bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity
Authors: Voigt Karsten , Sharma Cynthia M , Mitschke Jan , Lambrecht S Joke , Voß Björn , Hess Wolfgang R , Steglich Claudia 
Published: April 2014

Abstract
Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5′ untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine–Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
Role of AMACR (α-methylacyl-CoA racemase) and MFE-1 (peroxisomal multifunctional enzyme-1) in bile acid synthesis in mice
Authors: Autio Kaija J. , Schmitz Werner , Nair Remya R. , Selkälä Eija M. , Sormunen Raija T. , Miinalainen Ilkka J. , Crick Peter J. , Wang Yuqin , Griffiths William J. , Reddy Janardan K. , Baes Myriam , Hiltunen J. Kalervo 
Published: April 2014

Cholesterol is catabolized to bile acids by peroxisomal β-oxidation in which the side chain of C27-bile acid intermediates is shortened by three carbon atoms to form mature C24-bile acids. Knockout mouse models deficient in AMACR (α-methylacyl-CoA racemase) or MFE-2 (peroxisomal multifunctional enzyme type 2), in which this β-oxidation pathway is prevented, display a residual C24-bile acid pool which, although greatly reduced, implies the existence of alternative pathways of bile acid synthesis. One alternative pathway could involve Mfe-1 (peroxisomal multifunctional enzyme type 1) either with or without Amacr. To test this hypothesis, we generated a double knockout mouse model lacking both Amacr and Mfe-1 activities and studied the bile acid profiles in wild-type, Mfe-1 and Amacr single knockout mouse line and Mfe-1 and Amacr double knockout mouse lines. The total bile acid pool was decreased in Mfe-1−/− mice compared with wild-type and the levels of mature C24-bile acids were reduced in the double knockout mice when compared with Amacr-deficient mice. These results indicate that Mfe-1 can contribute to the synthesis of mature bile acids in both Amacr-dependent and Amacr-independent pathways.
Mobilisation, politics, investment and constant adaptation: lessons from the Australian health‐promotion response to HIV
Authors: Brown Graham , O'Donnell Daryl , Crooks Levinia , Lake Rob 
Published: April 2014

Issue addressedThe Australian response to HIV oversaw one of the most rapid and sustained changes in community behaviour in Australia's health‐promotion history. The combined action of communities of gay men, sex workers, people who inject drugs, people living with HIV and clinicians working in partnership with government, public health and research has been recognised for many years as highly successful in minimising the HIV epidemic.MethodsThis article will show how the Australian HIV partnership response moved from a crisis response to a constant and continuously adapting response, with challenges in sustaining the partnership. Drawing on key themes, lessons for broader health promotion are identified.ResultsThe Australian HIV response has shown that a partnership that is engaged, politically active, adaptive and resourced to work across multiple social, structural, behavioural and health‐service levels can reduce the transmission and impact of HIV.ConclusionsThe experience of the response to HIV, including its successes and failures, has lessons applicable across health promotion. This includes the need to harness community mobilisation and action; sustain participation, investment and leadership across the partnership; commit to social, political and structural approaches; and build and use evidence from multiple sources to continuously adapt and evolve.So what?The Australian HIV response was one of the first health issues to have the Ottawa Charter embedded from the beginning, and has many lessons to offer broader health promotion and common challenges. As a profession and a movement, health promotion needs to engage with the interactions and synergies across the promotion of health, learn from our evidence, and resist the siloing of our responses.
Stable expression of a GFP-reporter gene in the red alga Cyanidioschyzon merolae
Authors: Watanabe Satoru , Sato Jun , Imamura Sousuke , Ohnuma Mio , Ohoba Yusaku , Chibazakura Taku , Tanaka Kan , Yoshikawa Hirofumi 
Published: April 2014

Abstract
The unicellular red alga Cyanidioschyzon merolae is used as a model organism to investigate the basic architecture of photosynthetic eukaryotes. We established a stable expression system for the green fluorescent protein fused with the phycocyanin-associated rod linker (APCC) protein in C. merolae, which was clearly localized on the plastid. This system should be useful in the genetic engineering of C. merolae.
Construction and significance analysis of the MicroRNA expression profile of Hemerocallis fulva at low temperature
Authors: An Fengxia , Liang Yan , Li Jingfu , Chen Xiuling , Han Hui , Li Fuheng 
Published: April 2014

Abstract
MicroRNA (miRNA) identification was performed in Hemerocallis fulva by high-throughput sequencing in combination with bioinformatics prediction. A total of 14,843,184 and 16,072,575 RNA sequences were explored under normal and low temperature conditions, respectively. There was a significant difference in RNAs species and quantity between the two samples. Of all the miRNAs, 26 were significantly upregulated and 30 were significantly downregulated, while nine were either significantly upregulated or downregulated under low-temperature stress. Twenty-one highly expressed miRNA families were screened in at least six species. The number of miRNA families was very similar between monocotyledons and dicotyledons, and only a few were more frequently found in monocotyledons.
Purification and characterization of cocoonase from the silkwormBombyx mori
Authors: Fukumori Hisayoshi , Teshiba Satoshi , Shigeoka Yuichi , Yamamoto Kohji , Banno Yutaka , Aso Yoichi 
Published: April 2014

AbstractCocoonase (CCN) which facilitates the degradation of a cocoon is recognized as a trypsin-like serine protease. In this study, CCN from the silkworm Bombyx mori was purified and comprehensively characterized. Its activity was maximal at about pH 9.8. It was stable above pH 3.4 at 4 °C and below 50 °C at pH 7.5. CuSO4, FeSO4, and ZnSO4 showed inhibitory effects on CCN, but other salts improved activity. Typical trypsin inhibitors inhibited CCN, but the relative inhibitory activities were much lower than those against bovine trypsin. An extract of cocoon shells inhibited trypsin, but it was only slightly inhibitory against CCN. There were significant differences in catalytic efficiencies and substrate specificities as between CCN and bovine trypsin.
Quantitative analysis of CD3ε in a cloned canine lymphoma cell line by selected reaction monitoring assay
Authors: Kamiie Junichi , Shimoyama Naoto , Aihara Naoyuki , Hisasue Masaharu , Naya Yuko , Ogihara Kikumi , Shirota Kinji 
Published: April 2014

AbstractWe established a mass spectrometry-based quantitative method of assaying CD3ε, a component of the T-cell receptor complex. It revealed a CD3ε level of 1 mol per cell in a newly derived canine T-cell lymphoma cell line. Our results suggest that this method has sufficient sensitivity to quantify CD3ε levels in canine lymphoma cells reliably.
O2-dependent large electron flow functioned as an electron sink, replacing the steady-state electron flux in photosynthesis in the cyanobacterium Synechocystis sp. PCC 6803, but not in the cyanobacterium Synechococcus sp. PCC 7942
Authors: Hayashi Ryosuke , Shimakawa Ginga , Shaku Keiichiro , Shimizu Satoko , Akimoto Seiji , Yamamoto Hiroshi , Amako Katsumi , Sugimoto Toshio , Tamoi Masahiro , Makino Amane , Miyake Chikahiro 
Published: April 2014

Abstract
To determine whether alternative electron flow (AEF) can replace the photosynthetic electron flow in cyanobacteria, we used an open O2-electrode system to monitor O2-exchange over a long period. In air-grown Synechocystis sp. PCC 6803 (S. 6803(WT)), the quantum yield of PSII, Y(II), held even after photosynthesis was suppressed by CO2 shortage. The S. 6803 mutant, deficient in flavodiiron (FLV) proteins 1 and 3, showed the same phenotype as S. 6803(WT). In contrast, Y(II) decreased in Synechococcus sp. PCC 7942 (S. 7942). These results suggest that AEF functioned as the Y(II) in S. 6803 and replaced the photosynthetic electron flux. In contrast, the activity of AEF in S. 7942 was lower. The affinity of AEF for O2 in S. 6803 did not correspond to those of FLVs in bacteria or terminal oxidases in respiration. AEF might be driven by photorespiration.
Unsaturated long-chain fatty acids inhibit the binding of oxidized low-density lipoproteins to a model CD36
Authors: Takai Marie , Kozai Yuki , Tsuzuki Satoshi , Matsuno Yukari , Fujioka Maiko , Kamei Kozue , Inagaki Hitomi , Eguchi Ai , Matsumura Shigenobu , Inoue Kazuo , Fushiki Tohru 
Published: April 2014

Abstract
Transmembrane protein CD36 binds multiple ligands, including oxidized low-density lipoproteins (oxLDLs) and long-chain fatty acids (LCFAs). Our aim was to determine whether LCFAs compete with oxLDLs for binding to CD36. We addressed this issue by examining the inhibitory effect of LCFAs against the binding of Alexa-fluor-labeled oxLDLs (AFL-oxLDL) to a synthetic peptide representing the oxLDL-binding site on CD36 (3S-CD36150–168). All of the unsaturated LCFAs tested, inhibited the binding of AFL-oxLDL to 3S-CD36150–168, albeit to varying degrees. For instance, the concentrations required for 50% inhibition of binding for oleic, linoleic, and α-linolenic acids were 0.25, 0.97, and 1.2 mM, respectively. None of the saturated LCFAs tested (e.g. stearic acid) exhibited inhibitory effects. These results suggest that at least unsaturated LCFAs can compete with oxLDLs for binding to CD36. The study also provides information on the structural requirements of LCFAs for inhibition of oxLDLs–CD36 binding.
Biochemistry of lipolytic enzymes secreted byPenicillium solitumandCladosporium cladosporioides
Authors: Chinaglia Selene , Chiarelli Laurent R , Maggi Maristella , Rodolfi Marinella , Valentini Giovanna , Picco Anna Maria 
Published: April 2014

AbstractTwo distinct extracellular lipases were obtained from Penicillium solitum 194A, isolated from domestic compost, and Cladosporium cladosporioides 194B, isolated from dairy wastewater. These alkaline enzymes had molecular masses of 42 and 30 kDa, respectively. The P. solitum 194A lipase differed in mass from previously reported enzyme, indicating that it is a novel lipase, and indicating that penicillia can secrete lipase isoenzymes. The C. cladosporioides lipase was more active on esters of medium-chain acids, whereas the P. solitum lipase was more active on longer chained substrates. The C. cladosporioides enzyme displayed higher thermal stability than the P. solitum lipase, preserving full activity up to 48 °C and showing a T50 (10 min) of 60 °C. Their different catalytic properties and good protein stability should make these enzymes suitable for biotechnological applications. Furthermore, the combined use of these two fungal strains may prove to be valuable in lipid-rich waste management.
A high-throughput screen for inhibitors of the prolyl isomerase, Pin1, identifies a seaweed polyphenol that reduces adipose cell differentiation
Authors: Mori Tadashi , Hidaka Masafumi , Ikuji Hiroko , Yoshizawa Ibuki , Toyohara Haruhiko , Okuda Toru , Uchida Chiyoko , Asano Tomoichiro , Yotsu-Yamashita Mari , Uchida Takafumi 
Published: April 2014

Abstract
The peptidyl prolyl cis/trans isomerase Pin1 enhances the uptake of triglycerides and the differentiation of fibroblasts into adipose cells in response to insulin stimulation. Pin1 downregulation could be a potential approach to prevent and treat obesity-related disorders. In order to identify an inhibitor of Pin1 that exhibited minimal cytotoxicity, we established a high-throughput screen for Pin1 inhibitors and used this method to identify an inhibitor from 1,056 crude fractions of two natural product libraries. The candidate, a phlorotannin called 974-B, was isolated from the seaweed, Ecklonia kurome. 974-B inhibited the differentiation of mouse embryonic fibroblasts and 3T3-L1 cells into adipose cells without inducing cytotoxicity. We discovered the Pin1 inhibitor, 974-B, from the seaweed, E. kurome, and showed that it blocks the differentiation of fibroblasts into adipose cells, suggesting that 974-B could be a lead drug candidate for obesity-related disorders.
(Il)-licit Pronoun-Antecedent Relations in Bangla
Authors: Das Satarupa 
Published: April 2014

Abstract
Pronominal agreement with imposter DPs and secondary sources is subject to cross-linguistic variation, which is illustrated here with a comparative study of the relevant facts from English and Bangla. The chapter shows that Bangla systematically disallows pronominal agreement with a secondary source, and suggests that the verbal agreement system of a language is a crucial factor that constrains pronoun-antecedent relations. To derive the Bangla generalization, it is assumed that the inflection on the finite verb is itself pronominal, and the chapter shows that all cases of illicit pronoun-antecedent relations boil down to a violation of the homogeneity principle.
Imposters and Secondary Sources in Italian
Authors: Servidio Emilio 
Published: April 2014

Abstract
This chapter surveys a range of secondary source phenomena in the sense of Collins and Postal (2012) that are attested in Italian. It shows that while some classes of secondary sources (camouflage expressions, partitives, and subjects of predicative nominals in some idiolects and registers) pattern with their English counterparts in allowing non-third person agreement, in imposters this holds only of two items (il/la sottoscritto/a and il/la qui presente) that share some kind of participial morphology. This restriction is credited to a language specific constraint that interferes with the more liberal agreement system articulated by Collins and Postal (2012).
Person Imposters: The View from Two Romance Languages
Authors: Soare Gabriela 
Published: April 2014

AbstractThis chapter presents an overview of the syntactic behavior of imposter DPs in Romanian and French, the major focus of the investigation being verbal agreement. Plural imposters are shown to permit only third person plural verbal agreement but, if modified by an indexical element, first person agreement becomes possible. Coordinate DPs containing an imposter conjunct and plural imposters allow first person plural agreement if topicalized. In both cases, the underlying mechanism is argued to be clitic doubling. The imposter is doubled by [1PL] pro in Romanian and nous “we” in French. The chapter also identifies other loci (or sources) of phi-feature values of first (or second) person verbal agreement.
Intonation and prosody in Dalabon
Authors: Fletcher Janet 
Published: April 2014

AbstractThe Dalabon intonational inventory consists of one major pitch accent H* and two tonally-marked prosodic constituents, the accentual phrase and intonational phrase. Like other Australian Indigenous languages, focus is realized by syntactically fronting and expanding the pitch range of the focal constituent (the accentual phrase) with no evidence of de-accentuation.
Intonation in Basque
Authors: Elordieta Gorka , Hualde Jose I. 
Published: April 2014

AbstractThis chapter examines two Basque varieties. In Northern Bizkaian Basque, where there is a lexical contrast between accented and unaccented words, the only pitch-accent is H*+L and there is complex phrasing. Standard Basque lacks lexically contrastive prosody, and intonationally is more similar to Spanish. However, nuclear accent is generally preverbal.
Introducing concepts
Authors: Durkin Philip 
Published: April 2014

Abstract
The part played by loanwords in the vocabulary of modern English is illustrated by an examination of passages from different types of contemporary writing. The periodization of the history of English is introduced and discussed. Initial definitions are provided for key terms and concepts, including types of lexical borrowing, loanwords and semantic borrowing, code switching, and imposition. Different approaches to studying lexical borrowing are examined: identifying individual loanwords and tracing their histories; examining the effect of loanwords on the changing lexicon of English; examining stylistic or pragmatic deployment of loanwords in different text types. The different types of evidence for identifying loanwords are introduced, and the methodology for determining whether a loan has occurred. Finally, questions are investigated about how we define the extent of the vocabulary of English.
Long-term effects of loanwords on the shape of the English Lexicon
Authors: Durkin Philip 
Published: April 2014

Abstract
Some initial questions that we can ask about the degree of integration of a loanword into the English lexicon are outlined, including: Is it naturalized in pronunciation and morphology? Has it formed new compound or derivative formations? Has it developed new meanings? Who is the word used by? In which contexts is it found? Is it the usual word in contemporary English realizing a particular meaning, and if so how has this situation changed over time? What competition has there been with other words realizing the same meaning? What relationships exist with other words in the same semantic field? This chapter takes a pioneering approach to these questions, exploring how data from the OED and other dictionaries, from the Historical Thesaurus of the OED, and from studies of basic vocabulary can help illuminate the processes by which loanwords have become entrenched in the contemporary English lexicon.
Point group symmetry
Authors: Ladd Mark 
Published: April 2014

Abstract
The study of symmetry elements in two and three dimensions is followed by point groups, their derivation and recognition, including an interactive program for point group recognition. Euler’s theorem on the combination of rotations is discussed, and the physical properties of crystals and molecules in relation to their point groups explained. Chemical examples of crystallographic and non-crystallographic point groups illustrated by stereoscopic drawings. The discussion is extended to quasicrystals, and to fivefold symmetry in crystalline material.
Symmetry and X-ray diffraction
Authors: Ladd Mark 
Published: April 2014

Abstract
The generation and properties of X-rays and their diffraction by crystals are discussed. The collection of X-ray data by photographic and diffractometric methods is explained, leading to a discussion of the effects of space group symmetry on the recording of X-ray diffraction spectra. Geometrical structure factors are explained with examples, and the analytical deduction of the conditions limiting X-ray reflection according to space group symmetry described. Examples are given of the deduction of space groups from X-ray diffraction records.
Loyalty and Non-exclusive Competences
Authors: Klamert Marcus 
Published: April 2014

Abstract
This Chapter deals with various questions surrounding the role of loyalty with regard to non-exclusive competences of the Union. It discusses the correlation between the degree of preclusion of Member State rights as the consequence of their exercise with the degree of force and the level of detail of the duties flowing from the principle of loyalty. This is illustrated both with respect to shared competences, so called irregular shared competences such as development policy, and supporting competences such as for health. The different coordinating roles of the Commission with these different types of competences, and the potential for a conflict between national and Union action, even in areas that predominantly involve cooperation, are examined.
Manifestations of Loyalty in Secondary Law
Authors: Klamert Marcus 
Published: April 2014

Abstract
This Chapter presents loyalty as the basis for various duties for the Member States provided in secondary law. It is distinguished between regimes prescribing mere duties of notification, duties of notification coupled with rights of supervision for the Commission, and such regimes set up by secondary law where the supervision of notified measures may lead to standstill duties or even abstention duties for the Member States. By example of the screening mechanism provided in the Services Directive, the difficulty in assessing the nature of such regimes in acts of secondary law is illustrated. It is also shown how ‘managed’ preclusion generated by an act of secondary law can be not much different in effect from exclusive competence.
On the Nature of Loyalty
Authors: Klamert Marcus 
Published: April 2014

Abstract
This Chapter discusses whether loyalty is capable of producing binding legal obligations on its own by example of duties of Member States in relation to infringement procedures, and of mutual duties related to the implementation of Union law. It is shown how perceptions of loyalty have changed over time as regards this question. In this context, it is also discussed whether it is appropriate and useful to distinguish between obligations of result and obligations of conduct. Moreover, whether loyalty is a general principle of Union law and whether this assessment has any legal merit is also probed. For this, the functions of general principles of Union law such as fundamental rights and conferral are examined and compared with loyalty. The Chapter concludes with an interim summary of the various forms of application of loyalty in Union law.
Deconstructing Loyalty
Authors: Klamert Marcus 
Published: April 2014

Abstract
This Chapter discusses the loyalty-based case law of the Court from a methodological perspective. It starts by exploring the key methods of interpretation employed by the Court, such as effet utile in particular. Then, arguments made in defence of alleged judicial activism of the Court, such as ‘majoritarian activism’, the incomplete nature of EU law, and the concept of tolerance of error (Fehlerkalkül) are discussed. This is followed by an examination of objective criteria for assessing legal developments by the Court, such as gap-filling and principle-based reasoning. Moreover, this Chapter discusses the relation between loyalty and the principles of effectiveness and effet utile, illustrated by the case law on direct effect, exclusive competence, and state liability. Finally, the autopoiesis in the Court’s reasoning is probed by the examples of state liability and the Pupino case.