bluuebunny/crossref_metadata_2025 huggingface dataset:
Large-scale compression of genomic sequence databases with the Burrows–Wheeler transform
Authors: Cox Anthony J. , Bauer Markus J. , Jakobi Tobias , Rosone Giovanna
Published: May 2012

Motivation: The Burrows–Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets.

Results: We first used simulated reads to explore the relationship between the level of compression and the error rate, the length of the reads and the level of sampling of the underlying genome and compare choices of second-stage compression algorithm.

We demonstrate that compression may be greatly improved by a particular reordering of the sequences in the collection and give a novel ‘implicit sorting’ strategy that enables these benefits to be realized without the overhead of sorting the reads. With these techniques, a 45× coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3 Gb of sequence to fit into only 8.2 GB of space (trimming a small proportion of low-quality bases from the reads improves the compression still further).

This is >4 times smaller than the size achieved by a standard BWT-based compressor (bzip2) on the untrimmed reads, but an important further advantage of our approach is that it facilitates the building of compressed full text indexes such as the FM-index on large-scale DNA sequence collections.

Availability: Code to construct the BWT and SAP-array on large genomic datasets is part of the BEETL library, available as a github repository at https://github.com/BEETL/BEETL.

Contact:  acox@illumina.com
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
Authors: Pruesse Elmar , Peplies Jörg , Glöckner Frank Oliver
Published: May 2012

Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements.

Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands.

SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks.

Availability: Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

Contact:  epruesse@mpi-bremen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Changes in Atlantic water properties: an important factor in the European Arctic marine climate
Authors: Walczowski Waldemar , Piechura Jan , Goszczko Ilona , Wieczorek Piotr
Published: May 2012

Walczowski, W., Piechura, J., Goszczko, I., and Wieczorek, P. 2012. Changes in Atlantic water properties: an important factor in the European Arctic marine climate. – ICES Journal of Marine Science, 69: 864–869. The advection of warm Atlantic water (AW) through the Nordic Seas and its transformation (cooling and freshening) is one of the most important climatological processes in the region. Time-series of hydrographic observations in the northern Nordic Seas and the Fram Strait region are presented and analysed. Significant variability in the properties of AW has been observed in recent years. A 15-year time-series of summer observations indicate positive trends in salinity and temperature and two 5–6-year cycles. The northward advance of AW in 2006 was an unprecedented event. The position of the warm-water tongue shifted more than 350 km to the north, and temperatures in the West Spitsbergen Current reached the highest values ever recorded. These changes in AW temperature, heat content, and northward transport had a strong influence on the oceanic climate and sea-ice conditions north of Svalbard. These oceanic signals led to environmental changes that confirm the primary role of the ocean in shaping the climate of the region.
1-(4-Methoxyphenyl)ethane-1,2-diyl 1,1′-biphenyl-2,2′-dicarboxylate
Authors: Fun Hoong-Kun , Quah Ching Kheng , Wu Dongdong
Published: May 2012

In the title molecule, C23H18O5, the methoxy-substituted benzene ring makes dihedral angles of 65.12 (4) and 88.55 (4)° with the other two benzene rings. These two benzene rings form a dihedral angle of 45.70 (4)°. In the crystal, molecules are linked into inversion dimers by pairs of weak C—H...O hydrogen bonds.
2-Azido-1-(4-methylphenyl)ethanone
Authors: Arshad Muhammad , Yousuf Sammer , Butt Hafiza Madiha , Saeed Sumayya , Basha Fatima Z.
Published: May 2012

In the molecule of the title compound, C9H9N3O, the angle formed by the least-squares line through the azide group with the normal to the plane of the benzene plane ring is 46.62 (16)°. The crystal structure features C—H...O hydrogen bonds, which link the molecules into zigzag chains running parallel to [010].
1,1′-Bicyclohexyl-1,1′-diyl 2,2′-bipyridine-3,3′-dicarboxylate
Authors: Fun Hoong-Kun , Lim Ming Yeng , Quah Ching Kheng , Wu Dongdong
Published: May 2012

The title compound, C24H26N2O4, lies about a crystallographic twofold rotation axis. The cyclohexane rings adopts a chair conformation. The two pyridine rings form a dihedral angle of 41.02 (4)°. In the crystal, molecules are linked via C—H...O and C—H...N hydrogen bonds into a layer parallel to the bc plane.
6-Benzyloxy-2-phenylpyridazin-3(2H)-one
Authors: Ju Zhi-Yu , Li Gong-Chun , Li Chao , Wang Jie , Yang Feng-Ling
Published: May 2012

In the title compound, C17H14N2O2, the central pyridazine ring forms dihedral angles of 47.29 (5) and 88.54 (5)° with the benzene rings, while the dihedral angle between the benzene rings is 62.68 (6)°. In the crystal, molecules are linked by two weak C—H...O hydrogen bonds and three weak C—H...π interactions.
(Acetylacetonato-κ2
O,O′)carbonyl[dicyclohexyl(2,6-diisopropylphenyl)phosphane-κP]rhodium(I)
Authors: Davis Wade L. , Mathobela Sfiso D. , Meijboom Reinout
Published: May 2012

In the title compound, [Rh(C5H7O2){C12H17P(C6H11)2}(CO)], the RhI atom is coordinated by one carbonyl C, one P and two O atoms, forming a slighlty distorted square-planar configuration.
N-(4-Bromophenyl)-3,4,5-trimethoxybenzamide
Authors: Gu Wen , Qiao Chao
Published: May 2012

In the title compound, C16H16BrNO4, the dihedral angle between the two aromatic rings is 67.51 (25)°. In the crystal, molecules are linked by N—H...O hydrogen bonds involving the N—H and C=O groups of the amide function, leading to a chain along [-101].
5-Carbamoyl-2-methyl-1-(2-methylbenzyl)pyridinium bromide
Authors: Kim Kyung Beom , Yu Seung Man , Kim Cheal , Kim Youngmee
Published: May 2012

In the title molecular salt, C15H17N2O+·Br−, the benzene and pyridinium rings form a dihedral angle of 83.0 (1)°. In the crystal, N—H...Br and N—H...O hydrogen bonds link the components into chains along [010]. These chains are linked by weak C—H...O and C—H...Br hydrogen bonds, forming a three-dimensional network.
A triclinic polymorph of poly[[bis[μ-1,2-bis(pyridin-4-yl)ethene-κ2
N:N′]bis(thiocyanato-κN)cobalt(II)] 1,2-bis(pyridin-4-yl)ethene monosolvate]
Authors: Wöhlert Susanne , Jess Inke , Näther Christian
Published: May 2012

In the crystal structure of the title compound, [Co(NCS)2(C12H10N2)2]·C12H10N2, the CoII cations are octahedrally coordinated by two terminally N-bonded thiocyanate anions and four 1,2-bis(pyridin-4-yl)ethene (bpe) ligands. The asymmetric unit consists of three crystallographically independent CoII cations, six thiocyanate anions and six coordinating bpe ligands in general positions. Additionally, three non-coordinating bpe ligands are present in the asymmetric unit with two of them located on a center of inversion. The CoII cations are connected by the bpe ligands into layers parallel to the bc plane. The crystal investigated was non-merohedrically twinned, with a fractional contribution of 0.261 (2) for the minor domain.
Bis(3,5-di-tert-butyl-4H-1,2,4-triazol-4-amine-κN
1)(nitrato-κO)silver(I) ethanol monosolvate monohydrate
Authors: Liu Ya-Mei , Chen Jing-Huo , Yang Guang , Ng Seik Weng
Published: May 2012

The AgI atom in the title compound, [Ag(NO3)(C10H20N4)2]·C2H5OH·H2O, is coordinated by the N atoms of two N-heterocycles [N—Ag—N = 151.5 (1)°]; the approximately linear coordination geometry is distorted into a T-shaped geometry owing to a long Ag...Onitrate bond [2.717 (4) Å]. The N atoms of the N-heterocycles that are not involved in coordination point towards the lattice water molecule, which functions as a hydrogen-bond donor. The water molecule itself is a hydrogen-bond acceptor towards the ethanol solvent molecule. Hydrogen bonds of the type N–H...O give rise to a layer motif parallel to (001).
2,2′,2′′,2′′′-(1,4-Phenylenedinitrilo)tetraacetic acid dihydrate
Authors: Yan Juanzhi , Ma Ling , Zhu Miaoli , Zhang Xiangdong , Ge Chunhua
Published: May 2012

In the title compound, C14H16N2O8·2H2O, the complete organic molecule is generated by crystallographic inversion symmetry. The dihedral angles between the aniline ring and the acetic acid groups are almost identical, viz. 82.61 (7) and 80.33 (7)°. In the crystal, O—H...O hydrogen bonds link the organic molecules and water molecules, forming zigzag chains the c axis. An intramolecular O—H...O hydrogen bond is also observed.
4-[(E)-(4-Fluorobenzylidene)amino]-3-methyl-1H-1,2,4-triazole-5(4H)-thione
Authors: Devarajegowda H. C. , Jeyaseelan S. , Sathishkumar R. , D'souza Agnes Sylvia , D'souza Alphonsus
Published: May 2012

In the asymmetric unit of the title compound, C10H9FN4S, there are two independent molecules in which the dihedral angles between the 1,2,4-triazole and benzene rings are 36.85 (10) and 7.81 (10)°. In the crystal, N—H...S interactions link pairs of independent molecules into dimers. There are also π–π interactions between the triazole and benzene rings of inversion-related pairs of the more planar molecule [centroid–centroid distance = 3.6430 (13) Å].
N,N′-Bis(2,6-diisopropylphenyl)-3,6-dimethyl-1,2,4,5-tetrazine-1,4-dicarboxamide
Authors: Sun Na-Bo , Rao Guo-Wu , Zhang Li-Ling
Published: May 2012

In the title molecule, C30H42N6O2, the amide-substituted N atoms of the tetrazine ring deviate from the approximate plane of the four other atoms in the ring by 0.457 (3) and 0.463 (3) Å, forming a boat conformation. The two benzene rings form a dihedral angle of 47.69 (9)°. Intramolecular N—H...N and weak C—H...O hydrogen bonds are observed.
5,5′′-Dibromo-1,1′′-bis(prop-2-en-1-yl)-1,1′′,2,2′′-tetrahydrodispiro[indole-3,7′-[6,9]diazatricyclo[7.3.0.02,6]dodecane-8′,3′′-indole]-2,2′′-dione
Authors: Al Mamari Khalil , Ennajih Hamid , Bouhfid Rachid , Essassi El Mokhtar , Ng Seik Weng
Published: May 2012

In the molecule of the title compound, C30H30Br2N4O2, the piperazine ring adopts a chair conformation. The pyrrolidine rings that are fused to the piperazine ring adopt envelope conformations (in which the N atom represents the flap). The indoline fused-ring systems are nearly planar (r.m.s. deviations = 0.009 and 0.019 Å); the two fused rings are aligned at 60.63 (6)°.
Ethyl (3E)-3-[2-(4-bromophenylsulfonyl)hydrazin-1-ylidene]butanoate
Authors: Murtaza Shahzad , Kausar Naghmana , Abbas Aadil , Tahir M. Nawaz , Zulfiqar Muhammad
Published: May 2012

The asymmetric unit of title compound, C12H15BrN2O4S, contains two molecules (A and B), with slightly different conformations: the bromophenyl rings and the SO2 planes of the sulfonyl groups are oriented at dihedral angles of 50.2 (2) (molecule A) and 58.24 (7)° (molecule B), and the ethyl acetate groups make dihedral angles of 63.99 (19)° (A) and 65.35 (16)° (B) with their bromophenyl groups. In the crystal, both molecules exist as inversion dimers linked by pairs of N—H...O hydrogen bonds, which generate R
2
2(14) loops. The dimers are linked by C—H...O interactions.
Bis[(E)-N-(pyridin-3-ylmethylidene)hydroxylamine-κN
1]silver(I) perchlorate
Authors: Xu Jing , Gao Shan , Ng Seik Weng , Tiekink Edward R. T.
Published: May 2012

Each of the ions in the title salt, [Ag(C6H6N2O)2]ClO4, is completed by the application of crystallographic twofold symmetry. The AgI atom is coordinated by two pyridine N atoms in an almost linear fashion [N—Ag—N = 170.0 (2)°], with the T-shaped coordination geometry being completed by a weakly associated perchlorate-O atom. Supramolecular zigzag chains along [100] mediated by O—H...N hydrogen bonds [as parts of R
2
2(6) loops] feature in the crystal packing. The perchlorate O atoms are disordered over two sets of sites in a statistical ratio.
(E)-N′-(4-Ethoxybenzylidene)-4-hydroxybenzohydrazide dihydrate
Authors: Fun Hoong-Kun , Horkaew Jirapa , Chantrapromma Suchada , Karalai Chatchanok
Published: May 2012

The benzohydrazide molecule of the title compound, C16H16N2O3·2H2O, exists in a trans conformation with respect to the C=N double bond. The central O=C—NH—N=C plane [r.m.s. deviation of 0.0165 (1) Å for the five non-H atoms] makes dihedral angles of 6.04 (8) and 2.38 (8)°, respectively, with the hydroxy- and ethoxy-substituted benzene rings. The dihedral angle between these benzene rings is 3.82 (7)°. The ethoxy group is almost coplanar with the attached benzene ring with a C—O—C—C torsion angle of −176.58 (11)°. In the crystal, the benzohydrazide and water molecules are linked by N—H...O, O—H...O , O—H...N and C—H...O hydrogen bonds into a three-dimensional network.
(E)-1-(2,4-Dinitrophenyl)-2-[1-(3-fluorophenyl)ethylidene]hydrazine
Authors: Chantrapromma Suchada , Nilwanna Boonlerd , Kobkeatthawin Thawanrat , Jansrisewangwong Patcharaporn , Fun Hoong-Kun
Published: May 2012

The molecule of the title hydrazone derivative, C14H11FN4O4, is nearly planar, with a dihedral angle between the benzene rings of 3.71 (7)°. The central ethylidenehydrazine N—N=C—C plane makes dihedral angles of 5.32 (10) and 9.02 (10)° with the 2,4-dinitro- and 3-fluoro-substituted benzene rings, respectively. An intramolecular N—H...O bond generates an S(6) ring motif. In the crystal, molecules are linked by weak C—H...O interactions into a sheet parallel to (10-1). The molecules are further stacked along the a axis by π–π interactions with centroid–centroid distances of 3.6314 (9) and 3.7567 (10) Å. A C...F short contact [2.842 (3) Å] is observed. The 3-fluorophenyl group is disordered over two orientations with a site-occupancy ratio of 0.636 (3):0.364 (3).
Diaquadichloridobis[quinazolin-4(1H)-one-κN
3]nickel(II)
Authors: Shomurotova Shirin , Turgunov Kambarali K. , Mukhamedov Nasir , Tashkhodjaev Bakhodir
Published: May 2012

In the title complex, [NiCl2(C8H6N2O)2(H2O)2], the NiII ion is located on an inversion center and is six-coordinated by two N atoms of 1H-quinazolin-4-one ligands, two chloride ions and two water molecules. The water molecules are involved in intra- and intermolecular O—H...O and O—H...Cl hydrogen bonding. Intermolecular N—H...O and N—H...Cl hydrogen bonds are formed between ligands. In addition, weak π–π interactions are observed between the benzene rings of the ligands [centroid–centroid distance = 3.580 (3) Å]. The intermolecular hydrogen bonds and π–π interactions lead to the formation of a three-dimensional supramolecular network.
catena-Poly[[(2,9-dimethyl-1,10-phenanthroline-κ2
N,N′)lead(II)]-di-μ-bromido]
Authors: Sabour Behrous , Najafi Ezzatollah , Amini Mostafa M. , Ng Seik Weng
Published: May 2012

In the title compound, [PbBr2(C14H12N2)]
n
, the PbII atom lies on a twofold rotation axis. The N-heterocycle-chelated PbII atom exists in a distorted octahedral geometry owing to two long Pb...Br interactions [2.9562 (5) and 3.2594 (5) Å]. These result in a zigzag chain running along the c axis. The lone pair is stereochemically inactive.
3-(4-Bromophenylsulfonyl)-5-cyclopentyl-2-methyl-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: May 2012

In the title compound, C20H19BrO3S, the cyclopentyl ring adopts an envelope conformation. The 4-bromophenyl ring makes a dihedral angle of 82.09 (6)° with the mean plane [mean deviation = 0.026 (2) Å] of the benzofuran fragment. In the crystal, molecules are linked by weak C—H...O hydrogen bonds and Br...O contacts [3.309 (2) Å].
(E)-N′-(3-Fluorobenzylidene)-4-methylbenzohydrazide
Authors: Hu Hua-Nan , Liu Shi-Yong
Published: May 2012

In the title compound, C15H13FN2O, the dihedral angle between the benzene rings is 16.9 (2)°. The F atom and the O atom are in a syn conformation. In the crystal, molecules are linked by N—H...O hydrogen bonds to generate C(4) chains propagating along the b-axis direction.
Tris(5,6-dimethyl-1H-benzimidazole-κN
3)(pyridine-2,6-dicarboxylato-κ3
O
2,N,O
6)nickel(II)
Authors: Li Yue-Hua , Li Feng-Feng , Liu Xin-Hua , Zhao Ling-Yan
Published: May 2012

The title mononuclear complex, [Ni(C7H3NO4)(C9H10N2)3], shows a central NiII atom which is coordinated by two carboxylate O atoms and the N atom from a pyridine-2,6-dicarboxylate ligand and by three N atoms from different 5,6-dimethyl-1H-benzimidazole ligands in a distorted octahedral geometry. The crystal structure shows intermolecular N—H...O hydrogen bonds.
3-Methylpiperidinium bromide
Authors: Xu Qian
Published: May 2012

In the crystal structure of the title molecular salt, C6H14N+·Br−, N—H...Br hydrogen bonds link the cations and anions to form a one-dimensional network.
Methyl 2-butyl-4-hydroxy-1,1-dioxo-2H-1,2-benzothiazine-3-carboxylate
Authors: Arshad Muhammad Nadeem , Khan Islam Ullah , Zia-ur-Rehman Muhammad , Ahmed Waseem , Asiri Abdullah M.
Published: May 2012

In the title compound, C14H17NO5S, the thiazine ring adopts a half-chair conformation. The molecule exhibits an intramolecular O—H...O hydrogen bond, which forms a six-membered S(6) ring motif. The planes of the benzene and thiazine rings are inclined at a dihedral angle of 15.30 (12)°.
The reproductive behaviour of Pogonophryne scotti confirms widespread egg‐guarding parental care among Antarctic notothenioids
Authors: Jones C. D. , Near T. J.
Published: May 2012

In this paper, the first documentation of egg‐guarding behaviour in an artedidraconid species, Pogonophryne scotti, through in situ photographic imagery obtained during video transects is provided. The male specimen was observed closely guarding a well‐defined multi‐layered egg mass deposited on the sea floor at 240 m on the southern South Orkney Islands shelf in the northern Weddell Sea. Egg‐guarding parental care is present in species that are distributed among all of the major lineages of Antarctic notothenioids; however, lack of information on egg‐deposition behaviours in Bovichtidae and Pseudaphritis prevents assessment of whether parental care originated prior to the origin of the Antarctic notothenioid radiation.
Molecular identification of hybrids of the invasive gibel carp Carassius auratus gibelio and crucian carp Carassius carassius in Swedish waters
Authors: Wouters J. , Janson S. , Lusková V. , Olsén K. H.
Published: May 2012

Both mitochondrial DNA sequence and two nuclear microsatellite markers were used to confirm the identity of the first record of Carassius auratus gibelio in the western (Swedish) Baltic Sea region. A total of 49 fishes were analysed, where 22 were from three Swedish sites connected to the Baltic Sea. The D‐loop mitochondrial DNA sequences showed that 16 of 22 Swedish fishes were related to C. a. gibelio. The phylogenetic analysis of these sequences showed that these fish are probably not native, but represent different lineages of C. a. gibelio from China, Japan and Russia. All except three of these 16 fishes had microsatellite alleles suggesting hybridization with Carassius carassius. These findings suggest that a cryptic invasion of C. a. gibelio might be in progress.
A tale of missed opportunities: pursuit of a public health approach to gambling in New Zealand
Authors: Adams Peter J. , Rossen Fiona
Published: May 2012

Aim  This paper provides a critical overview a decade after the New Zealand Government announced its intention to formally incorporate a public health approach into its comprehensive revision of gambling legislation.

Method  The initial enthusiasm and the subsequent disillusionment with this approach are tracked. Four reasons for its lack of success are examined.

Findings  The New Zealand experiment with a public health approach to gambling is seen to have floundered in a network of vested interests. The pathways for influence included inappropriate industry input as well as community and government sector reliance on gambling profits. The new legislation neglected to set up systems for strong independent accountability, and this weakened the potential of public health initiatives.

Conclusion  As with tobacco control, the policy integrity of a public health approach to gambling requires close attention to ways of reducing vested interests in both government and community sectors and to establishing strong points of independent accountability.
The relative contribution of NSAIDs and Helicobacter pylori to the aetiology of endoscopically‐diagnosed peptic ulcer disease: observations from a tertiary referral hospital in the UK between 2005 and 2010
Authors: Musumba C. , Jorgensen A. , Sutton L. , Van Eker D. , Moorcroft J. , Hopkins M. , Pritchard D. M. , Pirmohamed M.
Published: May 2012

Background

Recent data from Western countries indicate that the aetiology of peptic ulcer disease (PUD) is changing as the prevalence of Helicobacter pylori is decreasing while the use of low‐dose aspirin (LDA, ≤325 mg/day) is increasing.

Aim

To investigate the changing aetiology and demographics of PUD in a well‐characterised patient cohort at a large tertiary hospital in the UK between July 2005 and June 2010.

Methods

Patients diagnosed with PUD following endoscopy were categorised as non‐steroidal anti‐inflammatory drug (NSAID)‐users or non‐users, and their H. pylori status determined. Comparisons between NSAID‐users and non‐users, and between non‐aspirin NSAID‐users and LDA‐users were summarised using counts and corresponding percentages (for categorical variables) and means and standard deviations (for continuous variables).

Results

Overall, 386 patients were enrolled; 57% used NSAIDs (51% LDA only) and 43% were non‐users. 57% of the whole cohort was H. pylori‐positive (including 66% with duodenal ulcers and 47% with gastric ulcers). Compared with non‐users, NSAID‐users were older (mean age 68 vs. 61 years) and fewer were H. pylori‐positive (52% vs. 63%). LDA‐users were older (mean age 71 vs. 62 years) and more likely to be H. pylori‐positive (61% vs. 41%) than those using non‐aspirin NSAIDs. Twelve per cent of the patients were neither using NSAIDs nor were H. pylori‐positive.

Conclusions

The NSAIDs, particularly LDA, were most commonly associated with PUD in this cohort. Our findings are compatible with the decline in the prevalence of H. pylori‐positive PUD and increase in non‐NSAID, non‐H. pylori PUD previously reported.
Correlation between liver histology and novel magnetic resonance imaging in adult patients with non‐alcoholic fatty liver disease – MRI accurately quantifies hepatic steatosis in NAFLD
Authors: Permutt Z. , Le T.‐A. , Peterson M. R. , Seki E. , Brenner D. A. , Sirlin C. , Loomba R.
Published: May 2012

Background

Conventional magnetic resonance imaging (MRI) techniques that measure hepatic steatosis are limited by T1 bias, T2* decay and multi‐frequency signal‐interference effects of protons in fat. Newer MR techniques such as the proton density‐fat fraction (PDFF) that correct for these factors have not been specifically compared to liver biopsy in adult patients with non‐alcoholic fatty liver disease (NAFLD).

Aim

To examine the association between MRI‐determined PDFF and histology‐determined steatosis grade, and their association with fibrosis.

Methods

A total of 51 adult patients with biopsy‐confirmed NAFLD underwent metabolic‐biochemical profiling, MRI‐determined PDFF measurement of hepatic steatosis and liver biopsy assessment according to NASH‐CRN histological scoring system.

Results

The average MRI‐determined PDFF increased significantly with increasing histology‐determined steatosis grade: 8.9% at grade‐1, 16.3% at grade‐2, and 25.0% at grade‐3 with P ≤ 0.0001 (correlation: r2 = 0.56, P < 0.0001). Patients with stage‐4 fibrosis, when compared with patients with stage 0–3 fibrosis, had significantly lower hepatic steatosis by both MRI‐determined PDFF (7.6% vs. 17.8%, P < 0.005) and histology‐determined steatosis grade (1.4 vs. 2.2, P < 0.05). NAFLD patients with grade 1 steatosis were more likely to have characteristics of advanced liver disease including higher average AST:ALT (0.87 vs. 0.60, P < 0.02), GGT (140 vs. 67, P < 0.01), and INR (1.06 vs. 0.99, P < 0.01), higher stage of fibrosis and hepatocellular ballooning.

Conclusions

MRI‐determined proton density‐fat fraction correlates with histology‐determined steatosis grade in adults with NAFLD. Steatosis is non‐linearly related to fibrosis progression. In patients with NAFLD, a low amount of hepatic steatosis on imaging does not necessarily indicate mild disease.
Vicious and virtuous circles of offshoring attitudes and relational behaviours. A configurational study of German IT developers
Authors: Zimmermann Angelika , Raab Katharina , Zanotelli Livio
Published: May 2012

Prior research has shown that the success of offshoring is affected by relational behaviours of the employees involved in an offshoring collaboration. However, hardly anything is known about the attitudes that onshore colleagues hold towards offshoring, and how such offshoring attitudes affect relational behaviours towards offshore colleagues. We therefore present an interpretivist, qualitative case study that explores the offshoring attitudes of German information technology developers. We found that offshoring attitudes affected relational behaviours towards Indian offshore colleagues, in terms of (1) treating Indian colleagues as fellow team members as opposed to suppliers; (2) spending more or less effort in communication and knowledge transfer; and (3) supporting vs. avoiding the task transfer. These relational behaviours fed back into participants' offshoring attitudes, leading to vicious and virtuous circles. The circles created two contrasting configurations of offshoring attitudes and relational behaviours, driven by opposing forces within the departmental context. Our findings highlight the value of taking a configurational perspective for understanding offshoring success and for identifying drivers that need to be managed in order to achieve favourable configurations. We suggest that future research should further expand the typology of attitude‐behaviour configurations and could apply theories of efficacy, self‐reinforcing spirals and planned behaviour.
The experiences of Australian lesbian couples becoming parents: deciding, searching and birthing
Authors: Chapman Rose , Wardrop Joan , Zappia Tess , Watkins Rochelle , Shields Linda
Published: May 2012

Aim and objectives.  To explore Australian lesbian mothers’ experiences of becoming parents.

Background.  Lesbians are becoming parents and, since legislative changes in Australia, their numbers are increasing. Prior to legislative changes, fertility and health services for women in Australia exclusively served the needs of the heterosexual community. Although lesbian experience of seeking health services has been studied in other contexts, little has been done to understand their experience of deciding, conceiving and birthing.

Design.  Qualitative descriptive study.

Method.  Seven interviews conducted with lesbian mothers in Australia.

Results.  The following themes were identified: ‘making the decision’; ‘the search’; ‘perseverance’; and ‘problems of isolation’.

Conclusions.  Although legislation now affords lesbians access to reproductive technologies throughout most of Australia, their involvement with health professionals can result in homophobic interactions. One way to address the needs of lesbian families is to provide an environment where the disclosure of sexual identity is encouraged. Further larger scale research should identify changes to service provision required to address the inequalities between heterosexual and lesbian women and ensure health services are provided that are free from discrimination.

Relevance to clinical practice.  Most health services have policies and procedures in place to prevent discrimination on all grounds, including sexual orientation. It is imperative that administrators and clinicians take steps to ensure that these guidelines are applied.
Police contact with people with an intellectual disability: the Independent Third Person perspective
Authors: Spivak B. L. , Thomas S. D. M.
Published: May 2012

Background A number of jurisdictions have instituted legislation requiring an independent person to be present during police interviews with vulnerable people. In Victoria, Australia, a group of volunteers known as Independent Third Persons help to fulfil this role with people who present with cognitive impairment arising from their mental illness or disability. This study sought to explore the perspectives of the Independent Third Person volunteers on police identification of and responses to people with intellectual disability (ID).

Methods All registered Independent Third Person volunteers across the State of Victoria in Australia were identified and sent a postal survey on their experiences and confidence in performing their role, their perceptions of police competency, and the challenges they faced working at this interface.

Results Of the 207 Independent Third Persons identified, 94 (45%) completed and returned the survey. Participants reported that despite being overly reliant on previous police contacts and cues relating to communication difficulties, they viewed police as generally competent in their ability to identify people with ID. They also considered themselves confident in performing their own roles at this interface, albeit more so at the perfunctory aspects of the role and less so with the emotional aspects of supporting the person being interviewed.

Conclusions Police are seen as competent at identifying those with cognitive deficits and seeking appropriate supports for the person with ID in the interview context. More specialised training for police members is recommended in communicating with people with IDs. Volunteers working at this interface require additional support and training in helping to meet the emotional needs of those being interviewed.
Origin and diversification of the cryptic ant genus Stenamma Westwood (Hymenoptera: Formicidae), inferred from multilocus molecular data, biogeography and natural history
Authors: BRANSTETTER MICHAEL G.
Published: May 2012

The genus Stenamma Westwood comprises a group of cryptic, cold tolerant ants that occur throughout the Holarctic and Middle American regions. Traditional approaches to taxonomy and phylogeny are confounded by multiple factors, including the conservative and often convergent morphology of workers and the rarity of reproductive castes in collections. Monophyly of Stenamma and relationships within the genus are uncertain as nearly all previous taxonomic work has been regional in scope. Furthermore, the sister group to Stenamma has not been well established. Here an extensive molecular dataset consisting of ten genes (∼8 kb of data), 48 ingroup taxa (20 Nearctic, 6 Palaearctic and 22 Neotropical) and 8 outgroup taxa (6 closely related non‐Stenamma and 2 additional myrmicines) is used to investigate the broad‐scale phylogeny and evolutionary history of Stenamma. Phylogenetic analysis is performed under maximum likelihood and Bayesian frameworks on individual genes and several alternate concatenated datasets, which are used to investigate the effects of inclusion or exclusion of COI and intronic regions. The timing of Stenamma evolution is inferred in beast and ancestral areas are reconstructed using both the s‐diva and DEC methods, as implemented in the programs rasp and lagrange, respectively. Stenamma is revealed as monophyletic with high support and tentatively is sister to a group of New World species placed currently in Aphaenogaster Mayr and Messor Forel. Within Stenamma, two major clades are recovered: a ‘Holarctic clade’ (HOC) and a ‘Middle American clade’ (MAC). The HOC consists of the European S. striatulum Emery sister to two well‐supported groups, the informal ‘debile’ and ‘brevicorne’ clades. The ‘brevicorne’ clade is entirely Nearctic, whereas the ‘debile’ clade includes both Nearctic and Palaearctic representatives. The MAC occurs from the southern United States to northern South America and, with the exception of S. huachucanum Smith, is almost completely isolated geographically from the HOC. It includes a depauperate northern clade and the ‘MAC core’, which is a diverse assemblage of wet forest adapted species found throughout Central America. Divergence dating and biogeographic reconstruction show that Stenamma is most likely to have originated in the Nearctic at the Eocene–Oligocene boundary (∼35 Ma) and diversified more rapidly at 16 and 8 Ma for the HOC and MAC, respectively. Potential environmental factors affecting the evolution of Stenamma include the intense global cooling of the late Eocene combined with aridification and mountain building. The phylogenetic results are discussed in relation to the current Stenamma species groups and several new morphological characters are presented to help in identification.
Use of immune function test in monitoring immunosuppression in liver transplant recipients
Authors: Te Helen S. , Dasgupta Kathleen A. , Cao Dingcai , Satoskar Rohit , Mohanty Smruti R. , Reau Nancy , Millis James Michael , Jensen Donald M.
Published: May 2012

Immune function test (Immuknow™) is a measure of cell‐mediated immunity based on peripheral CD4+ T cell adenosine triphosphate activity (desired range, 225–525 ng/mL). We evaluated the role of immune function test (IFT) in monitoring and adjustment of immunosuppression in orthotopic liver transplant (OLT) recipients. A total of 289 IFTs were obtained from 171 patients from March 2007 to June 2008. Graft/patient status was classified as stable, serious infection, or malignancy. IFT levels were analyzed with duration of follow‐up after OLT, graft/patient status, and the presence of hepatitis C (HCV) infection. The mean age was 54 ± 14 yr, with 62% men. The median follow‐up was 65 (2–249) months. Mean IFT levels were significantly lower in patients who were <24 months than in those ≥24 months post‐OLT (220 ± 19.5 vs. 257 ± 11.3 ng/mL, p = 0.03). Clinically stable patients had higher IFT levels than those with serious infection or malignancy (254 ± 11.1 vs. 162.5 ± 23.9, p < 0.001). HCV‐infected patients had lower IFT levels than uninfected patients (206.7 ± 15.7 vs. 273 ± 12.0 ng/mL, p < 0.001). Immunosuppression was reduced in 58 patients with IFT levels <225 ng/mL, and 90% maintained stable graft function after a median follow‐up of 22 (1–39) months. IFT may be a useful tool in monitoring and lowering of immunosuppression in long‐term OLT recipients.
Host and environmental factors influencing respiratory secretion of pro‐wheezing biomarkers in preterm children
Authors: Matías Vanesa , San Feliciano Laura , Fernández Jose E. , Lapeña Santiago , Garrido Estibaliz , Ardura Julio , Soga Maria José , Aragón María Paz , Remesal Ana , Benito Francisca , Andrés Jesús , Centeno Fernando , Marugán Victor , Bachiller Rosario , Bermejo‐Martin Jesus F.
Published: May 2012

To cite this article: Matías V, San Feliciano L, Fernández JE, Lapeña S, Garrido E, Ardura J, Soga MJ, Aragón MP, Remesal A, Benito F, Andrés J, Centeno F, Marugán V, Bachiller R, Bermejo‐Martin JF. Host and environmental factors influencing respiratory secretion of pro‐wheezing biomarkers in preterm children. Pediatric Allergy Immunology 2012: 23: 441–447.

Cytokines are actively secreted by the respiratory mucosa of preterm children and participate in the pathogenesis of wheezing. This study aimed to identify the factors that could potentially influence respiratory secretion of cytokines in these children. A nasopharyngeal aspirate (NPA) was collected from 77 preterm children 1 yr after birth. NPAs from 14 healthy, 1‐yr‐old term children were collected in parallel. 27 cytokines were measured in the NPAs using a multiplex assay. Multivariate stepwise regression analysis with Bonferroni correction evidenced that the variable [daycare attendance] was associated with higher levels of [monocyte chemoattractant protein‐1 (MCP‐1), IL‐6, vascular endothelial growth factor (VEGF), IL‐1β, IL‐10, tumor necrosis factor (TNF)‐α]; [male sex] with higher levels of (MCP‐1, VEGF, and IL‐1β); [smokers at home] was associated with higher levels of MCP‐1 (p < 0.0013). In turn, [prophylaxis with palivizumab] was associated with lower levels of (IL‐6, IL‐7) (p < 0.0013). All these mediators participate in the pathogenesis of asthma and recurrent wheezing. Preterm children secreted higher levels of chemokines (interferon‐gamma inducible protein‐10, macrophage inflammatory protein‐1α, Eotaxin, MCP‐1), growth factors (platelet‐derived growth factor‐bb, VEGF, fibroblast growth factor‐basic, granulocyte macrophage colony‐stimulating factor), Th1 (IL12, interferon‐γ), Th2 (IL‐9, IL‐13), Th17 (IL‐6, IL‐17) cytokines, and immunomodulatory mediators (IL1RA and granulocyte colony‐stimulating factor) than term children. In conclusion, we have identified for the first time a group of individual and environmental factors influencing respiratory secretion of cytokines in preterm children at the long term after birth. To know these factors could help to prevent the instauration of conditions linked to the appearance of chronic respiratory diseases such as wheezing or asthma.
Health‐related quality of life does not explain the protective effect of farming on allergies
Authors: Stöcklin Laura , Loss Georg , von Mutius Erika , Genuneit Jon , Horak Elisabeth , Braun‐Fahrländer Charlotte ,   on behalf of the GABRIELA study group
Published: May 2012

To cite this article: Stöcklin L, Loss G, von Mutius E, Genuneit J, Horak E, Braun‐Fahrländer C. Health‐related quality of life does not explain the protective effect of farming on allergies. Pediatr Allergy Immunol 2012: 23: 519–521.

Background:  Numerous studies report a protective effect of farming against allergic diseases. Some specific underlying exposures contributing to this effect have recently been described in the GABRIEL survey. So far, psycho‐social factors have not been included in these analyses.

Methods:  In order to assess the potential influence of health‐related quality of life (HRQOL) on the protective effect of farming, 8259 school aged children from the European GABRIEL study answered questions concerning farming and allergic diseases, as well as validated questions about HRQOL.

Results:  Farm children reported higher HRQOL than non farm children. However, HRQOL did not modify the protective effect of farming against allergies. Children with allergic diseases reported significantly lower HRQOL scores suggesting that the higher HRQOL of farm children was in part explained by the lower prevalence of these diseases among farm children.

Conclusion:  Although farm children reported higher HRQOL scores than did non‐farm children, HRQOL did not explain the protective effect of farming against allergic diseases. The relationship between allergic diseases and HRQOL is likely bidirectional and needs to be assessed prospectively.
Few associations between high‐sensitivity C‐reactive protein and environmental factors in 4.5‐year‐old children
Authors: Mustonen Kirsi , Keski‐Nisula Leea , Vaarala Outi , Pfefferle Petra Ina , Renz Harald , Riedler Josef , Dalphin Jean‐Charles , Buechele Gisela , Lauener Roger , Braun‐Fahrländer Charlotte , von Mutius Erika , Pekkanen Juha ,   the PASTURE Study Group
Published: May 2012

To cite this article: Mustonen K, Keski‐Nisula L, Vaarala O, Pfefferle PI, Renz H, Riedler J, Dalphin J‐C, Buechele G, Lauener R, Braun‐Fahrländer C, von Mutius E, Pekkanen J and the PASTURE Study Group. Few associations between high‐sensitivity C‐reactive protein and environmental factors in 4.5‐year‐old children. Pediatr Allergy Immunol 2012: 23: 522–528.

Background:  Low‐grade inflammation in early childhood might protect from allergic diseases later in life. Our aim was to examine the effects of different environmental factors on low‐grade inflammation measured with serum high‐sensitivity C‐reactive protein (hsCRP) at the age of 4.5 years.

Methods:  The high‐sensitivity CRP values (n = 653) and serum‐specific IgE concentrations were measured from 4.5‐year‐old children in rural areas in five European countries (Austria, Finland, France, Germany, and Switzerland). Children belonged to the prospective multi‐center PASTURE birth cohort. Data on early and current farming environment and domestic animal exposure were collected by questionnaires.

Results:  Females as well as obese or very obese children at age of 4.5 years had higher hsCRP values than males (aOR 1.84 95% CI 1.27–2.66) and healthy weight children (aOR 4.47 95% CI 1.94–10.31), respectively. Levels were lowest in the summer. Few associations were detected between hsCRP values and farm environmental factors or atopic sensitization. However, there was evidence of children with low levels of hsCRP (below the detection limit) who had increased prevalence of sensitization to inhaled and seasonal allergens. Among non‐sensitized children, spending time in stables was associated with reduced hsCRP (15 min–10 h aOR 0.40 95% CI 0.16–0.96 and ≥10 h aOR 0.25 95% CI 0.07–0.90), and among sensitized children, maternal smoking was associated with higher hsCRP values (aOR 2.51 95% CI 1.12–5.59).

Conclusion:  We found few associations between early environmental farming factors and hsCRP levels, and between hsCRP levels and atopic sensitization in 4.5‐year‐old children. However, our results suggest that the role played by the environmental factors in low‐grade inflammation may differ between sensitized and non‐sensitized children.
Primary school teachers’ knowledge about and attitudes toward anaphylaxis
Authors: Ercan Hulya , Ozen Ahmet , Karatepe Hande , Berber Mustafa , Cengizlier Reha
Published: May 2012

To cite this article: Ercan H, Ozen A, Karatepe H, Berber M, Cengizlier R. Primary school teachers’ knowledge about and attitudes toward anaphylaxis. Pediatr Allergy Immunol 2012: 23: 428–432.

Background:  One in 10,000 children experiences an anaphylactic attack, every year. It has been demonstrated that 82% of these attacks occur in children of school age and that most of the attack‐related deaths have occurred in schools. In this study, we aimed to investigate primary school teachers’ knowledge about and attitudes toward anaphylaxis.

Method:  A total of 237 teachers were questioned: 91 working in elementary state schools and 146 in private schools. A questionnaire was completed to obtain data on their knowledge of anaphylaxis and the availability of emergency treatment facilities in schools.

Results:  Fifty‐two percent of the teachers knew which students had an allergic disease. When questioned about agents that can potentially cause anaphylaxis, the most significant causes were thought to be pollen by 54% of the teachers, food by 47%, mites by 40%, and drugs by 30%. Of foods, eggs (30.4%) and strawberries (25.3%) were thought to be the two leading causes. The teachers’ responses on what would be their initial reaction in the event of an anaphylactic reaction were: he/she would give first aid in 24.3%, notify the school nurse in 39.7%, and call the emergency services in 19.8%. Only 10% were aware of an epinephrine autoinjector, and only 4% knew where to apply it. While 28% of the teachers reported that they had been informed about anaphylaxis previously, most had formed their ideas from brochures or the media. While 25% of the teachers knew all of the symptoms of anaphylaxis, 54% knew some, and 21% none. Only 6% of the teachers reported that there was a management plan for anaphylaxis in their schools.

Conclusion:  This study shows that primary school teachers are not well informed about anaphylaxis. Teachers should be given training on the subject, and there should be a re‐evaluation of school and health policies with a wider global perspective. There is an urgent need to inquire into the allergy management plans and policies in schools and to develop teacher education organizations on the subject.
Relationship between rhinitis and nocturnal cough in school children
Authors: Higuchi Osamu , Adachi Yuichi , Itazawa Toshiko , Ito Yasunori , Yoshida Koichi , Ohya Yukihiro , Odajima Hiroshi , Akasawa Akira , Miyawaki Toshio
Published: May 2012

To cite this article: Higuchi O, Adachi Y, Itazawa T, Ito Y, Yoshida K, Ohya Y, Odajima H, Akasawa A, Miyawaki T. Relationship between rhinitis and nocturnal cough in school children. Pediatr Allergy Immunol 2012: 23: 562–566.

Background:  There is a complex relationship between rhinitis, asthma, and nocturnal cough.

Methods:  To evaluate whether rhinitis is an important risk factor for nocturnal cough and whether this effect is independent of asthma, we analyzed data collected using the International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire in a population‐based nationwide survey. A child who had experienced a dry cough at night in the past 12 months in the absence of a cold was defined as having nocturnal cough.

Results:  After excluding 11,475 records with incomplete data, data from 136,506 children were analyzed. Nocturnal cough was significantly more prevalent in children with current rhinitis compared with children without rhinitis. The association between rhinitis and nocturnal cough was significant in children who had current asthma (adjusted OR [95% CI]: 2.26 [2.00–2.56] in children aged 6–7 yr, 1.90 [1.58–2.30] in those aged 13–14 yr, and 1.86 [1.60–2.19] in those aged 16–17 yr), and this association was even higher among children who had no asthma (adjusted OR [95% CI]: 3.65 [3.36–3.97] in children aged 6–7 yr, 3.05 [2.79–3.32] in those aged 13–14 yr, and 2.69 [2.51–2.88] in those aged 16–17 yr).

Conclusions:  There was a close association between rhinitis and nocturnal cough in young children through adolescents, and this effect was independent of asthma. Upper airways should be examined in children with nocturnal cough.