bluuebunny/crossref_metadata_2025_split huggingface dataset:
IN SEARCH OF IBN SĪNĀ'S “ORIENTAL PHILOSOPHY” IN MEDIEVAL CASTILE
Authors: SZPIECH RYAN 
Published: August 2010

AbstractScholars have long debated the possibility of a mystical or illuminationist strain of thought in Ibn Sīnā's body of writing. This debate has often focused on the meaning and contents of his partly lost workal-Mashriqiyyūn(The Easterners), also known asal-Ḥikma al-Mashriqiyya(Eastern Wisdom), mentioned by Ibn Sīnā himself as well as by numerous Western writers including Ibn Rushd and Ibn Ṭufayl. A handful of references to what is called Ibn Sīnā's “Oriental Philosophy” are also found in the Castilian and Hebrew works of the Castilian Jew Abner of Burgos (ca. 1270-ca. 1347), known after his conversion to Christianity as Alfonso of Valladolid. Although the content of these citations has not been identified, it has been proposed that they may preserve otherwise unknown passages from Ibn Sīnā's lost work. This study considers the references to Ibn Sīnā's so-called “Oriental Philosophy” within Abner's writings and concludes that rather than preserving lost passages from Ibn Sīnā's writing, Abner's references were drawn primarily from Ibn Ṭufayl and offer no support for the argument of a possible mystical or illuminationist strain in Ibn Sīnā's thinking.
ʿUMAR AL-KHAYYĀM’S CONTRIBUTION TO THE ARABIC MATHEMATICAL THEORY OF MUSIC
Authors: BARONTINI MICHELE , TONIETTI TITO M. 
Published: August 2010

AbstractWe here present the Arabic text, with an English translation, of certain pages dedicated by al-Khayyām to the mathematical theory of music. Our edition is based on a manuscript extant in a library in Manisa (Turkey), and corrects the mistakes found in another transcription. Lastly, we compare the theory of al-Khayyām with other Arabic theories of Music, and with those coming from other traditions.
Transmission dynamics of an emerging infectious disease in wildlife through host reproductive cycles
Authors: Uchii Kimiko , Telschow Arndt , Minamoto Toshifumi , Yamanaka Hiroki , Honjo Mie N , Matsui Kazuaki , Kawabata Zen'ichiro 
Published: August 2010

Abstract
Emerging infectious diseases are major threats to wildlife populations. To enhance our understanding of the dynamics of these diseases, we investigated how host reproductive behavior and seasonal temperature variation drive transmission of infections among wild hosts, using the model system of cyprinid herpesvirus 3 (CyHV-3) disease in common carp. Our main findings were as follows: (1) a seroprevalence survey showed that CyHV-3 infection occurred mostly in adult hosts, (2) a quantitative assay for CyHV-3 in a host population demonstrated that CyHV-3 was most abundant in the spring when host reproduction occurred and water temperature increased simultaneously and (3) an analysis of the dynamics of CyHV-3 in water revealed that CyHV-3 concentration increased markedly in breeding habitats during host group mating. These results indicate that breeding habitats can become hot spots for transmission of infectious diseases if hosts aggregate for mating and the activation of pathogens occurs during the host breeding season.
Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach
Authors: Sekelja Monika , Berget Ingunn , Næs Tormod , Rudi Knut 
Published: August 2010

Abstract
The potential presence of widespread and stable bacterial core phylogroups in the human colon has promoted considerable attention. Despite major efforts, no such phylogroups have yet been identified. Therefore, using a novel phylogroup- and tree-independent approach, we present a reanalysis of 1 114 722 V2 region and 71 550 near full-length 16S rRNA sequences from a total of 210 human beings, with widespread geographic origin, ethnic background and diet, in addition to a wide range of other mammals. We found two highly prevalent core phylogroups (cores 1 and 2), belonging to the clostridial family Lachnospiraceae. These core phylogroups showed a log-normal distribution among human individuals, while non-core phylogroups showed more skewed distributions towards individuals with low levels compared with the log-normal distribution. Molecular clock analyses suggest that core 2 co-evolved with the radiation of vertebrates, while core 1 co-evolved with the mammals. Taken together, the stability, prevalence and potential functionality support the fact that the identified core phylogroups are pivotal in maintaining gut homeostasis and health.
Inhibition of the mitochondrial permeability transition by protein kinase A in rat liver mitochondria and hepatocytes
Authors: Pediaditakis Peter , Kim Jae-Sung , He Lihua , Zhang Xun , Graves Lee M. , Lemasters John J. 
Published: August 2010

NO and cGMP administered at reperfusion after ischaemia prevent injury to hepatocytes mediated by the MPT (mitochondrial permeability transition). To characterize further the mechanism of protection, the ability of hepatic cytosol in combination with cyclic nucleotides to delay onset of the calcium-induced MPT was evaluated in isolated rat liver mitochondria. Liver cytosol plus cGMP or cAMP dose-dependently inhibited the MPT, required ATP hydrolysis for inhibition and did not inhibit mitochondrial calcium uptake. Specific peptide inhibitors for PKA (protein kinase A), but not PKG (protein kinase G), abolished cytosol-induced inhibition of MPT onset. Activity assays showed a cGMP- and cAMP-stimulated protein kinase activity in liver cytosol that was completely inhibited by PKI, a PKA peptide inhibitor. Size-exclusion chromatography of liver cytosol produced a single peak of cGMP/cAMP-stimulated kinase activity with an estimated protein size of 180–220 kDa. This fraction was PKI-sensitive and delayed onset of the MPT. Incubation of active catalytic PKA subunit directly with mitochondria in the absence of cytosol and cyclic nucleotide also delayed MPT onset, and incubation with purified outer membranes led to phosphorylation of a major 31 kDa band. After ischaemia, administration at reperfusion of membrane-permeant cAMPs and cAMP-mobilizing glucagon prevented reperfusion injury to hepatocytes. In conclusion, PKA in liver cytosol activated by cGMP or cAMP acts directly on mitochondria to delay onset of the MPT and protect hepatocytes from cell death after ischaemia/reperfusion.
BioRuby: bioinformatics software for the Ruby programming language
Authors: Goto Naohisa , Prins Pjotr , Nakao Mitsuteru , Bonnal Raoul , Aerts Jan , Katayama Toshiaki 
Published: August 2010

Abstract
Summary: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.
Availability: BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/.
Contact: katayama@bioruby.org
Health and age and sex distributions of Baltic grey seals (Halichoerus grypus) collected from bycatch and hunt in the Gulf of Bothnia
Authors: Bäcklin Britt-Marie , Moraeus Charlotta , Roos Anna , Eklöf Eva , Lind Ylva 
Published: August 2010

Abstract
Bäcklin, B-M., Moraeus, C., Roos, A., Eklöf, E., and Lind, Y. 2011. Health and age and sex distributions of Baltic grey seals (Halichoerus grypus) collected from bycatch and hunt in the Gulf of Bothnia. – ICES Journal of Marine Science, 68: 183–188. Age distribution, sex ratio, and season of death were investigated in grey seals taken as bycatch and hunted in the Gulf of Bothnia for the period 2002–2007. In seals 1–20 years old, certain health variables, earlier reported as parts of a disease complex related to persistent organic pollutants, were also investigated. Most of the hunted group were female (60%), but there were more males (62%) in the bycatch group. In spring, there were more bycatch than hunted yearlings. Seals taken as bycatch were leaner than hunted animals, and in hunted seals, there was a significant seasonal difference in blubber thickness that was not observed in seals taken in the bycatch. The prevalence of intestinal ulcers was 18–50% in bycatch and 24–74% in hunted animals. Hunted males 4–20 years old had a significantly greater prevalence of intestinal ulcers than bycatch males in the same age group. Adrenocortical thickening and mean weight of the adrenals increased with age. No lesions were observed in female reproductive organs, and in autumn, nearly all mature females were pregnant. The main differences between hunted and bycatch grey seals were in the season when death occurred, the prevalence of yearlings, the sex ratio, the blubber thickness, and the prevalence of intestinal ulcers.
Influence of Jet Cooking and pH on Extraction and Molecular Weight of β‐Glucan and Arabinoxylan from Barley (Hordeum vulgare Prowashonupana)
Authors: Rose Devin J. , Kim Sanghoon , Inglett George E. 
Published: August 2010

ABSTRACTFood processing conditions may affect the extractability and molecular weight of β‐glucans and arabinoxylans in cereal products. This can dramatically affect the functional and physiological properties of the final products. Therefore, the purpose of this research was to explore the effects of jet cooking on the content, extractability, and molecular weights of these polymers in barley flour from a high β‐glucan, waxy barley genotype, Prowashonupana. Barley flours were jet cooked without pH adjustment or after adjusting to pH 7, 9, or 11. Jet cooking without pH adjustment increased the extractability of β‐glucans from 15.4 to 38.0% when extracted with water at 30°C. As pH during jet cooking increased, the extractability further increased to 63.5% at pH 11. Arabinoxylan extractability was only substantially affected when the pH of jet cooking was alkaline (extractability increased from 11.4 to 48.5% when jet cooked at pH 11). Jet cooking without pH adjustment resulted in slight increases in peak molecular weights for both polymers (β‐glucan increased from 420,000 to 443,000; arabinoxylan increased from 119,000 to 125,000); higher pH values during jet cooking resulted in minor decrease in molecular weights.
Molecular Weight Distribution of Proteins in Hard Red Spring Wheat: Relationship to Quality Parameters and Intrasample Uniformity
Authors: Ohm Jae‐Bom , Hareland Gary , Simsek Senay , Seabourn Bradford , Maghirang Elizabeth , Dowell Floyd 
Published: August 2010

ABSTRACTMolecular weight distribution (MWD) of proteins extracted from hard red spring wheat was analyzed by size‐exclusion HPLC to investigate associations with wheat and breadmaking quality characteristics. Certain protein fractions were related to associations between wheat and breadmaking parameters, specifically when effect of quantitative variation of protein on those parameters was statistically eliminated by partial correlation analysis. SDS‐unextractable high molecular weight polymeric proteins had positive partial correlations with percent vitreous kernel content and breadmaking parameters, including mix time and bread loaf volume. SDS‐extractable protein fractions that were eluted before the primary gliadin peak had positive partial correlations with kernel hardness and water absorption parameters. The proportion of main gliadin fractions in total protein had a negative partial correlation with bread loaf volume and positive correlations with kernel hardness and water absorption parameters. Intrasample uniformity in protein MWD and kernel characteristics was estimated from three kernel subsamples that were separated according to single kernel protein content within individual wheat samples by a single‐kernel near‐infrared sorter. Wheat subsamples were significantly different in protein MWD. Intrasample uniformity in protein MWD did not differ greatly among wheat samples.
SHORT-ROOT and SCARECROW Regulate Leaf Growth in Arabidopsis by Stimulating S-Phase Progression of the Cell Cycle
Authors: Dhondt Stijn , Coppens Frederik , De Winter Freya , Swarup Kamal , Merks Roeland M.H. , Inzé Dirk , Bennett Malcolm J. , Beemster Gerrit T.S. 
Published: August 2010

AbstractSHORT-ROOT (SHR) and SCARECROW (SCR) are required for stem cell maintenance in the Arabidopsis (Arabidopsis thaliana) root meristem, ensuring its indeterminate growth. Mutation of SHR and SCR genes results in disorganization of the quiescent center and loss of stem cell activity, resulting in the cessation of root growth. This paper reports on the role of SHR and SCR in the development of leaves, which, in contrast to the root, have a determinate growth pattern and lack a persistent stem cell niche. Our results demonstrate that inhibition of leaf growth in shr and scr mutants is not a secondary effect of the compromised root development but is caused by an effect on cell division in the leaves: a reduced cell division rate and early exit of the proliferation phase. Consistent with the observed cell division phenotype, the expression of SHR and SCR genes in leaves is closely associated with cell division activity in most cell types. The increased cell cycle duration is due to a prolonged S-phase duration, which is mediated by up-regulation of cell cycle inhibitors known to restrain the activity of the transcription factor, E2Fa. Therefore, we conclude that, in contrast to their specific roles in cortex/endodermis differentiation and stem cell maintenance in the root, SHR and SCR primarily function as general regulators of cell proliferation in leaves.
Plant Cell Growth in Tissue
Authors: Ortega Joseph K.E. 
Published: August 2010

Abstract
Cell walls are part of the apoplasm pathway that transports water, solutes, and nutrients to cells within plant tissue. Pressures within the apoplasm (cell walls and xylem) are often different from atmospheric pressure during expansive growth of plant cells in tissue. The previously established Augmented Growth Equations are modified to evaluate the turgor pressure, water uptake, and expansive growth of plant cells in tissue when pressures within the apoplasm are lower and higher than atmospheric pressure. Analyses indicate that a step-down and step-up in pressure within the apoplasm will cause an exponential decrease and increase in turgor pressure, respectively, and the rates of water uptake and expansive growth each undergo a rapid decrease and increase, respectively, followed by an exponential return to their initial magnitude. Other analyses indicate that pressure within the apoplasm decreases exponentially to a lower value after a step-down in turgor pressure, which simulates its behavior after an increase in expansive growth rate. Also, analyses indicate that the turgor pressure decays exponentially to a constant value that is the sum of the critical turgor pressure and pressure within the apoplasm during stress relaxation experiments in which pressures within the apoplasm are not atmospheric pressure. Additional analyses indicate that when the turgor pressure is constant (clamped), a decrease in pressure within the apoplasm elicits an increase in elastic expansion followed by an increase in irreversible expansion rate. Some analytical results are supported by prior experimental research, and other analytical results can be verified with existing experimental methods.
Tail regeneration in the Xenopus tadpole
Authors: Mochii Makoto , Taniguchi Yuka , Shikata Isshin 
Published: August 2010

The tail of the Xenopus tadpole contains major axial structures, including a spinal cord, notochord and myotomes, and regenerates within 2 weeks following amputation. The tail regeneration in Xenopus can provide insights into the molecular basis of the regeneration mechanism. The regenerated tail has some differences from the normal tail, including an immature spinal cord and incomplete segmentation of the muscle masses. Lineage analyses have suggested that the tail tissues are reconstructed with lineage‐restricted stem cells derived from their own tissues in clear contrast to urodele regeneration, in which multipotent blastema cells derived from differentiated cells play a major role. Comprehensive gene expression analyses resulted in the identification of a panel of genes involved in sequential steps of the regeneration. Manipulation of genes’ activities suggested that the tail regeneration is regulated through several major signaling pathways.
Tip‐1 induces filopodia growth and is important for gastrulation movements during zebrafish development
Authors: Besser Jaya , Leito Jelani T. D. , Van Der Meer David L. M. , Bagowski Christoph P. 
Published: August 2010

Wnt signaling is essential during animal development and also plays important roles in pathological conditions. Two mayor pathways have been described: the β‐catenin‐dependent canonical (or classical) pathway and the β‐catenin‐independent non‐canonical Wnt pathway. Recent binding studies suggest links between the small PDZ protein TIP‐1 (Tax‐1 interacting protein) to components of both Wnt pathways. We have cloned and characterized the zebrafish tip‐1 gene. Whole mount in situ hybridization and semiquantitative reverse transcriptase‐polymerase chain reaction (RT‐PCR) indicated that zebrafish tip‐1 is present as a maternal RNA and is ubiquitously expressed during early development. After 24 h of development, tip‐1 expression was high in the central nervous system (CNS) whereas only weak expression was detected in the caudal regions of the zebrafish embryo. Tip‐1 knockdown using antisense morpholino oligonucleotides, as well as ectopic tip‐1 expression, led to elongation defects in zebrafish embryos and larvae. Both knockdown and overexpression of tip‐1 resulted in a widened goosecoid (gsc) expression domain in shield stage embryos, led to an abbreviated prechordal plate, and to reduced convergent extension movements during gastrulation. We constructed a green fluorescence protein (GFP)/TIP‐1 fusion protein which, when expressed in cultured fibroblasts (ZF4‐cells), induced filopodia growth. Our observations indicate a role for TIP‐1 in gastrulation movements and in filopodia growth induction.
Pleasing the Students: Teachers' Orientaton to Classroom Life in Adult Education
Authors: Salisbury Jane , Murcott Anne 
Published: August 2010

It is noted that existing sociological research on classrooms has focused too narrowly on compulsory schooling with the result that we have no data showing the rituals and routines of Adult Classrooms or the ways that teachers cope and resolve them. The paper presents fieldnote and interview data from a small ethnographic study of the two Adult Evening classes. The data suggest that in contrast to the teacher of school aged pupils, who seeks control and discipline, ‘pleasing students’ is the major orientation to classroom life of the evening class teacher. Do not say, the people must be educated when after all you only mean amused, refreshed, soothed put into good spirits and good humour or kept from vicious excesses. (Newman, 1873).
Ocean Cruising: A Sailing Subculture
Authors: Macbeth Jim 
Published: August 2010

Just after dawn, an English couple in their 30's haul up their anchor and motor across the stillness of Suva harbour. The hurricane season is approaching and they are embarking on the 2–3 week trip to Bay of Islands New Zealand for the southern summer. Three months earlier, as their yacht lay aground on the fringing reef of uninhabited Suvarov atoll, they wondered if they'd ever reach New Zealand. But, with the help of other cruisers and lucky tides their steel 36 footer was clear and safe in under 24 hours. What was to be a one year trip around the north Atlantic was now happily way off course in the South Pacific and likely to remain so for some time. That is just a glimpse of one small aspect of ocean cruising, the subculture of interest here. However, throughout the paper the ethnography of cruising is developed further. A model is proposed to show how individuals come to share the subculture ideology and then to participate in the lifestyle. Subsequently, 1 will place ocean cruising in the context of subculture theory by expanding the ethnography and relating cruising to other subcultures.
The Press and Public Access to the Environment and Development Debate
Authors: Lacey Colin , Longman David 
Published: August 2010

This paper presents an analysis of some aspects of newspaper coverage of environment and development issues. In particular, Global Warming and the Sudan famine are used as case studies of the features of this coverage. It argues that there are few grounds for adopting the optimistic view, as taken by some researchers, that the press will sustain and deepen its reporting of these issues. The analysis uses a computer-based methodology in which a key feature is the use of full-text on-line database of the contents of four newspapers. This paper presents the first steps in applying this methodology to the investigation of press reporting. It shows how the broad quantitative indicators available from this source can illustrate comparative patterns of newspaper coverage over long time periods and a wide range of themes. The ultimate purpose of this analysis is to understand the processes which contribute to informing or educating public debate about issues that crucially affect the political and economic future of society. The argument is that the press docs educate the public (its readers) but that this process is highly selective, it can contradict espoused editorial policy, and frequently environment and development issues receive less prominence as their political significance increases. The analysis shows therefore that in many cases the coverage given to these issues actually declines even as their significance increases. The authors argue that a social solution is required if the press is to be re-established as a public educator in a more positive sense. Methods must be developed for monitoring and influencing the processes by which the press manipulates the climate of opinion whilst nurturing its readership. One approach to this problem is taken by the Education Networks for Environment and Development Project at Sussex University where the results of this type of analysis are used to inform an open network of workers in a variety of professional institutions. Future investigations will look in more detail at this concept.
Gender and the Labour Market in Europe: Britain, Germany and France Compared
Authors: Lane Christel 
Published: August 2010

This paper has two objectives: to contrast patterns of female labour market participation in three West European societies and to develop a theoretical approach which can encompass both universal features of gender divisions in the labour market and nationally specific ones. Empirically, the focus is on the different levels and forms of labour force participation over the female life cycle, particularly on any resultant employment casualization. Consideration is also given to patterns of horizontal and vertical segregation and to pay. The differences between the three countries are explained by positing the existence of nationally specific gender profiles with a differential impact on labour market patterning along gender lines. These profiles are constructed by gender regimes at the level of the state which, in turn, are the result of political struggles and compromises of a variety of political actors. The paper utilizes European statistical data and secondary sources.