bluuebunny/crossref_metadata_2025 huggingface dataset:
Adsorption of pure SO2 on nanoscaled graphene oxide
Authors: Babu Deepu J. , Kühl Frank G. , Yadav Sandeep , Markert Daniel , Bruns Michael , Hampe Manfred J. , Schneider Jörg J.
Published: April 2016

Carbon materials are widely used for adsorptive removal of corrosive or green-house gases like SO2 or CO2. Graphene oxide is accessible in bulk quantities and thus may represent a viable replacement for other nanostructured carbon materials.
Preparation and characterization of interface-modified PLA/starch/PCL ternary blends using PLLA/triclosan antibacterial nanoparticles for medical applications
Authors: Davoodi Saeed , Oliaei Erfan , Davachi Seyed Mohammad , Hejazi Iman , Seyfi Javad , Heidari Behzad Shiroud , Ebrahimi Hossein
Published: April 2016

In this study, the antibacterial, interface-modified ternary blends based on polylactic acid/starch/polycaprolactone were prepared for medical applications.
Morphology evolution and the tri-continuous morphology formation of a PVDF/PS/HDPE ternary blend in melt mixing
Authors: Shao Yan , Dou Rui , Li Shuang-lin , Yin Bo , Yang Ming-bo
Published: April 2016

Manipulate the perfect tri-continuous structure of the PVDF/PS/HDPE system successfully and it can allow preparation for the functionalization of tri-continuous morphology!
Ion-pair recognition of amidinium salts by partially hydrogen-bonded heteroditopic cyclo[6]aramide
Authors: Shi Shanshan , Zhu Yumin , Li Xiaowei , Yuan Xiangyang , Ma Teng , Yuan Wen-Li , Tao Guo-Hong , Feng Wen , Yuan Lihua
Published: April 2016

Convergent heteroditopic cyclo[6]aramide is able to serve as ion-pair receptor for binding biologically important types of amidinium hydrochlorides as contact ion pair through host–guest interactions.
Influence of the properties of organic media in back-side silver pastes on the electrical performance of polycrystalline silicon solar cells
Authors: Li Ruixiao , Wang Hanying , Tai Yuping , Bai Jintao , Wang Hui
Published: April 2016

The best composition and ratio of solvents for the organic medium in back-side silver pastes was selected through a series of orthogonal experiments.
A widespread bacterial phenazine forms S-conjugates with biogenic thiols and crosslinks proteins
Authors: Heine D. , Sundaram S. , Beudert Matthias , Martin K. , Hertweck C.
Published: April 2016

Bacterial phenazines react with diverse biogenic thiols and proteins under radical-forming conditions, revealing new biological roles based on conjugation and crosslinking of proteins.
Multilayered semiconducting polymer nanoparticles with enhanced NIR fluorescence for molecular imaging in cells, zebrafish and mice
Authors: Zhu Houjuan , Fang Yuan , Zhen Xu , Wei Na , Gao Yu , Luo Kathy Qian , Xu Chenjie , Duan Hongwei , Ding Dan , Chen Peng , Pu Kanyi
Published: April 2016

Multilayered semiconducting polymer nanoparticles are developed forin vivoimaging of lymph nodes and tumors with a high signal-to-noise ratio.
A new strategy to prepare N-doped holey graphene for high-volumetric supercapacitors
Authors: Dong Xinwei , Hu Nantao , Wei Liangming , Su Yanjie , Wei Hao , Yao Lu , Li Xiaolin , Zhang Yafei
Published: April 2016

N-doped holey graphene with a volumetric capacitance of 397 F cm−3for supercapacitors was prepared by a novel “Bottom-up” strategy.
Microporous LiAlSiO4 with high ionic conductivity working as a coating material and water adsorbent for LiNi0.5Mn1.5O4 cathode
Authors: Deng J. C. , Xu Y. L. , Li L. , Feng T. Y. , Li L.
Published: April 2016

A LiAlSiO4 coating layer could work as a desiccant by excluding electrolyte molecules while adsorbing H2O molecules.
A photo-polymerized poly(Nε-acryloyll-lysine) hydrogel for 3D culture of MCF-7 breast cancer cells
Authors: Xu Weijun , Qian Junmin , Zhang Yaping , Suo Aili , Cui Ning , Wang Jinlei , Yao Yu , Wang Hejing
Published: April 2016

Standard two-dimensional monolayer culture platforms often fail to mimic the tumor microenvironment, while animal models complicate research on the effect of individual factors on cell behaviors. Three-dimensionalin vitrotumor models bridge gap between them.
A stimuli-responsive Janus peptide dendron–drug conjugate as a safe and nanoscale drug delivery vehicle for breast cancer therapy
Authors: Li Ning , Guo Chunhua , Duan Zhenyu , Yu Lingzhu , Luo Kui , Lu Jiao , Gu Zhongwei
Published: April 2016

A Janus mPEGylated dendron–PVGLIG–DOX conjugate self-assembled into nanoparticles was employed as a matrix metalloproteinase-2/9 enzyme-sensitive and safe nanoscale drug delivery system for breast cancer therapy.
Optical chemosensors for water sample analysis
Authors: Sharma Hemant , Kaur Navneet , Singh Amanpreet , Kuwar Anil , Singh Narinder
Published: April 2016

Molecular recognition is an emerging field of Supramolecular Chemistry.
Effect of alkyl length dependent crystallinity for the mechanofluorochromic feature of alkyl phenothiazinyl tetraphenylethenyl acrylonitrile derivatives
Authors: Ma Chunping , Zhang Xiqi , Yang Yang , Ma Zhiyong , Yang Liutao , Wu Yujiao , Liu Hongliang , Jia Xinru , Wei Yen
Published: April 2016

The influence of alkyl length dependent crystallinity for the mechanofluorochromic features of three acrylonitrile derivatives have been investigated.
Urethane–acrylate polymers in high-resolution contact printing
Authors: Li Jinhai , Xu Lisong , Kim Soyoun , Shestopalov Alexander A.
Published: April 2016

Polyurethane–acrylate (PUA) materials were used as printing stamps in the high-resolution contact printing of organic molecules and organic thin films to show that PUA-based printing can be used as a simple alternative to a kinetically modulated PDMS stamping.
Cytotoxicity investigation of luminescent nanohybrids based on chitosan and carboxymethyl chitosan conjugated with Bi2S3 quantum dots for biomedical applications
Authors: Carvalho Sandhra M. , Mansur Herman S. , Ramanery Fábio P. , Mansur Alexandra A. P. , Lobato Zelia I. P. , Leite Maria F.
Published: April 2016

Bioengineered hybrids are emerging as a new class of nanomaterials consisting of a biopolymer and inorganic semiconductors used in biomedical and environmental applications. The aim of the present work was to determine the cytocompatibility of novel water-soluble Bi2S3 quantum dots (QDs) functionalized with chitosan and O-carboxymethyl chitosan (CMC) as capping ligands using an eco-friendly aqueous process at room temperature. These hybrid nanocomposites were tested for cytocompatibility using a 3-(4,5-dimethylthiazol-2yl) 2,5-diphenyl tetrazolium bromide (MTT) cell proliferation assay with cultured human osteosarcoma cells (SAOS), human embryonic kidney cells (HEK293T cells) and a LIVE/DEAD® viability-cytotoxicity assay. The results of the in vitro assays demonstrated that the CMC and chitosan-based nanohybrids were not cytotoxic and exhibited suitable cell viability responses. However, despite the “safe by design” approach used in this research, we have proved that the impact of the size, surface charge and biofunctionalization of the nanohybrids on cytotoxicity was cell type-dependent due to complex mechanisms. Thus, these novel bionanocomposites offer promising prospects for potential biomedical and pharmaceutical applications as fluorescent nanoprobes.
Der zweite Gesundheitsmarkt aus Nachfragersicht: Ableitung eines Produkt-Marktraumes auf Basis von Konsumentenwahrnehmungen
Authors: Teichert T. , Mühlbach C.
Published: April 2016

Ziel der Studie: Ziel der Studie war eine Abbildung der individuellen Konsumentensicht auf den sehr speziellen Markt für Gesundheit bzw. Gesundheitsprodukte, den zweiten deutschen Gesundheitsmarkt. Eine visuelle Verortung der untersuchten Produktkategorien im Zuge einer Marktanalyse ergänzte diese Visualisierung.

Methodik: Eine großangelegte repräsentative Studie (N=1 033) ermittelte mit einer innovativen Adaption der Repertory-Grid-Methode die Konsumentensicht auf den betrachteten speziellen Markt. Grundlegende Fragen bzgl. der Gesundheitseinstellung sowie dem praktizierten gesunden Verhalten komplettierten die telefonisch umgesetzte Befragung.

Ergebnisse: Gesundheit stellt in gesättigten Märkten, vor allem auch unter dem Aspekt alternder Gesellschaften, einen Wachstumsmarkt dar, welcher sich bei Weitem nicht auf originäre medizinische Produkte beschränkt. In der hier vorgestellten Studie wurden Produktkategorien wie „Zahnpflege“, „Obst und Gemüse“ oder „Nüsse“ als gesunde Produkte klassifiziert.

Schlussfolgerung: Die Relevanz von Gesundheit, auch im gesamtwirtschaftlichen Kontext, ist lange unterschätzt worden. Nach wie vor nimmt Gesundheit für Konsumenten einen hohen Stellenwert ein. Eine Offenlegung der individuellen Wahrnehmungen im Gesundheitskontext bietet eine Möglichkeit der deutlich effektiveren Produktgestaltung. Die Identifikation gesunder Produktdimensionen aus Konsumentensicht bringt so Aufschluss über die tatsächlich gewünschten Produkteigenschaften und die daraus resultierenden vorhandenen Potenziale.
Die Entwicklung von Qualitätsstandards für die ambulante psychosoziale Krebsberatung – Ergebnisse einer Delphibefragung
Authors: Kuhnt S. , Mehnert A. , Giesler J. , Faust T. , Weis J. , Ernst J.
Published: April 2016

Hintergrund: Die ambulante psychosoziale Versorgung von Krebspatienten und deren Angehörigen ist ein zentraler Bestandteil der onkologischen Versorgung. Bislang sind die Angebote ambulanter Versorgung unter den Aspekten des erbrachten Leistungsspektrums und der Qualitätssicherung sehr heterogen und schwer vergleichbar.

Fragestellung: Ziel der Studie war die Entwicklung von Qualitätsstandards für die ambulante psychosoziale Krebsberatung in der Form eines mehrdimensionalen Klassifikationssystems.

Material und Methoden: Auf der Basis einer Delphierhebung (3 Befragungsrunden) mit 97 Experten aus mehr als 10 unterschiedlichen Tätigkeitsfeldern bzw. institutionellen Kontexten (z. B. ambulante und stationäre psychosoziale Versorgung, Krebs- und Fachgesellschaften, Medizin, Wissenschaft und Selbsthilfe) wurden insgesamt 134 Einzelkriterien zu 9 Qualitätsbereichen (z. B. Personalstruktur, Leistungsangebot, Dokumentation) erstellt und hinsichtlich der Relevanz, Eindeutigkeit, Vollständigkeit und dem Grad der Verbindlichkeit beurteilt.

Ergebnis: 119 Einzelkriterien (88,8%) wurden als konsensfähige Qualitätsmerkmale angenommen, davon 94 als Basiskriterium (79%) und 25 als optionales Kriterium (21%). Die höchste Anzahl an Einzelkriterien entfallen auf die Qualitätsbereiche Beratungsangebot (26 Einzelkriterien), Dokumentation (21) sowie Personal bzw. Erreichbarkeit (jeweils 16). Insgesamt 15 Kriterien (11,2%) erreichten über die 3 Delphirunden keinen Konsens und wurden entfernt.

Schlussfolgerung: Mit den im Expertenkonsens erarbeiteten Qualitätskriterien liegen erstmals Standards für die ambulante psychosoziale Krebsberatung vor, die eine vergleichbare Beurteilung der Leistungsangebote ambulanter Krebsberatungsstellen ermöglichen.
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system
Authors: Vandenbon Alexis , Dinh Viet H. , Mikami Norihisa , Kitagawa Yohko , Teraguchi Shunsuke , Ohkura Naganari , Sakaguchi Shimon
Published: April 2016

Significance

Correlation of expression between genes can offer useful hints regarding their function or underlying regulatory mechanism. Today, large amounts of expression data are publicly available, allowing researchers to estimate expression correlation over thousands of samples. However, extracting information from correlation data is not straightforward, because underlying expression data are generated by different laboratories working on different cell types and under different conditions. Here we present Immuno-Navigator, a database for correlation of expression in cells of the immune system, which addresses these issues. We present examples of ways our database can be used for generating hypotheses for further experimental analysis. We demonstrate how it recapitulates known facts in immunology and successfully predicts key regulators in naturally occurring regulatory T cells.
An approach to the study of the use of English in the activities of Spanish gyms
Authors: Rodríguez-Medina María Jesús
Published: April 2016

The study of Anglicisms in Spanish has been significant since the last half of the twentieth century. After an initial period of purist publications, the approach to this sociolinguistic phenomenon became more descriptive and academic in the 1980s. Today’s bibliography is relatively extensive, including works which have widely analysed the impact of the Anglo-American culture on different areas, as well as suggested a variety of definitions and taxonomies of Anglicisms. However, some domains that are greatly influenced by the English language in Spain such as the terminology used in gyms have not been examined so far, since the published literature has focused on specific sports (football, tennis, etc.). The aim of this paper is to compile and analyse the most frequent Anglicisms in the lexicon used in sports activities offered by Spanish gyms, as an introductory approach to prospective research. We have studied a sample of 268 Anglicisms taken from the web sites of 15 gyms. Our analysis is not limited to the description of the linguistic features of these Anglicisms but it also explores the possible reasons for their use.
Quantifying Recruitment Compensation in Florida Largemouth Bass, with Implications for Fisheries
Authors: Shaw Stephanie L. , Allen Micheal S.
Published: April 2016

Fish populations that undergo heavy exploitation and those for which the act of fishing can influence individual brood success are at risk of recruitment effects due to angling. The angling of brood‐guarding male black bass Micropterus spp. has been shown to decrease brood success, although there is no evidence that a loss of individual broods has population‐level impacts. Therefore, some level of recruitment compensation may influence juvenile bass survival. We sought to measure recruitment compensation and the form of the stock–recruit relationship for a brood‐guarding species, the Florida Largemouth Bass M. salmoides floridanus (hereafter, Florida Bass). The study was conducted in four north‐central Florida lakes during 4 years (2010–2013). We quantified adult stock density by using mark–recapture electrofishing surveys. The estimated broods produced in each spawning season, the number of those broods that were successful, and the age‐1 recruit density were quantified via snorkel surveys. We evaluated three models for describing the effects of stock density or successful brood density on recruitment: a proportional (linear; i.e., no compensation) model, a Ricker (dome‐shaped) model, and a Beverton–Holt (asymptotic) model. Recruit density was better indicated by the number of successful broods produced than by spawning stock density. Model comparisons indicated that the density‐dependent models had the most support, whereas there was no apparent support for the proportional or density‐independent model. The Ricker model had the most empirical support overall (estimated parameters: a = 2.2, b = 0.009). Our results indicate that the number of successful broods would have to fall below about 5 broods/ha to generate direct declines in observed average recruitment of Florida Bass.

Received August 5, 2015; accepted December 9, 2015 Published online April 14, 2016
Production of a thermal stress resistant mutant Euglena gracilis strain using Fe-ion beam irradiation
Authors: Yamada Koji , Kazama Yusuke , Mitra Sharbanee , Marukawa Yuka , Arashida Ryo , Abe Tomoko , Ishikawa Takahiro , Suzuki Kengo
Published: April 2016

Euglena gracilis is a common phytoplankton species, which also has motile flagellate characteristics. Recent research and development has enabled the industrial use of E. gracilis and selective breeding of this species is expected to further expand its application. However, the production of E. gracilis nuclear mutants is difficult because of the robustness of its genome. To establish an efficient mutation induction procedure for E. gracilis, we employed Fe-ion beam irradiation in the RIKEN RI beam factory. A decrease in the survival rate was observed with the increase in irradiation dose, and the upper limit used for E. gracilis selective breeding was around 50 Gy. For a practical trial of Fe-ion irradiation, we conducted a screening to isolate high-temperature-tolerant mutants. The screening yielded mutants that proliferated faster than the wild-type strain at 32 °C. Our results demonstrate the effectiveness of heavy-ion irradiation on E. gracilis selective breeding.
Global and local mechanical properties and microstructure of Bobbin tool friction-stir-welded Al–Li alloy
Authors: Wang F. F. , Li W. Y. , Shen J. , Zhang Z. H. , Li J. L. , dos Santos J. F.
Published: April 2016

AA2198–T851 sheets were welded by bobbin tool friction stir welding using a rotational speed of 800 rpm and welding speed of 42 mm min−1. The microstructure and precipitates within the joint were characterised by transmission electron microscopy. The global and local mechanical behaviour was determined using a digital image correlation system. Specific attention was given to the relationship between the local microstructure and properties across the joint, which govern the global strength and ductility of the welds. A lower global elongation of the joint is caused by the premature strain localisation in the softened zone.
On the algebraic relations between Mahler functions
Authors: Roques Julien
Published: April 2016

In the last years, a number of authors have studied the algebraic relations between the generating series of automatic sequences. It turns out that these series are solutions of Mahler type equations. This paper is mainly concerned with the difference Galois groups of Mahler type equations (these groups reflect the algebraic relations between the solutions of the equations). In particular, we study in detail the equations of order

2
2

and compute the difference Galois groups of classical equations related to the Baum-Sweet and to the Rudin-Shapiro automatic sequences.
NFκB is a central regulator of protein quality control in response to protein aggregation stresses via autophagy modulation
Authors: Nivon Mathieu , Fort Loïc , Muller Pascale , Richet Emma , Simon Stéphanie , Guey Baptiste , Fournier Maëlenn , Arrigo André-Patrick , Hetz Claudio , Atkin Julie D. , Kretz-Remy Carole
Published: April 2016

During cell life, proteins often misfold, depending on particular mutations or environmental changes, which may lead to protein aggregates that are toxic for the cell. Such protein aggregates are the root cause of numerous diseases called “protein conformational diseases,” such as myofibrillar myopathy and familial amyotrophic lateral sclerosis. To fight against aggregates, cells are equipped with protein quality control mechanisms. Here we report that NFκB transcription factor is activated by misincorporation of amino acid analogues into proteins, inhibition of proteasomal activity, expression of the R120G mutated form of HspB5 (associated with myofibrillar myopathy), or expression of the G985R and G93A mutated forms of superoxide dismutase 1 (linked to familial amyotrophic lateral sclerosis). This noncanonical stimulation of NFκB triggers the up-regulation of BAG3 and HspB8 expression, two activators of selective autophagy, which relocalize to protein aggregates. Then NFκB-dependent autophagy allows the clearance of protein aggregates. Thus NFκB appears as a central and major regulator of protein aggregate clearance by modulating autophagic activity. In this context, the pharmacological stimulation of this quality control pathway might represent a valuable strategy for therapies against protein conformational diseases.
The F-actin bundler α-actinin Ain1 is tailored for ring assembly and constriction during cytokinesis in fission yeast
Authors: Li Yujie , Christensen Jenna R. , Homa Kaitlin E. , Hocky Glen M. , Fok Alice , Sees Jennifer A. , Voth Gregory A. , Kovar David R.
Published: April 2016

The actomyosin contractile ring is a network of cross-linked actin filaments that facilitates cytokinesis in dividing cells. Contractile ring formation has been well characterized in Schizosaccharomyces pombe, in which the cross-linking protein α-actinin SpAin1 bundles the actin filament network. However, the specific biochemical properties of SpAin1 and whether they are tailored for cytokinesis are not known. Therefore we purified SpAin1 and quantified its ability to dynamically bind and bundle actin filaments in vitro using a combination of bulk sedimentation assays and direct visualization by two-color total internal reflection fluorescence microscopy. We found that, while SpAin1 bundles actin filaments of mixed polarity like other α-actinins, SpAin1 has lower bundling activity and is more dynamic than human α-actinin HsACTN4. To determine whether dynamic bundling is important for cytokinesis in fission yeast, we created the less dynamic bundling mutant SpAin1(R216E). We found that dynamic bundling is critical for cytokinesis, as cells expressing SpAin1(R216E) display disorganized ring material and delays in both ring formation and constriction. Furthermore, computer simulations of initial actin filament elongation and alignment revealed that an intermediate level of cross-linking best facilitates filament alignment. Together our results demonstrate that dynamic bundling by SpAin1 is important for proper contractile ring formation and constriction.
Has the time come for preprints in biology?
Authors: Bhalla Needhi
Published: April 2016

Preprints, non–peer-reviewed drafts of manuscripts available on the Internet, have been used in conjunction with peer review and publication in journals in the physical sciences for almost 25 years. Recently, more scientists have been discussing whether preprints can play a similar role in biological and biomedical research. Here, I discuss my excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences.
PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences
Authors: Peng Yousong , Yang Lei , Li Honglei , Zou Yuanqiang , Deng Lizong , Wu Aiping , Du Xiangjun , Wang Dayan , Shu Yuelong , Jiang Taijiao
Published: April 2016

Motivation: Timely surveillance of the antigenic dynamics of the influenza virus is critical for accurate selection of vaccine strains, which is important for effective prevention of viral spread and infection.

Results: Here, we provide a computational platform, called PREDAC-H3, for antigenic surveillance of human influenza A(H3N2) virus based on the sequence of surface protein hemagglutinin (HA). PREDAC-H3 not only determines the antigenic variants and antigenic cluster (grouped for similar antigenicity) to which the virus belongs, based on HA sequences, but also allows visualization of the spatial distribution and temporal dynamics of antigenic clusters of viruses isolated from around the world, thus assisting in antigenic surveillance of human influenza A(H3N2) virus.

Availability and Implementation: It is publicly available from: http://biocloud.hnu.edu.cn/influ411/html/index.php.

Contacts: yshu@cnic.org.cn or taijiao@moon.ibp.ac.cn
MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments
Authors: Pliatsika Venetia , Loher Phillipe , Telonis Aristeidis G. , Rigoutsos Isidore
Published: April 2016

Motivation: It has been known that mature transfer RNAs (tRNAs) that are encoded in the nuclear genome give rise to short molecules, collectively known as tRNA fragments or tRFs. Recently, we reported that, in healthy individuals and in patients, tRFs are constitutive, arise from mitochondrial as well as from nuclear tRNAs, and have composition and abundances that depend on a person’s sex, population origin and race as well as on tissue, disease and disease subtype. Our findings as well as similar work by other groups highlight the importance of tRFs and presage an increase in the community’s interest in elucidating the roles of tRFs in health and disease.

Results: We created MINTbase, a web-based framework that serves the dual-purpose of being a content repository for tRFs and a tool for the interactive exploration of these newly discovered molecules. A key feature of MINTbase is that it deterministically and exhaustively enumerates all possible genomic locations where a sequence fragment can be found and indicates which fragments are exclusive to tRNA space, and thus can be considered as tRFs: this is a very important consideration given that the genomes of higher organisms are riddled with partial tRNA sequences and with tRNA-lookalikes whose aberrant transcripts can be mistaken for tRFs. MINTbase is extremely flexible and integrates and presents tRF information from multiple yet interconnected vantage points (‘vistas’). Vistas permit the user to interactively personalize the information that is returned and the manner in which it is displayed. MINTbase can report comparative information on how a tRF is distributed across all anticodon/amino acid combinations, provides alignments between a tRNA and multiple tRFs with which the user can interact, provides details on published studies that reported a tRF as expressed, etc. Importantly, we designed MINTbase to contain all possible tRFs that could ever be produced by mature tRNAs: this allows us to report on their genomic distributions, anticodon/amino acid properties, alignments, etc. while giving users the ability to at-will investigate candidate tRF molecules before embarking on focused experimental explorations. Lastly, we also introduce a new labeling scheme that is tRF-sequence-based and allows users to associate a tRF with a universally unique label (‘tRF-license plate’) that is independent of a genome assembly and does not require any brokering mechanism.

Availability and Implementation: MINTbase is freely accessible at http://cm.jefferson.edu/MINTbase/. Dataset submissions to MINTbase can be initiated at http://cm.jefferson.edu/MINTsubmit/.

Contact:  isidore.rigoutsos@jefferson.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
hotspot: software to support sperm-typing for investigating recombination hotspots
Authors: Odenthal-Hesse Linda , Dutheil Julien Y. , Klötzl Fabian , Haubold Bernhard
Published: April 2016

Motivation: In many organisms, including humans, recombination clusters within recombination hotspots. The standard method for de novo detection of recombinants at hotspots is sperm typing. This relies on allele-specific PCR at single nucleotide polymorphisms. Designing allele-specific primers by hand is time-consuming. We have therefore written a package to support hotspot detection and analysis.

Results: hotspot consists of four programs: asp looks up SNPs and designs allele-specific primers; aso constructs allele-specific oligos for mapping recombinants; xov implements a maximum-likelihood method for estimating the crossover rate; six, finally, simulates typing data.

Availability and Implementation: hotspot is written in C. Sources are freely available under the GNU General Public License from http://github.com/evolbioinf/hotspot/

Contact:  haubold@evolbio.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Na + , HCO 3
− -cotransporter NBCn1 increases pH i gradients, filopodia, and migration of smooth muscle cells and promotes arterial remodelling
Authors: Boedtkjer Ebbe , Bentzon Jacob F. , Dam Vibeke S. , Aalkjaer Christian
Published: April 2016

Aims

Arterial remodelling can cause luminal narrowing and obstruct blood flow. We tested the hypothesis that cellular acid–base transport facilitates proliferation and migration of vascular smooth muscle cells (VSMCs) and enhances remodelling of conduit arteries.

Methods and results

N a + , HC O 3 − -cotransport via NBCn1 (Slc4a7) mediates net acid extrusion and controls steady-state intracellular pH (pH i ) in VSMCs of mouse carotid arteries and primary aortic explants. Carotid arteries undergo hypertrophic inward remodelling in response to partial or complete ligation in vivo , but the increase in media area and thickness and reduction in lumen diameter are attenuated in arteries from NBCn1 knock-out compared with wild-type mice. With CO2/HCO3− present, gradients for pH i (∼0.2 units magnitude) exist along the axis of VSMC migration in primary explants from wild-type but not NBCn1 knock-out mice. Knock-out or pharmacological inhibition of NBCn1 also reduces filopodia and lowers initial rates of VSMC migration after scratch-wound infliction. Interventions to reduce H + -buffer mobility (omission of CO2/HCO3− or inhibition of carbonic anhydrases) re-establish axial pH i gradients, filopodia, and migration rates in explants from NBCn1 knock-out mice. The omission of CO2/HCO3− also lowers global pH i and inhibits proliferation in primary explants.

Conclusion

Under physiological conditions (i.e. with CO2/HCO3− present), NBCn1-mediated HCO3− uptake raises VSMC pH i and promotes filopodia, VSMC migration, and hypertrophic inward remodelling. We propose that axial pH i gradients enhance VSMC migration whereas global acidification inhibits VSMC proliferation and media hypertrophy after carotid artery ligation. These findings support a key role of acid–base transport, particularly via NBCn1, for development of occlusive artery disease.
Systemically Significant Prices
Authors: Hockett Robert C. , Omarova Saule T.
Published: April 2016

Some prices and indices in domestic or global markets take on particular market-wide importance. This can occur either because (i) they are associated with ubiquitous inputs to production, (ii) they are associated with highly popular asset classes, (iii) by convention they tend to be used as benchmarks in determining other prices, or (iv) some combination of the above.  Examples include prevailing wage and salary rates, certain energy and commodity prices, and such indices and borrowing rates as the Standard & Poor’s 500, the Federal Funds Rate, and the Libor and Euribor interbank lending rate benchmarks.

We call such prices and indices ‘systemically important’ prices and indices, or ‘SIPIs’. Over the long term, these prices and indices tend towards certain statistical mean values that reflect determinants that can plausibly be treated as ‘fundamentals’, be these demographic, technological, or global-quantity-rooted in character.  At times, however, SIPIs can move out of alignment with mean values and associated fundamentals owing to distortions stemming from missing information, recursive collective action problems (including ‘noise’ trading and ‘herd’ behaviour), or even deliberately manipulative behaviour on the part of influential or colluding market actors. 

We develop a general account of systemically important prices and indices as well as of the market vulnerabilities to which they can give rise. We then develop a menu of regulatory strategies for addressing these vulnerabilities in manners that protect markets’ capacities to translate fundamental values into (more) accurate prices or indices when such prices or indices are systemically important.  Key to the effort is recognizing that what we propose is in some cases what regulators are committed to doing already in maintaining market integrity, and in other cases is what central banks do already in determining appropriate money rental (‘interest‘) rates and securing them through open market operations.
Transcriptome data analysis reveals correlation between developmentally altered gene expression and offspring phenotype in epigenetic inheritance
Authors: Sharma Abhay
Published: April 2016

A recent study investigated sperm mediated inheritance of diet induced metabolic phenotype, reported underlying regulation of MERVL targets and ribosomal protein genes in embryos, and suggested that the altered regulation observed may cause placentation defects which can secondarily result in abnormal metabolism. An analysis of available transcriptomic data however reveals a direct link between the developmentally altered genes and the offspring phenotype.
GenRank: an R/Bioconductor package for prioritization of candidate genes
Authors: Kanduri Chakravarthi , Järvelä Irma
Published: April 2016

Modern high-throughput studies often yield long lists of genes, of which a fraction are of high relevance to the phenotype of interest. To prioritize the candidate genes of complex genetic traits, our R/Bioconductor package GenRank provides methods that are based on convergent evidence obtained from multiple independent evidence layers. The package facilitates an extensible framework that allows a further addition of novel methods for candidate gene prioritization.

Availability and Implementation:

The methods are implemented in R and available as a package in Bioconductor repository (http://bioconductor.org/packages/GenRank/).

Contact:

chakra.kanduri@gmail.com
The effects of population size histories on estimates of selection coefficients from time-series genetic data
Authors: Jewett Ethan M. , Steinrücken Matthias , Song Yun S.
Published: April 2016

ABSTRACT

Many approaches have been developed for inferring selection coefficients from time series data while accounting for genetic drift. However, the improvement in inference accuracy that can be attained by modeling drift is unknown. Here, by comparing maximum likelihood estimates of selection coefficients that account for the true population size history with estimates that ignore drift, we address the following questions: how much can modeling the population size history improve estimates of selection coefficients? How much can mis-inferred population sizes hurt inferences of selection coefficients? We conduct our analysis under the discrete Wright-Fisher model by deriving the exact probability of an allele frequency trajectory in a population of time-varying size and we replicate our results under the diffusion model by extending the exact probability of a frequency trajectory derived by Steinrückenet al. (2014) to the case of a piecewise constant population. For both the discrete Wright-Fisher and diffusion models, we find that ignoring drift leads to estimates of selection coefficients that are nearly as accurate as estimates that account for the true population history, even when population sizes are small and drift is high. In populations of time-varying size, estimates of selection coefficients that ignore drift are similar in accuracy to estimates that rely on crude, yet reasonable, estimates of the population history. These results are of interest because inference methods that ignore drift are widely used in evolutionary studies and can be many orders of magnitude faster than methods that account for population sizes.
Using Google Earth to improve management of threatened limestone karst ecosystems in Peninsular Malaysia
Authors: Liew Thor-Seng , Price Liz , Clements Gopalasamy Reuben
Published: April 2016

Biodiversity conservation is now about prioritisation, especially in a world with limited resources and so many habitats and species in need of protection. However, we cannot prioritise effectively if historical and current information on a particular habitat or species remains scattered. Several good platforms have been created to help users to find, use and create biodiversity information. However, good platforms for sharing habitat information for threatened ecosystems are still lacking. Limestone hills are an example of threatened ecosystems that harbour unique biodiversity, but are facing intensifying anthropogenic disturbances. As limestone is a vital resource for the construction industry, it is not possible to completely halt forest degradation and quarrying in developing countries such as Malaysia, where 445 limestone hills have been recorded in the peninsula to date. As such, there is an urgent need to identify which hills must be prioritised for conservation. To make decisions based on sound science, collating spatial and biological information on limestone hills into a publicly accessible database is critical. Here, we compile Malaysia’s first limestone hill GIS map for 445 limestone hills in the peninsula based on information from geological reports and scientific literature. To assist in conservation prioritisation efforts, we quantify characteristics of limestone hills in terms of size, degree of isolation, and spatial distribution patterns and also assessed the degree of habitat disturbance of each limestone hill in terms of buffer area forest degradation and quarrying activity. All this information is stored in a KMZ file and can be accessed through the Google Earth interface. This product should not be viewed as a final output containing basic limestone hill information. Rather, this database is a foundational platform for users to collect, store, update and manipulate spatial and biological data from limestone hills to better inform decisions regarding their management.
Retrotransposon proliferation coincident with the evolution of dioecy inAsparagus
Authors: Harkess Alex , Mercati Francesco , Abbate Loredana , McKain Michael , Pires J. Chris , Sala Tea , Sunseri Francesco , Falavigna Agostino , Leebens-Mack Jim
Published: April 2016

Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genusAsparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across theAsparagusgenus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or retrotransposon proliferation in dioecious species. We first estimate genome sizes or use published values for four hermaphrodites and four dioecious species distributed across the phylogeny and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication event predating the diversification of theAsparagusgenus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing and common elements were annotated. Across our broad phylogenetic sampling,Ty-1 Copiaretroelements in particular have undergone a marked proliferation in dioecious species. In the absence of a detectable whole genome duplication event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioeciousAsparagusspecies.
Assessment of pharmacogenomic agreement
Authors: Safikhani Zhaleh , El-Hachem Nehme , Quevedo Rene , Smirnov Petr , Goldenberg Anna , Juul Birkbak Nicolai , Mason Christopher E. , Hatzis Christos , Shi Leming , Aerts Hugo JWL , Quackenbush John , Haibe-Kains Benjamin
Published: April 2016

In 2013 we published an analysis demonstrating that drug response data and gene-drug associations reported in two independent large-scale pharmacogenomic screens, Genomics of Drug Sensitivity in Cancer1(GDSC) and Cancer Cell Line Encyclopedia2(CCLE), were inconsistent3. The GDSC and CCLE investigators recently reported that their respective studies exhibit reasonable agreement and yield similar molecular predictors of drug response4, seemingly contradicting our previous findings3. Reanalyzing the authors’ published methods and results, we found that their analysis failed to account for variability in the genomic data and more importantly compared different drug sensitivity measures from each study, which substantially deviate from our more stringent consistency assessment. Our comparison of the most updated genomic and pharmacological data from the GDSC and CCLE confirms our published findings that the measures of drug response reported by these two groups are not consistent5. We believe that a principled approach to assess the reproducibility of drug sensitivity predictors is necessary before envisioning their translation into clinical settings.
A Possible Link Between Pyriproxyfen and Microcephaly
Authors: Evans Dan , Nijhout Fred , Parens Raphael , Morales Alfredo J. , Bar-Yam Yaneer
Published: April 2016

The Zika virus is the primary suspect in the large increase in microcephaly cases in 2015-6 in Brazil, however its role is unconfirmed despite individual cases of viral infections found in neural tissue. Here we consider the alternative that the insecticide pyriproxyfen, used in Brazilian drinking water for mosquito control, may actually be the cause. Pyriproxifen is an analog of juvenile hormone, which corresponds in mammals to regulatory molecules including retinoic acid, a vitamin A metabolite, with which it has cross-reactivity and whose application during development causes microcephaly. Methoprene, another juvenile hormone analog approved as an insecticide has metabolites that bind to the retinoid X receptor, and causes developmental disorders in mammals. Isotretinoin is another example of a retinoid causing microcephaly in human babies via activation of the retinoid X receptor. Moreover, tests of pyriproxyfen by the manufacturer, Sumitomo, widely quoted as giving no evidence for developmental toxicity, actually found some evidence for such an effect, including low brain mass and arhinencephaly—incomplete formation of the anterior cerebral hemispheres—in rat pups. Finally, the pyriproxyfen use in Brazil is unprecedented—it has never before been applied to a water supply on such a scale. Claims that it is not being used in Recife, the epicenter of microcephaly cases, do not distinguish the metropolitan area of Recife, where it is widely used, and the municipality, where it is not. Given this combination of information we strongly recommend that the use of pyriproxyfen in Brazil be suspended pending further investigation.
Wild-type U2AF1 antagonizes the splicing program characteristic of U2AF1-mutant tumors and is required for cell survival
Authors: Fei Dennis Liang , Motowski Hayley , Chatrikhi Rakesh , Prasad Sameer , Yu Jovian , Gao Shaojian , Kielkopf Clara , Bradley Robert K. , Varmus Harold
Published: April 2016

We have asked how the common S34F mutation in the splicing factor U2AF1 regulates alternative splicing in lung cancer, and why wild-type U2AF1 is retained in cancers with this mutation. A human lung epithelial cell line was genetically modified so thatU2AF1S34F is expressed from one of the two endogenous U2AF1 loci. By altering levels of mutant or wild-type U2AF1 in this cell line and by analyzing published data on human lung adenocarcinomas, we show that S34F-associated changes in alternative splicing are proportional to the ratio of S34F:wild-type gene products and not to absolute levels of either the mutant or wild-type factor. Preferential recognition of specific 3′ splice sites in S34F-expressing cells is largely explained by differential in vitro RNA-binding affinities of mutant versus wild-type U2AF1 for those same 3′ splice sites. Finally, we show that lung adenocarcinoma cell lines bearingU2AF1mutations do not require the mutant protein for growthin vitroorin vivo. In contrast, wild-type U2AF1 is required for survival, regardless of whether cells carry theU2AF1S34F allele. Our results provide mechanistic explanations of the magnitude of splicing changes observed inU2AF1-mutant cells and why tumors harboringU2AF1mutations always retain an expressed copy of the wild-type allele.

Author Summary

Large-scale genomics studies have identified recurrent mutations in many genes that fall outside the conventional domain of proto-oncogenes. They include genes encoding factors that mediate RNA splicing; mutations affecting four of these genes are present in up to half of proliferative myeloid disorders and in a significant number of solid tumors, including lung adenocarcinoma. Here we have characterized several properties of a common mutant version of the U2AF1 splicing factor, a component of the U2 auxiliary factor complex, in lung cells. We have found that mutant-associated changes in splice site selection are primarily influenced by the ratio of mutant and wild-type U2AF1 gene products; thus increasing wild-type U2AF1 levels represses the mutant-induced splicing program. We show that the altered splice site preferences of mutant U2AF1 can be attributed to changes in its binding to relevant 3′ splice sites. We also show that mutant U2AF1 is different from some oncogenes: the growth properties of lung cancer cell lines carrying the mutant allele are unaffected by loss of the mutant gene, while the wild-type allele is absolutely required for survival. These results advance our understanding of the molecular determinants of the mutant-associated splicing program, and they highlight previously unappreciated roles of wild-type U2AF1 in the presence of the recurrentU2AF1S34F mutation.
Inventory of cultivatable populations of S-cycling, fermentative, Fe-reducing, and aerobic heterotrophic bacteria from salt marsh sediments
Authors: Emerson David , Lydell Cynthia M.
Published: April 2016

A survey was carried out of the dominant chemotrophic groups of bacteria inhabiting surface salt marsh sediments in the Virginia Coastal Reserve (VCR) on the Atlantic coast of Virginia. Total direct cell counts were carried out on all samples. Aerobic heterotrophs, sulfur oxidizers, sulfate reducing bacteria (SRB), sulfur disproportionaters, Fe-reducing (FeRB) and fermentative bacteria were all quantified by most probable number (MPN) at four different sites that ranged in spatial scale from a few meters to 15 km apart. The sites were sampled every 3 – 4 months over a two year period. Total cell counts were quite consistent temporally at each of the sites, and ranged from a high of 1.4 × 1010cells. gdw-1to a low of 8 × 108cells. gdw-1. Recoveries of all culturable bacteria were also site dependent and ranged from a minimum of 0.4% to a maximum of 40% of the total cell count. Aerobic bacteria were the dominant recovered population at all of the sites, followed by sulfur-oxidizing bacteria. Together these two groups accounted for >75% of the total recovered bacteria at each of the sites. The populations of anaerobic groups fluctuated significantly; S-disproportionating and SRB were most abundant followed by FeRB and fermenters. On average, all the anaerobes were in the same order of magnitude of abundance (107cells. gdw-1). Overall, these results suggest that aerobic bacteria consistently predominated in the top 10 cm of the marsh sediments, and that autotrophy related to sulfur oxidation and disproportionation may be important, but under studied processes in salt marsh ecosystems.
Bidirectional transcription marks accessible chromatin and is not specific to enhancers
Authors: Young Robert S. , Kumar Yatendra , Bickmore Wendy A. , Taylor Martin S.
Published: April 2016

Bidirectional transcription initiating at enhancers has been proposed to represent the signature of enhancer activity. Here we show that bidirectional transcription is a pervasive feature of all forms of accessible chromatin, including enhancers, promoters, CTCF-bound sites and other DNase hypersensitive regions. Transcription is less predictive for enhancer activity than epigenetic modifications such as H3K4me1 or the accessibility of DNA when measured in both enhancer assays and at endogenous loci. Bidirectional transcription initiation from accessible chromatin is therefore not sufficient for, nor specific to, enhancer activity. The stability of enhancer initiated transcripts does not influence measures of enhancer activity and we cannot detect any evidence of purifying selection on the resulting enhancer RNAs within the human population. Our results suggest that transcription initiating at enhancers is frequently a by-product of promiscuous RNA polymerase activity at accessible chromatin, and may not generally play a functional role in enhancer activity.