bluuebunny/crossref_metadata_2025_split huggingface dataset:
bbcontacts: prediction of
β
-strand pairing from direct coupling patterns
Authors: Andreani Jessica , Söding Johannes 
Published: January 2015

Abstract
Motivation : It has recently become possible to build reliable de novo models of proteins if a multiple sequence alignment (MSA) of at least 1000 homologous sequences can be built. Methods of global statistical network analysis can explain the observed correlations between columns in the MSA by a small set of directly coupled pairs of columns. Strong couplings are indicative of residue-residue contacts, and from the predicted contacts a structure can be computed. Here, we exploit the structural regularity of paired β-strands that leads to characteristic patterns in the noisy matrices of couplings. The β–β contacts should be detected more reliably than single contacts, reducing the required number of sequences in the MSAs.
Results : bbcontacts predicts β–β contacts by detecting these characteristic patterns in the 2D map of coupling scores using two hidden Markov models (HMMs), one for parallel and one for antiparallel contacts. β-bulges are modelled as indel states. In contrast to existing methods, bbcontacts uses predicted instead of true secondary structure. On a standard set of 916 test proteins, 34% of which have MSAs with &lt; 1000 sequences, bbcontacts achieves 50% precision for contacting β–β residue pairs at 50% recall using predicted secondary structure and 64% precision at 64% recall using true secondary structure, while existing tools achieve around 45% precision at 45% recall using true secondary structure.
Availability and implementation: bbcontacts is open source software (GNU Affero GPL v3) available at https://bitbucket.org/soedinglab/bbcontacts
Contact : jessica.andreani@mines.org or soeding@mpibpc.mpg.de
Supplementary information : Supplementary data are available at Bioinformatics online.
Estimating survival of rock lobsters from long-term tagging programmes: how survey number and interval influence estimates
Authors: Kordjazi Ziya , Frusher Stewart , Buxton Colin D. , Gardner Caleb 
Published: January 2015

Abstract
A long-term tagging dataset on southern rock lobster (Jasus edwardsii) conducted at the Crayfish Point Scientific Reserve near Hobart, Tasmania, Australia, was used to determine how survey number and survey duration affected the precision of survival estimates of male and female lobsters to ensure sustainable exploitation of the population. Tagging surveys were undertaken twice yearly during 2000–2003 with unequal time-intervals between surveys and then once a year with equal time-intervals during 2004–2012 during the January–February period. The most parsimonious Cormack–Jolly–Seber model for estimating survival of lobsters was dependent on (i) timing of the tagging and recapture surveys, (ii) time between consecutive recapture surveys, and (iii) gender. The number of surveys required to provide a precise survival probability varied with gender and time between recapture surveys. For surveys where there was unequal time between recapture surveys, seven and five surveys were required for female and male lobsters, respectively, whereas only five surveys were required when annual surveys were undertaken. Thus, lobster tagging projects using annual surveys should ideally extend to at least 5 years, which is beyond the 3-year project duration common in marine science.
Function of the N-terminal segment of the RecA-dependent nuclease Ref
Authors: Gruber Angela J. , Olsen Tayla M. , Dvorak Rachel H. , Cox Michael M. 
Published: January 2015

Abstract
The bacteriophage P1 Ref (recombination enhancement function) protein is a RecA-dependent, HNH endonuclease. It can be directed to create targeted double-strand breaks within a displacement loop formed by RecA. The 76 amino acid N-terminal region of Ref is positively charged (25/76 amino acid residues) and inherently unstructured in solution. Our investigation of N-terminal truncation variants shows this region is required for DNA binding, contains a Cys involved in incidental dimerization and is necessary for efficient Ref-mediated DNA cleavage. Specifically, Ref N-terminal truncation variants lacking between 21 and 47 amino acids are more effective RecA-mediated targeting nucleases. We propose a more refined set of options for the Ref-mediated cleavage mechanism, featuring the N-terminal region as an anchor for at least one of the DNA strand cleavage events.
A basal level of DNA damage and telomere deprotection increases the sensitivity of cancer cells to G-quadruplex interactive compounds
Authors: Salvati Erica , Rizzo Angela , Iachettini Sara , Zizza Pasquale , Cingolani Chiara , D'Angelo Carmen , Porru Manuela , Mondello Chiara , Aiello Aurora , Farsetti Antonella , Gilson Eric , Leonetti Carlo , Biroccio Annamaria 
Published: January 2015

Abstract
Here, with the aim of obtaining insight into the intriguing selectivity of G-quadruplex (G4) ligands toward cancer compared to normal cells, a genetically controlled system of progressive transformation in human BJ fibroblasts was analyzed. Among the different comparative evaluations, we found a progressive increase of DNA damage response (DDR) markers throughout the genome from normal toward immortalized and transformed cells. More interestingly, sensitivity to G4 ligands strongly correlated with the presence of a basal level of DNA damage, including at the telomeres, where the chromosome ends were exposed to the DDR without concurrent induction of DNA repair activity, as revealed by the lack of 53BP1 recruitment and telomere aberrations. The link between telomere uncapping and the response to G4 stabilization was directly assessed by showing that a partial TRF2 depletion, causing a basal level of telomere localized DDR, rendered telomerized fibroblasts prone to G4-induced telomere damage and anti-proliferative defects. Taken together these data strongly indicate that the presence of a basal level of telomere-associated DDR is a determinant of susceptibility to G4 stabilization.
Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner
Authors: Ebina Isao , Takemoto-Tsutsumi Mariko , Watanabe Shun , Koyama Hiroaki , Endo Yayoi , Kimata Kaori , Igarashi Takuya , Murakami Karin , Kudo Rin , Ohsumi Arisa , Noh Abdul Latif , Takahashi Hiro , Naito Satoshi , Onouchi Hitoshi 
Published: January 2015

Abstract
Upstream open reading frames (uORFs) are often found in the 5′-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression.
Domain organization within the nuclear export factor Mex67:Mtr2 generates an extended mRNA binding surface
Authors: Aibara Shintaro , Valkov Eugene , Lamers Meindert , Stewart Murray 
Published: January 2015

Abstract
The Mex67:Mtr2 complex is the principal yeast nuclear export factor for bulk mRNA and also contributes to ribosomal subunit export. Mex67 is a modular protein constructed from four domains (RRM, LRR, NTF2-like and UBA) that have been thought to be joined by flexible linkers like beads on a string, with the RRM and LRR domains binding RNAs and the NTF2-like and UBA domains binding FG-nucleoporins to facilitate movement through nuclear pores. Here, we show that the NTF2-like domain from Saccharomyces cerevisiae Mex67:Mtr2 also contributes to RNA binding. Moreover, the 3.3 Å resolution crystal structure of the Mex67ΔUBA:Mtr2 complex, supplemented with small angle X-ray scattering data, indicated that the LRR domain has a defined spatial relationship to the Mex67NTF2L:Mtr2 region. Conversely, the RRM domain and especially the UBA domain are more mobile. The conformation assumed by the LRR and NTF2-like domains results in clusters of positively-charged residues on each becoming arranged to form a continuous interface for binding RNA on the opposite side of the complex to the region that interacts with FG-nucleoporins to facilitate passage through nuclear pores.
ANIR: Atacama near-infrared camera for the 1.0 m miniTAO telescope
Authors: Konishi Masahiro , Motohara Kentaro , Tateuchi Ken , Takahashi Hidenori , Kitagawa Yutaro , Kato Natsuko , Sako Shigeyuki , Uchimoto Yuka K. , Toshikawa Koji , Ohsawa Ryou , Yamamuro Tomoyasu , Asano Kentaro , Ita Yoshifusa , Kamizuka Takafumi , Komugi Shinya , Koshida Shintaro , Manabe Sho , Matsunaga Noriyuki , Minezaki Takeo , Morokuma Tomoki , Nakashima Asami , Takagi Toshinobu , Tanabé Toshihiko , Uchiyama Mizuho , Aoki Tsutomu , Doi Mamoru , Handa Toshihiro , Kato Daisuke , Kawara Kimiaki , Kohno Kotaro , Miyata Takashi , Nakamura Tomohiko , Okada Kazushi , Soyano Takao , Tamura Yoichi , Tanaka Masuo , Tarusawa Ken'ichi , Yoshii Yuzuru 
Published: February 2015

Abstract
We have developed a near-infrared camera called ANIR (Atacama Near-InfraRed camera) for the University of Tokyo Atacama Observatory 1.0 m telescope (miniTAO) installed at the summit of Cerro Chajnantor (5640 m above sea level) in the north of Chile. The camera provides a field of view of 5${^{\prime}_{.}}$1 × 5${^{\prime}_{.}}$1 with a spatial resolution of 0${^{\prime\prime}_{.}}$298 pixel−1 in the wavelength range of 0.95 to 2.4 μm, using Offner relay optics and a PACE HAWAII-2 focal plane array. Taking advantage of the dry site, the camera is capable of narrow-band imaging observations at the hydrogen Paschen-α (Paα, λ = 1.8751 μm in air) wavelength ground-based observations of which have been quite difficult due to deep atmospheric absorption, mainly from water vapor. We have been successfully obtaining Paα images of Galactic objects and nearby galaxies since the first-light observation in 2009 with ANIR. The throughputs at the narrow-band filters (N1875, N191) including the atmospheric absorption show larger dispersion (∼ 10%) than those at broad-band filters (a few percent), indicating that they are affected by temporal fluctuations in precipitable water vapor (PWV) above the site. We evaluate the PWV content via the atmospheric transmittance at the narrow-band filters, and deduce that the median and the dispersion of the distribution of the PWV are 0.40 ± 0.30 and 0.37 ± 0.21 mm, for the N1875 and N191 data respectively, which are remarkably smaller (49% ± 38% for N1875 and 59% ± 26% for N191) than radiometry measurements at the base of Cerro Chajnantor (an altitude of 5100 m). The decrease in PWV can be explained by the altitude of the site when we assume that the vertical distribution of the water vapor is approximated at an exponential profile with scale heights within 0.3–1.9 km (previously observed values at night). We thus conclude that miniTAO/ANIR at the summit of Cerro Chajnantor indeed provides us an excellent capability for a ground-based Paα observation.
Global distribution of ionizing and recombining plasmas in the supernova remnant G290.1−0.8
Authors: Kamitsukasa Fumiyoshi , Koyama Katsuji , Uchida Hiroyuki , Nakajima Hiroshi , Hayashida Kiyoshi , Mori Koji , Katsuda Satoru , Tsunemi Hiroshi 
Published: February 2015

We report on the Suzaku results of the mixed-morphology supernova remnant (SNR) G290.1−0.8 (MSH 11-61A). The SNR has an asymmetric structure extended to the south-east and the north-west. In the X-ray spectra of the center and the north-west regions, we discover recombining plasma features with a strong Si Lyα and radiative recombination continuum at ∼ 2.7 keV. These features are the most significant in the north-west region, and the spectra are well reproduced with a recombining plasma of kTe = 0.5 keV, whereas the spectra of other regions are expressed by an ionizing plasma of kTe = 0.6 keV. The recombining plasma has over-solar abundances, while the ionizing plasma has roughly solar abundances. Hence they are likely ejecta and of interstellar medium (ISM) origin, respectively. The recombining plasma in the north-west of G290.1−0.8 would be generated by a break-out of the supernova ejecta from a high density circumstellar medium to a low density ISM.
Alpha societies and requisite variety: a projected framework for governance, education, and work in the 21st century
Authors: Kubik George H. 
Published: February 2015

Purpose– The purpose of this article is to define a framework for projecting future leading-edge alpha societies based on the principle of requisite variety. Alpha societies are advanced as a platform for creating future forms of work and workforce preparation premised on continuous creativity, invention, design and innovation.Design/methodology/approach– The principle of requisite variety is presented as the basis for a structured schema that incorporates trends and developments in anticipatory behaviors, systems thinking, creativity, design and innovation to produce a strategy for continuous leading-edge learning and performance.Findings– Growing global hypercompetition requires real-time ability to create and deliver world-class ideas and value-adding products and services in the shortest possible timeframes. This challenge requires societies, enterprises and individuals that are capable of continuously expanding and expressing their internal variety and complexity while rapidly decreasing the gaps between learning and doing.Research limitations/implications– The principle of requisite variety has been well known to cybernetics and systems communities since 1956. However, literature linking the principle of requisite variety to the future of learning and work is not well developed.Practical implications– This article establishes requisite variety generation as a valuable resource for twenty-first century societies and economies engaged in producing leading-edge outcomes.Social implications– The requisite variety framework developed in this article is intended to enhance the ability of leading-edge societies to continuously leapfrog existing educational, social and economic trajectories.Originality/value– The author defines the future of education and work in terms of enhancing individual, enterprise and societal abilities to absorb, generate and exploit variety, complexity and ambiguity.
A tectonic shift
Authors: Abeles Tom P. 
Published: February 2015

Purpose
– The purpose of this paper is to present a brief review and analysis of “The Breakthrough Challenge: 10 Ways to Connect Today’s Profits With Tomorrow’s Bottom Line”.

Design/methodology/approach
– This article consists of a literature review of a recently published book.

Findings
– The volume puts forth the idea that the corporate world is in the process of adopting a new measure of bottom-line profitability around environmental, social and economic responsibilities. It proposes that for change needed in the rising anthropocene, the private sector must lead.

Originality/value
– The review analyzes the argument and raises substantive issues around the authors’ value proposition.
The future of the American campus
Authors: Haggans Michael 
Published: February 2015

Purpose
– This article aims to present a review of the American campus in 2015 as the physical and facilities implications of the digital transformation of higher education begin to appear. Business conditions and technological changes are beginning to require changes in the traditional physical campus.

Design/methodology/approach
– The author provides observations and recommendations of a former university architect and campus planner on the physical adaptation of the American campus.

Findings
– Predictions of the demise of traditional colleges and universities will prove accurate for some as they shrivel or merge out of existence. The survivors will adapt their business models and modify their physical campuses to better match student and faculty needs.

Originality/value
– A physical adaptation of the American campus will result from digital transformation of higher education, as there is less need for synchronous place and time.
Functional differences between dominant grasses drive divergent responses to large herbivore loss in mesic savanna grasslands of North America and South Africa
Authors: Forrestel Elisabeth J. , Donoghue Michael J. , Smith Melinda D. 
Published: January 2015

SummaryGrazing and fire are disturbances integral to the evolution and maintenance of savanna grasslands. Humans are altering or completely eliminating these disturbance regimes at a global scale, with important consequences for savanna ecosystem structure and function. It is unknown whether the alteration of these disturbance regimes will have similar effects on grass communities of savanna grasslands in different geographic regions that vary in their biogeographic and evolutionary histories, as well as in the diversity of extant grazers.Here, we examined the effects of large herbivore loss on different aspects of grass community structure – taxonomic, phylogenetic and functional – across a range of fire frequencies in C4‐dominated mesic savanna grassland sites of North America (Konza Prairie Biological Station, Kansas,USA) and South Africa (Kruger National Park). The goal of the study was to determine whether the loss of large herbivores exerted a consistent effect on the grass communities of two physiognomically similar grasslands with different biogeographic and grazing histories.The removal of large herbivores resulted in divergent responses in the grass communities at Konza and Kruger that was consistent across fire treatments. At Konza, there was a rapid and significant response to grazing exclusion while the response was muted and transient at Kruger. Functional syndromes associated with grazing resistance were generally conserved across sites, and it was the functional strategies of the dominant species at each site that drove the divergent responses. Further, our study supports the hypothesis that grazing and aridity may be selective forces that act in parallel as those species that were grazing resistant also occupied drier niches.Synthesis. Our study demonstrates that savanna grassland communities with different biogeographic and grazing histories respond differently to the removal of large herbivores and that climate, fire and grazing are interactive forces in maintaining savanna grassland diversity and function. We show that the functional attributes of the dominant grasses, which are in part driven by the biogeographic and grazing history experienced, are the most relevant in predicting the response of savanna ecosystems to the loss of large herbivores.
Tropical trees in a wind‐exposed island ecosystem: height‐diameter allometry and size at onset of maturity
Authors: Thomas Sean C. , Martin Adam R. , Mycroft Erin E. 
Published: January 2015

SummaryTropical tree species adapted to high wind environments might be expected to differ systematically in terms of stem allometry and life‐history patterns, as compared with species found in less windy forests. We quantified height‐diameter (H‐D) allometries and relative size at onset of maturity (RSOM) for rain forest tree and tree fern species native to Dominica, West Indies, an island that experiences some of the highest average wind speeds pantropically.H‐D allometries for 17 Dominican angiosperm tree species were strongly concave on a log–log scale with asymptotic heights ranging from 9 to 32 m among species, averaging 25 m for canopy trees. H‐D allometries for species‐pooled data deviated strongly from recorded patterns for other tropical forest trees: asymptotic heights for trees in Dominica were 30–116% lower than those recorded for continental rain forest trees in Australia, South America, Africa and South‐East Asia. In a subset of canopy trees sampled in steep, sheltered valleys, heights were 12–26% larger at a given diameter and approached those observed in other tropical regions, suggesting large phenotypic responses of H‐D allometries to wind conditions.RSOM(quantified as the ratio of height at onset of reproduction to asymptotic maximum height) for Dominican angiosperm species was highly variable, ranging from 0.23 to 0.89 (mean 0.54), similar to patterns observed in Malaysia and Panama; very lowRSOMvalues were estimated for two tree fern species. Pooling data from Dominica with published values from other tropical forests, we observed a significant negative correlation betweenRSOMand wood density.Synthesis. Our data suggest that wind regimes are a critical determinant of height‐diameter (H‐D) allometries of tropical trees at both the local and global scale. Although we found no evidence for a systematic differences in reproductive onset related to wind regime,RSOMwas negatively correlated with species’ wood density, suggesting that more shade‐tolerant tree species show a longer period of gradually increasing reproductive allocation through ontogeny.
An observational study of the success and complications of 2546 external cephalic versions in low‐risk pregnant women performed by trained midwives
Authors: Beuckens A , Rijnders M , Verburgt‐Doeleman GHM , Rijninks‐van Driel GC , Thorpe J , Hutton EK 
Published: February 2015

ObjectiveTo evaluate the success of an external cephalic version (ECV) training programme, and to determine the rates of successful ECV, complications, and caesarean birth in a low‐risk population.DesignProspective observational study.SettingPrimary health care and hospital settings throughout the Netherlands (January 2008–September 2011).PopulationLow‐risk women with a singleton fetus in breech presentation, without contraindications to ECV, were offered ECV at approximately 36 weeks of gestation.MethodsData were collected for all ECVs performed by midwives, and were entered into a national online database.Main measuresSuccessful ECV was defined as the fetus having a cephalic presentation immediately following the procedure and at birth. Complications were observed at ≤30 minutes and between 30 minutes and 48 hours after the ECV procedure. All serious pregnancy outcomes that occurred after the ECV procedure until birth were reported.ResultsA total of 47% had a successful ECv and a cephalic at the time of birth: 34% of nulliparous and 66% of multiparous women. After ECV, 57% of women gave birth vaginally: 45% of nulliparous women and 76% of multiparous women. Within 30 minutes after ECV, and between 30 minutes and 48 hours after ECV, the proportion of women experiencing a complication or serious pregnancy outcome was 0.9% and 1.8%, respectively. Serious pregnancy outcome at any time following ECV until birth was experienced by 58 (2.5%) of the women.ConclusionsThe success rate of ECVs performed by trained midwives in primary health care or hospital settings is comparable with that of other providers, and the procedure is safe for low‐risk women.