bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross Kelvin force microscopy and conductive atomic force microscopy studies of organic bulk heterojunction blends for local morphology and electrical behavior analysis
Authors: Villeneuve-Faure C. , Le Borgne D. , Bedel-Pereira E. , Moineau Chane-Ching K. I. , Hernandez-Maldonado D. , Séguy I.
Published: February 2015

Bulk Heterojunction (BHJ) organic photovoltaic devices performances depend on the relative organization and physical properties of the electron-donor and -acceptor materials. In this paper, BHJs of poly(3-hexyl-thiophene) (P3HT) associated with an electron acceptor material, 1-(3-methoxycarbonyl)-propyl-1-phenyl[6,6]C6 (PCBM) or [Ni(4dodpedt)2], are studied in terms of morphology, ordering, and electrical properties. First, comparison between the two BHJs performed by Atomic Force Microscopy (AFM) and Raman characterizations shows that P3HT structuration is improved by blending with [Ni(4dodpedt)2]. Then, the relationship between charges trapping, electrical properties, and film morphology is investigated using conductive AFM and Kelvin Force Microscopy. Measurements in dark condition and under solar cell simulator provide complementary information on electrical phenomena in these organic nanostructures. Finally, time dependent measurement highlights the influence of charges stacking on conduction. Specifically, we demonstrate that charge accumulation initiated by illumination remains valid after switching off the light, and induces the modification in current versus voltage characteristic of P3HT: PCBM blend. Finally, we observe a current increasing which can be attributed to the energy barrier decreasing due to charges trapping in PCBM.
Structural and thermal investigations of an amorphous GaSe9 alloy using EXAFS, cumulant expansion, and reverse Monte Carlo simulations
Authors: Siqueira M. C. , Maia R. N. A. , Araujo R. M. T. , Machado K. D. , Stolf S. F.
Published: February 2015

In this article, we investigated structural and thermal properties of an amorphous alloy of the Ga–Se system. The amorphous GaSe9 alloy was produced by mechanical alloying and it was studied using EXAFS spectroscopy and cumulant expansion method. We also made reverse Monte Carlo simulations using the total structure factor S(K) obtained from x-ray diffraction and the EXAFS χ(k) oscillations on Se and Ga K edges as input data. Several parameters, such as average coordination numbers and interatomic distances, structural and thermal disorders, asymmetry of the partial distribution functions gij(r), and Einstein and Debye temperatures, were determined. The gijE(r) functions were reconstructed from the cumulants C1, C2, and C3 obtained from the Einstein model, and they were compared to the gijRMC(r) functions obtained from the simulations. The simulations also furnished the partial bond angle distribution functions Θijℓ(cosθ), which describe the angular distribution of bonds between first neighbors, and give information about the kind of structural units present in the alloy.
Nanoscale heat transport from Ge hut, dome, and relaxed clusters on Si(001) measured by ultrafast electron diffraction
Authors: Frigge T. , Hafke B. , Tinnemann V. , Krenzer B. , Horn-von Hoegen M.
Published: February 2015

The thermal transport properties of crystalline nanostructures on Si were studied by ultra-fast surface sensitive time-resolved electron diffraction. Self-organized growth of epitaxial Ge hut, dome, and relaxed clusters was achieved by in-situ deposition of 8 monolayers of Ge on Si(001) at 550 °C under UHV conditions. The thermal response of the three different cluster types subsequent to impulsive heating by fs laser pulses was determined through the Debye-Waller effect. Time resolved spot profile analysis and life-time mapping was employed to distinguish between the thermal response of the different cluster types. While dome clusters are cooling with a time constant of τ = 150 ps, which agrees well with numerical simulations, the smaller hut clusters with a height of 2.3 nm exhibit a cooling time constant of τ = 50 ps, which is a factor of 1.4 slower than expected.
Two-dimensional materials let protons pass
Authors: Miller Johanna L.
Published: January 2015

Graphene and its cousin, boron nitride, may find new applications in hydrogen-based technologies.
An ultrafast camera films light at light speed
Authors: Smart Ashley G.
Published: January 2015

Exploiting a strategy known as compressed sensing, the camera can capture video at 100 billion frames per second.
The heat is on in concentrated emulsions
Authors: Miller Johanna L.
Published: January 2015

To understand the propagation of sound through a scattering medium, it’s necessary to account for the conversion of energy from acoustic to thermal and back again.
US nuclear scientists hash out priorities for their field
Authors: Feder Toni
Published: January 2015

Education, computing, experiments, and facilities jostle for position in a grassroots exercise that seeks to maintain a nuclear-physics workforce and scientific leadership.
Pakistan’s nuclear Taj Mahal
Authors: Leslie Stuart W.
Published: January 2015

Inspired by the promise of Atoms for Peace, the Pakistan Institute of Nuclear Science and Technology eventually succumbed to the demands of the country’s nuclear weapons program.
The influence of external factors on false alarms in an infrared fire detection system
Authors: Mengod Pedro Canales , Bravo José Andrés Torrent , Sardá Leticia López
Published: February 2015

There have been many studies on the use of different automatic wildfire detection systems, yet few long-term analyses of any of these techniques have been reported. In this paper we present the results obtained from the study of an infrared fire detection system that has been working in the field for more than 10 years, over which period it produced 10 519 false alarms. This article gives a brief description of the system and discusses the false alarms, showing that factors that are often not taken into account in the development of fire detection algorithms, such as camera orientation, the type of surface being monitored, or the time of day, can lead to false alarms being triggered.
Rapid loss of lakes on the Mongolian Plateau
Authors: Tao Shengli , Fang Jingyun , Zhao Xia , Zhao Shuqing , Shen Haihua , Hu Huifeng , Tang Zhiyao , Wang Zhiheng , Guo Qinghua
Published: February 2015

Significance

The Mongolian Plateau, composed mainly of Inner Mongolia in China and the Republic of Mongolia, has been experiencing remarkable lake shrinkage during the recent decades because of intensive human activities and climate changes. This study provides a comprehensive satellite-based evaluation of lake shrinkage across the plateau, and finds a greater decreasing rate of the number of lakes in Inner Mongolia than in Mongolia (34.0% vs. 17.6%) between the late 1980s and 2010, due mainly to an unsustainable mining boom and agricultural irrigation in the former. Disastrous damages to the natural systems are threatening the livelihood of local people, and we thus call for an urgent action to prevent further deterioration.
Phylogenomics with paralogs
Authors: Hellmuth Marc , Wieseke Nicolas , Lechner Marcus , Lenhof Hans-Peter , Middendorf Martin , Stadler Peter F.
Published: February 2015

Significance

We demonstrate that the distribution of paralogs in large gene families contains in itself sufficient phylogenetic signal to infer fully resolved species phylogenies. This source of phylogenetic information is independent of information contained in orthologous sequences and is resilient against horizontal gene transfer. An important consequence is that phylogenomics data sets need not be restricted to 1:1 orthologs.
Scaling laws describe memories of host–pathogen riposte in the HIV population
Authors: Barton John P. , Kardar Mehran , Chakraborty Arup K.
Published: February 2015

Significance

A cure or a vaccine for HIV remains elusive, and HIV is not known to be cleared by natural immune responses. Thus, one can study how a virus evolves in humans in the absence of effective directed selection pressures and harness this knowledge to inform vaccine design. We find that the sequence space accessed by circulating HIV strains is characterized by sets of sequences related by collectively coupled mutations that evade host immunity (an informative lower-dimensional representation of sequence space). These sets of sequences represent stored memories of host–pathogen combat won by the virus (analogous to neural networks) and obey power law scaling. The collective escape pathways we reveal must be thwarted by an effective vaccine.
A conserved amphipathic helix is required for membrane tubule formation by Yop1p
Authors: Brady Jacob P. , Claridge Jolyon K. , Smith Peter G. , Schnell Jason R.
Published: February 2015

Significance

The first structural studies, to our knowledge, of a reticulon homology domain (RHD), which is essential for maintaining smooth endoplasmic reticulum (ER) tubules and the edges of ER sheets, are described. We show here that the RHD of the protein Yop1p from the YOP1 gene has hydrophobic helices long enough to cross the membrane fully but contains a previously uncharacterized amphipathic helix (APH) that is necessary for membrane tubule formation. The APH is highly conserved in its amino acid properties and its location relative to the RHD both in the DP1 (deleted in polyposis) and reticulon families. These results place the DP1/reticulon proteins into the large and growing class of membrane-remodeling proteins that use APHs to influence membrane curvature.
CRYPTOCHROME-mediated phototransduction by modulation of the potassium ion channel β-subunit redox sensor
Authors: Fogle Keri J. , Baik Lisa S. , Houl Jerry H. , Tran Tri T. , Roberts Logan , Dahm Nicole A. , Cao Yu , Zhou Ming , Holmes Todd C.
Published: February 2015

Significance

CRYPTOCHROMES (CRYs) are blue light photoreceptors that mediate phototransduction in brain arousal neurons, as well as circadian light entrainment in
Drosophila
fruit flies. We describe how light-activated
Drosophila
CRY couples to membrane depolarization and increased action potential firing rate in large ventral lateral arousal neurons. Pharmacological treatments that specifically disrupt the CRY redox-sensitive flavin chromophore or block voltage-gated K
+
channels abolish the light response. Correspondingly, we find that the Kvβ channel subunit
Hyperkinetic
with a well conserved redox sensor domain links light-evoked redox changes in CRY to rapid changes in membrane electrical potential.
Penta-graphene: A new carbon allotrope
Authors: Zhang Shunhong , Zhou Jian , Wang Qian , Chen Xiaoshuang , Kawazoe Yoshiyuki , Jena Puru
Published: February 2015

Significance

Carbon has many faces––from diamond and graphite to graphene, nanotube, and fullerenes. Whereas hexagons are the primary building blocks of many of these materials, except for C
20
fullerene, carbon structures made exclusively of pentagons are not known. Because many of the exotic properties of carbon are associated with their unique structures, some fundamental questions arise: Is it possible to have materials made exclusively of carbon pentagons and if so will they be stable and have unusual properties? Based on extensive analyses and simulations we show that penta-graphene, composed of only carbon pentagons and resembling Cairo pentagonal tiling, is dynamically, thermally, and mechanically stable. It exhibits negative Poisson's ratio, a large band gap, and an ultrahigh mechanical strength.
Crossovers are associated with mutation and biased gene conversion at recombination hotspots
Authors: Arbeithuber Barbara , Betancourt Andrea J. , Ebner Thomas , Tiemann-Boege Irene
Published: February 2015

Significance

We present experimental evidence showing that meiosis is an important source of germline mutations. Because sites of meiotic recombination experience recurrent double-strand breaks at hotspots, recombination has been previously suspected to be mutagenic. Yet inferences made from sequence comparisons have not found strong evidence for a mutagenic effect of recombination. Here, we directly sequenced a large number of single sperm DNA molecules and found more new mutations in molecules with a crossover than in molecules without a recombination event. We also observed that GC alleles are transmitted more often than AT alleles at polymorphic sites. Our data demonstrate that both mutagenesis and biased transmission occur during crossing over in meiosis and are important modifiers of the sequence content at recombination hotspots.
Glycosylation profiles determine extravasation and disease-targeting properties of armed antibodies
Authors: Venetz Dario , Hess Christian , Lin Chia-wei , Aebi Markus , Neri Dario
Published: February 2015

Significance

Therapeutic antibodies represent the largest and fastest growing class of biopharmaceuticals. There is a trend in moving from intact antibodies toward “armed” antibody products, in which the antibody moiety serves as pharmacodelivery vehicle. The impact of glycosylation on the targeting performance of armed antibodies is still largely unknown. Our article sheds light on the surprising finding that relatively small variations in glycostructures and sialic acid content can have dramatic effects on therapeutic agent performance. A better understanding of the impact of glycosylation on pharmaceutical activity is likely to be relevant not only for future antibody development activities, but also for changes in current manufacturing processes and for the development of biosimilar products.
Suppression of phase separation and giant enhancement of superconducting transition temperature in FeSe

1−
x

Te

x

thin films
Authors: Imai Yoshinori , Sawada Yuichi , Nabeshima Fuyuki , Maeda Atsutaka
Published: February 2015

Significance

To clarify the mechanism of superconductivity in iron-based superconductors, it is crucial to investigate FeSe

1−
x

Te

x

, which has the simplest crystal structure among them. There is, however, a serious obstacle to the understanding of its superconductivity; phase separation occurs in the region of

0.1
≤
x
≤
0.4

, and thus a whole phase diagram has not been available. Here we report the successful fabrication of FeSe

1−
x

Te

x

films with

0
≤
x
≤
1

. This is, to our knowledge, the first demonstration of the suppression of the phase separation. What is more notable is that a giant enhancement of

T
c

is observed in the “phase-separation region.” The complete phase diagram that we present provides a previously unidentified perspective for the mechanism of superconductivity of this material.
Droplet fragmentation: 3D imaging of a previously unidentified pore-scale process during multiphase flow in porous media
Authors: Pak Tannaz , Butler Ian B. , Geiger Sebastian , van Dijke Marinus I. J. , Sorbie Ken S.
Published: February 2015

Significance

Fluid displacement processes in carbonate rocks are important because they host over 50% of the world's hydrocarbon reserves and are aquifers supplying water to one quarter of the global population. A previously unidentified pore-scale fluid displacement event, droplet fragmentation, is described that occurs during the flow of two immiscible fluids specifically in carbonate rocks. The complex, heterogeneous pore structure of carbonate rocks induces this droplet fragmentation process, which explains the increased recovery of the nonwetting phase from porous carbonates as the wetting phase injection rate is increased. The previously unidentified displacement mechanism has implications for (
i
) enhanced oil recovery, (
ii
) remediation of nonaqueous liquid contaminants in aquifers, and (
iii
) subsurface CO
2
storage.
Tonoplast CBL–CIPK calcium signaling network regulates magnesium homeostasis in Arabidopsis
Authors: Tang Ren-Jie , Zhao Fu-Geng , Garcia Veder J. , Kleist Thomas J. , Yang Lei , Zhang Hong-Xia , Luan Sheng
Published: February 2015

Significance

Plant growth requires a balanced supply of mineral nutrients. However, the availability of minerals varies constantly in the environment. How do plants adapt to low or high levels of minerals in the soil? The answer to this question holds the key to sustainable crop production. Mg is an essential macronutrient for plants, but high levels of Mg
2+
can become toxic. This study uncovered a regulatory mechanism, consisting of two calcineurin B-like (CBL) Ca sensors partnering with four CBL-interacting protein kinases (CIPKs) forming a CBL–CIPK network that allows plant cells to sequester the extra Mg
2+
into vacuoles, thereby protecting plant cells from high-Mg toxicity. To our knowledge, this report is the first that describes such a signaling mechanism for regulation of Mg homeostasis.
Plasma butyrylcholinesterase regulates ghrelin to control aggression
Authors: Chen Vicky Ping , Gao Yang , Geng Liyi , Parks Robin J. , Pang Yuan-Ping , Brimijoin Stephen
Published: February 2015

Significance

Butyrylcholinesterase (BChE), a common plasma enzyme, has been known for decades but its real physiological roles are just beginning to emerge. Although BChE eliminates the neurotransmitter acetylcholine, it is not vital for locomotion, cognition, or other cholinergic functions. Nevertheless, we now find that circulating BChE has a large impact on aggressive behavior in mice that is attributable to its ability to inactivate ghrelin, a peptide hormone involved in hunger, feeding, and stress. A key observation was decreased fighting among group-housed male mice overexpressing BChE after viral gene transfer. In contrast, BChE knockout mice exhibited increased fighting. These effects mirrored changes in plasma levels of active ghrelin. Controlling them might offer therapeutic potential for certain behavioral disorders.
Copper economy in
Chlamydomonas
: Prioritized allocation and reallocation of copper to respiration vs. photosynthesis
Authors: Kropat Janette , Gallaher Sean D. , Urzica Eugen I. , Nakamoto Stacie S. , Strenkert Daniela , Tottey Stephen , Mason Andrew Z. , Merchant Sabeeha S.
Published: February 2015

Significance

Many inorganic elements, because they are required for catalysis or as structural components in biomolecules, are essential nutrients for life. In a situation of poor nutrition, organisms economize on the use of these elements by choosing alternate chemistries to achieve the same function. The mechanism of copper economy in
Chlamydomonas
involves replacement of copper-containing plastocyanin with heme-containing cytochrome (Cyt)
c
6
. The copper that is saved by this substitution is used instead for Cyt oxidase biosynthesis. Copper recycling requires proteolysis of plastocyanin dependent on a copper-sensing transcription factor. A candidate protease has been identified.
Double-stranded RNA made in
C. elegans
neurons can enter the germline and cause transgenerational gene silencing
Authors: Devanapally Sindhuja , Ravikumar Snusha , Jose Antony M.
Published: February 2015

Significance

The germline, which produces sperm or oocyte, is separated from other cells that generate the rest of the body, the soma, during early development in most animals. Somatic cells experience and respond to the environment in each generation, and it is unknown whether they can transmit information to the germline for inheritance into subsequent generations. We found that neurons of the worm
Caenorhabditis elegans
can transmit double-stranded RNA to the germline to initiate transgenerational silencing of a gene of matching sequence. To our knowledge, these results demonstrate for the first time that a somatic tissue of an animal can have transgenerational effects on a gene through the transport of double-stranded RNA to the germline.
Macrophages eat cancer cells using their own calreticulin as a guide: Roles of TLR and Btk
Authors: Feng Mingye , Chen James Y. , Weissman-Tsukamoto Rachel , Volkmer Jens-Peter , Ho Po Yi , McKenna Kelly M. , Cheshier Samuel , Zhang Michael , Guo Nan , Gip Phung , Mitra Siddhartha S. , Weissman Irving L.
Published: February 2015

Significance

Macrophage-mediated programmed cell removal (PrCR) plays an essential role in tumor surveillance and elimination. Blockade of the don't-eat-me signal CD47 on tumor cells allows already expressed eat-me signals to induce PrCR to eliminate tumor cells. To date the molecular mechanism by which macrophages recognize and phagocytose tumor cells remains unclear. This paper demonstrates that the activation of Toll-like receptor (TLR) pathways in macrophages induces the phosphorylation of Bruton's tyrosine kinase (Btk), which catalyzes cell-surface exposure of calreticulin. Calreticulin on or secreted by macrophages plays a critical role in mediating adjacent tumor cell recognition and phagocytosis. These findings reveal a strategy to enhance the efficacy of PrCR through a combination of TLR/Btk activation and CD47 blockade, and advance our understanding of the underlying mechanism of macrophage-mediated PrCR of tumor cells.
Generation of reactive oxygen species by lethal attacks from competing microbes
Authors: Dong Tao G. , Dong Shiqi , Catalano Christy , Moore Richard , Liang Xiaoye , Mekalanos John J.
Published: February 2015

Significance

How microbes respond to lethal attacks from competing species is not fully understood. Here, we investigated the response of
Escherichia coli
to attacks from the type VI secretion system (T6SS), bacteriophage P1
vir
, and polymyxin B. We report that generation of reactive oxygen species (ROS) is a general outcome of potentially lethal activities mediated by contact-dependent or contact-independent interactions of aggressive competing bacterial species and phage. An ROS response gene,
soxS
, is highly induced in response to all sources of attacks tested. This discovery will likely prompt other investigations into why evolution has selected expression of this gene as a “first responder” to potentially lethal interspecies competition.
Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients
Authors: Jiang Peiyong , Chan Carol W. M. , Chan K. C. Allen , Cheng Suk Hang , Wong John , Wong Vincent Wai-Sun , Wong Grace L. H. , Chan Stephen L. , Mok Tony S. K. , Chan Henry L. Y. , Lai Paul B. S. , Chiu Rossa W. K. , Lo Y. M. Dennis
Published: February 2015

Significance

We used massively parallel sequencing to study the size profiles of plasma DNA samples at single-base resolution and in a genome-wide manner. We used chromosome arm-levelz-score analysis (CAZA) to identify tumor-derived plasma DNA for studying their specific size profiles. We showed that populations of aberrantly short and long DNA molecules existed in the plasma of patients with hepatocellular carcinoma. The short ones preferentially carried the tumor-associated copy number aberrations. We further showed that there were elevated amounts of mitochondrial DNA in the plasma of hepatocellular carcinoma patients. Such molecules were much shorter than the nuclear DNA in plasma. These findings have shed light on fundamental biological characteristics of plasma DNA and related diagnostic applications for cancer.
A tale of two statues in Astana: the fuzzy process of nationalistic city making
Authors: Fauve Adrien
Published: February 2015

In the summer of 2009, statues stood leaning in a yard, beyond Independence Square in Astana. The situation was incongruous and constituted an enigma: Why were these monuments left alone in shambles? This paper argues that nationalistic city making is more of a resource for people involved in patron/client relationships and a contingent outcome, rather than a planned strategy. This case study, drawing on evidence gathered through qualitative methods with artists and urban-planners, hence reveals a paradox: in Kazakhstan, there surely is a state incentive to produce nationalistic symbols, but in the absence of a mid-term strategy, city-planners and the people they work with improvise in order to answer local authorities' demands, and use this opportunity to advance their own interests. Hence, the political production of space is considered a fuzzy process, contingent on the agency of multiple subjects, and treated as an outcome of Foucauldian “micro-physics of power.” But even though it is erratic, it still creates the built environment which will be reacted upon by citizens. Finally, this sociopolitical perspective on nationalistic urbanism demonstrates that Astana's scenery is a fuzzy “landscape of power” instituting an erratic Kazakhstani regime, based on the political economy of symbolic goods.
ICOS maintains the T follicular helper cell phenotype by down-regulating Krüppel-like factor 2
Authors: Weber Jan P. , Fuhrmann Franziska , Feist Randi K. , Lahmann Annette , Al Baz Maysun S. , Gentz Lea-Jean , Vu Van Dana , Mages Hans W. , Haftmann Claudia , Riedel René , Grün Joachim R. , Schuh Wolfgang , Kroczek Richard A. , Radbruch Andreas , Mashreghi Mir-Farzin , Hutloff Andreas
Published: February 2015

The co-stimulators ICOS (inducible T cell co-stimulator) and CD28 are both important for T follicular helper (TFH) cells, yet their individual contributions are unclear. Here, we show that each molecule plays an exclusive role at different stages of TFH cell development. While CD28 regulated early expression of the master transcription factor Bcl-6, ICOS co-stimulation was essential to maintain the phenotype by regulating the novel TFH transcription factor Klf2 via Foxo1. Klf2 directly binds to Cxcr5, Ccr7, Psgl-1, and S1pr1, and low levels of Klf2 were essential to maintain this typical TFH homing receptor pattern. Blocking ICOS resulted in relocation of fully developed TFH cells back to the T cell zone and reversion of their phenotype to non-TFH effector cells, which ultimately resulted in breakdown of the germinal center response. Our study describes for the first time the exclusive role of ICOS and its downstream signaling in the maintenance of TFH cells by controlling their anatomical localization in the B cell follicle.
A packed Ramsey’s theorem and computability theory
Authors: Flood Stephen
Published: February 2015

Ramsey’s theorem states that each coloring has an infinite homogeneous set, but these sets can be arbitrarily spread out. Paul Erdős and Fred Galvin proved that for each coloring

f
f

, there is an infinite set that is “packed together” which is given “a small number” of colors by

f
f

.

We analyze the strength of this theorem from the perspective of computability theory and reverse mathematics. We show that this theorem is close in computational strength to the standard Ramsey’s theorem by giving arithmetical upper and lower bounds for solutions to computable instances. In reverse mathematics, we show that that this packed Ramsey’s theorem is equivalent to Ramsey’s theorem for exponents

n
≠
2

n\neq 2

. When

n
=
2

n=2

, we show that it implies Ramsey’s theorem and that it does not imply

A
C
A

0

\mathsf {ACA}_0

.
On the stable moment graph of an affine Kac–Moody algebra
Authors: Lanini Martina
Published: February 2015

In 1980 Lusztig proved a stabilisation property of the affine Kazhdan-Lusztig polynomials. In this paper we give a categorical version of such a result using the theory of sheaves on moment graphs. This leads us to associate with any Kac-Moody algebra its stable moment graph.
GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms
Authors: Manor Ohad , Segal Eran
Published: January 2015

Summary: Understanding the effect of single nucleotide polymorphisms (SNPs) on the expression level of genes is an important goal. We recently published a study in which we devised a multi-SNP predictive model for gene expression in Lymphoblastoid cell lines (LCL), and showed that it can robustly predict the expression of a small number of genes in test individuals. Here, we validate the generality of our models by predicting expression profiles for genes in LCL in an independent study, and extend the pool of predictable genes for which we are able to explain more than 25% of their expression variability to 232 genes across 14 different cell types. As the number of people who obtained their SNP profiles through companies such as 23andMe is rising rapidly, we developed GenoExp , a web-based tool in which users can upload their individual SNP data and obtain predicted expression levels for the set of predictable genes across the 14 different cell types. Our tool thus allows users with biological knowledge to study the possible effects that their set of SNPs might have on these genes and predict their cell-specific expression levels relative to the population average.

Availability and implementation:  GenoExp is freely available at http://genie.weizmann.ac.il/pubs/GenoExp/ .

Contact:  eran.segal@weizmann.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
RAMPART: a workflow management system for
de novo
genome assembly
Authors: Mapleson Daniel , Drou Nizar , Swarbreck David
Published: January 2015

Motivation: The de novo assembly of genomes from whole- genome shotgun sequence data is a computationally intensive, multi-stage task and it is not known a priori which methods and parameter settings will produce optimal results. In current de novo assembly projects, a popular strategy involves trying many approaches, using different tools and settings, and then comparing and contrasting the results in order to select a final assembly for publication.

Results: Herein, we present RAMPART, a configurable workflow management system for de novo genome assembly, which helps the user identify combinations of third-party tools and settings that provide good results for their particular genome and sequenced reads. RAMPART is designed to exploit High performance computing environments, such as clusters and shared memory systems, where available.

Availability and implementation: RAMPART is available under the GPLv3 license at: https://github.com/TGAC/RAMPART .

Contact:  daniel.mapleson@tgac.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online. In addition, the user manual is available online at: http://rampart.readthedocs.org/en/latest .
NetExplore: a web server for modeling small network motifs
Authors: Papatsenko Dmitri , Lemischka Ihor R.
Published: January 2015

Motivation: Quantitative and qualitative assessment of biological data often produces small essential recurrent networks, containing 3–5 components called network motifs. In this context, model solutions for small network motifs represent very high interest.

Results: Software package NetExplore has been created in order to generate, classify and analyze solutions for network motifs including up to six network components. NetExplore allows plotting and visualization of the solution's phase spaces and bifurcation diagrams.

Availability and implementation: The current version of NetExplore has been implemented in Perl-CGI and is accessible at the following locations: http://line.bioinfolab.net/nex/NetExplore.htm and http://nex.autosome.ru/nex/NetExplore.htm .

Contact:  dmitri.papatsenko@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Omics Pipe: a community-based framework for reproducible multi-omics data analysis
Authors: Fisch Kathleen M. , Meißner Tobias , Gioia Louis , Ducom Jean-Christophe , Carland Tristan M. , Loguercio Salvatore , Su Andrew I.
Published: January 2015

Motivation: Omics Pipe ( http://sulab.scripps.edu/omicspipe ) is a computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole-Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis. The goal of Omics Pipe is to democratize next-generation sequencing analysis by dramatically increasing the accessibility and reproducibility of best practice computational pipelines, which will enable researchers to generate biologically meaningful and interpretable results.

Results: Using Omics Pipe, we analyzed 100 TCGA breast invasive carcinoma paired tumor-normal datasets based on the latest UCSC hg19 RefSeq annotation. Omics Pipe automatically downloaded and processed the desired TCGA samples on a high throughput compute cluster to produce a results report for each sample. We aggregated the individual sample results and compared them to the analysis in the original publications. This comparison revealed high overlap between the analyses, as well as novel findings due to the use of updated annotations and methods.

Availability and implementation: Source code for Omics Pipe is freely available on the web ( https://bitbucket.org/sulab/omics_pipe ). Omics Pipe is distributed as a standalone Python package for installation ( https://pypi.python.org/pypi/omics_pipe ) and as an Amazon Machine Image in Amazon Web Services Elastic Compute Cloud that contains all necessary third-party software dependencies and databases ( https://pythonhosted.org/omics_pipe/AWS_installation.html ).

Contact:  asu@scripps.edu or kfisch@ucsd.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Dizzy-Beats: a Bayesian evidence analysis tool for systems biology
Authors: Aitken Stuart , Kilpatrick Alastair M. , Akman Ozgur E.
Published: January 2015

Motivation: Model selection and parameter inference are complex problems of long-standing interest in systems biology. Selecting between competing models arises commonly as underlying biochemical mechanisms are often not fully known, hence alternative models must be considered. Parameter inference yields important information on the extent to which the data and the model constrain parameter values.

Results: We report Dizzy-Beats, a graphical Java B ayesian e vidence a nalysis t ool implementing nested s ampling - an algorithm yielding an estimate of the log of the Bayesian evidence Z and the moments of model parameters, thus addressing two outstanding challenges in systems modelling. A likelihood function based on the L1 -norm is adopted as it is generically applicable to replicated time series data.

Availability and implementation:  http://sourceforge.net/p/bayesevidence/home/Home/

Contact:  s.aitken@ed.ac.uk
ClassifyR: an R package for performance assessment of classification with applications to transcriptomics
Authors: Strbenac Dario , Mann Graham J. , Ormerod John T. , Yang Jean Y.H.
Published: February 2015

Although a large collection of classification software packages exist in R, a new generic framework for linking custom classification functions with classification performance measures is needed. A generic classification framework has been designed and implemented as an R package in an object oriented style. Its design places emphasis on parallel processing, reproducibility and extensibility. Finally, a comprehensive set of performance measures are available to ease post-processing. Taken together, these important characteristics enable rapid and reproducible benchmarking of alternative classifiers.

Availability and implementation: ClassifyR is implemented in R and can be obtained from the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/ClassifyR.html

Contact : dario.strbenac@sydney.edu.au

Supplementary information : Supplementary data are available at Bioinformatics online.
Antiretroviral Treatment Failure, Drug Resistance, and Subtype Diversity in the Only Pediatric HIV Clinic in Rhode Island
Authors: Rogo Tanya , DeLong Allison K. , Chan Philip , Kantor Rami
Published: January 2015

Background.  Drug resistance development in the human immunodeficiency virus (HIV)-infected pediatric population in the United States can impact long-term antiretroviral therapy (ART) efficacy. Limited formularies and adherence constraints in children jeopardize lifelong-needed ART.

Methods.  We examined treatment failure, drug resistance, and their correlates in ART-naive and ART-experienced children attending the pediatric HIV clinic in Rhode Island between 1991 and 2012. Pol sequences were obtained for phylogenetic, subtype, and resistance analyses. Associations between selected covariates and virologic failure and resistance were evaluated using generalized additive models and Fisher exact tests.

Results.  Data were available for all 56 clinic-attending children. At diagnosis, 33% were aged <1 year, 31% aged 1–4 years, and 37% aged ≥5 years; 54% were male, 73% black or Hispanic, 55% US-born, 20% refugees, and 64% perinatally infected. Of 44 ART-experienced children, 57% had virologic failure, most never virologically suppressed. Failure was associated with missed appointments (P = .05) and missed doses (P < .01). Of 40 children with available genotypes, 35% were infected with non-B subtypes; 6% of ART-naive children had resistance; and 73% of ART-experienced children had ≥1 major mutation: (16% conferring triple-class, 47% dual-class, and 37% single-class resistance). An epidemiologically confirmed resistance transmission from a perinatally infected teenage male to a newly infected teenage female was demonstrated.

Conclusions.  We report high HIV type 1 diversity, extensive drug resistance among ART-experienced children, and horizontal transmission of resistance in the Rhode Island pediatric HIV clinic. As HIV-infected children mature into adulthood, close monitoring of ART, adherence, and diagnosis disclosure are essential to optimize patient care.
Adverse Events Following Measles, Mumps, and Rubella Vaccine in Adults Reported to the Vaccine Adverse Event Reporting System (VAERS), 2003–2013
Authors: Sukumaran Lakshmi , McNeil Michael M. , Moro Pedro L. , Lewis Paige W. , Winiecki Scott K. , Shimabukuro Tom T.
Published: January 2015

Background.  Limited data exist on the safety of the measles, mumps, and rubella (MMR) vaccine in adults. We reviewed reports of adverse events (AEs) to the Vaccine Adverse Event Reporting System (VAERS) to assess safety in this previously understudied group.

Methods.  VAERS is the national spontaneous vaccine safety surveillance system coadministered by the Centers for Disease Control and Prevention and the US Food and Drug Administration. We searched the VAERS database for US reports of adults aged ≥19 years who received the MMR vaccine from 1 January 2003 to 31 July 2013. We clinically reviewed reports and available medical records for serious AEs, pregnancy reports, and reports for selected prespecified outcomes.

Results.  During this period, VAERS received 3175 US reports after MMR vaccine in adults. Of these, 168 (5%) were classified as serious, including 7 reports of death. Females accounted for 77% of reports. The most common signs and symptoms for all reports were pyrexia (19%), rash (17%), pain (13%), and arthralgia (13%). We did not detect any new safety findings in empirical Bayesian data mining. We identified 131 reports of MMR vaccine administered to a pregnant woman; the majority of these vaccinations were in the first trimester and in 83 (62%), no AE was reported.

Conclusions.  In our review of VAERS data, we did not detect any new or unexpected safety concerns for MMR vaccination in adults. We identified reports of pregnant women exposed to MMR, which is a group in whom the vaccine is contraindicated, suggesting the need for continued provider education on vaccine recommendations and screening.
The efficacy of azithromycin and doxycycline for the treatment of rectal chlamydia infection: a systematic review and meta-analysis
Authors: Kong Fabian Yuh Shiong , Tabrizi Sepehr N. , Fairley Christopher Kincaid , Vodstrcil Lenka A. , Huston Wilhelmina M. , Chen Marcus , Bradshaw Catriona , Hocking Jane S.
Published: January 2015

Background

There are increasing concerns about treatment failure following treatment for rectal chlamydia with 1 g of azithromycin. A systematic review and meta-analysis was conducted to investigate the efficacy of 1 g of azithromycin as a single dose or 100 mg of doxycycline twice daily for 7 days for the treatment of rectal chlamydia.

Methods

Medline, Embase, PubMed, Cochrane Controlled Trials Register, Australia New Zealand Clinical Trial Register and ClinicalTrials.gov were searched to the end of April 2014. Studies using 1 g of azithromycin or 7 days of doxycycline for the treatment of rectal chlamydia were eligible. Gender, diagnostic test, serovar, symptomatic status, other sexually transmitted infections, follow-up time, attrition and microbial cure were extracted. Meta-analysis was used to calculate pooled (i) azithromycin and doxycycline efficacy and (ii) efficacy difference.

Results

All eight included studies were observational. The random-effects pooled efficacy for azithromycin (based on eight studies) was 82.9% (95% CI 76.0%–89.8%; I2 = 71.0%; P < 0.01) and for doxycycline (based on five studies) was 99.6% (95% CI 98.6%–100%; I2 = 0%; P = 0.571), resulting in a random-effects pooled efficacy difference (based on five studies) of 19.9% (95% CI 11.4%–28.3%; I2 = 48.5%; P = 0.101) in favour of doxycycline.

Conclusions

The efficacy of single-dose azithromycin may be considerably lower than 1 week of doxycycline for treating rectal chlamydia. However, the available evidence is very poor. Robust randomized controlled trials are urgently required.
The nature of obscuration in AGNs – II. Insights from clustering properties
Authors: Shao Li , Li Cheng , Kauffmann Guinevere , Wang Jing
Published: January 2015

Based on large optical and mid-infrared (mid-IR) surveys, we investigate the relation between nuclear activity in local Seyfert 2 galaxies and galaxy interactions using a statistical neighbour-counting technique. At the same level of host galaxy star formation (SF), we find that active galactic nuclei (AGNs) with stronger ${\rm [O\,\small {III}]}$ emission lines do not show an excess of near neighbours, while AGNs with stronger mid-IR emission do have more near neighbours within a projected distance of 100 kpc. The excess neighbour count increases with decreasing projected radius. These results suggest a phase of torus formation during galaxy interactions.
Environmental Security
Authors: Scott Christopher A. , Thapa Bhuwan
Published: February 2015

Environmental security, as a subset of broader concerns over human security, is addressed from the disciplinary perspectives of international relations, political science, geography, development studies, and environmental studies. The concept of environmental security views ecological processes and natural resources as sources or catalysts of conflict, barriers or limits to human well-being, or conversely, as the means to mitigate or resolve insecurity. Security over natural resources—particularly energy and increasingly water—seen in terms of territorial control, treaty arrangements, and trade agreements (including the application of economic instruments) over production and conveyance of resources to demand locations, has tended to frame the analysis in international relations and political science. While spatial and transboundary concerns over resources continue to occupy geographers, attention in the field of geography is drawn increasingly to social equity and environmental justice dimensions of resource use and outcomes. Development studies focused on emerging economies and societies in rapid transition addresses environmental security in terms of differential national or regional access to resources and impacts, e.g., associated with pollution, deprivation, etc. And among other points of concern, environmental studies addresses environmental security in terms of local, intra-household, and gender-differentiated access to water, energy, and food as well as outcomes such as public health, nutrition, and quality of life. While the term environmental security has existed since at least the 1980s, its prominence in academic and political circles rose significantly after the 1994 Human Development Report of the United Nations Development Programme, which formulated the broadly accepted concept of human security. This report identified environmental security together with economic, food, health, personal, community, and political security as core components of human security. Since the 1990s, the definition and scope of environmental security have broadened to include multiple subsets, including food security, energy security, and water security, as well as emerging notions of adaptation and resilience to hazards, e.g., climate security, and all of these are referred to in this article. No attempt is made to treat the broad and ever-widening field of environmental security exhaustively. The principal aims are to trace the evolution of security discourses, consider securitization of the environment and natural resources, and assess new conceptions of environmental security in the context of global change. This work is funded by the Lloyd’s Register Foundation, a charitable foundation helping to protect life and property by supporting engineering-related education, public engagement, and the application of research.
Disease Ecology
Authors: Ostfeld Richard S.
Published: February 2015

Disease ecology is a rapidly developing subdiscipline of ecology concerned with how species interactions and abiotic components of the environment affect patterns and processes of disease. To date, disease ecology has focused largely on infectious disease. The scientific study of infectious disease has a long history dominated by specialists on the taxa of infectious agents (e.g., bacteriologists, virologists), mechanisms of host defense (e.g., immunologists), effects of infection on individual hosts (e.g., pathologists), effects on host populations (epidemiologists), and treatment (e.g., practicing physicians and veterinarians). Disease ecology arose as scientists increasingly recognized that the interactions between pathogen and host could be conceptually united with other interspecific interactions, such as those between predator and prey, competitors, or mutualists. At its simplest, an infectious disease consists of an interaction between one species of pathogen and one species of host. The evolution of disease ecology since the late 20th century has incorporated additional layers of complexity, including recognition that most pathogens infect multiple species of host, that hosts are infected with multiple pathogens, and that abiotic conditions (e.g., temperature, moisture) interact with biotic conditions to affect transmission and disease. As a consequence, a framework broader than the simplest host-pathogen system is often required to understand disease dynamics. Disease ecologists are interested both in the ecological causes of disease patterns (for instance, how the population density of a host influences transmission rates), and the ecological consequences of disease (for instance, how the population dynamics of a host species change as an epidemic progresses). Consequently, disease ecology today often integrates across several levels of biological organization, from molecular mechanisms of pathology and immunity; to individual-organism changes in health, survival, and reproduction; to population dynamics of hosts and pathogens; to community dynamics of hosts and pathogens; to impacts of disease on ecosystem processes; to ecosystem-level effects of climate change and landscape change on disease.