bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-formed copper oxide contact interlayer for high-performance oxide thin film transistors
Authors: Gao Xu , Aikawa Shinya , Mitoma Nobuhiko , Lin Meng-Fang , Kizu Takio , Nabatame Toshihide , Tsukagoshi Kazuhito
Published: July 2014

Oxide thin film transistor employing copper source/drain electrodes shows a small turn on voltage and reduced hysteresis. Cross-sectional high-resolution transmission electron microscopy image confirmed the formation of ∼4 nm CuOx related interlayer. The lower bond-dissociation energy of Cu-O compared to Si-O and In-O suggests that the interlayer was formed by adsorbing oxygen molecules from surrounding environment instead of getting oxygen atoms from the semiconductor film. The formation of CuOx interlayer acting as an acceptor could suppress the carrier concentration in the transistor channel, which would be utilized to control the turn on voltage shifts in oxide thin film transistors.
Simultaneous monitoring of singlet and triplet exciton variations in solid organic semiconductors driven by an external static magnetic field
Authors: Ding Baofu , Alameh Kamal
Published: July 2014

The research field of organic spintronics has remarkably and rapidly become a promising research area for delivering a range of high-performance devices, such as magnetic-field sensors, spin valves, and magnetically modulated organic light emitting devices (OLEDs). Plenty of microscopic physical and chemical models based on exciton or charge interactions have been proposed to explain organic magneto-optoelectronic phenomena. However, the simultaneous observation of singlet- and triplet-exciton variations in an external magnetic field is still unfeasible, preventing a thorough theoretical description of the spin dynamics in organic semiconductors. Here, we show that we can simultaneously observe variations of singlet excitons and triplet excitons in an external magnetic field, by designing an OLED structure employing a singlet-exciton filtering and detection layer in conjunction with a separate triplet-exciton detection layer. This OLED structure enables the observation of a Lorentzian and a non-Lorentzian line-shape magnetoresponse for singlet excitons and triplet excitons, respectively.
Very high efficiency phosphorescent organic light-emitting devices by using rough indium tin oxide
Authors: Zhang Yingjie , Aziz Hany
Published: July 2014

The efficiency of organic light-emitting devices (OLEDs) is shown to significantly depend on the roughness of the indium tin oxide (ITO) anode. By using rougher ITO, light trapped in the ITO/organic wave-guided mode can be efficiently extracted, and a light outcoupling enhancement as high as 40% is achieved. Moreover, contrary to expectations, the lifetime of OLEDs is not affected by ITO roughness. Finally, an OLED employing rough ITO anode that exhibits a current efficiency of 56 cd/A at the remarkably high brightness of 105 cd/m2 is obtained. This represents the highest current efficiency at such high brightness to date for an OLED utilizing an ITO anode, without any external light outcoupling techniques. The results demonstrate the significant efficiency benefits of using ITO with higher roughness in OLEDs.
Detecting the dipole moment of a single carbon monoxide molecule
Authors: Schwarz A. , Köhler A. , Grenz J. , Wiesendanger R.
Published: July 2014

Using non-contact atomic force microscopy with metallic tips enabled us to detect the electrostatic dipole moment of single carbon monoxide (CO) molecules adsorbed on three very different substrates. The observed distance dependent contrast can be explained by an interplay between the attractive van der Waals interaction and the repulsive electrostatic interaction, respectively, with the latter stemming from antiparallel aligned dipoles in tip and molecule. Our results suggest that metallic as well as CO-functionalized tips are able to probe electrostatic properties of polar molecules and that repulsive dipole-dipole interactions have to be considered when interpreting complex contrast patterns.
Electrically induced insulator to metal transition in epitaxial SmNiO3 thin films
Authors: Shukla Nikhil , Joshi Toyanath , Dasgupta Sandeepan , Borisov Pavel , Lederman David , Datta Suman
Published: July 2014

We report on the electrically induced insulator to metal transition (IMT) in SmNiO3 thin films grown on (001) LaAlO3 by pulsed laser deposition. The behavior of the resistivity as a function of temperature suggests that the primary transport mechanism in the SmNiO3 insulating state is dominated by Efros-Shklovskii variable range hopping (ES-VRH). Additionally, the magnetic transition in the insulating state of SmNiO3 modifies the characteristics of the ES-VRH transport. Systematic DC and pulsed current-voltage measurements indicate that current-induced joule heating is the fundamental mechanism driving the electrically induced IMT in SmNiO3. These transport properties are explained in context of the IMT in SmNiO3 being related to the strong electron-lattice coupling.
Influence of irradiation upon few-layered graphene using electron-beams and gamma-rays
Authors: Wang Yuqing , Feng Yi , Mo Fei , Qian Gang , Chen Yangming , Yu Dongbo , Wang Yang , Zhang Xuebin
Published: July 2014

Few-layered graphene (FLG) is irradiated by electron beams and gamma rays. After 100 keV electron irradiation, the edges of FLG start bending, shrinking, and finally generate gaps and carbon onions due to sputtering and knock-on damage mechanism. When the electron beam energy is increased further to 200 keV, FLG suffers rapid and catastrophic destruction. Unlike electron irradiation, Compton effect is the dominant damage mechanism in gamma irradiation. The irradiation results indicate the crystallinity of FLG decreases first, then restores as increasing irradiation doses, additionally, the ratio (O/C) of FLG surface and the relative content of oxygen groups increases after irradiation.
Quantum nonlocality does not exist
Authors: Tipler Frank J.
Published: July 2014

Significance

I show that quantum nonlocality is an artifact of the assumption that observers obey the laws of classical mechanics, whereas observed systems obey quantum mechanics. Locality is restored if observed and observer both obey quantum mechanics, as in the many-worlds interpretation (MWI). Using the MWI, I show that the quantum side of Bell’s inequality is entirely local. Thus, experiments confirming “nonlocality” are actually confirming the MWI. The mistaken interpretation of Bell’s inequality depends on the idea that the wave function is a probability amplitude, but the MWI holds that the wave function is a world density amplitude. Assuming the wave function is a world density amplitude, I derive the Born interpretation directly from Schrödinger’s equation.
Structural basis for the binding and incorporation of nucleotide analogs with
L
-stereochemistry by human DNA polymerase λ
Authors: Vyas Rajan , Zahurancik Walter J. , Suo Zucai
Published: July 2014

Significance

DNA polymerases are known to select against
L
-nucleotides, the enantiomers of natural
D
-nucleotides. However, the structural basis for
D-
stereoselectivity of a DNA polymerase has not been established, although two
L
-nucleoside analogs, lamivudine and emtricitabine, have been widely used as anti-HIV and anti-hepatitis B drugs. Here, we report ternary crystal structures of human DNA polymerase λ in complex with DNA and
L
-deoxycytidine 5′-triphosphate, or its analogs (the triphosphates of lamivudine and emtricitabine). These structures reveal that unlike a polymerase-bound
D
-nucleotide, an
L
-nucleotide initially interacts with an active site arginine residue through hydrogen bonds and then pairs with the templating nucleotide. Our work provides a structural basis for the
D-
stereoselectivity of a polymerase and valuable insight toward design of less toxic antiviral nucleoside analogs.
Strigolactones regulate rice tiller angle by attenuating shoot gravitropism through inhibiting auxin biosynthesis
Authors: Sang Dajun , Chen Dongqin , Liu Guifu , Liang Yan , Huang Linzhou , Meng Xiangbing , Chu Jinfang , Sun Xiaohong , Dong Guojun , Yuan Yundong , Qian Qian , Li Jiayang , Wang Yonghong
Published: July 2014

Significance

Shoot gravitropism is a key determinant of tiller angle, one of the most important factors that affect ideal plant architecture and grain yield of cereal crops. Strigolactones (SLs) are newly identified plant hormones that play diverse roles in plant growth and development. In this study, we provide compelling evidences that SLs are involved in shoot gravitropism, showing that SLs attenuate shoot gravitropism by inhibiting auxin biosynthesis. Our study uncovers a new role of SLs and suggests a previously unidentified mechanism underlying shoot gravitropism and tiller angle. Based on our study, SLs could be considered an important tool for achieving ideal plant architecture in the future.
proovread
: large-scale high-accuracy PacBio correction through iterative short read consensus
Authors: Hackl Thomas , Hedrich Rainer , Schultz Jörg , Förster Frank
Published: July 2014

Motivation : Today, the base code of DNA is mostly determined through sequencing by synthesis as provided by the Illumina sequencers. Although highly accurate, resulting reads are short, making their analyses challenging. Recently, a new technology, single molecule real-time (SMRT) sequencing, was developed that could address these challenges, as it generates reads of several thousand bases. But, their broad application has been hampered by a high error rate. Therefore, hybrid approaches that use high-quality short reads to correct erroneous SMRT long reads have been developed. Still, current implementations have great demands on hardware, work only in well-defined computing infrastructures and reject a substantial amount of reads. This limits their usability considerably, especially in the case of large sequencing projects.

Results : Here we present proovread , a hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high-performance computing cluster. On genomic and transcriptomic test cases covering Escherichia coli , Arabidopsis thaliana and human, proovread achieved accuracies up to 99.9% and outperformed the existing hybrid correction programs. Furthermore, proovread -corrected sequences were longer and the throughput was higher. Thus, proovread combines the most accurate correction results with an excellent adaptability to the available hardware. It will therefore increase the applicability and value of SMRT sequencing.

Availability and implementation:  proovread is available at the following URL: http://proovread.bioapps.biozentrum.uni-wuerzburg.de

Contact : frank.foerster@biozentrum.uni-wuerzburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
MAGNA: Maximizing Accuracy in Global Network Alignment
Authors: Saraph Vikram , Milenković Tijana
Published: July 2014

Motivation : Biological network alignment aims to identify similar regions between networks of different species. Existing methods compute node similarities to rapidly identify from possible alignments the high-scoring alignments with respect to the overall node similarity. But, the accuracy of the alignments is then evaluated with some other measure that is different than the node similarity used to construct the alignments. Typically, one measures the amount of conserved edges. Thus, the existing methods align similar nodes between networks hoping to conserve many edges ( after the alignment is constructed!).

Results : Instead, we introduce MAGNA to directly ‘optimize’ edge conservation while the alignment is constructed, without decreasing the quality of node mapping. MAGNA uses a genetic algorithm and our novel function for ‘crossover’ of two ‘parent’ alignments into a superior ‘child’ alignment to simulate a ‘population’ of alignments that ‘evolves’ over time; the ‘fittest’ alignments survive and proceed to the next ‘generation’, until the alignment accuracy cannot be optimized further. While we optimize our new and superior measure of the amount of conserved edges, MAGNA can optimize any alignment accuracy measure, including a combined measure of both node and edge conservation. In systematic evaluations against state-of-the-art methods (IsoRank, MI-GRAAL and GHOST), on both synthetic networks and real-world biological data, MAGNA outperforms all of the existing methods, in terms of both node and edge conservation as well as both topological and biological alignment accuracy.

Availability : Software: http://nd.edu/∼cone/MAGNA

Contact : tmilenko@nd.edu

Supplementary information : Supplementary data are available at Bioinformatics online.
SNP-SIG 2013: the state of the art of genomic variant interpretation
Authors: Bromberg Yana , Capriotti Emidio
Published: July 2014

Contact:  yanab@rci.rutgers.edu or emidio@uab.edu .
GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination
Authors: Gotz Lou , Abrahams Jodie L. , Mariethoz Julien , Rudd Pauline M. , Karlsson Niclas G. , Packer Nicolle H. , Campbell Matthew P. , Lisacek Frederique
Published: July 2014

Summary: Sequencing oligosaccharides by exoglycosidases, either sequentially or in an array format, is a powerful tool to unambiguously determine the structure of complex N- and O- link glycans. Here, we introduce GlycoDigest, a tool that simulates exoglycosidase digestion, based on controlled rules acquired from expert knowledge and experimental evidence available in GlycoBase. The tool allows the targeted design of glycosidase enzyme mixtures by allowing researchers to model the action of exoglycosidases, thereby validating and improving the efficiency and accuracy of glycan analysis.

Availability and implementation:  http://www.glycodigest.org .

Contact:  matthew.campbell@mq.edu.au or frederique.lisacek@isb-sib.ch
Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression
Authors: Cheng Chun-Pei , Kuo I-Ying , Alakus Hakan , Frazer Kelly A. , Harismendy Olivier , Wang Yi-Ching , Tseng Vincent S.
Published: July 2014

Motivation: A rapid progression of esophageal squamous cell carcinoma (ESCC) causes a high mortality rate because of the propensity for metastasis driven by genetic and epigenetic alterations. The identification of prognostic biomarkers would help prevent or control metastatic progression. Expression analyses have been used to find such markers, but do not always validate in separate cohorts. Epigenetic marks, such as DNA methylation, are a potential source of more reliable and stable biomarkers. Importantly, the integration of both expression and epigenetic alterations is more likely to identify relevant biomarkers.

Results: We present a new analysis framework, using ESCC progression-associated gene regulatory network (GRN escc ), to identify differentially methylated CpG sites prognostic of ESCC progression. From the CpG loci differentially methylated in 50 tumor–normal pairs, we selected 44 CpG loci most highly associated with survival and located in the promoters of genes more likely to belong to GRN escc . Using an independent ESCC cohort, we confirmed that 8/10 of CpG loci in the promoter of GRN escc genes significantly correlated with patient survival. In contrast, 0/10 CpG loci in the promoter genes outside the GRN escc were correlated with patient survival. We further characterized the GRN escc network topology and observed that the genes with methylated CpG loci associated with survival deviated from the center of mass and were less likely to be hubs in the GRN escc . We postulate that our analysis framework improves the identification of bona fide prognostic biomarkers from DNA methylation studies, especially with partial genome coverage.

Contact:  tsengsm@mail.ncku.edu.tw or ycw5798@mail.ncku.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
A new approach for detecting riboswitches in DNA sequences
Authors: Havill Jessen T. , Bhatiya Chinmoy , Johnson Steven M. , Sheets Joseph D. , Thompson Jeffrey S.
Published: July 2014

Motivation : Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression.

Results : The Denison Riboswitch Detector (DRD) is a new computational tool with a Web interface that can quickly identify putative riboswitches in DNA sequences on the scale of bacterial genomes. Riboswitch descriptions are easily modifiable and new ones are easily created. The underlying algorithm converts the problem to a ‘heaviest path’ problem on a multipartite graph, which is then solved using efficient dynamic programming. We show that DRD can achieve ∼88–99% sensitivity and >99.99% specificity on 13 riboswitch families.

Availability and implementation : DRD is available at http://drd.denison.edu .

Contact : havill@denison.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing
Authors: Calabrese Claudia , Simone Domenico , Diroma Maria Angela , Santorsola Mariangela , Guttà Cristiano , Gasparre Giuseppe , Picardi Ernesto , Pesole Graziano , Attimonelli Marcella
Published: July 2014

Motivation: The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data.

Results: MToolBox implements an effective computational strategy for mitochondrial genomes assembling and haplogroup assignment also including a prioritization analysis of detected variants. MToolBox provides a Variant Call Format file featuring, for the first time, allele-specific heteroplasmy and annotation files with prioritized variants. MToolBox was tested on simulated samples and applied on 1000 Genomes WXS datasets.

Availability and implementation: MToolBox package is available at https://sourceforge.net/projects/mtoolbox/ .

Contact:  marcella.attimonelli@uniba.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
The China power grid: a network science perspective
Authors: Chen Guanrong (Ron)
Published: July 2014

Power grid is a very large scale and highly non-linear dynamical system, and its stable and reliable operation poses a great challenge to scientists and engineers. As a complex dynamic network has a tendency of catastrophic failure, sophisticated analysis and control are required. In an interview with NSR, Professor Yusheng Xue, member of the Chinese Academy of Engineering, Honorary President of China's State Grid Electric Power Research Institute, talked about the economic impact, technical challenges, and future development of power grid in China.
Alexandria
Authors: Taylor Joan
Published: July 2014

Founded by Alexander the Great in 331 bce, Alexandria under the Ptolemaic dynasty soon became a unique cultural center that led the Hellenistic world. Cultural interchange created a milieu in which some of the most important Jewish and Christian thinkers would thrive. The Septuagint (lxx) was produced here, largely in the 3rd century bce. With the vibrant intellectual hubs of the Alexandrian museon and library, a distinctive Alexandrian school of philosophy, science, and medicine developed that included such figures as Eratosthenes and Ptolemy. It is likely that many works of Jewish literature written in Greek were composed here, though their provenance cannot be established with certainty. There was a Jewish school of allegorical exegesis, evidenced in the work of Aristobulus and Philo. Paul’s influential associate Apollos came from this city (Acts 18: 24–8). After the uprising of 115–17 ce, when the Alexandrian Jewish community was decimated, allegorical exegesis was continued in the Christian catechetical school, headed by Pantaenus, Clement, and then Origen. Christian teachers such as Basilides, Valentinus, and Isidore were also active in the city. Traditionally the evangelist Mark was said to have died in Alexandria (see, for example, Eusebius, Hist. Eccles. 2: 16, 24), where his tomb was venerated for centuries before his remains were brought to Venice in 828 ce. A useful bibliographical Internet resource for the site may be found online. A remarkable 3-D tour of ancient Alexandria is also provided online.
Caterina Sforza
Authors: de Vries Joyce
Published: July 2014

Caterina Sforza (b. 1462/63–d. 1509) was the daughter of Galeazzo Maria Sforza (b. 1444–d. 1476), duke of Milan (r. 1467–1476), and his mistress Lucrezia Landriani (b. 1440/45–d. 1507). In 1477, she married Girolamo Riario (b. 1443–d. 1488), nephew of Pope Sixtus IV and ruler of Imola since 1473. He gained possession of Forlì in 1480. Sforza bore at least eight children with Riario, six of whom survived infancy, and she became regent for her son Ottaviano (b. 1479–d. 1533) when Riario was assassinated in 1488. She survived several conspiracies against her rule of Imola and Forlì in the 1490s, and she was deposed only when Cesare Borgia (b. 1475/76–d. 1507) invaded the Romagna region in late 1499. Taken prisoner in early 1500, she was released in July 1501. Sforza moved to Florence, where she plotted to retake the family territories. Neither she nor the Riario family ever resumed power and she died after a long illness in 1509. She was buried in the Murate convent, where she had maintained a cell for spiritual retreat. Sforza’s political cunning and forceful rule fascinated many in early modern Italy, including Niccolò Machiavelli, who came to Forlì in 1499 to negotiate her son Ottaviano’s military contract with Florence. In The Prince, Machiavelli highlights Sforza’s use of fortresses for protection. His version of her actions after Riario’s assassination in 1488 did much to promote her reputation as a sexually bold and merciless ruler. By all accounts, when Sforza entered the Rocca di Ravaldino to facilitate its surrender to the rebels, she instead mounted the ramparts with the intention to rule and challenged her enemies to kill her children, who were hostages. According to Machiavelli, in the Discourses, she then lifted her skirts to reveal her genitals, a gesture meant to emphasize her claim that she could bear more children, who would eventually avenge Riario’s murder. This purported act is an exaggeration of her actions, but this version of the events remains influential as part of her legend. Sforza has often been cast as an exceptional woman not only because of her long regency, but also because of her sexual independence during her widowhood and regency. Without a husband or father to patrol her sexuality, Sforza inspired many rumors about possible sexual partners. During her widowhood, she did indeed maintain relationships with at least two men, whom she claimed after their deaths to have married. Giacomo Feo (b. 1470–d. 1495) achieved much power in her court and was assassinated. They had a son, Carlo (b. 1490–d. 1550s). The second, Giovanni di Pierfrancesco de’ Medici (b. 1467–d. 1498), of the cadet branch of the Florentine family, did not gain political power and died of natural causes. During her final years in Florence, Sforza won custody of their son, Giovanni (b. 1498–d. 1526). She then oversaw his education and estates, and he grew up to became a famous military commander in Italy, known as Giovanni dalle Bande Nere, and father of the future duke of Florence, Cosimo I de’ Medici (b. 1519–d. 1574). Sforza’s Medici connections augmented her fame after her death.
Indigenous Peoples
Authors: Gilbert Jérémie
Published: July 2014

The rights of indigenous peoples under international law have evolved greatly since the late 1980s. Efforts by indigenous peoples to get their rights recognized under international law started during the League of Nations in the early 1920s, but it was only in 2007 that the General Assembly of the United Nations (UN) adopted the United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP). The adoption of the declaration not only marks an important moment in terms of lawmaking; it also represents the achievement of long decades of lobbying and advocacy from indigenous peoples’ representatives. The UN declared the decade 1994–2004 as the First International Decade of the World’s Indigenous Peoples, and later 2005–2015 was declared the second such decade. The main objective was the strengthening of international cooperation for the solution of problems faced by indigenous people in such areas as human rights, the environment, education, and health. As a result, in 2002, the Permanent Forum on Indigenous Issues was established as an advisory body to the UN Economic and Social Council. But it was only in 2007 that the UN General Assembly adopted the UNDRIP, which universally proclaims and consolidates a specific international legal corpus of rights for indigenous peoples. The adoption of the declaration is representative of the significant legal developments of the rights of indigenous peoples under international law. The international legal framework concerns general human rights such as nondiscrimination and equality, as well as very specific collective rights such as self-determination, cultural rights, land rights, and control over natural resources. The establishment of a specific corpus of law dedicated to the rights of indigenous peoples, or sui generis rights, has also meant a proliferation of scholarly literature on the topic. This article does not propose to be exhaustive or comprehensive, but rather to offer a review of some of the texts that can guide the researcher or the reader through the vast and extensive existing literature. First, it focuses on some of the leading sources that provide a general overview on the rights of indigenous peoples. It then examines the institutional and regional approaches. And finally, it focuses on specific issues affecting indigenous peoples, namely historical claims, self-determination, land rights, natural resources, and development.
Food
Authors: Most Andrea , Mulhern Aldea
Published: July 2014

Food studies is a burgeoning field that crosses many disciplinary lines, and that has increasingly turned academic attention toward foodways, or the processes by which meaning is made around food. Jewish food studies, while not yet a field, is a topic of increasing interest for scholars in Jewish studies. The coexistence of an Oxford Bibliographies article Dietary Laws (by David Kraemer) and this one on Jews and food attests to the first important distinction to be made about the field: kashrut and Jewish food are not coterminous. Indeed, Jews and food is the larger category, encompassing not only the food laws and the commentary and practice that surround them, but all food acts and ideas that are undertaken in reference either to the laws of kashrut, to Judaism, or to Jews. Food is an extraordinarily capacious topic, touching on every discipline, historical period, and geographical delineation in Jewish studies. Scholars have long considered Jewish food and eating practices within their particular areas of interest and have used food practices to explain developments in religious practice and ritual, to set historical and cultural context, to describe Jewish relations with non-Jews, and to trace the pathways of Jewish Diaspora experience. Food practices have served as political and economic markers of change in Jewish life, and data on holiday observance, ritual, variations in kashrut practice, and other foodways provide a fascinating window into the social realities of Jews in many times and places. Jewish food has also offered a rich avenue into the study of gender and of women’s experience in Jewish life. Recently, Food studies has become its own scholarly category, and a number of scholars in Jewish studies have begun to work seriously in this area, developing new field-specific methodologies for making use of information about food and eating practices. This article catalogues both works that incorporate food as a topic, and works that are intentionally situated within the field of food studies. At least two important journals in the field of Jewish studies are currently in the process of compiling special issues on the topic of Jews and food, and so we anticipate this article will grow considerably over the next few years. At this point, the article addresses scholarship in English only and so leans heavily on North American scholarship and topics, but we likewise anticipate adding sources in other languages in the future.
Low Multiplicity of HIV-1 Infection and No Vaccine Enhancement in VAX003 Injection Drug Users
Authors: Sterrett Sarah , Learn Gerald H. , Edlefsen Paul T. , Haynes Barton F. , Hahn Beatrice H. , Shaw George M. , Bar Katharine J.
Published: July 2014

Background.  We performed human immunodeficiency virus type 1 (HIV-1) transmitted/founder (T/F) virus analysis of the VAX003 vaccine efficacy trial participants to characterize the transmission bottleneck and test for vaccine-associated reduction or enhancement of infection in this injection drug user (IDU) cohort.

Methods.  We performed single genome sequencing of plasma vRNA from 50 subjects sampled in early HIV infection. Sequences were analyzed phylogenetically, T/F viruses enumerated, and a sieve analysis performed.

Results.  Eight of 19 (42%) placebo recipients were productively infected by more than 1 virus (range 1–5, median 1, mean 1.7). This frequency of multiple virus transmission was greater than reported for heterosexual cohorts (19%, P = .03) but not statistically different from vaccine recipients (22.6%, P > .05), where the range was 1–3, median 1, and mean 1.3 (P > .05 for all comparisons). An atypical sieve effect was detected in Env V2 but was not associated with reduction or enhancement of virus acquisition.

Conclusions.  The number of T/F viruses in IDUs was surprising low, with 95% of individuals infected by only 1–3 viruses. This finding suggests that a successful vaccine or other prevention modality generally needs to protect against only one or a few viruses regardless of risk behavior. T/F analysis ide.jpegied an atypical genetic sieve in the V2 region of Envelope and found no evidence for vaccine-mediated enhancement in VAX003.
Discovery of an overlapping cluster in the Abell 1674 field with Suzaku
Authors: Inoue Shota , Hayashida Kiyoshi , Akamatsu Hiroki , Ueda Shutaro , Nagino Ryo , Tsunemi Hiroshi , Tawa Noriaki , Koyama Katsuji
Published: July 2014

We present the results of a Suzaku observation of Abell 1674, an optically very rich (richness class 3) cluster cataloged as z = 0.1066. We discover the He-like Fe K-shell line from the central region for the first time, and find that the X-ray spectrum yields a high redshift of $0.215^{+0.007}_{-0.006}$. On the other hand, the spectrum of the south-western region is fitted with a redshift of 0.11 ± 0.02 by the He-like Fe L-shell lines, consistent with the optically determined value. The gas temperature, metal abundance, and core radius of the X-ray emission in the central region are 3.8 ± 0.2 keV, 0.20 ± 0.05 Z⊙, and 450 ± 40 kpc, respectively, while those in the south-western region are 2.0 ± 0.2 keV, $0.41^{+0.17}_{-0.13}\,Z$⊙, and $220^{+90}_{-70}$ kpc, respectively. These parameters are typical for clusters. We thus conclude that Abell 1674 consists of two independent clusters, A 1674-C at z ∼ 0.22 and A 1674-SW at z ∼ 0.11, overlapping along the line of sight. The X-ray luminosity of A 1674-C within r = 2 Mpc is (15.9 ± 0.6) × 1043 erg s−1 in the 0.1–2.4 keV energy band, while that for A 1674-SW is (1.25 ± 0.07) × 1043 erg s−1. Both are consistent with those expected from the L–T relation of clusters within a factor of 2. This is another supporting factor for our conclusion.
Halovivax limisalsi sp. nov., an extremely halophilic archaeon from hypersaline mud
Authors: Amoozegar Mohammad Ali , Makhdoumi-Kakhki Ali , Mehrshad Maliheh , Riazi Siavash , Ventosa Antonio
Published: July 2014

A Gram-stain-negative, cream‐pigmented, motile, extremely halophilic archaeon, designated strain IC38T, was isolated from a saline mud sample taken from a hypersaline lake, Aran-Bidgol, in Iran. The strain required at least 2.5 M NaCl for growth. However, MgCl2 was not required. Optimal growth occurred with 4.3 M NaCl and 0.2 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 35 °C, respectively, and strain IC38T was able to grow over a pH range of 6.5–9.0, and a temperature range of 25–45 °C. Analysis of the 16S rRNA gene sequence revealed that strain IC38T clustered with the two species of the genus

Halovivax

,

Halovivax asiaticus

EJ-46T and

Halovivax ruber

XH-70T, with sequence similarities of 96.4 % and 96.1 %, respectively. The similarities between the rpoB′ gene of the novel strain and

Halovivax asiaticus

and

Halovivax ruber

were 90.7 % and 90.3 %, respectively. The polar lipid pattern of strain IC38T consisted of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Three unidentified glycolipids and two minor phospholipids were also observed. The DNA G+C content of strain IC38T was 62.6 mol%. On the basis of the phylogenetic analysis, as well as the biochemical and physiological characteristics, the new isolate is suggested to be a representative of a novel species of the genus

Halovivax

, for which the name
Halovivax

limisalsi sp. nov. is proposed. The type strain of
Halovivax

limisalsi is IC38T ( = IBRC-M 10022T = KCTC 4051T).
Idiomarina planktonica sp. nov., isolated from a saline lake
Authors: Zhong Zhi-Ping , Liu Ying , Liu Hong-Can , Wang Fang , Song Lei , Liu Zhi-Pei
Published: July 2014

A Gram-stain-negative bacterium, strain TS-T11T, was isolated from Tuosu lake, a saline lake (salinity 5.4 %, w/v) in the Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain TS-T11T were non-spore-forming rods, 0.6–0.8 µm wide and 0.8–2.2 µm long, and motile by means of a single polar flagellum. Strain TS-T11T was strictly heterotrophic and aerobic. Cells were positive for catalase and oxidase. Growth was observed in the presence of 0.5–11.0 % (w/v) NaCl (optimum 4.0–6.0 %), at 4–40 °C (optimum 30–35 °C) and at pH 6.0–10.5 (optimum pH 7.5–8.5). Strain TS-T11T contained iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c as the predominant fatty acids (>10 %). The major respiratory quinone was Q-8. The polar lipids consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and nine uncharacterized phospholipids. The G+C content of genomic DNA was 46.8 mol% (T
m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T11T was associated with the genus

Idiomarina

, and showed highest 16S rRNA gene sequence similarity to

Idiomarina aestuarii

KYW314T (97.4 %) and

Idiomarina salinarum

ISL-52T (97.4 %). DNA–DNA relatedness of strain TS-T11T to

I. aestuarii

JCM 16344T and

I. salinarum

DSM 21900T was 22.2±2.4 and 11.5±1.6 %, respectively. Based on the data presented above, it was concluded that strain TS-T11T represents a novel species of the genus

Idiomarina

, for which the name Idiomarina planktonica sp. nov. is proposed. The type strain is TS-T11T ( = CGMCC 1.12458T = JCM 19263T).
Acinetobacter guangdongensis sp. nov., isolated from abandoned lead–zinc ore
Authors: Feng Guang-Da , Yang Song-Zhen , Wang Yong-Hong , Deng Ming-Rong , Zhu Hong-Hui
Published: July 2014

A Gram-stain-negative, non-motile bacterial strain designated 1NM-4T was isolated from an abandoned lead–zinc ore mine site in Mei County, Meizhou, Guangdong Province, southern China. The isolate was light yellow, strictly aerobic, oxidase-negative and catalase-positive. Phylogenetic analyses based on 16S rRNA, rpoB and gyrB gene sequences, together with DNA–DNA hybridization values less than 70 %, revealed that strain 1NM-4T belongs to the genus

Acinetobacter

and may represent a novel species. The major respiratory quinone was ubiquinone 9 (Q-9) and the major cellular fatty acids consisted of C18 : 1ω9c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content of strain 1NM-4T was 47.17±0.02 mol%. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain 1NM-4T should be assigned to a novel species of the genus

Acinetobacter

, for which the name Acinetobacter guangdongensis sp. nov. is proposed. The type strain is 1NM-4T ( = GIMCC 1.656T = CCTCC AB 2014199T = KCTC 42012T).
The lack of OmpF, but not OmpC, contributes to increased antibiotic resistance in Serratia marcescens
Authors: Moya-Torres Aniel , Mulvey Michael R. , Kumar Ayush , Oresnik Ivan J. , Brassinga Ann Karen C.
Published: July 2014

The environmental organism Serratia marcescens is one of the primary causes of numerous nosocomial outbreaks and opportunistic infections. Multi-drug resistance is now a common feature among S. marcescens clinical isolates, complicating the efficacy of treatment. Recent reports have attributed antibiotic resistance to altered porin expression as well as perturbation of the intrinsic AmpC beta-lactamase production pathway. In this study, we aimed to genetically correlate the absence of OmpF and OmpC classical porins with increased antibiotic resistance. In generating isogenic porin mutant strains, we avoided incorporating additional resistance through the use of antibiotic cassettes in gene replacement and adopted an alternative strategy in creating clean unmarked mutant strains. We found that lack of OmpF, but not OmpC, significantly increased antibiotic MIC values to the beta-lactam drugs such as ampicillin and cefoxitin as well as to nitrofurantoin. Furthermore, we found that cefoxitin did not induce intrinsic AmpC beta-lactamase production, indicating that the increased MIC values were a result of reduced permeability of cefoxitin due to the lack of OmpF. Genetic deletion of both ompF and ompC did not compromise the integrity of the bacterial cell envelope in optimal growth conditions, suggesting that other outer-membrane porins may function in a compensatory role to facilitate nutrient uptake and cell envelope integrity. Taken together, to our knowledge this is the first study that genetically correlates increased antibiotic resistance with altered porin expression in S. marcescens.
A plea for evidence in ecosystem service science: a framework and its application
Authors: Mupepele Anne-Christine , Dormann Carsten F.
Published: July 2014

The ecosystem service concept is at the interface of ecology, economics and politcs, with scientific results rapidly translated into management or political action. This emphasises the importance ofreliable recommendationsprovided by scientist. We propose to use evidence-based practice in ecosystem service science in order to evaluate and improve the reliability of scientific statements. For this purpose, we introduce a level-of-evidence scale ranking study designs (e.g. review, case-control, descriptive) in combination with a study quality checklist. For illustration, the concept was directly applied to 12 case studies. We also review criticisms levered against evidence-based practice and how it applies to ecosystem services science. We further discuss who should use the evidence-based concept and suggest important next steps, with a focus on the development of guidelines for methods used in ecosystem service assessments.
Chromosomal distribution of cyto-nuclear genes in a dioecious plant with sex chromosomes
Authors: Hough Josh , Ågren J. Arvid , Barrett Spencer C. H. , Wright Stephen I.
Published: July 2014

The coordination between nuclear and organellar genes is essential to many aspects of eukaryotic life, including basic metabolism, energy production, and ultimately, organismal fitness. Whereas nuclear genes are bi-parentally inherited, mitochondrial and chloroplast genes are almost exclusively maternally inherited, and this asymmetry may lead to a bias in the chromosomal distribution of nuclear genes whose products act in the mitochondria or chloroplasts. In particular, because X-linked genes have a higher probability of co-transmission with organellar genes (2/3) compared to autosomal genes (1/2), selection for co-adaptation has been predicted to lead to an over-representation of nuclear-mitochondrial and nuclear-chloroplast genes on the X chromosome relative to autosomes. In contrast, the occurrence of sexually antagonistic organellar mutations might lead to selection for movement of cyto-nuclear genes from the X chromosome to autosomes to reduce male mutation load. Recent broad-scale comparative studies of N-mt distributions in animals have found evidence for these hypotheses in some species, but not others. Here, we use transcriptome sequences to conduct the first study of the chromosomal distribution of cyto-nuclear interacting genes in a plant species with sex chromosomes (Rumex hastatulus; Polygonaceae). We found no evidence of under- or over-representation of either N-mt or N-cp genes on the X chromosome, and thus no support for either the co-adaptation or the sexual-conflict hypothesis. We discuss how our results from a species with recently evolved sex chromosomes fit into an emerging picture of the evolutionary forces governing the chromosomal distribution of nuclear-mitochondrial and nuclear-chloroplast genes.
Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI’s RNA-seq archive
Authors: Olarerin-George Anthony O. , Hogenesch John B.
Published: July 2014

Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Because they are small, they can escape filtration in culture media. Because they lack cell walls, they are resistant to commonly used antibiotics. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series (or projects) in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥ 100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. Interestingly, series using poly(A)-selection, which should bias against mycoplasma detection, had comparable contamination rates as non-poly(A)-selected series. We also examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes (P< 0.001) were significantly associated with mycoplasma-mapped read counts. Lastly, to estimate the potential economic cost of this widespread contamination, we queried NIH RePORTER to find grants with the terms “cell culture” or “cell lines”. Funding for these totaled over $3 billion, suggesting hundreds of millions of dollars in research are potentially affected. In all, this study suggests mycoplasma contamination is still prevalent today and poses substantial risk to research quality, with considerable financial consequences.
Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood
Authors: Gao Fan , Wang Kai
Published: July 2014

Background

As one of the genetic mechanisms for adaptive immunity, V(D)J recombination generates an enormous repertoire of T-cell receptors (TCRs). With the development of high-throughput sequencing techniques, systematic exploration of V(D)J recombination becomes possible. Multiplex PCR method has been previously developed to assay immune repertoire, however the usage of primer pools has inherent bias in target amplification. In our study, we developed a ligation-anchored PCR method to unbiasedly amplify the repertoire.

Results

By utilizing a universal primer paired with a single primer targeting the conserved constant region, we amplified TCR-beta (TRB) variable regions from total RNA extracted from blood. Next-generation sequencing libraries were then prepared for Illumina HiSeq 2500 sequencer, which provided 151 bp read length to cover the entire V(D)J recombination region. We evaluated this approach on blood samples from patients with malignant and benign meningiomas. Mapping of sequencing data showed 64% to 91% of mapped TCRV-containing reads belong to TRB subtype. An increased usage of TRBV29-1 was observed in malignant meningiomas. Also distinct signatures were identified from CDR3 sequence logos, with predominant subset as 42 nt for benign and 45 nt for malignant samples, respectively.

Conclusions

In summary, we report an integrative approach to monitor immune repertoire in a systematic manner.
Genomic analysis of the causative agents of coccidiosis in domestic chickens
Authors: Reid Adam J. , Blake Damer P. , Ansari Hifzur R. , Billington Karen , Browne Hilary P. , Bryant Josephine , Dunn Matt , Hung Stacy S. , Kawahara Fumiya , Miranda-Saavedra Diego , Malas Tareq B. , Mourier Tobias , Naghra Hardeep , Nair Mridul , Otto Thomas D. , Rawlings Neil D. , Rivailler Pierre , Sanchez-Flores Alejandro , Sanders Mandy , Subramaniam Chandra , Tay Yea-Ling , Woo Yong , Wu Xikun , Barrell Bart , Dear Paul H. , Doerig Christian , Gruber Arthur , Ivens Alasdair C. , Parkinson John , Rajandream Marie-Adèle , Shirley Martin W. , Wan Kiew-Lian , Berriman Matthew , Tomley Fiona M. , Pain Arnab
Published: July 2014

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.