bluuebunny/crossref_metadata_2025 huggingface dataset:
A Label-Free Colorimetric Biosensor for 17β-Estradiol Detection Using Nanoparticles Assembled by Aptamer and Cationic Polymer
Authors: Zhang Dongwei , Zhang Weilin , Ye Jiayun , Zhan Shenshan , Xia Bing , Lv Jing , Xu Hanchu , Du Gaoshang , Wang Lumei
Published: June 2015

Concern is mounting regarding the human health and environment effects of 17β-estradiol (E2), a natural oestrogen excreted by human beings and animals. In this paper, a sensitive and selective biosensor for the detection of E2 using gold nanoparticles (AuNPs), label-free E2-specific aptamer, and poly(diallyldimethylammonium chloride) (PDDA) was developed. In the absence of E2, PDDA can electrostatically interact with E2-specific aptamer, and the charge responsible for inducing AuNPs aggregation was destroyed. However, the introduction of E2 can specifically interact with the aptamer to form E2–aptamer complex so that PDDA can aggregate AuNPs and cause a remarkable change in colour from wine red to blue, which enables colorimetric detection of E2 with selectivity and a detection limit of 1.57 nM.
Iron(III)-induced activation of chloride from artificial sea-salt aerosol
Authors: Wittmer Julian , Bleicher Sergej , Ofner Johannes , Zetzsch Cornelius
Published: July 2015

Environmental context
Inorganic, natural aerosols (sea-salt, mineral dust, glacial flour) and contributions of anthropogenic components (fly ash, dust from steel production and processing, etc.) contain iron that can be dissolved as FeIII in saline media. This study investigates photochemical processes in clouds and aerosols producing gas-phase Cl as a function of salt- and gas-phase composition employing a simulation chamber. Atomic Cl may contribute to the oxidative capacity of the troposphere, and our findings imply local sources.

Abstract
Artificial sea-salt aerosol, containing FeIII at various compositions, was investigated in a simulation chamber (made of Teflon) for the influence of pH and of the tropospheric trace gases NO2, O3 and SO2 on the photochemical activation of chloride. Atomic chlorine (Cl) was detected in the gas phase and quantified by the radical clock technique. Dilute brines with known FeIII content were nebulised until the relative humidity reached 70–90%. The resulting droplets (most abundant particle diameter: 0.35–0.46µm, initial surface area: up to 3×10–2cm2cm–3) were irradiated with simulated sunlight, and the consumption of a test mixture of hydrocarbons was evaluated for Cl, Br and OH. The initial rate of atomic Cl production per aerosol surface increased with FeIII and was ~1.9×1018 atoms cm–2s–1atCl–/FeIII=13. The presence of NO2 (~20 ppb) increased it to ~7×1018 atoms cm–2s–1, the presence of O3 (630 ppb) to ~9×1018 atoms cm–2s–1 and the presence of SO2 at 20 and 200 ppb inhibited the release slightly to ~1.7 and ~1.1×1018 atoms cm–2s–1. The observed production of atomic Cl is discussed with respect to pH and speciation of the photolabile aqueous FeIII complexes.
Investigation of species boundaries and relationships in the Asplenium paleaceum complex (Aspleniaceae) using AFLP fingerprinting and chloroplast and nuclear DNA sequences
Authors: Ohlsen Daniel J. , Perrie Leon R. , Shepherd Lara D. , Brownsey Patrick J. , Bayly Michael J.
Published: June 2015

Species boundaries and relationships were investigated in the Asplenium paleaceum (Aspleniaceae) species complex from eastern Australia, using AFLP fingerprinting and chloroplast trnL–trnF and rps4–trnS and nuclear pgiC DNA sequences. Phenetic analyses of AFLP data resulted in the following five distinct groups: (1) A. carnarvonense, (2) A. bicentenniale (including nearby collections originally identified as A. paleaceum), (3) A. paleaceum with both aborted and normal spores, (4) one population of putative tetraploid A. attenuatum var. indivisum from south Queensland, and (5) remaining octoploid A. attenuatum populations and several putative hybrids. Taxonomic revision of this complex will require morphological re-circumscription of the current species and recognition of a new species if these AFLP groups are taken to represent separate species. The chloroplast regions, morphology and pgiC together provide good evidence that an Asplenium of unconfirmed identity, A. sp. ‘Kroombit Tops’, is an allopolyploid with a species of the A. paleaceum chloroplast clade, probably A. paleaceum, and distantly related A. polyodon as parents. Further study is required to determine the complete ancestry of the other species of the A. paleaceum complex.
Distribution of morphological diversity within widespread Australian species of Poa (Poaceae, tribe Poeae) and implications for taxonomy of the genus
Authors: Birch Joanne L. , Berwick Freya M. , Walsh Neville G. , Cantrill David J. , Murphy Daniel J.
Published: June 2015

Taxonomic uncertainty exists regarding the circumscription of the following seven phenotypically similar Australian species: Poa crassicaudex Vickery, P. hookeri Vickery, P. labillardierei Steud., P. phillipsiana Vickery, P. poiformis (Labill.) Druce, P. porphyroclados Nees (including P. serpentum Nees) and P. sieberiana Spreng. Multivariate ordination and clustering analyses of morphological data were conducted and the distribution of morphological diversity among taxa was assessed for congruence with current taxonomic boundaries. One-way analyses of variance and Tukey’s honest significant difference tests were applied to identify continuous characters that differentiate taxa. Utility of morphological characters was assessed in light of the distribution of variation among and within taxa. Revisions of P. labillardierei, P. porphyroclados and P. sieberiana circumscriptions are proposed. Accounting for nomenclatural priority, proposed revisions include recognition of P. porphyroclados vars. acris, labillardierei, porphyroclados, and. serpentum, P. sieberiana var. cyanophylla Vickery at species rank, and P. phillipsiana at varietal rank within P. sieberiana. Species boundaries are supported by leaf, culm, panicle, spikelet and floret dimensions. The present study enables increased accuracy in taxonomic identifications for Poa species that are keystones in a range of grassland vegetation types, including critically endangered natural temperate grassland and eucalypt woody grassland ecosystems, therefore contributing to the effective biodiversity monitoring and management of these ecosystems.
A revision of Chara sect. Charopsis (Characeae: Charophyceae) in Australia, including specimens collected for Bush Blitz
Authors: Casanova Michelle T.
Published: June 2015

Australian species of Chara L. sect. Charopsis (Kütz.) Leonh. are revised. Multivariate analysis supports recognition of four species: Chara braunii C.C.Gmel., C. evanida Casanova, C. karolii Casanova and C. muelleri (A.Braun) F.Muell. These taxa are described and illustrated, and a key is provided.
A chloroplast phylogeny of Zieria (Rutaceae) in Australia and New Caledonia shows widespread incongruence with species-level taxonomy
Authors: Barrett Rosemary A. , Bayly Michael J. , Duretto Marco F. , Forster Paul I. , Ladiges Pauline Y. , Cantrill David J.
Published: June 2015

This study presents a molecular phylogeny of Zieria Sm., a genus of shrubs and small trees, with 59 species in Australia and one endemic to New Caledonia. The phylogeny is based on four cpDNA markers and 116 samples representing all species of Zieria except one, and the monotypic outgroup Neobyrnesia suberosa. The New Caledonian species, Z. chevalieri, was resolved as sister to a well supported clade of all Australian taxa. There was widespread incongruence between the cpDNA tree and species-level taxonomy, with 14 species shown as polyphyletic or paraphyletic. These included widespread species (e.g. Z. smithii and Z. arborescens, each falling in at least four well supported clades) and some with narrow geographic ranges (e.g. Z. alata and Z. oreocena). No species represented by three or more samples was resolved as monophyletic. We suggest that a combination of factors explains this incongruence, including regional cpDNA introgression (chloroplast capture), incomplete lineage sorting and inappropriate taxonomic boundaries. The cpDNA phylogeny provides useful insight into the evolution of Zieria but, because of its complexity, does not provide a clear basis for assessing phylogenetic relationships and monophyly of taxa. Better understanding of relationships, taxon limits and evolutionary processes in Zieria will require comparisons with nuclear DNA markers and critical assessment of morphological and genetic variation in widespread species.
Molecular data consistently recover a 'Queensland clade' of Synostemon Phyllanthaceae, Phyllantheae) with distinctive floral morphology
Authors: Telford Ian R. H. , Pruesapan Kanchana , van Welzen Peter C. , Bruhl Jeremy J.
Published: June 2015

Molecular analysis of the newly reinstated genus Synostemon F.Muell. (Phyllanthaceae, Phyllantheae), using ITS sequence data from the now densely sampled genus, confirmed that the previously recognised ‘Queensland clade’ consists of Synostemon albiflorus (F.Muell. ex Müll.Arg.) Airy Shaw, S. sphenophyllus Airy Shaw, Sauropus podenzanae (S.Moore) Airy Shaw and the undescribed Synostemon spinescens, sp. nov. ined., the latter being validated here as S. spinosus I.Telford & J.J.Bruhl. Morphological synapomorphies for the clade are as follows: linear, apiculate anthers that are connivent but only basally connate, and thickened, clavate, recurved stigmas. A new combination is provided under Synostemon for Sauropus podenzanae as Synostemon podenzanae (S.Moore) I.Telford & Pruesapan and Sauropus convallarioides J.T.Hunter & J.J.Bruhl is formally placed in synonymy under Synostemon sphenophyllus. Descriptions, distributional data and notes on ecology and conservation status are provided for these species. Phyllanthus albiflorus F.Muell. ex Müll.Arg., the basionym of Synostemon albiflorus, is lectotypified.
Four new species of Goodeniaceae from Western Australia, including the smallest species in the family, a putative seed-article elaiosome and possible floral mimicry in Lechenaultia
Authors: Barrett Russell L. , Barrett Matthew D.
Published: June 2015

Goodenia cravenii R.L.Barrett & M.D.Barrett, G. maretensis R.L.Barrett, Goodenia heterotricha M.D.Barrett & R.L.Barrett and Lechenaultia mimica M.D.Barrett & R.L.Barrett are described as new species from the northern Kimberley region of Western Australia. Goodenia cravenii (subg. Goodenia sect. Amphichila DC.) is the smallest species known in the family. Goodenia maretensis (subg. Goodenia sect. Goodenia subsect. Ebracteolatae K.Krause) is known only from the Maret Islands group in the Bonaparte Archipelago. Goodenia heterotricha (subg. Goodenia sect. Goodenia subsect. Ebracteolatae K.Krause) was discovered during a Bush Blitz survey on Home Valley Station in May 2014. Modified keys to these species are presented. Lechenaultia mimica (sect. Latouria (Endl.) Benth.) is known only from the Harding Range and may represent the first instance of floral mimicry to be reported in the genus Lechenaultia. Seed article micromorphology in tropical annual species of Lechenaultia R.Br. is discussed and a key to species is provided. A putative elaiosome, the first report for the genus, was observed on the seed article of L. ovata. All species described here are of conservation priority and are illustrated.
Additions to the genus Trapelia (Trapeliaceae: lichenised Ascomycetes)
Authors: Kantvilas Gintaras , Leavitt Steven D. , Elix John A. , Lumbsch H. Thorsten
Published: June 2015

Two new species in the genus Trapelia, namely, T. calvariana Kantvilas & Lumbsch from the Tasmanian highlands and T. thieleana Kantvilas & Lumbsch from south-western Western Australia, are described. Examination of ascus types and analyses of DNA-sequence data confirmed the inclusion of these taxa in Trapelia sensu lato, but raised questions concerning the homogeneity of the genus as currently circumscribed and, in particular, the generic classification of T. lilacea Kantvilas & Elix.
Phylogeny of the fern family Aspleniaceae in Australasia and the south-western Pacific
Authors: Ohlsen Daniel J. , Perrie Leon R. , Shepherd Lara D. , Brownsey Patrick J. , Bayly Michael J.
Published: June 2015

Aspleniaceae is one of the largest fern families. It is species-rich in Australasia and the south-western Pacific (ASWP), where approximately 115 species occur. In the current study, the chloroplast regions rbcL, trnL–trnF and rps4–trnS were sequenced for 100 Aspleniaceae samples from ASWP. These data were combined with published sequences for species from New Zealand and other regions for phylogenetic analyses. Species of Aspleniaceae from ASWP were placed in six of the eight previously identified inter-continental clades. The majority of species from ASWP were placed in two of these clades, with the remaining four clades each being represented by three or fewer species. Strong biogeographic affinities with South-east Asia were observed and immigration, rather than local radiations of endemic taxa, appears to have made a more important contribution to patterns of diversity in ASWP. This study supports the current taxonomic practice of recognising two genera, Asplenium L. and Hymenasplenium Hayata, in Aspleniaceae, and identifies future taxonomic work required for the family in this region, including potential synonymising of species, and revision of species complexes or widespread species that are demonstrably non-monophyletic.
Lomandra marginata (Asparagaceae), a shy-flowering new species from south-western Australia
Authors: Macfarlane Terry D. , Conran John G.
Published: June 2015

Lomandra marginata T.D.Macfarl. & Conran is described as a new species and illustrated by photographs and a distribution map. Recognised initially from vegetative plants during a biological survey at Lochada Station, it was realised subsequently that the species is widespread from Geraldton to Corrigin. However, it apparently flowers only occasionally under favourable conditions, so earlier collections were mostly vegetative. Lomandra marginata is placed in L. series Sparsiflorae on the basis of possessing a narrow floral bract that does not encircle the pedicel and a bracteole, when present, offset rather than opposite the bract. It has distinctive membranous leaf margins resembling those of the related genus Chamaexeros and the longest pedicels in the genus, mostly 10–16mm long, on which are borne white flowers resembling those of L. effusa (Lindl.) Ewart. Although L. effusa is the most similar species in flower and inflorescence and is also a member of L. series Sparsiflorae, it differs vegetatively by having distinctly two-toothed leaf tips.
Two new species of Tricoryne (Hemerocallidaceae) from the Midwest region of Western Australia
Authors: Macfarlane Terry D. , Keighery Gregory J.
Published: June 2015

Field studies have provided an improved understanding of a known undescribed species of Tricoryne R.Br. and also shown that two or three separate species are included in an existing taxonomic concept. Two new species are described here, namely, T. tuberosa Keighery & T.D.Macfarl. and T. soullierae T.D.Macfarl. & Keighery. Tricoryne tuberosa has an extensive range in the northern wheatbelt and adjacent pastoral areas of south-western Western Australia. It has large root tubers, the leaves are withered at flowering time, and it forms clonal groups by long rhizomatous shoots. Tricoryne soullierae has a restricted distribution in remnant vegetation in the northern wheatbelt. It has fibrous roots and is conspicuously leafy when flowering.
Taxonomic status and distribution of the critically endangered Christmas Island spleenwort (Asplenium listeri, Aspleniaceae): it is not as rare as we thought
Authors: Ohlsen Daniel J. , Perrie Leon R. , Shepherd Lara D. , Bayly Michael J.
Published: June 2015

Asplenium listeri C.Chr. has been considered endemic to Christmas Island and is one of only two fern species listed as Critically Endangered under Australia’s Environment Protection and Biodiversity Conservation Act. Its status as a distinct species has been questioned because of morphological similarity to the widespread A. polyodon G.Forst., which also occurs on Christmas Island. Molecular analyses revealed that A. listeri and plants attributed to A. polyodon from coastal limestone in New Caledonia and Vanuatu share the same rbcL, trnL–trnF and rps4–trnS haplotype and that other samples of A. polyodon in Australia and the south-western Pacific belong to three separate molecular lineages. One of these lineages is formed by epiphytic A. polyodon from Christmas Island and has a chloroplast haplotype closely related to that of A. listeri, differing by four mutations. The A. listeri haplotype and each of the three A. polyodon lineages are associated with morphological characters and are all worthy of recognition as separate species. Asplenium listeri is here expanded to include limestone dwelling populations in the Pacific previously assigned to A. polyodon. This greatly extends the geographic range of A. listeri, and its conservation status should be revised accordingly. Application of correct names to all species in the A. polyodon complex requires further molecular sampling throughout its geographic range and clarification of how type material relates to each of the molecular groups.
A new, rare species of Brachychiton from Fish River Station, Northern Territory
Authors: Cowie Ian D. , Guymer Gordon P.
Published: June 2015

Brachychiton chrysocarpus Cowie & Guymer from Fish River Station in the north-western part of the Northern Territory is described as a new species. It is compared with B. tuberculatus Guymer and B. xanthophyllus Guymer, but differs especially in the softer finer indumentum, shorter caducous stipules, slender paniculate, open inflorescence, the weakly tuberculate follicles and other characters. It appears to be restricted to Eucalyptus tectifica woodland on slopes of ~17° associated with ferruginous sandstone of the Waterbag Creek formation. Its conservation status is discussed and assessed.
Bush Blitz: journeys of discovery in the Australian outback
Authors: Preece Michael , Harding Jo , West Judy G.
Published: June 2015

Bush Blitz is an innovative and ambitious partnership between the Australian Biological Resources Study, BHP Billiton Sustainable Communities and the Earthwatch Institute (Australia) that aims to fill critical gaps in the knowledge of the biodiversity of Australia (http://www.bushblitz.org.au). Since its inception in 2009, over 900 putative new species of animals and plants have been discovered in Australian conservation reserves. As a unique approach to surveys in often-remote areas of the Australian outback, the Bush Blitz program has been highly successful and highlights the need for ongoing exploration and research to adequately document the biodiversity of Australia. This special issue of Australian Systematic Botany describes some of the newly discovered species and showcases the botanical results of the Bush Blitz program.
Developmental investigation of age at sexual debut and subsequent sexual risk behaviours: a study of high-risk young black males
Authors: Crosby Richard , Geter Angelica , Ricks JaNelle , Jones Jamal , Salazar Laura F.
Published: June 2015

Background The purpose of this study was to identify unmediated associations of early sexual debut (ESD) on the current safer sex practices of young Black men (YBM). Methods: A cross-sectional study of YBM (n = 697) attending clinics treating sexually transmissible diseases (STIs) in three cities was conducted. ESD was dichotomised at the age of 13 years and under. A series of regression models were used to test the moderating effects of ESD and perceived parental monitoring (PPM). A regression model also tested the effect of years of sexual experience (YSE) on sexual risk behaviours, while controlling for ESD. Results: Mean age of debut was 13.95 years. ESD results varied with significance for pregnancy (P < 0.001), sexual partners (P < 0.001), and ever having chlamydia (assessed by self report), but this final association was only found for older males (P = 0.03). PPM held no moderating effect on any of the sexual risk outcomes. YSE was correlated with an increase in recent unprotected vaginal sex (AOR = 1.19, 95%CI = 1.10–1.27) and having a pregnant partner at the time of enrolment (AOR = 1.30, 95%CI = 1.17–1.43). Conclusions: The findings provide mixed evidence for unmediated associations of ESD among young Black males. The study strongly posits that ESD may actually be a mediating variable rather than a causal explanation for sexual risk. The findings also suggest that advancing YSE foster diminishing vigilance in safer sex practices. These outcomes should be utilised to inform intervention development.
Rate of repeat diagnoses in men who have sex with men for Chlamydia trachomatis and Neisseria gonorrhoeae: a retrospective cohort study
Authors: Marinelli Tess , Chow Eric P. F. , Tomnay Jane , Fehler Glenda , Bradshaw Catriona S. , Chen Marcus Y. , Forcey Dana S. , Fairley Christopher K.
Published: June 2015

Background
Sexually transmissible infections (STIs) have increased rapidly among men who have sex with men (MSM). One of the most effective strategies to control STIs is partner notification. Inadequate partner notification may be associated with high rates of repeat diagnoses with STIs. The aim of this study is to estimate and compare the rate of chlamydia and gonorrhoea infection following primary infection to the overall clinic rate. Methods: A retrospective cohort analysis of MSM attending the Melbourne Sexual Health Clinic was conducted. For both infections, the overall incidence and that following diagnosis and treatment was calculated. Results: Of the 13053 MSM, the incidence of diagnoses for chlamydia and gonorrhoea was 8.5 (95% CI: 8.2–8.9) and 6.2 (95% CI: 5.9–6.5) per 100 person-years, respectively. Seventy per cent of chlamydia and 64% of gonorrhoea cases were retested at 10–365 days after diagnosis and treatment. Following diagnosis and treatment of chlamydia, the rate ratio in these individuals in the first quarter was 16- and 8-fold higher for chlamydia and gonorrhoea, respectively, compared with the background incidence of diagnoses. Similarly, following diagnosis and treatment of gonorrhoea, the rate ratio in these individuals in the first quarter was 18- and 10-fold higher for gonorrhoea and chlamydia, respectively. Conclusions: These data suggest that approximately half of MSM who test positive for chlamydia or gonorrhoea within 90 days after an initial infection represent contact with either a previous sexual partner or member of the same sexual network, the remainder representing the particularly high STI risk for these MSM.
Influence of stigma and homophobia on mental health and on the uptake of HIV/sexually transmissible infection services for Cameroonian men who have sex with men
Authors: Cange Charles W. , LeBreton Matthew , Billong Serge , Saylors Karen , Tamoufe Ubald , Papworth Erin , Yomb Yves , Baral Stefan
Published: June 2015

Background
Men who have sex with men (MSM) in Cameroon consistently face significant stigma and discrimination. The urban HIV prevalence in MSM is estimated at 35%. This study investigates the effect of stigma, discrimination and alienation on Cameroonian MSM’s engagement of the HIV treatment cascade. Methods: Qualitative interviews were semi-structured using a guide. Participants in Douala, Ngaoundere, Bamenda, Bertoua and Yaoundé were asked to describe the MSM social and structural context, MSM knowledge of existing HIV-related services in public and MSM-focussed non-governmental organisation (NGO) clinics. Using a codebook, coded text was extracted from 40 transcripts with Microsoft Word Macros. These texts were analysed for recurring themes that were developed into results. Results: There were three main themes that emerged. First, among those MSM participants seeking HIV services, many commonly reported experiences of discrimination and physical violence outside the healthcare setting. Second, a few respondents used services provided by the Ministry of Health and local NGOs. However, most participants observed limited clinical and cultural competency of public clinic staff. Third, MSM declared that lack of social support and healthcare access caused them much stress. Several individuals recounted their alienation greatly discouraged them from seeking HIV prevention, treatment and care services. Conclusions: Community-level and public healthcare-related stigma impacts the mental wellbeing of Cameroonian MSM. Alienation among MSM also represents a common obstacle to the uptake of MSM-oriented HIV/AIDS services. Improving provider cultural and clinical competency among Cameroonian health care workers combined with a broader stigma-reduction intervention for Cameroonian healthcare may increase the uptake of HIV prevention, treatment and care among MSM.
Acceptance of and experiences utilising expedited partner therapy among African-American juvenile girls
Authors: Ricks JaNelle M. , Swartzendruber Andrea L. , Sales Jessica M. , Boyce Lorin S. , DiClemente Ralph J. , Rose Eve
Published: June 2015

Background
The aim of this study was to describe acceptance of and experiences utilising expedited partner therapy (EPT) among African-American girls recruited from short-term juvenile detention centres. Methods: Ninety-five detained African-American girls (aged 13–17 years) completed audio computer-assisted self-interviews (ACASI) and self-collected vaginal swab specimens assayed for chlamydia and gonorrhoea. EPT was offered to sexually transmissible infection (STI)-positive participants (n = 51); follow-up phone interviews assessed medication delivery to partners. Summary statistics described EPT acceptance frequency. Generalised estimating equations assessed correlates of acceptance. Nine semi-structured interviews elicited EPT experiences. Results: EPT was offered 69 times, accepted by 70% (n = 37) girls and provided to 68% (n = 36) of girls. Acceptance was significantly associated with sexual risk behaviours such as infrequent partner STI prevention discussion (OR = 3.2, 95% CI: 1.0,–10.1, P = 0.048) and ≥ 4 lifetime sex partners (OR = 3.3, 95% CI: 1.0–11.0, P = 0.048). Discontinued relationships were the most common barrier to EPT acceptance. Emergent interview themes included sense of responsibility, which appeared to motivate acceptance and help overcome identified discomfort with partner disclosure conversations. Conclusions: Future research is needed to determine EPT efficacy among African-American juvenile populations and feasibility of its use outside of research settings.
Oil palm deserves government attention in Brazil
Authors: Moreira José R , Goldemberg José
Published: July 2015

Englund et al (2015 Environ. Res. Lett.

10 044002) have recently analyzed biodiesel production from oil palm plantations as one possible way to mitigate climate change while providing cost effective results. They show that data for detailed quantification of biological carbon sequestration is available allowing a high confidence evaluation of positive impacts when oil palm plantation for food and biodiesel production is carried out in degraded, cultivated soil, and also with some varieties of natural vegetation in the Amazon. Nevertheless, economic risk associated with the future price of fossil fuels and uncertainties related with carbon subsidy are barriers. Here we discuss the assumptions under which such controversial proposal is based and suggest further analysis for Brazilian decision makers.
New operator inequalities in finite-dimensional vector spaces
Authors: Gordon Alexander
Published: July 2015

We establish some new operator inequalities in an

n
n

-dimensional vector space

X
X

equipped with a seminorm

‖
⋅
‖

\|\cdot \|

. Here is an example. If

A
A

is an invertible linear operator in

X
X

and  

ξ
\xi

is a vector, then
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="double-vertical-bar xi double-vertical-bar Superscript r Baseline less-than-or-equal-to sigma-summation Underscript 1 less-than-or-equal-to StartAbsoluteValue j EndAbsoluteValue less-than-or-equal-to StartBinomialOrMatrix n plus r minus 1 Choose r EndBinomialOrMatrix Endscripts double-vertical-bar upper A Superscript j Baseline xi double-vertical-bar Superscript r Baseline period">

‖
ξ

‖
r

≤

∑

1
≤

|

j

|

≤

(

n
+
r
−
1

r

)

‖

A
j

ξ

‖
r

.

\|\xi \|^r \le \sum _{1\le |j|\le {n+r-1\choose r}}\|A^j\xi \|^r.

\]
Some special cases have been known and used in mathematical physics.
Dynactin-dependent cortical dynein and spherical spindle shape correlate temporally with meiotic spindle rotation in Caenorhabditis elegans
Authors: Crowder Marina E. , Flynn Jonathan R. , McNally Karen P. , Cortes Daniel B. , Price Kari L. , Kuehnert Paul A. , Panzica Michelle T. , Andaya Armann , Leary Julie A. , McNally Francis J.
Published: July 2015

Oocyte meiotic spindles orient with one pole juxtaposed to the cortex to facilitate extrusion of chromosomes into polar bodies. In Caenorhabditis elegans, these acentriolar spindles initially orient parallel to the cortex and then rotate to the perpendicular orientation. To understand the mechanism of spindle rotation, we characterized events that correlated temporally with rotation, including shortening of the spindle in the pole-to pole axis, which resulted in a nearly spherical spindle at rotation. By analyzing large spindles of polyploid C. elegans and a related nematode species, we found that spindle rotation initiated at a defined spherical shape rather than at a defined spindle length. In addition, dynein accumulated on the cortex just before rotation, and microtubules grew from the spindle with plus ends outward during rotation. Dynactin depletion prevented accumulation of dynein on the cortex and prevented spindle rotation independently of effects on spindle shape. These results support a cortical pulling model in which spindle shape might facilitate rotation because a sphere can rotate without deforming the adjacent elastic cytoplasm. We also present evidence that activation of spindle rotation is promoted by dephosphorylation of the basic domain of p150 dynactin.
ISQuest: finding insertion sequences in prokaryotic sequence fragment data
Authors: Biswas Abhishek , Gauthier David T. , Ranjan Desh , Zubair Mohammad
Published: June 2015

Motivation: Insertion sequences (ISs) are transposable elements present in most bacterial and archaeal genomes that play an important role in genomic evolution. The increasing availability of sequenced prokaryotic genomes offers the opportunity to study ISs comprehensively, but development of efficient and accurate tools is required for discovery and annotation. Additionally, prokaryotic genomes are frequently deposited as incomplete, or draft stage because of the substantial cost and effort required to finish genome assembly projects. Development of methods to identify IS directly from raw sequence reads or draft genomes are therefore desirable. Software tools such as Optimized Annotation System for Insertion Sequences and IScan currently identify IS elements in completely assembled and annotated genomes; however, to our knowledge no methods have been developed to identify ISs from raw fragment data or partially assembled genomes. We have developed novel methods to solve this computationally challenging problem, and implemented these methods in the software package ISQuest. This software identifies bacterial ISs and their sequence elements—inverted and direct repeats—in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours, making it a valuable high-throughput tool for a global search of IS elements. We tested ISQuest on simulated read libraries of 3810 complete bacterial genomes and plasmids in GenBank and were capable of detecting 82% of the ISs and transposases annotated in GenBank with 80% sequence identity.

Contact: abiswas@cs.odu.edu
Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level
Authors: Gehrmann Thies , Reinders Marcel J.T.
Published: June 2015

Background: With more and more genomes being sequenced, detecting synteny between genomes becomes more and more important. However, for microorganisms the genomic divergence quickly becomes large, resulting in different codon usage and shuffling of gene order and gene elements such as exons.

Results: We present Proteny, a methodology to detect synteny between diverged genomes. It operates on the amino acid sequence level to be insensitive to codon usage adaptations and clusters groups of exons disregarding order to handle diversity in genomic ordering between genomes. Furthermore, Proteny assigns significance levels to the syntenic clusters such that they can be selected on statistical grounds. Finally, Proteny provides novel ways to visualize results at different scales, facilitating the exploration and interpretation of syntenic regions. We test the performance of Proteny on a standard ground truth dataset, and we illustrate the use of Proteny on two closely related genomes (two different strains of Aspergillus niger) and on two distant genomes (two species of Basidiomycota). In comparison to other tools, we find that Proteny finds clusters with more true homologies in fewer clusters that contain more genes, i.e. Proteny is able to identify a more consistent synteny. Further, we show how genome rearrangements, assembly errors, gene duplications and the conservation of specific genes can be easily studied with Proteny.

Availability and implementation: Proteny is freely available at the Delft Bioinformatics Lab website http://bioinformatics.tudelft.nl/dbl/software.

Contact:  t.gehrmann@tudelft.nl

Supplementary information: Supplementary data are available at Bioinformatics online.
Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff
Authors: Manter Daniel K. , Bakker Matthew G.
Published: July 2015

Motivation: In profiling the composition and structure of complex microbial communities via high throughput amplicon sequencing, a very low proportion of community members are typically sampled. As a result of this incomplete sampling, estimates of dissimilarity between communities are often inflated, an issue we term pseudo β-diversity.

Results: We present a set of tools to identify and correct for the presence of pseudo β-diversity in contrasts between microbial communities. The variably weighted Odum dissimilarity (DwOdum) allows for down-weighting the influence of either abundant or rare taxa in calculating a measure of similarity between two communities. We show that down-weighting the influence of rare taxa can be used to minimize pseudo β-diversity arising from incomplete sampling. Down-weighting the influence of abundant taxa can increase the sensitivity of hypothesis testing. OTUshuff is an associated test for identifying the presence of pseudo β-diversity in pairwise community contrasts.

Availability and implementation: A Perl script for calculating the DwOdum score from a taxon abundance table and performing pairwise contrasts with OTUshuff can be obtained at http://www.ars.usda.gov/services/software/software.htm?modecode=30-12-10-00.

Contact:  daniel.manter@ars.usda.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
An empirical analysis of the financial benefits of health information exchange in emergency departments
Authors: Yaraghi Niam
Published: June 2015

Objective To examine the impact of health information exchange (HIE) on reducing laboratory tests and radiology examinations performed in an emergency department (ED).

Materials and Methods The study was conducted in an ED setting in Western New York over a period of 2 months. The care of the patients in the treatment group included an HIE query for every encounter, while the care of other patients in the control group did not include such queries. A group of medical liaisons were hired to query the medical history of patients from an HIE and provide it to the ED clinicians. Negative binomial regression was used to analyze the effects of HIE queries on the number of performed laboratory tests and radiology examinations. The log files of the HIE system since 1 year before the ED admission were used to analyze the differences in outcome measures between the 2 groups of patients.

Results Ceteris paribus, HIE usage is associated with, respectively, 52% and 36% reduction in the expected total number of laboratory tests and radiology examinations ordered per patient at the ED.

Conclusions The results indicate that access to additional clinical data through the HIE will significantly reduce the number of laboratory tests and radiology examinations performed in the ED settings and thus support the ongoing HIE efforts.
Induced pluripotent stem cell technology for modelling and therapy of cerebellar ataxia
Authors: Watson Lauren M. , Wong Maggie M. K. , Becker Esther B. E.
Published: July 2015

Induced pluripotent stem cell (iPSC) technology has emerged as an important tool in understanding, and potentially reversing, disease pathology. This is particularly true in the case of neurodegenerative diseases, in which the affected cell types are not readily accessible for study. Since the first descriptions of iPSC-based disease modelling, considerable advances have been made in understanding the aetiology and progression of a diverse array of neurodegenerative conditions, including Parkinson's disease and Alzheimer's disease. To date, however, relatively few studies have succeeded in using iPSCs to model the neurodegeneration observed in cerebellar ataxia. Given the distinct neurodevelopmental phenotypes associated with certain types of ataxia, iPSC-based models are likely to provide significant insights, not only into disease progression, but also to the development of early-intervention therapies. In this review, we describe the existing iPSC-based disease models of this heterogeneous group of conditions and explore the challenges associated with generating cerebellar neurons from iPSCs, which have thus far hindered the expansion of this research.
Mendelian randomization: a premature burial?
Authors: Davey Smith George
Published: July 2015

Mendelian randomization is a promising approach to help improve causal inference in observational studies, with widespread potential applications, including to prioritization of pharmacotherapeutic targets for evaluation in RCTs. From its initial proposal the limitations of Mendelian randomization approaches have been widely recognised and discussed, and recently Pickrell has reiterated these1. However this critique did not acknowledge recent developments in both methodological and empirical research, nor did it recognise many future opportunities for application of the Mendelian randomization approach. These issues are briefly reviewed here.
Mitochondrial DNA Copy Number Variation Across Human Cancers
Authors: Reznik Ed , Miller Martin L. , Senbabaoglu Yasin , Riaz Nadeem , Lee William , Sander Chris
Published: June 2015

In cancer, mitochondrial dysfunction, through mutations, deletions, and changes in copy number of mitochondrial DNA (mtDNA), contributes to the malignant transformation and progress of tumors. Here, we report the first large-scale survey of mtDNA copy number variation across 21 distinct solid tumor types, examining over 13,000 tissue samples profiled with next-generation sequencing methods. We find a tendency for cancers, especially of the bladder and kidney, to be significantly depleted of mtDNA, relative to matched normal tissue. We show that mtDNA copy number is correlated to the expression of mitochondrially-localized metabolic pathways, suggesting that mtDNA copy number variation reflect gross changes in mitochondrial metabolic activity. Finally, we identify a subset of tumor-type-specific somatic alterations, including IDH1 and NF1 mutations in gliomas, whose incidence is strongly correlated to mtDNA copy number. Our findings suggest that modulation of mtDNA copy number may play a role in the pathology of cancer.
Salmonprovides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference
Authors: Patro Rob , Duggal Geet , Love Michael I , Irizarry Rafael A , Kingsford Carl
Published: June 2015

We introduceSalmon, a new method for quantifying transcript abundance from RNA-seq reads that is highly-accurate and very fast.Salmonis the first transcriptome-wide quantifier to model and correct for fragment GC content bias, which we demonstrate substantially improves the accuracy of abundance estimates and the reliability of subsequent differential expression analysis compared to existing methods that do not account for these biases.Salmonachieves its speed and accuracy by combining a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure. These innovations yield both exceptional accuracy and order-of-magnitude speed benefits over alignment-based methods.
Adaptive evolution is substantially impeded by Hill-Robertson interference in Drosophila
Authors: Castellano David , Coronado Marta , Campos Jose , Barbadilla Antonio , Eyre-Walker Adam
Published: June 2015

It is known that rates of mutation and recombination vary across the genome in many species. Here we investigate whether these factors affect the rate at which genes undergo adaptive evolution both individually and in combination and quantify the degree to which Hill-Robertson interference (HRi) impedes the rate of adaptive evolution. To do this we compiled a dataset of 6,141 autosomal protein coding genes from Drosophila, for which we have polymorphism data fromD. melanogasterand divergence out toD. yakuba. We estimated the rate of adaptive evolution using a derivative of the McDonald-Kreitman test that controls for the slightly deleterious mutations. We find that the rate of adaptive amino acid substitution is positively correlated to both the rates of recombination and mutation. We also find that these correlations are robust to controlling for each other, synonymous codon bias and gene functions related to immune response and testes. We estimate that HRi reduces the rate of adaptive evolution by ∼27%. We also show that this fraction depends on a gene’s mutation rate; genes with low mutation rates lose ∼11% of their adaptive substitutions while genes with high mutation rates lose ∼43%. In conclusion, we show that the mutation rate and the rate of recombination, are important modifiers of the rate of adaptive evolution in Drosophila.
Comprehensive nucleosome mapping of the human genome in cancer progression
Authors: Druliner Brooke R. , Vera Daniel , Johnson Ruth , Ruan Xiaoyang , Apone Lynne M. , Dimalanta Eileen T. , Stewart Fiona J. , Boardman Lisa , Dennis Jonathan H.
Published: June 2015

Altered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Important studies have mapped human nucleosome distributions genome wide, but the role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Transcription Start Site Sequence Capture method (mTSS-seq) to map the nucleosome distribution at human transcription start sites genome-wide in primary human lung and colon adenocarcinoma tissue. Here, we confirm that nucleosome redistribution is an early, widespread event in lung (LAC) and colon (CRC) adenocarcinoma. These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they may serve as important early adenocarcinoma markers. We demonstrate that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. We conclude that DNA-directed nucleosome redistributions are widespread early in cancer progression. We have proposed an entirely new hierarchical model for chromatin-mediated genome regulation.

Significance

This is the first report of human nucleosome distribution in cancer progression using sequence capture and HiSeq. We show in lung and colorectal adenocarcinoma patients that nucleosome distribution is a widespread, early response driven by genetically-encoded signals and potentiate regulatory factor binding. We present a model for chromatin-based hierarchical regulation.
TransRate: reference free quality assessment of de-novo transcriptome assemblies
Authors: Smith-Unna Richard D , Boursnell Chris , Patro Rob , Hibberd Julian M , Kelly Steven
Published: June 2015

TransRateis a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only sequenced reads as the input,TransRatemeasures the quality of individual contigs and whole assemblies, enabling assembly optimization and comparison.TransRatecan accurately evaluate assemblies of conserved and novel RNA molecules of any kind in any species. We show that it is more accurate than comparable methods and demonstrate its use on a variety of data.
Origins of cell-to-cell variability, kinetic proof-reading and the robustness of MAPK signal transduction
Authors: Filippi Sarah , Barnes Chris P. , Kirk Paul , Kudo Takamasa , McMahon Siobhan , Tsuchiya Takaho , Wada Takumi , Kuroda Shinya , Stumpf Michael P.H.
Published: July 2015

Cellular signalling processes can exhibit pronounced cell-to-cell variability in genetically identical cells. This affects how individual cells respond differentially to the same environmental stimulus. However, the origins of cell-to-cell variability in cellular signalling systems remain poorly understood. Here we measure the temporal evolution of phosphorylated MEK and ERK dynamics across populations of cells and quantify the levels of population heterogeneity over time using high-throughput image cytometry. We use a statistical modelling framework to show that upstream noise is the dominant factor causing cell-to-cell variability in ERK phosphorylation, rather than stochasticity in the phosphorylation/dephosphorylation of ERK. In particular, the cell-to-cell variability during sustained phosphorylation stems from random fluctuations in the background upstream signalling processes, while during transient phosphorylation, the heterogeneity is primarily due to noise in the intensity of the upstream signal(s). We show that the core MEK/ERK system uses kinetic proof-reading to faithfully and robustly transmits these variable inputs. The MAPK cascade thus propagates cell-to-cell variability at the population level, rather than attenuating or increasing it.
Crystal structure of dichloridobis(1,3,4,5-tetramethyl-1H-imidazol-2-ium-2-thiolate-κS)nickel(II)
Authors: Ahmida Aziza , Flörke Ulrich , Egold Hans , Henkel Gerald
Published: July 2015

In the molecular structure of the title compound, [NiCl2(C7H12N2S)2], the NiIIatom has a distorted tetrahedral geometry, coordinated by two Cl atoms [Ni—Cl= 2.2336 (6) Å] and two thione S atoms [Ni—S= 2.3024 (6) Å]. The angles at the NiIIcation, which lies on a twofold rotation axis, are Cl—Ni—Cl = 115.58 (3)° and S—Ni—S = 94.55 (3)°. All other angles at the central NiIIatom range from 109.46 (2) to 112.96 (2)°. The C—S—Ni angle is 99.91 (6)°. The planes of two imidazolium rings make a dihedral angle of 70.56 (6)°.