bluuebunny/crossref_metadata_2025 huggingface dataset:
Effectiveness of Harvest Control Rules in Managing American Lobster Fishery in the Gulf of Maine
Authors: Zhang Yuying , Chen Yong
Published: October 2012

Harvest control rules (HCRs) are commonly applied in managing fisheries resources. However, no HCR is explicitly defined for the fishery of American lobster Homarus americanus in the Gulf of Maine (GOM), one of the most valuable commercial fisheries in the USA. In this study we evaluated five HCRs: the “linear” HCR, the “nonlinear middle convex” HCR, the “nonlinear convex” HCR, the “nonlinear concave” HCR, and the “catch” HCR. The first four HCRs use fishing mortality curves as boundaries that could adjust the next year's target fishing mortality linearly or nonlinearly based on the stock abundance, while the fifth HCR links the catch-based boundaries to the stock abundance. A sex-specific and size-dependent operating model was developed to simulate the GOM lobster fishery managed by the above five HCRs. Four performance measures were used to quantify the effectiveness of HCRs in the lobster fishery management. For each HCR we considered both short-term and long-term management time periods and scenarios of different recruitment dynamics and natural mortality rates, as well as uncertainties in key fishery parameters. This study shows that the linear HCR can effectively maintain the fishing mortality and stock abundance around the target levels. The nonlinear concave HCR could result in a higher lowest legal biomass and a higher terminal legal biomass in a short-term management period, especially when the abundance was low. Comparing the nonlinear middle convex HCR and the “nonlinear convex” HCR, when the abundance was high, an increase of the fishing mortality would not increase the total catch but would decrease the terminal legal biomass. The fishing mortality-based HCR was more effective than the catch-based HCR in managing the GOM American lobster fishery.

Received March 14, 2011; accepted July 12, 2012
Instance memorization and category influence: Challenging the evidence for multiple systems in category learning
Authors: Johansen Mark K. , Fouquet Nathalie , Savage Justin , Shanks David R.
Published: October 2012

A class of dual-system theories of categorization assumes a categorization system based on actively formed prototypes in addition to a separate instance memory system. It has been suggested that, because they have used poorly differentiated category structures (such as the influential “5-4” structure), studies supporting the alternative exemplar theory reveal little about the properties of the categorization system. Dual-system theories assume that the instance memory system only influences categorization behaviour via similarity to single isolated instances, without generalization across instances. However, we present the results of two experiments employing the 5-4 structure to argue against this. Experiment 1 contrasted learning in the standard 5-4 structure with learning in an even more poorly differentiated 5-4 structure. In Experiment 2, participants memorized the 5-4 structure based on a five minute simultaneous presentation of all nine category instances. Both experiments revealed category influences as reflected by differences in instance learnability and generalization, at variance with the dual-system prediction. These results have implications for the exemplars versus prototypes debate and the nature of human categorization mechanisms.
Cédric Blanpain: The stories stem cells tell
Authors: Sedwick Caitlin
Published: October 2012

Blanpain studies stem cell maintenance and repair of embryonic and adult tissues.
Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling
Authors: Shen Qing-Tao , Hsiue Peter P. , Sindelar Charles V. , Welch Matthew D. , Campellone Kenneth G. , Wang Hong-Wei
Published: October 2012

The microtubule (MT) and actin cytoskeletons drive many essential cellular processes, yet fairly little is known about how their functions are coordinated. One factor that mediates important cross talk between these two systems is WHAMM, a Golgi-associated protein that utilizes MT binding and actin nucleation activities to promote membrane tubulation during intracellular transport. Using cryoelectron microscopy and other biophysical and biochemical approaches, we unveil the underlying mechanisms for how these activities are coordinated. We find that WHAMM bound to the outer surface of MT protofilaments via a novel interaction between its central coiled-coil region and tubulin heterodimers. Upon the assembly of WHAMM onto MTs, its N-terminal membrane-binding domain was exposed at the MT periphery, where it can recruit vesicles and remodel them into tubular structures. In contrast, MT binding masked the C-terminal portion of WHAMM and prevented it from promoting actin nucleation. These results give rise to a model whereby distinct MT-bound and actin-nucleating populations of WHAMM collaborate during membrane tubulation.
Antisense-based therapy for the treatment of spinal muscular atrophy
Authors: Rigo Frank , Hua Yimin , Krainer Adrian R. , Bennett C. Frank
Published: October 2012

One of the greatest thrills a biomedical researcher may experience is seeing the product of many years of dedicated effort finally make its way to the patient. As a team, we have worked for the past eight years to discover a drug that could treat a devastating childhood neuromuscular disease, spinal muscular atrophy (SMA). Here, we describe the journey that has led to a promising drug based on the biology underlying the disease.
Getting mobile right: start with who and why, not what and how
Authors: RAPPLE Charlie
Published: October 2012

Mobile dominance is imminent. Getting mobile wrong means losing market share to disruptors; getting it right gives us an opportunity to rebuild relationships with our audience. It is the audience, therefore, that should direct mobile strategy. This means starting by researching the workflows and challenges of different segments, to understand how to add value (not just bells‐and‐whistles). We must prioritize mobile in our product development and innovation, freeing it from the ‘print + online’ paradigm so that it can fulfil different kinds of information needs and objectives. This article advocates a back‐to‐basics approach that puts audiences (not content, and not technology) at the centre of mobile strategy, and explores market segmentation and research, innovation, business models, development choices, and the wider organizational implications of getting mobile right.
Statistics usage by French academic libraries: a survey
Authors: BOUKACEM‐ZEGHMOURI Chérifa , SCHÖPFEL Joachim
Published: October 2012

The article presents a survey on usage statistics management in academic libraries in France. The objective is to provide empirical evidence on real methods and processes, best practices and problems experienced by librarians. The survey adapted Baker and Read's methodology to the French context. One‐third of French academic libraries answered the survey. Results show that usage statistics are crucial for librarians' daily work. COUNTER reports are mostly used, specifically the JR1 format. Two‐thirds of the libraries enhance the usage statistics with other data. Librarians face three major difficulties: lack of time, lack of usage data produced by French vendors, and the need for customized tools. The article contains a short literature review and ends with recommendations for further studies. It is the first published survey on usage data management in France and allows for comparison with results from other countries.
Article and book reading patterns of scholars: findings for publishers
Authors: TENOPIR Carol , VOLENTINE Rachel , KING Donald W.
Published: October 2012

Surveys of academic staff in six universities in the UK provide insights for publishers into scholarly article and book reading patterns of academics and differences based on personal characteristics of readers. These surveys were part of the 2011 UK Scholarly Reading and the Value of the Library Study funded by JISC Collections and based on studies conducted by Tenopir and King since 1977. Scholarly articles, especially those obtained from the library's e‐journal collections, are a vital part of academic work. Reading patterns of books are quite different than articles; books most often come from personal print collections. Book readings are still important for research and teaching, however, especially for humanists. Academics come into contact with multiple sources of information every day and therefore, convenience and easy access are important factors. Knowing more about academic reading patterns helps publishers and librarians design more effective journal systems and services now and into the future.
A survey on the use of CrossCheck for detecting plagiarism in journal articles
Authors: ZHANG Yuehong (Helen) , JIA Xiaoyan
Published: October 2012

The purpose of this survey was to investigate journal editors' use of CrossCheck, powered by iThenticate, to detect plagiarism, and their attitude to potential plagiarism once discovered. A 22‐question survey was sent to 3,305 recipients, primarily scholarly journal editors from Anglophone countries, and a reduced 10‐question version to 607 editors from non‐Anglophone countries. The response rate was 5.6%. 42% of all respondents had used CrossCheck in their work. The main findings are as follows: (1) the plagiarism detection tool and its similarity report are extremely useful and effective and can assist editors in screening documents suspected of plagiarism; (2) responses show the journal editors' attitude and level of tolerance towards different kinds of plagiarism in different disciplines; (3) the survey results underscore a clear consensus on editorial standards on plagiarism, but there were small variations between different disciplines and countries, as well as between Anglophone and non‐Anglophone. The study also suggests that further work is needed to establish a universal principle and practical approaches to prevent plagiarism and duplicate publication.
A new bmj.com: now with added Drupal
Authors: BERHANE Daniel , PAYNE David
Published: October 2012

This case study describes a two year co‐development project involving BMJ Group and HighWire Press to redesign and migrate the company's flagship website, bmj.com, to Drupal. The new site went live in November 2011. The project achieved its five main objectives: (i) to boost discoverability of new content; (ii) increase user engagement; (iii) increase traffic; (iv) promote the site's channels (research, education, comment, news, multimedia, specialties); and (v) drive referrals to other BMJ Group product sites.
Site identification in high-throughput RNA–protein interaction data
Authors: Uren Philip J. , Bahrami-Samani Emad , Burns Suzanne C. , Qiao Mei , Karginov Fedor V. , Hodges Emily , Hannon Gregory J. , Sanford Jeremy R. , Penalva Luiz O. F. , Smith Andrew D.
Published: October 2012

Motivation: Post-transcriptional and co-transcriptional regulation is a crucial link between genotype and phenotype. The central players are the RNA-binding proteins, and experimental technologies [such as cross-linking with immunoprecipitation- (CLIP-) and RIP-seq] for probing their activities have advanced rapidly over the course of the past decade. Statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however.

Results: We introduce a method for site identification which provides four key advantages over previous methods: (i) it can be applied on all variations of CLIP and RIP-seq technologies, (ii) it accurately models the underlying read-count distributions, (iii) it allows external covariates, such as transcript abundance (which we demonstrate is highly correlated with read count) to inform the site identification process and (iv) it allows for direct comparison of site usage across cell types or conditions.

Availability and implementation: We have implemented our method in a software tool called Piranha. Source code and binaries, licensed under the GNU General Public License (version 3) are freely available for download from http://smithlab.usc.edu.

Contact:  andrewds@usc.edu

Supplementary information:  Supplementary data available at Bioinformatics online.
FeatureStack: Perl module for comparative visualization of gene features
Authors: Frech Christian , Choo Caleb , Chen Nansheng
Published: October 2012

Summary: FeatureStack is a Perl module for the automatic generation of multi-gene images. FeatureStack takes BioPerl-compliant gene or transcript features as input and renders them side by side using a user-defined BioPerl glyph. Output images can be generated in SVG or PNG format. FeatureStack comes with a new BioPerl glyph, decorated_gene, which can highlight protein features on top of gene models. Used in combination, FeatureStack and decorated_gene enable rapid and automated generation of annotation-rich images of stacked gene models that greatly facilitate evolutionary studies of related gene structures and gene families.

Availability and implementation:  Bio-Draw-FeatureStack and Bio-Graphics-glyph-decorated_gene are freely available at the Comprehensive Perl Archive Network (CPAN) and GitHub.

Contact:  chenn@sfu.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
Authors: Smith Richard N. , Aleksic Jelena , Butano Daniela , Carr Adrian , Contrino Sergio , Hu Fengyuan , Lyne Mike , Lyne Rachel , Kalderimis Alex , Rutherford Kim , Stepan Radek , Sullivan Julie , Wakeling Matthew , Watkins Xavier , Micklem Gos
Published: October 2012

Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of ‘widgets’ performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages.

Availability: Freely available from http://www.intermine.org under the LGPL license.

Contact:  g.micklem@gen.cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages
Authors: Molak Martyna , Lorenzen Eline D. , Shapiro Beth , Ho Simon Y.W.
Published: October 2012

In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.
Storage ring measurements of the dissociative recombination of H
3
+
Authors: Kreckel Holger , Petrignani Annemieke , Novotný Oldřich , Crabtree Kyle , Buhr Henrik , McCall Benjamin J. , Wolf Andreas
Published: October 2012

The dissociative recombination (DR) of

is a key process in interstellar chemistry. More than 30 experimental studies of the DR process have been published in the literature. The

DR rate coefficient results obtained from these measurements, however, have not always been consistent. The outcome seems to depend on the experimental method, on the exact measurement procedure and sometimes even on the interpretation of the experimental data. In the past two decades, heavy-ion storage rings have become the working horse for DR measurements, as they provide a direct measurement of the DR products. Furthermore, storage ring measurements yield energy-resolved rate coefficients with unprecedented resolution that allow for detailed comparison with theory. DR results from different storage ring facilities have shown a remarkable consistency throughout the years and they provide additional information on break-up dynamics and internal excitation. In this study, we will review the storage ring DR measurements that have been carried out for

.
Dissociative recombination of H
3
+
: 10 years in retrospect
Authors: Larsson Mats
Published: October 2012

The dissociative recombination of

has been an intriguing problem for more than half a century. The early experiments on

during the first 20 years were carried out without mass analysis in decaying plasma afterglows, and thus the measured rates pertained to an uncontrolled mixture of

and impurity ions. When mass analysis was used, the rate coefficient was determined to be an uneventful value of about 10
−7
 cm
3
 s
−1
, a very common rate coefficient for many molecular ions. But this was not the end of the story, not even the beginning of the end; it marked only the end of the beginning. The story I will tell in this article started about 10 years ago, when the dissociative recombination of

was approaching its deepest crisis. Today, owing to an extensive experimental and theoretical effort, the state of affairs has reached a historically unique level of harmony, although there still remains many things to sort out.
The distribution of cosmic-ray ionization rates in diffuse molecular clouds as probed by H
3
+
Authors: Indriolo Nick
Published: October 2012

Owing to its simple chemistry, H

is widely regarded as the most reliable tracer of the cosmic-ray ionization rate in diffuse interstellar clouds. At present, H

observations have been made in over 50 sight lines that probe the diffuse interstellar medium (ISM) throughout the Galaxy. This small survey presents the opportunity to investigate the distribution of cosmic-ray ionization rates in the ISM, as well as any correlations between the ionization rate and line-of-sight properties. Some of the highest inferred ionization rates are about 25 times larger than the lowest upper limits, suggesting variations in the underlying low-energy cosmic-ray flux across the Galaxy. Most likely, such variations are caused predominantly by the distance between an observed cloud and the nearest site of particle acceleration.
Hot, metastable hydronium ion in the Galactic centre: formation pumping in X-ray-irradiated gas?
Authors: Lis Dariusz C. , Schilke Peter , Bergin Edwin A. , Emprechtinger Martin ,   the HEXOS Team
Published: October 2012

With a 3.5 m diameter telescope passively cooled to approximately 80 K, and a science payload comprising two direct detection cameras/medium resolution imaging spectrometers (PACS and SPIRE) and a very high spectral resolution heterodyne spectrometer (HIFI), the Herschel Space Observatory is providing extraordinary observational opportunities in the 55–670 μm spectral range. HIFI has opened for the first time to high-resolution spectroscopy the submillimetre band that includes the fundamental rotational transitions of interstellar hydrides, the basic building blocks of astrochemistry. We discuss a recent HIFI discovery of metastable rotational transitions of the hydronium ion (protonated water, H
3
O
+
), with rotational level energies up to 1200 K above the ground state, in absorption towards Sagittarius B2(N) in the Galactic centre. Hydronium is an important molecular ion in the oxygen chemical network. Earlier HIFI observations have indicated a general deficiency of H
3
O
+
in the diffuse gas in the Galactic disc. The presence of hot H
3
O
+
towards Sagittarius B2(N) thus appears to be related to the unique physical conditions in the central molecular zone, manifested, for example, by the widespread presence of abundant H

. One intriguing theory for the high rotational temperature characterizing the population of the H
3
O
+
metastable levels may be formation pumping in molecular gas irradiated by X-rays emitted by the Galactic centre black hole. Alternatively, the pervasive presence of enhanced turbulence in the central molecular zone may give rise to shocks in the lower-density medium that is exposed to energetic radiation.
To be or not to be: the early history of H
3
and H
3
+
Authors: Kragh Helge
Published: October 2012

Triatomic hydrogen became a major research area only after 1980, but its history goes back to J. J. Thomson’s discovery in 1911. In fact, the possible existence of H
3
was suggested as early as 1895. This paper outlines the history of H
3
and

up to the mid-1930s, when chemists and physicists ceased to believe in the existence of the H
3
molecule. In the intervening years, there was a great deal of interest in ‘active hydrogen’ and also in the configuration of H
3
, which was examined by Bohr in 1919. While H
3
was abandoned,

was not. Although the properties of

were largely unknown, the existence of the ion was firmly established, and its structure studied by means of the new methods of quantum chemistry.
Kinetic processes in recombining H
3
+
plasmas
Authors: Johnsen Rainer
Published: October 2012

Recombination in plasmas containing

ions occurs not only by binary recombination but also by third-body-assisted mechanisms, the principal subject of this contribution. Third-body effects on recombination are of interest for model calculations of hydrogen discharges, their spectral emissions and the inference of binary recombination coefficients from plasma afterglow data.
H
3
+
at the interface between astrochemistry and astroparticle physics
Authors: Black John H.
Published: October 2012

The

molecular ion has been used by Oka and collaborators to trace the rate of ionization by cosmic rays in the interstellar medium. More energetic cosmic rays also produce diffuse γ-radiation. Now that several supernova remnants (SNRs) have been identified as γ-ray sources, it is possible to use spectroscopy of molecular ions to search for enhanced ionization rates that would pinpoint the SNRs as the accelerators of cosmic rays. It is proposed that the warm, dilute molecular gas revealed by

absorption in the central molecular zone of the Galaxy can also be investigated via radio recombination lines of atoms and possibly triatomic hydrogen.
Paracoccus tibetensis sp. nov., isolated from Qinghai-Tibet Plateau permafrost
Authors: Zhu Shan , Zhao Qi , Zhang Gaosen , Jiang Zhonghao , Sheng Hongmei , Feng Huyuan , An Lizhe
Published: October 2012

Strain Tibet-S9a3T was isolated from Qinghai-Tibet Plateau permafrost, China. The isolate was a Gram-negative, non-motile, non-spore-forming short rod. The 16S rRNA gene sequence indicated that strain Tibet-S9a3T was a member of the genus

Paracoccus

and was closely related to

Paracoccus aestuarii

B7T (98.2 % 16S rRNA gene sequence similarity), ‘P. beibuensis’ JLT1284 (97.9 %),

P. homiensis

DD-R11T (97.4 %),

P. zeaxanthinifaciens

ATCC 21588T (97.4 %) and other type strains of the genus (93.7–96.7 %). The G+C content of the genomic DNA was 69.1 mol% and the major isoprenoid quinone was ubiquinone-10. The major fatty acids were C18 : 1ω7c (87.6 %), C18 : 0 (4.3 %) and C10 : 0 3-OH (2.0 %). DNA–DNA relatedness between strain Tibet-S9a3T and

P. aestuarii

B7T was 37.9 %. On the basis of phenotypic and genotypic characteristics, it is suggested that strain Tibet-S9a3T represents a novel species of the genus

Paracoccus

, for which the name Paracoccus tibetensis sp. nov. is proposed. The type strain is Tibet-S9a3T ( = CGMCC 1.8925T  = NBRC 105667T).
Fonticella tunisiensis gen. nov., sp. nov., isolated from a hot spring
Authors: Fraj Belkis , Ben Hania Wajdi , Postec Anne , Hamdi Moktar , Ollivier Bernard , Fardeau Marie-Laure
Published: October 2012

A strictly anaerobic, moderately thermophilic, halotolerant rod, designated BELH25T, was isolated from a water sample of a Tunisian hot spring. Cells were non-motile, 2–6 µm long and 0.4–0.6 µm wide, appearing singly or in pairs. The isolate grew at 45–70 °C (optimum 55 °C), at pH 6.2–8.0 (optimum pH 7.0) and with 0–4 % NaCl (optimum 0–2.0 %). Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain BELH25T used cellobiose, fructose, galactose, glucose, maltose, mannose, sucrose, starch and yeast extract as electron donors. The main fermentation products from glucose metabolism were formate, acetate, ethanol and CO2. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and anteiso-C15 : 0. The DNA G+C content was 37.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain BELH25T was most closely related to

Caloramator viterbiensis

JW/MS-VS5T and

Fervidicella metallireducens

AeBT (92.2 and 92.1 % sequence similarity, respectively), and the isolate was positioned approximately equidistantly between these genera. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain BELH25T is proposed to be a member of a novel species of a novel genus within the order

Clostridiales

, family

Clostridiaceae

, for which the name Fonticella tunisiensis gen. nov., sp. nov. is proposed. The type strain of the type species is BELH25T ( = DSM 24455T = JCM 17559T).
Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment
Authors: Tsubouchi Taishi , Shimane Yasuhiro , Mori Kozue , Usui Keiko , Hiraki Toshiki , Tame Akihiro , Uematsu Katsuyuki , Maruyama Tadashi , Hatada Yuji
Published: October 2012

A novel filamentous bacterium, designated strain JIR-001T, was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55–73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family

Thermoactinomycetaceae

. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001T belongs to the family

Thermoactinomycetaceae

within the class

Bacilli

. Similarity levels between the 16S rRNA gene sequence of strain JIR-001T and those of the type strains of

Thermoactinomycetaceae

species were 85.5–93.5 %; highest sequence similarity was with

Melghirimyces algeriensis

NariEXT. In the DNA–DNA hybridization assays between strain JIR-001T and its phylogenetic neighbours the mean hybridization levels with

Melghirimyces algeriensis

NariEXT,

Planifilum fimeticola

H0165T,

Planifilum fulgidum

500275T and

Planifilum yunnanense

LA5T were 5.3–7.5, 2.3–4.7, 2.1–4.8 and 2.5–4.9 %, respectively. The DNA G+C content of strain JIR-001T was 55.1 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001T is considered to represent a novel species in a new genus of the family

Thermoactinomycetaceae

, for which the name Polycladomyces abyssicola gen. nov., sp. nov. is proposed. The type strain of Polycladomyces abyssicola is JIR-001T ( = JCM 18147T = CECT 8074T).
Preparation of Small RNA Libraries for High-Throughput Sequencing
Authors: Malone Colin , Brennecke Julius , Czech Ben , Aravin Alexei , Hannon Gregory J.
Published: October 2012

This protocol details the process of small RNA cloning for sequencing on the Illumina/Solexa sequencing platform, but it can be easily modified for use on other next-generation platforms (e.g., SOLiD, 454). This procedure is designed to clone canonical small RNA molecules with 5′-monophosphate and 3′-hydroxyl termini. Modifications, such as the presence of a 2′-O-methyl group, can reduce efficiency, although not sufficiently to negate the utility of the approach. Other termini modifications, such as a 5′ triphosphate or a 3′ phosphate, can be altered by enzymatic treatment before cloning.
Estimating Object Number in Biological Structures
Authors: West Mark J.
Published: October 2012

The number of cells and subcellular structures can often be readily related to quantitative evaluations of organ and tissue function. Neurons and synapses, for example, are directly involved in the integration and transfer of information in neural systems. Their numbers are consequently important parameters in the evaluations of the functional capacity of neural systems. Only information regarding the total number of objects, such as synapses and neurons, can be used to draw conclusions regarding changes or differences in the number of these structural entities. The large numbers of neurons and synapses in the vast majority of neural systems preclude absolute determinations of their total number, that is, counting each and every neuron or synapse. However, estimates or approximations based on limited sampling can be useful if the estimates are unbiased and if the individual estimates have an acceptable amount of precision. This article discusses the estimation of object number, including sampling, indirect and direct counting techniques, sources and types of bias, and the disector counting technique. An example is also given.
Cadmium(II) chloride, bromide and iodide complexes with 4,4′-bipyridazine: when are diazine and halide bridges (in)compatible?
Authors: Domasevitch Konstantin V. , Rusanova Julia A. , Gural'skiy Ilya A. , Solntsev Pavlo V.
Published: October 2012

In poly[di-μ-chlorido-μ-(4,4′-bipyridazine)-κ2N1:N1′-cadmium(II)], [CdCl2(C8H6N4)]n, (I), and its isomorphous bromide analogue, [CdBr2(C8H6N4)]n, (II), the halide atom lies on a mirror plane and the CdIIion resides at the intersection of two perpendicular mirror planes withm2msite symmetry. The pyridazine rings of the ligand lie in a mirror plane and are related to each other by a second mirror plane perpendicular to the first. The compounds adopt the characteristic structure of the [MIIX2(bipy)] type (bipy is bipyridine) based on crosslinking of [Cd(μ-X)2]nchains [Cd—Cl = 2.5955 (9) and 2.6688 (9) Å; Cd—Br = 2.7089 (4) and 2.8041 (3) Å] by bitopic rod-like organic ligands [Cd—N = 2.368 (3)–2.380 (3) Å]. This feature is discussed in terms of supramolecular stabilization, implying that the periodicity of the inorganic chain [Cd...Cd = 3.7802 (4) Å in (I) and 3.9432 (3) Å in (II)] is favourable for extensive parallel π–π stacking of monodentate pyridazine rings, with centroid–centroid distances of 3.7751 (4) Å in (I) and 3.9359 (4) Å in (II). This is not the case for the longer iodide bridges, which cannot stabilize such a pattern. In poly[tetra-μ-iodido-μ4-(4,4′-bipyridazine)-κ4N1:N2:N1′:N2′-dicadmium(II)], [Cd2I4(C8H6N4)]n, (III), the ligands are situated across a centre of inversion; they are tetradentate [Cd—N = 2.488 (2) and 2.516 (2) Å] and link successive [Cd(μ-I)2]nchains [Cd—I = 2.8816 (3)–3.0069 (4) Å] into corrugated layers.
Aging leads to a programmed loss of brown adipocytes in murine subcutaneous white adipose tissue
Authors: Rogers Nicole H. , Landa Alejandro , Park Seongjoon , Smith Roy G.
Published: October 2012

Insulin sensitivity deteriorates with age, but mechanisms remain unclear. Age‐related changes in the function of subcutaneous white adipose tissue (sWAT) are less characterized than those in visceral WAT. We hypothesized that metabolic alterations in sWAT, which in contrast to epididymal WAT, harbors a subpopulation of energy‐dissipating UCP1+ brown adipocytes, promote age‐dependent progression toward insulin resistance. Indeed, we show that a predominant consequence of aging in murine sWAT is loss of ‘browning’. sWAT from young mice is histologically similar to brown adipose tissue (multilocular, UCP1+), but becomes morphologically white by 12 months of age. Correspondingly, sWAT expression of ucp1 precipitously declines (~300‐fold) between 3 and 12 months. Loss continues into old age (24 months) and is inversely correlated with the development of insulin resistance. Additional age‐dependent changes in sWAT include lower expression of adbr3 and higher expression of maoa, suggesting reduced local adrenergic tone as a potential mechanism. Indeed, treatment with a β3‐adrenergic agonist to compensate for reduced tone rescues the aged sWAT phenotype. Age‐related changes in sWAT are not explained by the differences in body weight; mice subjected to 40% caloric restriction for 12 months are of body weight similar to 3‐month‐old ad lib fed mice, but display sWAT resembling that of age‐matched ad lib fed mice (devoid of brown adipose‐like morphology). Overall, findings identify the loss of ‘browning’ in sWAT as a new aging phenomenon and provide insight into the pathogenesis of age‐associated metabolic disease by revealing novel molecular changes tied to systemic metabolic dysfunction.
Estrogen Receptor α Antagonists Mediate Changes in CCL20 and CXCL1 Secretions in the Murine Female Reproductive Tract
Authors: Hickey Danica K. , Fahey John V. , Wira Charles R.
Published: October 2012

Problem

Estradiol regulates chemokine secretion from uterine epithelial cells, but little is known about estradiol regulation in vivo or the role of estrogen receptors (ERs).

Method

CCL20 and CXCL1 present in reproductive washes following treatment with selective estrogen receptor modulators (SERMs) were compared with that during estrous and following estradiol‐treated ovariectomized BALB/c mice. Cellular regulation was determined using isolated vaginal and uterine epithelial/stromal cells in vitro.

Results

Uterine and vaginal chemokine secretion is cyclically regulated with CCL20 at low levels but CXCL1 at high levels during high estradiol, generally mimicking estradiol effect in vivo. ERα but not ERβ regulated CCL20/CXCL1 secretion by uterine epithelial cells in vitro and vaginal CCL20 in vivo. Estradiol/SERMs failed to alter uterine CCL20 secretion in ovariectomized mice. Diminished uterine epithelial ERα staining following ovariectomy corresponded with estradiol unresponsiveness of uterine tissue.

Conclusion

Estrogen receptors α regulates CCL20/CXCL1 secretion in the female reproductive tract, and ERα antagonists directly oppose the regulation by estradiol. Understanding ER‐mediated antimicrobial chemokine expression is important to elucidate cyclic susceptibility to sexually transmitted pathogens.
Cigarette smoking and impulsivity in bipolar disorder
Authors: Heffner Jaimee L , Fleck David E , DelBello Melissa P , Adler Caleb M , Strakowski Stephen M
Published: October 2012

Heffner JL, Fleck DE, DelBello MP, Adler CM, Strakowski SM. Cigarette smoking and impulsivity in bipolar disorder. Bipolar Disord 2012: 14: 735–742. © 2012 The Authors. Journal compilation © 2012 John Wiley & Sons A/S.

Objectives:  There is a high prevalence of smoking among individuals with bipolar disorder, yet there have been few efforts to identify potential contributing factors as a means of improving prevention and treatment approaches. The goal of this study was to examine the association between impulsivity and the initiation or maintenance of smoking in bipolar disorder.

Methods:  Participants comprised 97 adolescents and adults, ages 16–50, with bipolar I disorder who were experiencing a mixed or manic episode at the time of study enrollment. Participants completed the Barratt Impulsiveness Scale‐11 (BIS‐11) as a self‐report indicator of trait impulsivity, and the Logan Stop‐Signal Task (SST), Delayed Reward Task (DRT), and Degraded Stimulus Continuous Performance Task (DSCPT) as behavioral measures of impulsivity.

Results:  Current smokers (34%) and former smokers (23%) generally reported higher trait impulsivity on the BIS‐11 than never smokers (43%), with minimal evidence for differences among the two ever‐smoking groups. No differences in impulsivity by smoking status emerged on the behavioral measures.

Conclusions:  Trait impulsivity is associated with the initiation, but not necessarily the maintenance, of cigarette smoking in adolescents and adults with bipolar disorder. Our findings provide no evidence that smoking is associated with impulsive responding on cognitive tasks during a symptomatic period during which impulsivity is elevated.
Phase I trial of OTS11101, an anti‐angiogenic vaccine targeting vascular endothelial growth factor receptor 1 in solid tumor
Authors: Hayashi Hidetoshi , Kurata Takayasu , Fujisaka Yasuhito , Kawakami Hisato , Tanaka Kaoru , Okabe Takafumi , Takeda Masayuki , Satoh Taroh , Yoshida Koji , Tsunoda Takuya , Arao Tokuzo , Nishio Kazuto , Nakagawa Kazuhiko
Published: October 2012

OTS11101 is a novel peptide vaccine that acts as an angiogenesis inhibitor by inducing cytotoxic T lymphocyte (CTL) cells that specifically target vascular endothelial cells expressing vascular endothelial growth factor (VEGF) receptor 1. We conducted a phase I study to evaluate the safety, tolerability, maximum tolerated dose, and pharmacodynamic biomarker status of this vaccine. Nine patients with advanced solid tumors received 1.0, 2.0, or 3.0 mg of OTS11101 subcutaneously, once a week in a 28‐day cycle. Three patients experienced grade 1 injection site reactions, which were the most frequent adverse events. Grade 2 proteinuria and hypertension each occurred in one patient. As other toxicities were generally mild, the maximum tolerated dose was not reached. Furthermore, we explored the induction of specific activated CTLs, and biomarkers related to angiogenesis. A pharmacodynamics study revealed that induction of specific CTLs was observed for a dose of 2.0 and 3.0 mg. The serum concentrations of soluble VEGF receptor 1 and 2 after vaccination increased significantly compared with baseline. A microarray was performed to give a comprehensive analysis of gene expression, suggesting that OTS11101 vaccination resulted in T cell activation in a clinical setting. In conclusion, OTS11101 was well tolerated in patients up to 3.0 mg once weekly and our biomarker analysis suggested that this anti‐angiogenesis vaccine is biologically active. (Cancer Sci 2013; 104: 98–104)
Segmental allergen challenge enhances chitinase activity and levels of CCL18 in mild atopic asthma
Authors: Gavala M. L. , Kelly E. A. B. , Esnault S. , Kukreja S. , Evans M. D. , Bertics P. J. , Chupp G. L. , Jarjour N. N.
Published: October 2012

Background

Allergic airway inflammation contributes to the airway remodelling that has been linked to increased obstruction and morbidity in asthma. However, the mechanisms by which allergens contribute to airway remodelling in humans are not fully established. CCL18, chitotriosidase (CHIT1) and YKL‐40 are readily detectable in the lungs and contribute to remodelling in other fibrotic diseases, but their involvement in allergic asthma is unclear.

Objective

We hypothesized that CCL18, YKL‐40 and CHIT1 bioactivity are enhanced in allergic asthma subjects after segmental allergen challenge and are related to increased pro‐fibrotic and Th2‐associated mediators in the lungs.

Methods

Levels of CCL18 and YKL‐40 protein and chitotriosidase (CHIT1) bioactivity in bronchoalveolar lavage (BAL) fluid, as well as CCL18, YKL‐40 and CHIT1 mRNA levels in BAL cells were evaluated in patients with asthma at baseline and 48 h after segmental allergen challenge. We also examined the correlation between CCL18 and YKL‐40 levels and CHIT1 activity with the levels of other pro‐fibrotic factors and chemokines previously shown to be up‐regulated after allergen challenge.

Results

Chitotriosidase activity and YKL‐40 and CCL18 levels were elevated after segmental allergen challenge and these levels correlated with those of other pro‐fibrotic factors, T cell chemokines, and inflammatory cells after allergen challenge. CCL18 and YKL‐40 mRNA levels also increased in BAL cells after allergen challenge.

Conclusions and Clinical Relevance

Our results suggest that CCL18 and YKL‐40 levels and CHIT1 activity are enhanced in allergic airway inflammation and thus may contribute to airway remodelling in asthma.
Population structure of Chrysoporthe austroafricana in southern Africa determined using Vegetative Compatibility Groups (VCGs)
Authors: Vermeulen M. , Gryzenhout M. , Wingfield M. J. , Roux J.
Published: October 2012

Chrysoporthe austroafricana is one of the most damaging pathogens of Eucalyptus trees in southern Africa. It also occurs on non‐native Tibouchina granulosa trees and native Syzygium species. Additional isolates of the pathogen from previously unstudied countries in the region have become available from survey studies. The aim of this study was to use VCGs to consider the diversity in populations of isolates collected in various countries in southern Africa (Malawi, Mozambique, Namibia, South Africa and Zambia) and from different hosts. We also wanted to determine whether there are shared VCGs among these countries and hosts in southern Africa and establish a VCG tester strain database. Results showed a high diversity amongst isolates from different countries and hosts, but suggested little movement of VCGs among countries or hosts based on the available isolates. A total of 108 VCG tester strains were identified for southern Africa.
Plant diversity controls arthropod biomass and temporal stability
Authors: Borer Elizabeth T. , Seabloom Eric W. , Tilman David
Published: October 2012

Understanding the linkages among species diversity, biomass production and stability underlies effective predictions for conservation, agriculture and fisheries. Although these relationships have been well studied for plants and, to a lesser extent, consumers, relationships among plant and consumer diversity, productivity, and temporal stability remain relatively unexplored. We used structural equation models to examine these relationships in a long‐term experiment manipulating plant diversity and enumerating the arthropod community response. We found remarkably similar strength and direction of interrelationships among diversity, productivity and temporal stability of consumers and plants. Further, our results suggest that the frequently observed relationships between plant and consumer diversity occur primarily via changes in plant production leading to changed consumer production rather than via plant diversity directly controlling consumer diversity. Our results demonstrate that extinction or invasion of plant species can resonate via biomass and energy flux to control diversity, production and stability of both plant and consumer communities.
Human melanoma cells in the rhombencephalon of the chick embryo: a novel model for brain metastasis
Authors: Busch Christian , Krochmann Jelena , Drews Ulrich
Published: October 2012

Malignant melanoma has the highest propensity to metastasize to the brain of all primary neoplasms in adults. Here, we describe invasive growth and the development of melanoma metastases from suspensions of human melanoma cells in the brain of the chick embryo. Patient‐derived melanoma cells and established melanoma cell lines were injected into the rhombencephalic brain vesicle of the two‐day‐chick embryo. After 48 and 96 h, tumor formation was studied in serial paraffin sections with melanoma‐specific HMB45 and human‐specific MIB1 proliferation markers. The majority of the cells injected into the embryonic liquor cavity perished. Only melanoma cells in newly formed aggregates or when attached to the dorsal roof plate escaped apoptosis. Local invasion occurred not in the ventral differentiating neural epithelium but only in the roof plate. Although after 48 h melanoma cells invaded the rhombencephalic roof plate profusely at both sides, after 96 h typically one large tumor developed in the midline between roof plate and the dorsal surface epithelium. From the tumor, single cells invaded the mesenchyme and blood vessels. Cell lines with different invasive properties retained their graded invasive behaviour. Maximally invasive cells formed continuous tracks via vessels and along nerve fibres. The central tumor in the roof plate of the chick embryo rhombencephalon resembles a metastatic nodule in the patients with melanoma. Penetration of the roof plate epithelium, tumor formation and invasion of surrounding tissues by single cells can reliably be reproduced. The chick embryo model can be used for molecular studies of early phases of melanoma brain metastasis.
Climate‐driven range retraction of an Arctic freshwater crustacean
Authors: LINDHOLM MARKUS , STORDAL FRODE , MOE S. JANNICKE , HESSEN DAG O. , AASS PER
Published: October 2012

1. Species responses to global warming are predicted to be manifest as poleward and upward extension of species ranges, whereas cold‐adapted species experience range retractions. We report on recent range retraction of a freshwater crustacean, the Arctic fairy shrimp Branchinecta paludosa (Branchiopoda, Anostraca) from alpine ponds of southern Norway, a southernmost extension of its otherwise arctic range.

2. The species was mapped during two separate surveys, in 1970 and 2011. In 1970, it occurred in numerous ponds from the tree line at 900 m altitude to high alpine sites at 1500 m. Re‐sampling of the same ponds 41 years later revealed extinction of populations from ponds along the lowest 200 m of its altitudinal range.

3. Reconstruction of summer temperatures for the periods 1965–70 and 2005–10 revealed a thermal increase for the period, corresponding to a c. 200‐m upward shift of the local isotherms. More specifically, the number of warm summer days had doubled in the lowest 200 m of the region, which might be particularly detrimental for the species.

4. The extinctions at lower altitudes were not compensated for by corresponding upward colonisations. The range retraction of B. paludosa is possibly associated with oxygen stress and hypoxia, induced by increased water temperatures.