bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies
Authors: Meskauskiene Rasa , Laule Oliver , Ivanov Nikolai V , Martin Florian , Wyss Markus , Gruissem Wilhelm , Zimmermann Philip 
Published: August 2013

Abstract

Background
It is generally accepted that controlled vocabularies are necessary to systematically integrate data from various sources. During the last decade, several plant ontologies have been developed, some of which are community specific or were developed for a particular purpose. In most cases, the practical application of these ontologies has been limited to systematically storing experimental data. Due to technical constraints, complex data structures and term redundancies, it has been difficult to apply them directly into analysis tools.

Results
Here, we describe a simplified and cross-species compatible set of controlled vocabularies for plant anatomy, focussing mainly on monocotypledonous and dicotyledonous crop and model plants. Their content was designed primarily for their direct use in graphical visualization tools. Specifically, we created annotation vocabularies that can be understood by non-specialists, are minimally redundant, simply structured, have low tree depth, and we tested them practically in the frame of Genevestigator.

Conclusions
The application of the proposed ontologies enabled the aggregation of data from hundreds of experiments to visualize gene expression across tissue types. It also facilitated the comparison of expression across species. The described controlled vocabularies are maintained by a dedicated curation team and are available upon request.
Synaptic protein and pan-neuronal gene expression and their regulation by Dicer-dependent mechanisms differ between neurons and neuroendocrine cells
Authors: Stubbusch Jutta , Narasimhan Priyanka , Huber Katrin , Unsicker Klaus , Rohrer Hermann , Ernsberger Uwe 
Published: August 2013

Abstract

Background
Neurons in sympathetic ganglia and neuroendocrine cells in the adrenal medulla share not only their embryonic origin from sympathoadrenal precursors in the neural crest but also a range of functional features. These include the capacity for noradrenaline biosynthesis, vesicular storage and regulated release. Yet the regulation of neuronal properties in early neuroendocrine differentiation is a matter of debate and the developmental expression of the vesicle fusion machinery, which includes components found in both neurons and neuroendocrine cells, is not resolved.

Results
Analysis of synaptic protein and pan-neuronal marker mRNA expression during mouse development uncovers profound differences between sympathetic neurons and adrenal chromaffin cells, which result in qualitatively similar but quantitatively divergent transcript profiles. In sympathetic neurons embryonic upregulation of synaptic protein mRNA follows early and persistent induction of pan-neuronal marker transcripts. In adrenal chromaffin cells pan-neuronal marker expression occurs only transiently and synaptic protein messages remain at distinctly low levels throughout embryogenesis. Embryonic induction of synaptotagmin I (Syt1) in sympathetic ganglia and postnatal upregulation of synaptotagmin VII (Syt7) in adrenal medulla results in a cell type-specific difference in isoform prevalence. Dicer 1 inactivation in catecholaminergic cells reduces high neuronal synaptic protein mRNA levels but not their neuroendocrine low level expression. Pan-neuronal marker mRNAs are induced in chromaffin cells to yield a more neuron-like transcript pattern, while ultrastructure is not altered.

Conclusions
Our study demonstrates that remarkably different gene regulatory programs govern the expression of synaptic proteins in the neuronal and neuroendocrine branch of the sympathoadrenal system. They result in overlapping but quantitatively divergent transcript profiles. Dicer 1-dependent regulation is required to establish high neuronal mRNA levels for synaptic proteins and to maintain repression of neurofilament messages in neuroendocrine cells.
Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824
Authors: Kovács Katalin , Willson Benjamin J , Schwarz Katrin , Heap John T , Jackson Adam , Bolam David N , Winzer Klaus , Minton Nigel P 
Published: August 2013

Abstract

Background
Consolidated bioprocessing (CBP) is reliant on the simultaneous enzyme production, saccharification of biomass, and fermentation of released sugars into valuable products such as butanol. Clostridial species that produce butanol are, however, unable to grow on crystalline cellulose. In contrast, those saccharolytic species that produce predominantly ethanol, such as Clostridium thermocellum and Clostridium cellulolyticum, degrade crystalline cellulose with high efficiency due to their possession of a multienzyme complex termed the cellulosome. This has led to studies directed at endowing butanol-producing species with the genetic potential to produce a cellulosome, albeit by localising the necessary transgenes to unstable autonomous plasmids. Here we have explored the potential of our previously described Allele-Coupled Exchange (ACE) technology for creating strains of the butanol producing species Clostridium acetobutylicum in which the genes encoding the various cellulosome components are stably integrated into the genome.

Results
We used BioBrick2 (BB2) standardised parts to assemble a range of synthetic genes encoding C. thermocellum cellulosomal scaffoldin proteins (CipA variants) and glycoside hydrolases (GHs, Cel8A, Cel9B, Cel48S and Cel9K) as well as synthetic cellulosomal operons that direct the synthesis of Cel8A, Cel9B and a truncated form of CipA. All synthetic genes and operons were integrated into the C. acetobutylicum genome using the recently developed ACE technology. Heterologous protein expression levels and mini-cellulosome self-assembly were assayed by western blot and native PAGE analysis.

Conclusions
We demonstrate the successful expression, secretion and self-assembly of cellulosomal subunits by the recombinant C. acetobutylicum strains, providing a platform for the construction of novel cellulosomes.
Diversity of picoeukaryotes at an oligotrophic site off the Northeastern Red Sea Coast
Authors: Acosta Francisco , Ngugi David Kamanda , Stingl Ulrich 
Published: August 2013

Abstract

Background
Picoeukaryotes are protists ≤ 3 μm composed of a wide diversity of taxonomic groups. They are an important constituent of the ocean’s microbiota and perform essential ecological roles in marine nutrient and carbon cycles. Despite their importance, the true extent of their diversity has only recently been uncovered by molecular surveys that resulted in the discovery of a substantial number of previously unknown groups. No study on picoeukaryote diversity has been conducted so far in the main Red Sea basin-a unique marine environment characterized by oligotrophic conditions, high levels of irradiance, high salinity and increased water temperature.

Results
We sampled surface waters off the coast of the northeastern Red Sea and analyzed the picoeukaryotic diversity using Sanger-based clone libraries of the 18S rRNA gene in order to produce high quality, nearly full-length sequences. The community captured by our approach was dominated by three main phyla, the alveolates, stramenopiles and chlorophytes; members of Radiolaria, Cercozoa and Haptophyta were also found, albeit in low abundances. Photosynthetic organisms were especially diverse and abundant in the sample, confirming the importance of picophytoplankton for primary production in the basin as well as indicating the existence of numerous ecological micro-niches for this trophic level in the upper euphotic zone. Heterotrophic organisms were mostly composed of the presumably parasitic Marine Alveolates (MALV) and the presumably bacterivorous Marine Stramenopiles (MAST) groups. A small number of sequences that did not cluster closely with known clades were also found, especially in the MALV-II group, some of which could potentially belong to novel clades.

Conclusions
This study provides the first snapshot of the picoeukaryotic diversity present in surface waters of the Red Sea, hence setting the stage for large-scale surveying and characterization of the eukaryotic diversity in the entire basin. Our results indicate that the picoeukaryotic community in the northern Red Sea, despite its unique physiochemical conditions (i.e. increased temperatures, increased salinity, and high UV irradiance) does not differ vastly from its counterparts in other oligotrophic marine habitats.
Thinking about internal states, a qualitative investigation into metacognitions in women with eating disorders
Authors: Vann Alix , Strodl Esben , Anderson Erin 
Published: August 2013

Abstract

Background
There is a need for qualitative research to help develop case conceptualisations to guide the development of Metacognitive Therapy interventions for Eating Disorders.

Method
A qualitative study informed by grounded theory methodology was conducted involving open-ended interviews with 27 women aged 18–55 years, who were seeking or receiving treatment for a diagnosed ED.

Results
The categories identified in this study appeared to be consistent with a metacognitive model including constructs of a Cognitive Attentional Syndrome and metacognitive beliefs. These categories appear to be transdiagnostic, and the interaction between the categories is proposed to explain the maintenance of EDs.

Conclusions
The transdiagnostic model proposed may be useful to guide the development of future metacognitive therapy interventions for EDs with the hope that this will lead to improved outcomes for individuals with EDs.
Production of 2,3-butanediol from cellulose and Jatropha hulls after ionic liquid pretreatment and dilute-acid hydrolysis
Authors: Jiang Li-qun , Fang Zhen , Li Xing-Kang , Luo Jia 
Published: August 2013

Abstract
Abundant Jatropha waste is a promising renewable feedstock for the production of sugars and 2,3-butanediol fermentation. To obtain high yield of water-soluble products and high concentration of reducing-sugars, ionic liquid (IL) pretreatment and dilute acid hydrolysis at 150°C were combined in this work. The destruction of crystalline structure and increase surface area of biomasses after IL-pretreatment, made their hydrolysis more efficient. Compared with original cellulose, after IL-pretreatment, both the yield and concentration of reducing-sugars increased by 139%, and the water-soluble products yield increased by 128% after hydrolysis. Compared with water-washed Jatropha hulls, after IL-pretreatment, the yield and concentration of reducing-sugars increased by 80% and 76%, respectively, and the water-soluble products yield increased by 70% after hydrolysis. IL-pretreatment benefited the fermentation of Jatropha hull hydrolysate with 66.58% diol yield and its productivity increased from 0.35 to 0.40 g/(L · h).
Recruitment to the Norwegian fishing fleet: storylines, paradoxes, and pragmatism in Norwegian fisheries and recruitment policy
Authors: Sønvisen Signe Annie 
Published: August 2013

AbstractThe majority of actors in the Norwegian fisheries consider recruitment of fishers to be the main future challenge for the Norwegian fishing fleet. As fleet recruitment is a highly politicized field, the problem of how to mitigate the recruitment problem is a subject of heavy debate. Some argue that recruitment problems are caused by low fleet profitability, while others argue that recruitment problems are caused by fleet restructuring polices.This article aims to explore the recruitment phenomenon. Thus, it examines the relationship between recruitment discourse and recruitment policies and practices. Discourse analysis is used to show how diverging storylines about recruitment result in incoherent recruitment policy. The article concludes that while current recruitment policies are heavily influenced by ideology, the answer to creating more efficient recruitment policies may lie in a more pragmatic approach.
Incremental value of rare genetic variants for the prediction of multifactorial diseases
Authors: Mihaescu Raluca , Pencina Michael J , Alonso Alvaro , Lunetta Kathryn L , Heckbert Susan R , Benjamin Emelia J , JW Janssens A Cecile 
Published: August 2013

Abstract
Background
It is often assumed that rare genetic variants will improve available risk prediction scores. We aimed to estimate the added predictive ability of rare variants for risk prediction of common diseases in hypothetical scenarios.

Methods
In simulated data, we constructed risk models with an area under the ROC curve (AUC) ranging between 0.50 and 0.95, to which we added a single variant representing the cumulative frequency and effect (odds ratio, OR) of multiple rare variants. The frequency of the rare variant ranged between 0.0001 and 0.01 and the OR between 2 and 10. We assessed the resulting AUC, increment in AUC, integrated discrimination improvement (IDI), net reclassification improvement (NRI(>0.01)) and categorical NRI. The analyses were illustrated by a simulation of atrial fibrillation risk prediction based on a published clinical risk model.

Results
We observed minimal improvement in AUC with the addition of rare variants. All measures increased with the frequency and OR of the variant, but maximum increment in AUC remained below 0.05. Increment in AUC and NRI(>0.01) decreased with higher AUC of the baseline model, whereas IDI remained constant. In the atrial fibrillation example, the maximum increment in AUC was 0.02 for a variant with frequency = 0.01 and OR = 10. IDI and NRI showed at most minimal increase for variants with frequency greater than or equal to 0.005 and OR greater than or equal to 5.

Conclusions
Since rare variants are present in only a minority of affected individuals, their predictive ability is generally low at the population level. To improve the predictive ability of clinical risk models for complex diseases, genetic variants must be common and have substantial effect on disease risk.
The effects of anaesthesia on the developing brain: a summary of the clinical evidence
Authors: Yu Clara KY , Yuen Vivian Man Ying , Wong Gordon TC , Irwin Michael G 
Published: August 2013

Introduction: There is data amassing in the literature regarding the potentially adverse effects of anaesthesia exposure on the developing human brain. The purpose of this article is to summarise current relevant data from clinical studies in this area. Methods: Articles from journals written in English were searched for using PubMed, Ovid and Medline. Keywords used included: brain (newborn, infant, child and neonate), neurodegeneration, apoptosis, toxicity, neurocognitive impairment (developmental impairment and learning disorders) and anaesthesia (intravenous, inhalational and sedation).Results: From the initial search, 23 articles were identified as potentially relevant, with publication dates spanning from 1978 to 2012. Twelve studies were deemed irrelevant to the research questions. The results of neurocognitive assessment from eight of the remaining eleven studies had showed some differences in the performances of children exposed to anaesthesia. The control population in these studies was highly variable. The age at which the subjects were exposed to anaesthesia ranged from prenatal to 4 years in the majority of studies with one including children aged up to 12 years when exposed. Discussion: Although there is clinical data suggesting a possible detrimental effect, the evidence is best considered preliminary and inconclusive at this stage. Many of the outcome measures were lacking in specificity and standardization in most cases. Parents should be counselled to not avoid necessary invasive procedures for fear of a currently ill-defined risk. However, deferral of elective procedures beyond the first few years of life should be contemplated.
Austrian Books Online: Die Public Private Partnership der Österreichischen Nationalbibliothek mit Google
Authors: Kaiser Max , Majewski Stefan 
Published: August 2013

Zusammenfassung
Austrian Books Online ist ein Massendigitalisierungsprojekt der Österreichischen Nationalbibliothek in Kooperation mit Google. Der Artikel beschreibt zunächst die Einbettung des Projekts in die Bibliothek und die Rahmenbedingungen der öffentlich-privaten Partnerschaft. Anschließend werden exemplarisch die Herausforderungen im Bereich der Buchlogistik und Metadatenbearbeitung sowie in der Qualitätssicherung beschrieben. Der Artikel schließt mit einem Ausblick auf zukünftige Entwicklungen in Austrian Books Online.
Die Stärken digitalen Publizierens endlich vollständig nutzen: Patron Driven Acquisition aus der Verlagssicht
Authors: Siems Katrin 
Published: August 2013

Zusammenfassung
Patron Driven Acquisition hat in den vergangenen Jahren wachsende Beachtung unter Bibliothekaren gefunden. Wenig diskutiert ist bisher die Perspektive von Verlagen. Während digitale Medien mittlerweile zum verlegerischen Alltag gehören, sind die Geschäftsmodelle überraschend stark in der Welt gedruckter Bücher verhaftet. Der Beitrag wirft einen Blick auf die Motivation von Verlagen zum Angebot von PDA und beantwortet die Frage, wie ein solches Modell konkret entwickelt werden kann.
Die Markt- und Wettbewerbsanalyse – ein betriebswirtschaftliches Instrument zur Anwendung in Bibliotheken
Authors: Seidler-de Alwis Ragna 
Published: August 2013

Zusammenfassung
Auch wenn Bibliotheken Non-Profit-Organisationen sind, ist es sinnvoll, wesentliche Teile der Markt- und Wettbewerbsanalyse auf Bibliotheken zu übertragen. Die Markt- und Wettbewerbsanalyse gibt einer Bibliothek die Möglichkeit, ihre Kunden, Produkte, Dienstleistungen und Wettbewerber systematisch zu analysieren, so dass Chancen, Risiken und Trends für die jeweilige Bibliothek und/oder der Bibliotheksbranche sichtbar werden.
Das Projekt „move it“ – die Stadtbibliothek Biel bewegt!
Authors: Moser Clemens 
Published: August 2013

Zusammenfassung
Die Stadtbibliothek Biel sieht sich mit stagnierenden Benutzerzahlen und rückläufigen Medienausleihen konfrontiert. Nach einem Workshop mit der gesamten Belegschaft und dem Stiftungsrat wurde grünes Licht für einen Strategieprozess „move it“ gegeben. Im Laufe des Projekts sollen neue Perspektiven erarbeitet und realisiert werden. „move it“ beinhaltet eine Mitarbeit sämtlicher Kolleginnen und Kollegen sowie Politiker, Benutzer, Nicht-Benutzer, Schüler, Studenten und Familien (teilweise mit Migrationshintergrund). Die Fortschritte und Resultate werden laufend in einer eigenen Webseite aktualisiert. Die Bibliothek sieht sich als „lernende Organisation“.
The National Year of Reading 2012: An Australian Campaign to Promote Books, Reading and Literacy
Authors: McKerracher Sue , McDowell Donna , Ellard Robyn , Currie Brenda , Ward-Smith Karen , Hallam Gillian 
Published: August 2013

Abstract
In 2012, Australian libraries and library associations joined together to actively promote reading and literacy. Throughout the National Year of Reading, libraries across the country worked with a broad range of stakeholders including the government, the media, publishers and bookstores to develop and strengthen the passion for reading. The article outlines the goals of the program and discusses the four principal programs that created the framework for the 4,000 activities run by public libraries and reading organisations. The importance of branding and communication is highlighted to underscore the successful outcomes from the national campaign.
Unraveling RNA-mediated networks: new insights from new technologies
Authors: Rossbach Oliver , Bindereif Albrecht 
Published: August 2013

Abstract
Eukaryotic gene expression is regulated in a combinatorial manner and on several interconnected layers, ranging from epigenetic mechanisms, transcription, RNA processing to protein stages. mRNA processing plays a major role in tissue- and development-dependent regulation, in particular alternative pre-mRNA splicing, which greatly enhances the capacity and composition of the proteome. Within the last decade, novel methods have been developed to systematically study the complex networks between regulatory alternative splicing factors and their RNA targets. This minireview focuses on cross-linking and immunoprecipitation methods, which – in combination with deep RNA sequencing – have made an important contribution in unraveling these networks.
Microstructure and Tensile Deformation Features of Tandem Hot Rolling GH4169 Superalloy
Authors: Li Zhenrong , Ma Chunlei , Tian Sugui , Chen Liqing , Liu Xianghua 
Published: August 2013

AbstractBy means of solution treatment, microstructure observation and mechanical property measurement, the microstructure and tensile deformation features of tandem hot rolling GH4169 alloy have been investigated. Results shown that, after solution treatment and aging, large numbers of the spherical γ′ phase and the flat-ellipsoidal γ″ phase dispersedly precipitate in the matrix, and acicular or short rod-like δ-phase discontinuously distribute along grain boundaries. As the tensile temperatures increases, the tensile strength and yield strength of the alloy gradually decrease. The tensile deformation features of the alloy are that the twinning and slipping dislocations with double orientations are activated in the matrix. In the later tension, the deformed dislocations pile up near the grain boundary to induce initiation and propagation of cracks due to stress concentration.
Pre-pregnancy overweight overtakes gestational diabetes as a risk factor for subsequent metabolic syndrome
Authors: Ijäs H , Morin-Papunen L , Keränen A K , Bloigu R , Ruokonen A , Puukka K , Ebeling T , Raudaskoski T , Vääräsmäki M 
Published: August 2013

ObjectiveGestational diabetes mellitus (GDM) is associated with an increased risk of subsequent diabetes and metabolic syndrome (MS). The independent significance of overweight, often associated with GDM, is controversial. This study was aimed to investigate the prevalence of MS and carotid intima-media thickness (CIMT) values in normal and overweight women with previous insulin-treated GDM and control without GDM 19 years after the index pregnancy.MethodsThe study group consisted of 61 women with prior GDM and 55 controls who gave birth in Oulu University Hospital between 1988 and 1993. These women were further divided into subgroups according to pre-pregnancy BMI (<25 or ≥25 kg/m2). In 2008–2010, anthropometrics and blood pressure were measured, blood samples were taken, and an oral glucose tolerance test was performed to investigate the components of MS. CIMT was measured by Doppler ultrasound.ResultsTotal prevalence of MS was 62% in the GDM group and 31% in the control group (P=0.001); it was highest (86%) in GDM women with pre-pregnancy overweight. CIMT was significantly thicker (0.67 vs 0.56 mm,P=0.007) and more often abnormal (71.7 vs 45.3%,P=0.004) in the GDM group compared with the controls. In logistic regression analysis, the strongest factor predicting MS in the whole study population was pre-pregnancy overweight.ConclusionsPre-pregnancy overweight was the strongest predictive factor for later MS, whereas GDM indicated increased risk of subsequent diabetes and subclinical atherosclerosis. The risk of MS was highest when both of these factors were present.