(6) andR22(8) ring motifs; the acceptor carbonyl O atom is bifurcated. These dimers are further linked by C—H...O hydrogen bonds, forming supramolecular tapes running along theaaxis.
Crystal structure of (E)-2-[4-(4-hydroxyphenyl)butan-2-ylidene]hydrazine-1-carbothioamide
Authors: Oliveira Adriano Bof de , Beck Johannes , Landvogt Christian , Feitosa Bárbara Regina Santos , Rocha Fillipe Vieira
Published: December 2014

The title compound, C11H15N3OS, is a thiosemicarbazone derivative of the raspberry ketone rheosmin [systematic name: 4-(4-hydroxyphenyl)butane-2-one]. The molecule deviates from planarity, with the bridging C—C—C=N torsion angle equal to −101.3 (2)°. The maximum deviation from the mean plane of the non-H atoms of the thiosemicarbazone fragment [C=N—N—C(= S)—N] is 0.085 (5) Å for the Schiff base N atom, and the dihedral angle between this mean plane and the aromatic ring is 50.31 (8)°. In the crystal, molecules are linked by N—H...O, N—H...S and O—H...S hydrogen bonds, forming a three-dimensional structure, with the molecules stacked along [011].
Proteomics of Colwellia psychrerythraea at subzero temperatures – a life with limited movement, flexible membranes and vital DNA repair
Authors: Nunn Brook L. , Slattery Krystal V. , Cameron Karen A. , Timmins‐Schiffman Emma , Junge Karen
Published: December 2014

The mechanisms that allow psychrophilic bacteria to remain metabolically active at subzero temperatures result from form and function of their proteins. We present first proteomic evidence of physiological changes of the marine psychrophile Colwellia psychrerythraea 34H (Cp34H) after exposure to subzero temperatures (−1, and −10°C in ice) through 8 weeks. Protein abundance was compared between different treatments to understand the effects of temperature and time, independently and jointly, within cells transitioning to, and being maintained in ice. Parallel [3H]‐leucine and [3H]–thymidine incubations indicated active protein and DNA synthesis to −10°C. Mass spectrometry‐based proteomics identified 1763 proteins across four experimental treatments. Proteins involved in osmolyte regulation and polymer secretion were found constitutively present across all treatments, suggesting that they are required for metabolic success below 0°C. Differentially abundant protein groups indicated a reallocation of resources from DNA binding to DNA repair and from motility to chemo‐taxis and sensing. Changes to iron and nitrogen metabolism, cellular membrane structures, and protein synthesis and folding were also revealed. By elucidating vital strategies during life in ice, this study provides novel insight into the extensive molecular adaptations that occur in cold‐adapted marine organisms to sustain cellular function in their habitat.
Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America
Authors: Souffreau Caroline , Van der Gucht Katleen , van Gremberghe Ineke , Kosten Sarian , Lacerot Gissell , Lobão Lúcia Meirelles , de Moraes Huszar Vera Lúcia , Roland Fabio , Jeppesen Erik , Vyverman Wim , De Meester Luc
Published: December 2014

Metacommunity studies on lake bacterioplankton indicate the importance of environmental factors in structuring communities. Yet most of these studies cover relatively small spatial scales. We assessed the relative importance of environmental and spatial factors in shaping bacterioplankton communities across a > 6000 km latitudinal range, studying 48 shallow lowland lakes in the tropical, tropicali (isothermal subzone of the tropics) and tundra climate regions of South America using denaturing gradient gel electrophoresis. Bacterioplankton community composition (BCC) differed significantly across regions. Although a large fraction of the variation in BCC remained unexplained, the results supported a consistent significant contribution of local environmental variables and to a lesser extent spatial variables, irrespective of spatial scale. Upon correction for space, mainly biotic environmental factors significantly explained the variation in BCC. The abundance of pelagic cladocerans remained particularly significant, suggesting grazer effects on bacterioplankton communities in the studied lakes. These results confirm that bacterioplankton communities are predominantly structured by environmental factors, even over a large‐scale latitudinal gradient (6026 km), and stress the importance of including biotic variables in studies that aim to understand patterns in BCC.
Endophytic colonization and biocontrol performance of Pseudomonas fluorescens PICF7 in olive (Olea europaea L.) are determined neither by pyoverdine production nor swimming motility
Authors: Maldonado‐González M. Mercedes , Schilirò Elisabetta , Prieto Pilar , Mercado‐Blanco Jesús
Published: December 2014

Pseudomonas fluorescens PICF7 is an indigenous inhabitant of olive (Olea europaea L.) rhizosphere, able to display endophytic lifestyle in roots, to induce a wide range of defence responses upon colonization of this organ and to exert effective biological control against Verticillium wilt of olive (VWO) (Verticillium dahliae). We aimed to evaluate the involvement of specific PICF7 phenotypes in olive root colonization and VWO biocontrol effectiveness by generating mutants impaired in swimming motility (fliI) or siderophore pyoverdine production (pvdI). Besides, the performance of mutants with diminished in vitro growth in potato dextrose agar medium (gltA) and cysteine (Cys) auxotrophy was also assessed. Results showed that olive root colonization and VWO biocontrol ability of the fliI, pvdI and gltA mutants did not significantly differ from that displayed by the parental strain PICF7. Consequently, altered in vitro growth, swimming motility and pyoverdine production contribute neither to PICF7 VWO suppressive effect nor to its colonization ability. In contrast, the Cys auxotroph mutant showed reduced olive root colonization capacity and lost full biocontrol efficacy. Moreover, confocal laser scanning microscopy revealed that all mutants tested were able to endophytically colonize root tissue to the same extent as wild‐type PICF7, discarding these traits as relevant for its endophytic lifestyle.
Oxygen‐dependent copper toxicity: targets in the chlorophyll biosynthesis pathway identified in the copper efflux ATPase CopA deficient mutant
Authors: Liotenberg Sylviane , Steunou Anne‐Soisig , Durand Anne , Bourbon Marie‐Line , Bollivar David , Hansson Mats , Astier Chantal , Ouchane Soufian
Published: December 2014

Characterization of a copA− mutant in the purple photosynthetic bacterium Rubrivivax gelatinosus under low oxygen or anaerobic conditions, as well as in the human pathogen Neisseria gonorrhoeae identified HemN as a copper toxicity target enzyme in the porphyrin synthesis pathway. Heme synthesis is, however, unaffected by copper under high oxygen tension because of the aerobic coproporphyrinogen III oxidase HemF. Nevertheless, in the copA− mutant under aerobiosis, we show that the chlorophyll biosynthesis pathway is affected by excess copper resulting in a substantial decrease of the photosystem. Analyses of pigments and enzyme activity showed that under low copper concentrations, the mutant accumulated protochlorophyllide, suggesting that the protochlorophyllide reductase activity is affected by excess copper. Increase of copper concentration led to a complete lack of chlorophyll synthesis as a result of the loss of Mg‐chelatase activity. Both enzymes are widely distributed from bacteria to plants; both are [4Fe‐4S] proteins and oxygen sensitive; our data demonstrate their in vivo susceptibility to copper in the presence of oxygen. Additionally, our study provides the understanding of molecular mechanisms that may contribute to chlorosis in plants when exposed to metals. The role of copper efflux systems and the impact of copper on heme and chlorophyll biosynthesis in phototrophs are addressed.
Nihilism and Urban Multiculture in Outer East London
Authors: James Malcolm
Published: December 2014

This paper discusses nihilism as it relates to contemporary urban multiculture in outer East London. It addresses how contemporary discourses on, and performances of, nihilism signal shifts in the constitution of urban multiculture. Attention is paid to acts of anti-sociability (and sociability) for what they reveal about contemporary urban rearrangement, and in particular the re-formation of urban multiculture in a moment defined by globalization, virtual communication, ethnic diversity and neoliberal marginalization. Through addressing discourses on, and performances of, nihilism the overall argument of the paper is for a renewal of the terms on which we understand and engage with urban multiculture, and for an appreciation of how relations between class, race and culture have shifted since key texts on the subject were published.
Magnetic Resonance Imaging of the Dorsal Proximal Synovial Plica of the Equine Metacarpo‐/Metatarsophalangeal Joint
Authors: Hauspie S. , Vanderperren K. , Gielen I. , Pardon B. , Kromhout K. , Martens A. , Saunders J. H.
Published: December 2014

A synovial plica is present at the dorsoproximal aspect of the fetlock joint. The objective of this study was to describe the location of the synovial plica during induced hyperextension using Magnetic Resonance Imaging. For this study 20 cadaver limbs from five Warmblood horses were used. Measurements were made of the dorsal; palmar/plantar length and the thickness of the plica with the joint in a normal position. During induced hyperextension of the joint, the position of the plica was described; the dorsal angle of extension and angle of contact between the proximal phalanx (P1) and the condyle were measured. The dorsal length differed between front/hind limbs and between the medial/lateral aspect of the joint. The angle of contact between P1 and condyle differed between front/hind limbs; between the lateral and medial aspect of the joint and between different positions of the plica. Four different positions of the plica were observed: shortened with the tip curved towards palmar/plantar; projecting distally; projecting towards dorsal and projecting distally with the tip interposed between P1 and the condyle. During induced hyperextension, a close relation is present between the synovial plica, P1 and the condyle with a variable position of the plica; which is suggestive for a contact interface between P1 and the metacarpal/metatarsal bone. However the plica does not seem to act consistently as a cushioning surface.
Barriers to access reproductive health care for pregnant adolescent girls: a qualitative study in Tanzania
Authors: Hokororo Adolfine , Kihunrwa Albert F. , Kalluvya Samuel , Changalucha John , Fitzgerald Daniel W. , Downs Jennifer A.
Published: December 2014

Aims

In Tanzania, approximately 25% of adolescents give birth and 50% more become sexually active during adolescence. We hypothesised that reproductive health education and services for adolescent girls are inaccessible and conducted this study to gain insights into their perceptions of sexually transmitted infections (STIs) and barriers to reproductive health service utilisation in rural Mwanza, Tanzania.

Methods

We conducted nine focus groups among pregnant adolescents aged 15–20 years. Data were transcribed, translated and coded for relevant themes using NVivo10 software for qualitative data analysis.

Results

Most participants were aware of the dangers of STIs to themselves and their unborn babies, but did not perceive themselves as at risk of acquiring STIs. They viewed condoms as ineffective for preventing STIs and pregnancies and unnecessary for those in committed relationships. Stigma, long waiting times, and lack of privacy in the clinics discouraged adolescent girls from seeking reproductive health care.

Conclusion

Reproductive health care for adolescent girls who are not pregnant is practically nonexistent in Tanzania. Healthcare access for pregnant young women is also limited. Targeted changes to increase clinic accessibility and to provide reproductive health education to all rather than only pregnant women have the potential to address these gaps.
Differences in nephrotoxicity risk and renal effects among anti‐viral therapies against hepatitis B
Authors: Koklu S. , Gulsen M. T. , Tuna Y. , Koklu H. , Yuksel O. , Demir M. , Guner R. , Dogan Z. , Kucukazman M. , Poyrazoglu O. K. , Biyik M. , Ozturk N. A. , Aydogan T. , Coban S. , Kocaman O. , Sapmaz F. , Gokturk S. H. , Karaca C. , Demirezer A. , Tanoglu A. , Yildirim B. , Altinbas A. , Atak B. M. , Cosar A. M. , Alkan E. ,   Other collaborators
Published: December 2014

Background

Results are conflicting with respect to the renal effects of anti‐viral agents used for hepatitis B virus infection.

Aim

To compare short and long‐term renal effects in real‐life settings and to determine risk factors for renal impairment during treatment.

Methods

2221 treatment‐naïve patients were enrolled. Among these, 895 (302 lamivudine, 27 telbivudine, 282 entecavir, 273 tenofovir and 11 adefovir initiated patients) had ‘repeated measures’ of creatinine (baseline, 1st, 6th, 12th and 24th month of treatment). Telbivudine and adefovir groups were excluded from further analysis because of the low number of patients. We calculated the glomerular filtration rate (GFR) using the Modification of Diet in Renal Disease (MDRD) formula at each time point. Hypophosphataemia was also recorded. Risk factors for renal impairment were analysed.

Results

Tenofovir caused a decline in GFR at each time point when compared to baseline levels. However, lamivudine and entecavir did not change GFR. GFR‐shifting from ≥90 to 60–89 mL/min/1.73 m2 was comparable among groups. The proportion of patients whose baseline creatinine increased more than 25% was comparable among all anti‐virals. GFR showed a decline in patients who switched from entecavir to tenofovir. One patient with compensated cirrhosis needed to change from tenofovir because of renal safety. Seven and three patients developed transient hypophosphataemia in the tenofovir and lamivudine groups, respectively.

Conclusions

Although tenofovir caused a decline in GFR, differences between the anti‐viral agents do not appear to be so impressive. In patients with and without renal risk factors at baseline, there is no impact of anti‐virals, including tenofovir.