bluuebunny/crossref_metadata_2025 huggingface dataset:
GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences
Authors: Sato Tetsuya , Suyama Mikita
Published: December 2014

Summary: Genome sequence alignments provide valuable information on many aspects of molecular biological processes. In this study, we developed a web server, GenomeCons, for manipulating multiple genome sequence alignments and their consensus sequences for high-throughput genome sequence analyses. This server facilitates the visual inspection of multiple genome sequence alignments for a set of genomic intervals at a time. This allows the user to examine how these sites are evolutionarily conserved over time for their functional importance. The server also reports consensus sequences for the input genomic intervals, which can be applied to downstream analyses such as the identification of common motifs in the regions determined by ChIP-seq experiments.

Availability and implementation: GenomeCons is freely accessible at http://bioinfo.sls.kyushu-u.ac.jp/genomecons/

Contact:  mikita@bioreg.kyushu-u.ac.jp
Semiconductor sequencing: how many flows do you need?
Authors: Budczies Jan , Bockmayr Michael , Treue Denise , Klauschen Frederick , Denkert Carsten
Published: December 2014

Motivation: Semiconductor sequencing directly translates chemically encoded information (A, C, G or T) into voltage signals that are detected by a semiconductor device. Changes of pH value and thereby of the electric potential in the reaction well are detected during strand synthesis from nucleotides provided in cyclic repeated flows for each type of nucleotide. To minimize time requirement and costs, it is necessary to know the number of flows that are required for complete coverage of the templates.

Results: We calculate the number of required flows in a random sequence model and present exact expressions for cumulative distribution function, expected value and variance. Additionally, we provide an algorithm to calculate the number of required flows for a concrete list of amplicons using a BED file of genomic positions as input. We apply the algorithm to calculate the number of flows that are required to cover six amplicon panels that are used for targeted sequencing in cancer research. The upper bounds obtained for the number of flows allow to enhance the instrument throughput from two chips to three chips per day for four of these panels.

Availability and implementation: The algorithm for calculation of the flows was implemented in R and is available as package ionflows from the CRAN repository.

Contact:  jan.budczies@charite.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Are the broad optical Balmer lines in PG 1613+658 from the central accretion disc?
Authors: Zhang Xue-Guang
Published: December 2014

In this letter, we report on the positive correlations between the broad-line width and broad-line flux for the broad Balmer lines of the active galactic nucleus (AGN) PG 1613+658, which has been observed for a long time. Rather than the expected negative correlations that come with the widely accepted virialization assumption for AGN broad emission-line regions (BLRs), the positive correlations indicate very different BLR structures of PG 1613+658 from the commonly considered BLR structures that are dominated by the equilibrium between radiation pressure and gas pressure. Therefore, it is preferable to assume that the observed broad single-peaked optical Balmer lines of PG 1613+658 originate from the accretion disc, because the mainly gravity-dominated disc-like BLRs with radial structures have few effects from radiation pressure.
The inefficiency of satellite accretion in forming extended star clusters
Authors: Bianchini Paolo , Renaud Florent , Gieles Mark , Varri Anna Lisa
Published: December 2014

The distinction between globular clusters and dwarf galaxies has been progressively blurred by the recent discoveries of several extended star clusters, with size (20–30 pc) and luminosity (−6 < Mv < −2) comparable to the one of the faint dwarf spheroidals. In order to explain their sparse structure, it has been suggested that they formed as star clusters in dwarf galaxy satellites that later accreted on to the Milky Way. If these clusters form in the centre of dwarf galaxies, they evolve in a tidally compressive environment where the contribution of the tides to the virial balance can become significant, and lead to a supervirial state and subsequent expansion of the cluster, once removed. Using N-body simulations, we show that a cluster formed in such an extreme environment undergoes a sizable expansion, during the drastic variation of the external tidal field due to the accretion process. However, we show that the expansion due to the removal of the compressive tides is not enough to explain the observed extended structure, since the stellar systems resulting from this process are always more compact than the corresponding clusters that expand in isolation due to two-body relaxation. We conclude that an accreted origin of extended globular clusters is unlikely to explain their large spatial extent, and rather favour the hypothesis that such clusters are already extended at the stage of their formation.
Non-linear mirror instability
Authors: Rincon F. , Schekochihin A. A. , Cowley S. C.
Published: December 2014

Slow dynamical changes in magnetic-field strength and invariance of the particles’ magnetic moments generate ubiquitous pressure anisotropies in weakly collisional, magnetized astrophysical plasmas. This renders them unstable to fast, small-scale mirror and firehose instabilities, which are capable of exerting feedback on the macroscale dynamics of the system. By way of a new asymptotic theory of the early non-linear evolution of the mirror instability in a plasma subject to slow shearing or compression, we show that the instability does not saturate quasi-linearly at a steady, low-amplitude level. Instead, the trapping of particles in small-scale mirrors leads to non-linear secular growth of magnetic perturbations, δB/B ∝ t2/3. Our theory explains recent collisionless simulation results, provides a prediction of the mirror evolution in weakly collisional plasmas and establishes a foundation for a theory of non-linear mirror dynamics with trapping, valid up to δB/B = O(1).
Impairment of medical decisional capacity in relation to Karnofsky Performance Status in adults with malignant brain tumor
Authors: Martin Roy C. , Gerstenecker Adam , Nabors Louis B. , Marson Daniel C. , Triebel Kristen L.
Published: December 2014

Background

We aimed to investigate the relationship between medical decisional capacity (MDC) and Karnofsky Performance Status (KPS) in adults with malignant brain tumors.

Methods

Participants were 71 adults with primary (n = 26) or metastatic (n = 45) brain tumors. Testing to determine KPS scores and MDC was performed as close together as possible for each patient. Participants were administered a standardized measure of medical decision-making capacity (Capacity to Consent to Treatment Instrument [CCTI]) to assess 3 treatment consent abilities (ie, appreciation, reasoning, and understanding). Capacity classifications (ie, capable, marginally capable, and incapable) were established using cut scores previously derived from healthy control CCTI performance.

Results

The majority of participants had KPS scores of 90–100 (n = 39), with the remainder divided between KPS scores of 70–80 (n = 26) and 50–60 (n = 6). Comparisons between persons with KPS scores of 90–100 or 70–80 revealed significant differences on the CCTI consent standards of understanding and appreciation. Participants with KPS ratings of 90–100 achieved 46% capable classifications across all CCTI standards, in contrast with 23% of participants with KPS ratings of 70–80, and 0% of participants with KPS ratings of 50–60.

Conclusions

A substantial portion of brain-tumor patients with KPS scores reflecting only minimal disability nonetheless demonstrated impairments on standardized measures of MDC. Clinicians working with this adult population should carefully screen for capacity to make clinical treatment decisions regardless of functional/performance status.
Dynamics of airflow in a short inhalation
Authors: Bates A. J. , Doorly D. J. , Cetto R. , Calmet H. , Gambaruto A. M. , Tolley N. S. , Houzeaux G. , Schroter R. C.
Published: December 2014

During a rapid inhalation, such as a sniff, the flow in the airways accelerates and decays quickly. The consequences for flow development and convective transport of an inhaled gas were investigated in a subject geometry extending from the nose to the bronchi. The progress of flow transition and the advance of an inhaled non-absorbed gas were determined using highly resolved simulations of a sniff 0.5 s long, 1 l s
−1
peak flow, 364 ml inhaled volume. In the nose, the distribution of airflow evolved through three phases: (i) an initial transient of about 50 ms, roughly the filling time for a nasal volume, (ii) quasi-equilibrium over the majority of the inhalation, and (iii) a terminating phase. Flow transition commenced in the supraglottic region within 20 ms, resulting in large-amplitude fluctuations persisting throughout the inhalation; in the nose, fluctuations that arose nearer peak flow were of much reduced intensity and diminished in the flow decay phase. Measures of gas concentration showed non-uniform build-up and wash-out of the inhaled gas in the nose. At the carina, the form of the temporal concentration profile reflected both shear dispersion and airway filling defects owing to recirculation regions.
First carrot, then stick: how the adaptive hybridization of incentives promotes cooperation
Authors: Chen Xiaojie , Sasaki Tatsuya , Brännström Åke , Dieckmann Ulf
Published: December 2014

Social institutions often use rewards and penalties to promote cooperation. Providing incentives tends to be costly, so it is important to find effective and efficient policies for the combined use of rewards and penalties. Most studies of cooperation, however, have addressed rewarding and punishing in isolation and have focused on peer-to-peer sanctioning as opposed to institutional sanctioning. Here, we demonstrate that an institutional sanctioning policy we call ‘first carrot, then stick’ is unexpectedly successful in promoting cooperation. The policy switches the incentive from rewarding to punishing when the frequency of cooperators exceeds a threshold. We find that this policy establishes and recovers full cooperation at lower cost and under a wider range of conditions than either rewards or penalties alone, in both well-mixed and spatial populations. In particular, the spatial dynamics of cooperation make it evident how punishment acts as a ‘booster stage’ that capitalizes on and amplifies the pro-social effects of rewarding. Together, our results show that the adaptive hybridization of incentives offers the ‘best of both worlds’ by combining the effectiveness of rewarding in establishing cooperation with the effectiveness of punishing in recovering it, thereby providing a surprisingly inexpensive and widely applicable method of promoting cooperation.
Adhesion-dependent rupturing of
Saccharomyces cerevisiae
on biological antimicrobial nanostructured surfaces
Authors: Nowlin Kyle , Boseman Adam , Covell Alan , LaJeunesse Dennis
Published: December 2014

Recent studies have shown that some nanostructured surfaces (NSS), many of which are derived from surfaces found on insect cuticles, rupture and kill adhered prokaryotic microbes. Most important, the nanoscale topography is directly responsible for this effect. Although parameters such as cell adhesion and cell wall rigidity have been suggested to play significant roles in this process, there is little experimental evidence regarding the underlying mechanisms involving NSS-induced microbial rupture. In this work, we report the NSS-induced rupturing of a eukaryotic microorganism,
Saccharomyces cerevisiae
. We show that the amount of NSS-induced rupture of
S. cerevisiae
is dependent on both the adhesive qualities of the yeast cell and the nanostructure geometry of the NSS. Thus, we are providing the first empirical evidence that these parameters play a direct role in the rupturing of microbes on NSS. Our observations of this phenomenon with
S. cerevisiae,
particularly the morphological changes, are strikingly similar to that reported for bacteria despite the differences in the yeast cell wall structure. Consequently, NSS provide a novel approach for the control of microbial growth and development of broad-spectrum microbicidal surfaces.
Revealing the dependence of cell spreading kinetics on its spreading morphology using microcontact printed fibronectin patterns
Authors: Huang Cheng-Kuang , Donald Athene
Published: December 2014

Since the dawn of
in vitro
cell cultures, how cells interact and proliferate within a given external environment has always been an important issue in the study of cell biology. It is now well known that mammalian cells typically exhibit a three-phase sigmoid spreading on encountering a substrate. To further this understanding, we examined the influence of cell shape towards the second rapid expansion phase of spreading. Specifically, 3T3 fibroblasts were seeded onto silicon elastomer films made from polydimethylsiloxane (PDMS), and micro-contact printed with fibronectin stripes of various dimensions. PDMS is adopted in our study for its biocompatibility, its ease in producing very smooth surfaces, and in the fabrication of micro-contact printing stamps. The substrate patterns are compared with respect to their influence on cell spreading over time. Our studies reveal, during the early rapid expansion phase, 3T3 fibroblasts are found to spread radially following a

law; meanwhile, they proliferated in a lengthwise fashion on the striped patterns, following a

law. We account for the observed differences in kinetics through a simple geometric analysis which predicted similar trends. In particular, a
t
2
law for radial spreading cells, and a
t
1
law for lengthwise spreading cells.
Quantifying long-term evolution of intra-urban spatial interactions
Authors: Sun Lijun , Jin Jian Gang , Axhausen Kay W. , Lee Der-Horng , Cebrian Manuel
Published: December 2014

Understanding the long-term impact that changes in a city's transportation infrastructure have on its spatial interactions remains a challenge. The difficulty arises from the fact that the real impact may not be revealed in static or aggregated mobility measures, as these are remarkably robust to perturbations. More generally, the lack of longitudinal, cross-sectional data demonstrating the evolution of spatial interactions at a meaningful urban scale also hinders us from evaluating the sensitivity of movement indicators, limiting our capacity to understand the evolution of urban mobility in depth. Using very large mobility records distributed over 3 years, we quantify the impact of the completion of a metro line extension: the Circle Line (CCL) in Singapore. We find that the commonly used movement indicators are almost identical before and after the project was completed. However, in comparing the temporal community structure across years, we do observe significant differences in the spatial reorganization of the affected geographical areas. The completion of CCL enables travellers to re-identify their desired destinations collectively with lower transport cost, making the community structure more consistent. These changes in locality are dynamic and characterized over short timescales, offering us a different approach to identify and analyse the long-term impact of new infrastructures on cities and their evolution dynamics.
How receptor diffusion influences gradient sensing
Authors: Nguyen H. , Dayan P. , Goodhill G. J.
Published: December 2014

Chemotaxis, or directed motion in chemical gradients, is critical for various biological processes. Many eukaryotic cells perform spatial sensing, i.e. they detect gradients by comparing spatial differences in binding occupancy of chemosensory receptors across their membrane. In many theoretical models of spatial sensing, it is assumed, for the sake of simplicity, that the receptors concerned do not move. However, in reality, receptors undergo diverse modes of diffusion, and can traverse considerable distances in the time it takes such cells to turn in an external gradient. This sets a physical limit on the accuracy of spatial sensing, which we explore using a model in which receptors diffuse freely over the membrane. We find that the Fisher information carried in binding and unbinding events decreases monotonically with the diffusion constant of the receptors.
Classification of the pre-settlement behaviour of barnacle cyprids
Authors: Maleschlijski Stojan , Bauer Stella , Aldred Nick , Clare Anthony S. , Rosenhahn Axel
Published: December 2014

Barnacle cyprids exhibit a complex swimming and exploratory behaviour on surfaces and settlement is a consequence of extensive surface probing and selection of suitable settlement sites. In this work, the behaviour of cyprids in their pre-settlement phase was studied by three-dimensional video stereoscopy. With this technique, three-dimensional trajectories were obtained that were quantitatively analysed. The velocity during vertical sinking of cyprids of
Balanus amphitrite
was used with a modified form of Stokes' law to calculate their mean body density. Furthermore, a classification of the swimming patterns allowed the extension of existing models describing cyprid locomotion and swimming behaviour. The patterns were characterized with respect to their occurrence, transition between patterns and their velocity distribution, and motions were identified that led to surface contacts. This analysis provides a classification framework, which can assist future attempts to identify behavioural responses of cyprids to specific settlement cues.
Computational investigation of cicada aerodynamics in forward flight
Authors: Wan Hui , Dong Haibo , Gai Kuo
Published: December 2014

Free forward flight of cicadas is investigated through high-speed photogrammetry, three-dimensional surface reconstruction and computational fluid dynamics simulations. We report two new vortices generated by the cicada's wide body. One is the thorax-generated vortex, which helps the downwash flow, indicating a new phenomenon of lift enhancement. Another is the cicada posterior body vortex, which entangles with the vortex ring composed of wing tip, trailing edge and wing root vortices. Some other vortex features include: independently developed left- and right-hand side leading edge vortex (LEV), dual-core LEV structure at the mid-wing region and near-wake two-vortex-ring structure. In the cicada forward flight, approximately 79% of the total lift is generated during the downstroke. Cicada wings experience drag in the downstroke, and generate thrust during the upstroke. Energetics study shows that the cicada in free forward flight consumes much more power in the downstroke than in the upstroke, to provide enough lift to support the weight and to overcome drag to move forward.
Memory-endowed US cities and their demographic interactions
Authors: Hernando A. , Hernando R. , Plastino A. , Zambrano E.
Published: December 2014

A quantitative understanding of cities' demographic dynamics is becoming a potentially useful tool for planning sustainable growth. The concomitant theory should reveal details of the cities' past and also of its interaction with nearby urban conglomerates for providing a reasonably complete picture. Using the exhaustive database of the Census Bureau in a time window of 170 years, we exhibit here empirical evidence for time and space correlations in the demographic dynamics of US counties, with a characteristic memory time of 25 years and typical distances of interaction of 200 km. These correlations are much larger than those observed in a European country (Spain), indicating more coherent evolution in US cities. We also measure the resilience of US cities to historical events, finding a demographical
post-traumatic amnesia
after wars (such as the American Civil War) or economic crisis (such as the 1929 Stock Market Crash).
The status of the species Bacillus aerophilus and Bacillus stratosphericus. Request for an Opinion
Authors: Branquinho Raquel , Klein Günter , Kämpfer Peter , Peixe Luísa V.
Published: December 2014

During a study assessing the diversity of the

Bacillus pumilus

group it became apparent that the type strains of both

Bacillus aerophilus

and

Bacillus stratosphericus

were not available from any established culture collection, nor from the authors who originally described them. Therefore, type strains of these species cannot be included in any further scientific studies. It is therefore proposed that the Judicial Commission of the International Committee of Systematics of Prokaryotes place the names

Bacillus aerophilus

and

Bacillus stratosphericus

on the list of rejected names, if suitable replacements for the type strains are not found or if neotype strains are not proposed within two years following the publication of this Request for an Opinion.
Halostagnicola bangensis sp. nov., an alkaliphilic haloarchaeon from a soda lake
Authors: Corral Paulina , Corcelli Angela , Ventosa Antonio
Published: December 2014

An extremely haloalkaphilic archaeon, strain T26T, belonging to the genusHalostagnicola, was isolated from sediment of the soda lake Bange in the region of Tibet, China. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain T26Twas closely related toHalostagnicola alkaliphila167-74T(98.4 %),Halostagnicola larseniiXH-48T(97.5 %) andHalostagnicola kamekurae194-10T(96.8 %). Strain T26Tgrew optimally in media containing 25 % (w/v) salts, at pH 9.0 and 37 °C in aerobic conditions. Mg2+was not required for growth. The cells were motile, pleomorphic and Gram-stain-variable. Colonies of this strain were pink pigmented. Hypotonic treatment caused cell lysis. The polar lipids of the isolate consisted of C20C20and C20C25derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phospholipids components. Glycolipids were not detected, in contrast to the two neutrophilic species of this genus. The genomic DNA G+C content of strain T26Twas 60.1 mol% and DNA–DNA hybridization showed a relatedness of 19 and 17 % withHalostagnicola alkaliphilaCECT 7631TandHalostagnicola larseniiCECT 7116T, respectively. The comparison of 16S rRNA gene sequences, detailed phenotypic characterization, polar lipid profile and DNA–DNA hybridization studies revealed that strain T26Tbelongs to the genusHalostagnicola, and represents a novel species for which the nameHalostagnicolabangensissp. nov. is proposed. The type strain is T26T( = CECT 8219T = IBRC-M 10759T = JCM 18750T).
Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., thermophilic anaerobic representatives of the phylum Planctomycetes
Authors: Slobodkina Galina B. , Kovaleva Olga L. , Miroshnichenko Margarita L. , Slobodkin Alexander I. , Kolganova Tatyana V. , Novikov Andrei A. , van Heerden Esta , Bonch-Osmolovskaya Elizaveta A.
Published: December 2014

Two novel strains of thermophilic planctomycetes were recovered from terrestrial and subterranean habitats. Strain R1Twas isolated from a hot spring (Kunashir Island, Russia) and strain SBP2Twas isolated from a deep gold mine (South Africa). Both isolates grew in the temperature range 30–60 °C and pH range 5.0–8.0. Strain R1Tgrew optimally at 60 °C and pH 6.0–6.5; for SBP2Toptimal conditions were at 52 °C and pH 7.5–8.0. Both strains were capable of anaerobic respiration with nitrate and nitrite as electron acceptors as well as of microaerobic growth. They also could grow by fermentation of mono-, di- and polysaccharides. Based on their phylogenetic position and phenotypic features we suggest that the new isolates represent two novel species belonging to a new genus in the orderPlanctomycetales, for which the namesThermogutta terrifontisgen. nov., sp. nov. andThermogutta hypogeasp. nov. are proposed. The type strain ofThermogutta terrifontis, the type species of the genus, is R1T( = DSM 26237T = VKM B-2805T), and the type strain ofThermogutta hypogeais SBP2T( = JCM 19991T = VKM B-2782T).
Fodinicurvata halophila sp. nov., a moderately halophilic bacterium from a marine saltern
Authors: Infante-Dominguez Carmen , Lawson Paul A. , Johnson Crystal N. , Sánchez-Porro Cristina , Ventosa Antonio
Published: December 2014

A Gram-stain-negative, rod-shaped, facultatively anaerobic, moderately halophilic bacterium, designated strain BA45ALT, was isolated from water of a saltern located in Santa Pola, Alicante, Spain. Cells were motile, and catalase- and oxidase-positive. Strain BA45ALT grew at temperatures in the range 14–45 °C (optimally at 37 °C), at pH 5.0–9.0 (optimally at pH 7.5), and in media containing 5–20 % (w/v) salts [optimally in media containing 10 % (w/v) salts]. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain BA45ALT is a member of the genus

Fodinicurvata

. The closest relatives to the novel strain were

Fodinicurvata fenggangensis

YIM D812T and

Fodinicurvata sediminis

YIM D82T with sequence similarities of 98.2 % and 97.4 %, respectively. DNA–DNA hybridization between the novel isolate and these phylogenetically related species revealed relatedness values of 30 % and 15 %, respectively, with respect to the aforementioned species. The major cellular fatty acids of strain BA45ALT were C18 : 1ω7c, C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA of strain BA45ALT was 58.0 mol%, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine and a number of unknown phospholipids and lipids. Based on phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain BA45ALT constituted a novel species of the genus

Fodinicurvata

, for which the name Fodinicurvata halophila sp. nov. is suggested. The type strain is BA45ALT ( = CCM 8504T = CECT 8472T = JCM 19075T = LMG 27945T).
The status of the species Actinobaculum massiliense (Greub and Raoult 2006). Request for an Opinion
Authors: Yassin A. F. , Spröer C. , Pukall R. , Schumann P.
Published: December 2014

A recent study on members of the genus

Actinobaculum

revealed that cultures of the species

Actinobaculum massiliense

CCUG 47753T ( = DSM 19118T) currently being distributed do not conform to the properties of the type strain of

A. massiliense

CIP 107404T given by Greub & Raoult [Greub, G. & Raoult, D. (2002). J Clin Microbiol 40, 3938–3941]. The original strain, CIP 107404T is no longer available from the Biological Resource Center of Institut Pasteur, Paris. Based on data currently available, the organism currently deposited as CCUG 47753T and DSM 19118T is a member of the species

Actinobaculum schaalii

. Clearly, the organism deposited as CCUG 47753T and DSM 19118T as the type strain of the species

Actinobaculum massiliense

does not have the properties given by Greub & Raoult. Based on the absence of an authentic type strain, the Judicial Commission is requested to examine the status of the name

Actinobaculum massiliense

Greub and Raoult 2006 and to issue an Opinion.
Gemmobacter intermedius sp. nov., isolated from a white stork (Ciconia ciconia)
Authors: Kämpfer Peter , Jerzak Leszek , Wilharm Gottfried , Golke Jan , Busse Hans-Jürgen , Glaeser Stefanie P.
Published: December 2014

A cream-coloured, Gram-stain-negative, aerobic, non-motile, rod- to irregular shaped bacterium, strain 119/4T, was isolated from a choana swab of a white stork nestling on sheep blood agar. 16S rRNA gene sequence analysis and subsequent comparisons showed that it was a member of the family

Rhodobacteraceae,
showing 94.9 % similarity to the type strain of

Gemmobacter tilapiae

and 94.6 % similarity to that of

Gemmobacter nectariphilus

, but also similarly low sequence similarity to the type strains of

Rhodobacter viridis

(94.8 %),

Rhodobacter veldkampii

(94.6 %) and

Paenirhodobacter enshiensis

(94.6 %). Reconstruction of phylogenetic trees showed that strain 119/4T clustered close to species of the genus

Gemmobacter

. The quinone system contained high amounts of ubiquinone Q-10 with traces of Q-8, Q-9 and Q-11, and the fatty acid profile consisted mainly of C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH and C10 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phoshatidylglycerol and phosphatidylcholine. Major polyamines were putrescine and spermidine. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strain 119/4T represents a novel species of the genus

Gemmobacter

, for which the name Gemmobacter intermedius sp. nov. is proposed. The type strain is 119/4T ( = CIP 110795T = LMG 28215T = CCM 8510T).
Psychrobacter ciconiae sp. nov., isolated from white storks (Ciconia ciconia)
Authors: Kämpfer Peter , Jerzak Leszek , Wilharm Gottfried , Golke Jan , Busse Hans-Jürgen , Glaeser Stefanie P.
Published: December 2014

Five beige bacterial strains (176/10T, 178/10, 182/10, 185/7 and 193/8) were isolated from white storks in Poland and found to share identical 16S rRNA gene sequences; they were also investigated in a polyphasic taxonomic study. The cells of all isolates were rod-shaped and Gram-stain-negative. A comparison of the 16S rRNA gene sequences of these organisms with the sequences of the type strains of the most closely related species of the genus

Psychrobacter

showed highest sequence similarities to the type strains of

Psychrobacter pulmonis

and

Psychrobacter faecalis

(both 97.1 %). The 16S rRNA gene sequence similarities to all other species of the genus

Psychrobacter

were below 96.3 %. All five isolates showed an identical profile of physiological reactions and almost identical fatty acid profiles consisting of mainly C18 : 1ω9c, but also C12 : 0 3-OH as a characteristic hydroxylated fatty acid. A quinone system with mainly ubiquinone Q-8 was detected and the polar lipid profile of the type strain, 176/10T, was mainly composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and diphosphatidylglycerol, plus some hitherto uncharacterized phospholipids and one aminolipid. The major polyamines were spermidine and putrescine. DNA–DNA hybridizations between 176/10T and the type strains of

P. pulmonis

and

P.

faecialis
resulted in relatedness values below 70 %. These results indicate that the strains represent a novel species, for which the name
Psychrobacter

ciconiae sp. nov. (type strain 176/10T = CIP 110777T = LMG 28175T = CCM 8519T) is proposed.
Description of Corynebacterium trachiae sp. nov., isolated from a white stork (Ciconia ciconia)
Authors: Kämpfer Peter , Jerzak Leszek , Wilharm Gottfried , Golke Jan , Busse Hans-Jürgen , Glaeser Stefanie P.
Published: December 2014

A Gram-stain-positive bacterial isolate, strain 280/10T was isolated from the trachea of a white stork. The isolate was morphologically rod- to coccoid-shaped, non-motile and showed no oxidase activity. The highest 16S rRNA gene sequence similarity was found to the type strain of

Corynebacterium ciconiae

(97.3 % similarity) as the nearest relative of strain 280/10T, all other 16S rRNA gene sequence similarities to type strains of species of the genus

Corynebacterium

were below 94.2 %. Strain 280/10T had a quinone system consisting predominantly of menaquinone MK-8(H2), minor quantities of MK-9(H2) and small amounts of MK-8. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major compounds in the polar lipid profiles were diphosphatidylglycerol, phoshatidylglycerol, phosphatidylinositol and an acidic glycolipid. Two phosphatidylinositol-mannosides and several unidentified lipids were also present. The strain contained corynemycolic acids, while only small amounts of cellular polyamines were detected. Spermidine and spermine were predominant in the polyamine pattern of 280/10T and putrescine was present in moderate amounts. In the fatty acid profile C18 : 1ω9c, and C16 : 0 were predominant. The strain was distinguishable from

C. ciconiae

,
which is the most closely related species. In conclusion, strain 280/10T is proposed to represent a novel species of the genus

Corynebacterium

with the name Corynebacterium trachiae sp. nov. and the type strain 280/10T ( = CIP 110796T = LMG 28214T).
Structured dynamics of neural activity across developing neocortex
Authors: Ackman James B , Zeng Hongkui , Crair Michael C
Published: December 2014

The cerebral cortex exhibits spontaneous and sensory evoked patterns of activity during early development that is vital for the formation and refinement of neural circuits. Identifying the source and flow of this activity locally and globally is critical for understanding principles guiding self-organization in the developing brain. Here we use whole brain transcranial optical imaging at high spatial and temporal resolution to demonstrate that dynamical patterns of neuronal activity in developing mouse neocortex consist of spatially discrete domains that are coordinated in an age, areal, and behavior- dependent fashion. Ongoing cortical activity displays mirror-symmetric activation patterns across the cerebral hemispheres and stereotyped network architectures that are shaped during development, with parietal-sensorimotor subnetworks functionally connected to occipital regions through frontal-medial cortical areas. This study provides the first broad description of population activity in the developing neocortex at a scope and scale that bridges the microscopic and macroscopic spatiotemporal resolutions provided by traditional neurophysiological and functional neuroimaging techniques. Mesoscale maps of cortical population dynamics within animal models will be crucial for future efforts to understand and treat neurodevelopmental disorders.
Synthesis of phylogeny and taxonomy into a comprehensive tree of life
Authors: Hinchliff Cody , Smith Stephen A , Allman James F , Burleigh J Gordon , Chaudhary Ruchi , Cognill Lyndon M , Crandall Keith A , Deng Jiabin , Drew Bryan T , Gazis Romina , Gude Karl , Hibbett David S , Katz Laura A , Laughinghouse IV H Dail , McTavish Emily Jane , Midford Peter E. , Owen Christopher L , Ree Richard , Rees Jonathan A , Soltis Doug E , Williams Tiffani , Cranston Karen Ann
Published: December 2014

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips -- the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: 1) a novel comprehensive global reference taxonomy; and 2) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. While data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.
Likelihood Estimation with Incomplete Array Variate Observations
Authors: Akdemir Deniz
Published: December 2014

Missing data present an important challenge when dealing with high dimensional data arranged in the form of an array. In this paper, we propose methods for estimation of the parameters of array variate normal probability model from partially observed multi-way data. The methods developed here are useful for missing data imputation, estimation of mean and covariance parameters for multi-way data. A multi-way semi-parametric mixed effects model that allows separation of multi-way covariance effects is also defined and an efficient algorithm for estimation based on the spectral decompositions of the covariance parameters is recommended. We demonstrate our methods with simulations and with real life data involving the estimation of genotype and environment interaction effects on possibly correlated traits.
Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline
Authors: Watanabe Toshiaki , Cheng Ee-chun , Zhong Mei , Lin Haifan
Published: December 2014

The eukaryotic genome has vast intergenic regions containing transposons, pseudogenes, and other repetitive sequences. They produce numerous long noncoding RNAs (lncRNAs) and Piwi-interacting RNAs (piRNAs), yet the functions of the vast intergenic regions remain largely unknown. Mammalian piRNAs are abundantly expressed from the spermatocyte to round spermatid stage, coinciding with the widespread expression of lncRNAs in these cells. Here, we show that piRNAs derived from transposons and pseudogenes mediate the degradation of a large number of mRNAs and lncRNAs in mouse late spermatocytes. In particular, they have a large impact on the lncRNA transcriptome, as a quarter of lncRNAs expressed in late spermatocytes are up-regulated in mice deficient in the piRNA pathway. Furthermore, our genomic and in vivo functional analyses reveal that retrotransposon sequences in the 3′ UTR of mRNAs are targeted by piRNAs for degradation. Similarly, the degradation of spermatogenic cell-specific lncRNAs by piRNAs is mediated by retrotransposon sequences. Moreover, we show that pseudogenes regulate mRNA stability via the piRNA pathway. The degradation of mRNAs and lncRNAs by piRNAs requires PIWIL1 (also known as MIWI) and, at least in part, depends on its slicer activity. Together, these findings reveal the presence of a highly complex and global RNA regulatory network mediated by piRNAs with retrotransposons and pseudogenes as regulatory sequences.
Site-SpecificN-Glycosylation of the S-Locus Receptor Kinase and Its Role in the Self-Incompatibility Response of the Brassicaceae
Authors: Yamamoto Masaya , Tantikanjana Titima , Nishio Takeshi , Nasrallah Mikhail E. , Nasrallah June B.
Published: December 2014

The S-locus receptor kinase SRK is a highly polymorphic transmembrane kinase of the stigma epidermis. Through allele-specific interaction with its pollen coat-localized ligand, the S-locus cysteine-rich protein SCR, SRK is responsible for recognition and inhibition of self pollen in the self-incompatibility response of the Brassicaceae. The SRK extracellular ligand binding domain contains several potential N-glycosylation sites that exhibit varying degrees of conservation among SRK variants. However, the glycosylation status and functional importance of these sites are currently unclear. We investigated this issue in transgenic Arabidopsis thaliana stigmas that express the Arabidopsis lyrata SRKb variant and exhibit an incompatible response toward SCRb-expressing pollen. Analysis of single- and multiple-glycosylation site mutations of SRKb demonstrated that, although five of six potential N-glycosylation sites in SRKb are glycosylated in stigmas, N-glycosylation is not important for SCRb-dependent activation of SRKb. Rather, N-glycosylation functions primarily to ensure the proper and efficient subcellular trafficking of SRK to the plasma membrane. The study provides insight into the function of a receptor that regulates a critical phase of the plant life cycle and represents a valuable addition to the limited information available on the contribution of N-glycosylation to the subcellular trafficking and function of plant receptor kinases.
Seismic interferometry by tangent‐phase correction
Authors: Poletto Flavio , Farina Biancamaria , Böhm Gualtiero , Wapenaar Kees
Published: December 2014

We present a modified interferometry method based on local tangent‐phase analysis, which corrects the cross‐correlated data before summation. The approach makes it possible to synthesize virtual signals usually vanishing in the conventional seismic interferometry summation. For a given pair of receivers and a set of different source positions, a plurality of virtual traces is obtained at new stationary projected points located along the signal wavefronts passing through the real reference receiver. The position of the projected points is estimated by minimizing travel times using wavefront constraint and correlation‐signal tangent information. The method uses mixed processing, which is partially based on velocity‐model knowledge and on data‐based blind interferometry. The approach can be used for selected events, including reflections with different stationary conditions and projected points with respect to those of the direct arrivals, to extend the interferometry representation in seismic exploration data where conventional illumination coverage is not sufficient to obtain the stationary‐phase condition. We discuss possible applications in crosswell geometry with a velocity anomaly and a time lapse.
EDITOR'S CHOICE: Neonicotinoid insecticide travels through a soil food chain, disrupting biological control of non‐target pests and decreasing soya bean yield
Authors: Douglas Margaret R. , Rohr Jason R. , Tooker John F.
Published: December 2014

Neonicotinoids are the most widely used insecticides world‐wide, but their fate in the environment remains unclear, as does their potential to influence non‐target species and the roles they play in agroecosystems.

We investigated in laboratory and field studies the influence of the neonicotinoid thiamethoxam, applied as a coating to soya bean seeds, on interactions among soya beans, non‐target molluscan herbivores and their insect predators.

In the laboratory, the pest slug Deroceras reticulatum was unaffected by thiamethoxam, but transmitted the toxin to predaceous beetles (Chlaenius tricolor), impairing or killing >60%.

In the field, thiamethoxam‐based seed treatments depressed activity–density of arthropod predators, thereby relaxing predation of slugs and reducing soya bean densities by 19% and yield by 5%.

Neonicotinoid residue analyses revealed that insecticide concentrations declined through the food chain, but levels in field‐collected slugs (up to 500 ng g−1) were still high enough to harm insect predators.

Synthesis and applications. Our findings reveal a previously unconsidered ecological pathway through which neonicotinoid use can unintentionally reduce biological control and crop yield. Trophic transfer of neonicotinoids challenges the notion that seed‐applied toxins precisely target herbivorous pests and highlights the need to consider predatory arthropods and soil communities in neonicotinoid risk assessment and stewardship.
Changes and Fluctuations in Issue Ownership: The Case of Sweden, 1979–2010
Authors: Christensen Love , Dahlberg Stefan , Martinsson Johan
Published: December 2014

Issue ownership (IO) has been an important concept in the analysis of party behaviour, party strategy and party competition for several decades. More recently, it has also been of growing interest for research on voting behaviour. Traditionally, IO has been regarded as a stable phenomenon where parties have different issue profiles and are advantaged by different political issues or issue‐areas. Recently, however, many studies have reported change and fluctuations of IO, and the same studies also makes it clear that we know surprisingly little about what might cause, or facilitate, change in issue ownership. In fact, we do not even have systematic studies of how stable issue ownership is, or how frequent shifts in issue ownership actually are. The aim of this article is to explore the extent of change and stability in issue ownership in Sweden. For this purpose, the Swedish national election studies from 1979 to 2010 are utilised. Although recent research has indicated that changes in IO have increased over time, this is not supported in the Swedish case. Instead, issue ownership seems never to have been a particularly stable phenomenon. However, in line with our theoretical expectations, we show that ownership of economic issues is more volatile compared to ownership of other issues.
The effect of patient body mass index on surgical difficulty in gynaecological laparoscopy
Authors: McIlwaine Kate , Manwaring Janine , Ellett Lenore , Cameron Melissa , Readman Emma , Villegas Rocio , Maher Peter
Published: December 2014

Introduction

Over the past three decades, rates of overweight and obesity internationally have risen to epidemic proportions. There are currently no published prospective studies examining the effect of obesity on gynaecologic laparoscopy for benign indications within a population with obesity rates comparable to Australian women.

Aims

To assess and quantify whether increasing patient body mass index negatively impacted upon the ability to successfully complete planned laparoscopic surgery.

Methods

From January 2009 until October 2012, 307 women undergoing laparoscopic gynaecological surgery for benign pathology were recruited. Intra‐operative variables included the following: ease of identification of anatomical landmarks, entry technique and number of attempts, conversion to laparotomy and any complications encountered. Any post‐operative complications were recorded at the six week post‐operative review.

Results

94.46% of operations were completed as planned. As BMI increased, the ease of identification of important anatomical landmarks significantly decreased. There was no correlation between increasing BMI and surgical complication rates.

Conclusions

Planned gynaecological laparoscopy can be performed in obese patients with a high likelihood of completion. In this study, obesity was not associated with a significant increase in complication rates or failure to complete the surgery as planned.
A review of six sacrospinous suture devices
Authors: Manning Jane A. , Arnold Peter
Published: December 2014

Background

The sacrospinous ligament is frequently accessed blindly during vaginal vault suspension with risk to inferior gluteal vessels. This article examines the vascular safety of six devices currently used for this purpose using cadaveric examination.

Method

Devices were evaluated for cost and for their ability to reliably avoid vessels behind the sacrospinous ligament by applying each to the traditionally described location, two fingerbreadths medial to the right ischial spine. We selected the five predissected, preserved pelves and right hemipelves where vessels remained attached.

Results

The i stitch® was seen to penetrate coccygeal branches of inferior gluteal artery. The Capio®, Caspari™ and Endostitch® remained confined within all, including thin, ligaments. The Miya® hook and Deschamp® impinged upon but deflected vessels behind thin ligaments.

Conclusions

VascuIar anatomy behind the sacrospinous ligament is enormously variable. Suture placement two fingerbreadths medial to the spine does not guarantee safety. The ligament may be thin in the elderly, who are unlikely to cope with haemorrhage yet who may represent a growing proportion of those requiring surgery. For vascular safety, the ideal device is compact. It impresses and enfolds but does not penetrate behind the ligament. The sharp penetrating component that carries suture should traverse the shortest distance at the shallowest depth allowing adequate bite. This was satisfied by the Caspari®, Capio® and less so by Endostitch®. The i stitch® was not safe in thin ligaments. The Deschamp® and Miya® devices may be a good compromise for the developing world where cost is important.