bluuebunny/crossref_metadata_2025 huggingface dataset:
Global expression profiling reveals genetic programs underlying the developmental divergence between mouse and human embryogenesis
Authors: Xue Lu , Cai Jin-Yang , Ma Jian , Huang Zan , Guo Ming-Xiong , Fu Lie-Zhen , Shi Yun-Bo , Li Wen-Xin
Published: August 2013

Background

Mouse has served as an excellent model for studying human development and diseases due to its similarity to human. Advances in transgenic and knockout studies in mouse have dramatically strengthened the use of this model and significantly improved our understanding of gene function during development in the past few decades. More recently, global gene expression analyses have revealed novel features in early embryogenesis up to gastrulation stages and have indeed provided molecular evidence supporting the conservation in early development in human and mouse. On the other hand, little information is known about the gene regulatory networks governing the subsequent organogenesis. Importantly, mouse and human development diverges during organogenesis. For instance, the mouse embryo is born around the end of organogenesis while in human the subsequent fetal period of ongoing growth and maturation of most organs spans more than 2/3 of human embryogenesis. While two recent studies reported the gene expression profiles during human organogenesis, no global gene expression analysis had been done for mouse organogenesis.

Results

Here we report a detailed analysis of the global gene expression profiles from egg to the end of organogenesis in mouse. Our studies have revealed distinct temporal regulation patterns for genes belonging to different functional (Gene Ontology or GO) categories that support their roles during organogenesis. More importantly, comparative analyses identify both conserved and divergent gene regulation programs in mouse and human organogenesis, with the latter likely responsible for the developmental divergence between the two species, and further suggest a novel developmental strategy during vertebrate evolution.

Conclusions

We have reported here the first genome-wide gene expression analysis of the entire mouse embryogenesis and compared the transcriptome atlas during mouse and human embryogenesis. Given our earlier observation that genes function in a given process tends to be developmentally co-regulated during organogenesis, our microarray data here should help to identify genes associated with mouse development and/or infer the developmental functions of unknown genes. In addition, our study might be useful for invesgtigating the molecular basis of vertebrate evolution.
A plasmid toolkit for cloning chimeric cDNAs encoding customized fusion proteins into any Gateway destination expression vector
Authors: Buj Raquel , Iglesias Noa , Planas Anna M , Santalucía Tomàs
Published: August 2013

Background

Valuable clone collections encoding the complete ORFeomes for some model organisms have been constructed following the completion of their genome sequencing projects. These libraries are based on Gateway cloning technology, which facilitates the study of protein function by simplifying the subcloning of open reading frames (ORF) into any suitable destination vector. The expression of proteins of interest as fusions with functional modules is a frequent approach in their initial functional characterization. A limited number of Gateway destination expression vectors allow the construction of fusion proteins from ORFeome-derived sequences, but they are restricted to the possibilities offered by their inbuilt functional modules and their pre-defined model organism-specificity. Thus, the availability of cloning systems that overcome these limitations would be highly advantageous.

Results

We present a versatile cloning toolkit for constructing fully-customizable three-part fusion proteins based on the MultiSite Gateway cloning system. The fusion protein components are encoded in the three plasmids integral to the kit. These can recombine with any purposely-engineered destination vector that uses a heterologous promoter external to the Gateway cassette, leading to the in-frame cloning of an ORF of interest flanked by two functional modules. In contrast to previous systems, a third part becomes available for peptide-encoding as it no longer needs to contain a promoter, resulting in an increased number of possible fusion combinations. We have constructed the kit’s component plasmids and demonstrate its functionality by providing proof-of-principle data on the expression of prototype fluorescent fusions in transiently-transfected cells.

Conclusions

We have developed a toolkit for creating fusion proteins with customized N- and C-term modules from Gateway entry clones encoding ORFs of interest. Importantly, our method allows entry clones obtained from ORFeome collections to be used without prior modifications. Using this technology, any existing Gateway destination expression vector with its model-specific properties could be easily adapted for expressing fusion proteins.
Differences and associations of metabolic and vitamin D status among patients with and without sub-clinical hypothyroid dysfunction
Authors: Aljohani Naji J , Al-Daghri Nasser M , Al-Attas Omar S , Alokail Majed S , Alkhrafy Khalid M , Al-Othman Abdulaziz , Yakout Sobhy , Alkabba Abdulaziz F , Al-Ghamdi Ahmed S , Almalki Mussa , Buhary Badurudeen Mahmood , Sabico Shaun
Published: August 2013

Background

Sub-clinical hypothyroid dysfunction, a relatively understudied disorder in the Kingdom of Saudi Arabia (KSA), has significant clinical implications if not properly monitored. Also from KSA, more than 50% of the population suffer from hypovitaminosis D (<50 nmol/l). In this cross-sectional case-control study, we described the differences and associations in the metabolic patterns of adult Saudis with and without hypothyroid dysfunction in relation to their vitamin D status, PTH, calcium and lipid profile.

Methods

A total of 94 consenting adult Saudis [52 controls (without subclinical hypothyroidism), 42 cases (previously diagnosed subjects)] were included in this cross-sectional study. Anthropometrics were obtained and fasting blood samples were taken for ascertaining lipid and thyroid profile, as well as measuring PTH, 25(OH) vitamin D and calcium.

Results

Cases had a significantly higher body mass index than the controls (p < 0.001). Circulating triglycerides was also significantly higher in cases than the controls (p = 0.001). A significant positive association between HDL-cholesterol and PTH (R = 0.56; p = 0.001), as well as a negative and modestly significant negative association between LDL-cholesterol and PTH (R = - 20.0; p = 0.04) were observed. FT3 was inversely associated with circulating 25 (OH) vitamin D (R = -0.25; p = 0.01).

Conclusions

Patients with hypothyroid dysfunction possess several cardiometabolic risk factors that include obesity and dyslipidemia. The association between PTH and cholesterol levels as well as the inverse association between vitamin D status and FT3 needs to be reassessed prospectively on a larger scale to confirm these findings.
Spindle and kinetochore associated complex subunit 1 regulates the proliferation of oral adenosquamous carcinoma CAL-27 cells in vitro
Authors: Zhang Bin , Li Ke Yi , Chen Hai Ying , Pan Shao Dong , Jiang Li Cheng , Wu Ya Ping , Liu Shu Wei
Published: August 2013

Background

The prognosis of oral squamous cell carcinoma is very poor due to local recurrence and metastasis. This study explores the molecular events involved in oral carcinoma with the goal of developing novel therapeutic strategies. The mitotic spindle is a complex mechanical apparatus required for the accurate segregation of sister chromosomes during mitosis. Spindle and kinetochore associated complex subunit 1 (SKA1) is a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation. In recent years, much attention has been focused on determining how SKA proteins interact with each other, as well as their biological role in cancer cells. However, the precise role of SKA1 in oral carcinoma remains unknown.

Methods

In order to investigate the role of SKA1 in oral cancer, we employed lentivirus-mediated shRNA to silence SKA1 expression in the CAL-27 human oral adenosquamous carcinoma cell line.

Results

Depletion of SKA1 in CAL-27 cells significantly decreased cell proliferation, as determined by MTT and colony formation assays. These results strongly demonstrate that reduced SKA1 protein levels may cause inhibition of tumor formation. The shRNA-mediated depletion of SKA1 also led to G2/M phase cell cycle arrest and apoptosis.

Conclusion

This is the first report to show that SKA1 plays an important role in the progression of oral adenosqamous carcinoma. Thus, silencing of SKA1 by RNAi might be a potential therapy for this disease.
Stress echocardiography: safety and tolerability
Authors: Fennich Nada , Ellouali Fedoua , Abdelali Salima , Chaara Assad , Berrada Allal , Elhajjaji Imane , Cherradi Rhizlane , Abir Saadia , Doghmi Nawal , Cherti Mohammed
Published: August 2013

Background

Stress echocardiography is a valuable tool for the noninvasive diagnosis of ischemic heart disease. Despite its widely use in the clinical practice, safety and side effects profile have never been evaluated in Moroccans.

The aim

To assess the safety and tolerability of the two stress echo modalities in Moroccans.

Methods

The study was made by 311 patients with known or suspected coronary artery disease, 203 underwent exercise echocardiography and 108 underwent dobutamine echocardiography, major and minor rhythmic complications and side effects were recorded for the two groups.

Results

We registered 3 (2, 8%) major rhythmic events in the dobutamine group (2 sustained supraventricular tachycardia and 1 sustained ventricular tachycardia), there was no major rhythmic events in the exercise group. Minor rhythmic events were frequent (43, 5% in the dobutamine group and 19, 2% in the exercise group with a p = 0, 0001). Severe hypotension occurs in 4 (3, 7%) patients during a dobutamine stress, there was no significant drop in the blood pressure during exercise stress procedures. Non cardiac side effects were more common among patients who underwent a dobutamine stress echo (13, 9% vs. 3, 4% with p = 0,001).

Conclusion

Exercise is safer than dobutamine stress echocardiography, complications and adverse effects with the use of dobutamine are usually minor and self-limiting.
Additional value of lateral tissue Doppler imaging in the assessment of diastolic dysfunction among subjects with pseudonormal pattern of mitral inflow
Authors: Kim Hack-Lyoung , Zo Joo-Hee , Seo Jae-Bin , Chung Woo-Young , Kim Yong-Jin , Kim Sang-Hyun , Kim Myung-A , Sohn Dae-Won
Published: August 2013

Background

There has been a lack of research on further stratification of subjects who have pseudonormal pattern of mitral inflow. The study aim was to clarify 2 different groups with different diastolic function grades among these subjects using lateral tissue Doppler imaging (TDI).

Methods

A total of 122 consecutive subjects showing pseudonormal pattern of mitral inflow (E/A ≥ 1 and septal e’/a’ < 1) without structural abnormality were prospectively recruited. TDI measurements were performed from both septal and lateral mitral annuli.

Results

Study subjects were stratified according to lateral TDI pattern (e’/a’ < 1 [n = 50] versus e’/a’ ≥ 1 [n = 72]). Subjects with lateral e’/a’ < 1 had higher values of left atrial volume index (LAVI) and E/e’ compared to those for lateral e’/a’ ≥ 1 (p < 0.001 for each). Among subjects with lateral e’/a’ ≥ 1, only 9.3% of subjects had grade II diastolic dysfunction, whereas among subjects with lateral e’/a’ < 1, majority of subjects (64.1%) had grade II diastolic dysfunction (p < 0.001). Multiple linear regression analysis showed that lateral e’/a’ was independently associated with LAVI (β = −0.484, p < 0.001), even after adjusting for potential confounders including age, sex, body mass index, hypertension and diabetes.

Conclusions

In subjects without structural abnormality showing E/A ≥ 1 and septal e’/a’ < 1, lateral TDI measurement is useful in the assessment of diastolic dysfunction. Lateral e’/a’ ≥ 1 is a valuable indicator of early diastolic dysfunction but not of advanced diastolic dysfunction in this population.
Pharmacological treatments in ARDS; a state-of-the-art update
Authors: Boyle Andrew James , Sweeney Rob Mac , McAuley Daniel Francis
Published: August 2013

Despite its high incidence and devastating outcomes, acute respiratory distress syndrome (ARDS) has no specific treatment, with effective therapy currently limited to minimizing potentially harmful ventilation and avoiding a positive fluid balance. Many pharmacological therapies have been investigated with limited success to date. In this review article we provide a state-of-the-art update on recent and ongoing trials, as well as reviewing promising future pharmacological therapies in ARDS.
Western-type diet modulates inflammatory responses and impairs functional outcome following permanent middle cerebral artery occlusion in aged mice expressing the human apolipoprotein E4 allele
Authors: Dhungana Hiramani , Rolova Taisia , Savchenko Ekaterina , Wojciechowski Sara , Savolainen Kaisa , Ruotsalainen Anna-Kaisa , Sullivan Patrick M , Koistinaho Jari , Malm Tarja
Published: August 2013

Background

Numerous clinical trials in stroke have failed, most probably partially due to preclinical studies using young, healthy male rodents with little relevance to the heterogenic conditions of human stroke. Co-morbid conditions such as atherosclerosis and infections coupled with advanced age are known to contribute to increased risk of cerebrovascular diseases. Clinical and preclinical studies have shown that the E4 allele of human apolipoprotein (ApoE4) is linked to poorer outcome in various conditions of brain injury and neurodegeneration, including cerebral ischemia. Since ApoE is a known regulator of lipid homeostasis, we studied the impact of a high-cholesterol diet in aged mice in the context of relevant human ApoE isoforms on the outcome of focal brain ischemia.

Methods

Aged mice expressing human E3 and E4 isoforms of ApoE in C57BL/6J background and C57BL/6J mice fed on either a high-fat diet or a normal diet underwent permanent middle cerebral artery occlusion. The impact of a high-cholesterol diet was assessed by measuring the serum cholesterol level and the infarction volume was determined by magnetic resonance imaging. Sensorimotor deficits were assessed using an adhesive removal test and the findings were correlated with inflammatory markers.

Results

We show that expression of human ApoE4 renders aged mice fed with a western-type diet more susceptible to sensorimotor deficits upon stroke. These deficits are not associated with atherosclerosis but are accompanied with altered astroglial activation, neurogenesis, cyclooxygenase-2 immunoreactivity and increased plasma IL-6.

Conclusions

Our results support the hypothesis that ApoE alleles modify the inflammatory responses in the brain and the periphery, thus contributing to altered functional outcome following stroke.
A qualitative study of Ottawa university students’ awareness, knowledge and perceptions of infertility, infertility risk factors and assisted reproductive technologies (ART)
Authors: Sabarre Kelley-Anne , Khan Zainab , Whitten Amanda N , Remes Olivia , Phillips Karen P
Published: August 2013

Background

Awareness of infertility risk factors is an essential first step to safeguard future fertility. Whereas several studies have examined university students’ awareness of female fertility and related risk factors, the topic of male infertility has not been well examined. The objective of this study was to assess young men and women’s awareness, knowledge and perceptions of infertility, male and female infertility risk factors and assisted reproductive technologies (ART).

Methods

Semi-structured interviews were conducted in 2008 with a multi-ethnic sample of sixteen male and twenty-three female Ottawa university students, followed by qualitative data analysis to identify major themes. Interview topics included awareness of male and female infertility risk factors, infertility diagnosis/treatments and personal options in the event of future infertility.

Results

Participants were generally familiar with infertility as a biomedical health problem, could identify sex-specific risk factors but overestimated fertility of women in their thirties and ART success rates. Reproductive health knowledge gaps and confusion of the physiological life-stage of menopause with infertility were apparent. Most participants would pursue in vitro fertilization or international adoption in the event of personal infertility. Some participants wished to use a ‘natural’ approach and were concerned with potential side effects of ART-related medications.

Conclusions

The general awareness of infertility in young adults is promising and supports the potential uptake for health promotion of fertility preservation. This study underscores the continued need for comprehensive sexual and reproductive health education and promotion for adolescents and young adults.
TRialing individualized interventions to prevent functional decline in at-risk older adults (TRIIFL): study protocol for a randomized controlled trial nested in a longitudinal observational study
Authors: Grimmer Karen , Luker Julie , Beaton Kate , Kumar Saravana , Crockett Alan , Price Kay
Published: August 2013

Background

Functional decline (FD) is a largely preventable feature of aging, characterized as gradual erosion of functional autonomy. This reduces an older person’s capacity for safe, independent community living. The healthcare needs of an unprecedented aging population places pressure on health systems to develop innovative approaches to ensuring older people live healthy and independent lives for as long as possible.

TRIIFL aims to demonstrate that:

Incipient FD in older people can be identified using a simple telephone-screening process within four weeks of discharge from an emergency department presentation for a minor health event; and

Early engagement into a person-centered individualized intervention arrests or reduces the rate of FD over the next 12 months.

Methods/Design

A randomized controlled trial (RCT) nested within a 13-month longitudinal cohort study. The RCT (conducted over 12 months) tests the effectiveness of a novel, early, home-based, personalized program (compared with no intervention) in arresting or slowing FD.

TRIIFL focuses on older adults living independently in the community, who have not yet had a serious health event, yet are potentially on the cusp of FD. Participants in the longitudinal cohort study will be recruited as they present to one large tertiary hospital Emergency Department, providing they are not subsequently admitted to a ward. Sample size calculations indicate that 570 participants need to be recruited into the longitudinal study, with 100 participants randomized into the trial arms.

Measures from all subjects will be taken face-to-face at baseline (recruitment), then subsequently by telephone at one, four, seven and thirteen months later. Measures include functional abilities, quality of life, recent falls, mobility dependence, community supports and health service usage. Specific to the nested RCT, the quality of life tool (SF12) applied at one month, will identify individuals with low mental component quality of life scores, who will be invited to enter the RCT.

Assessors will be blinded to RCT arm allocation, and subjects in the RCT will be blinded to the intervention being received by other subjects.

Trials Registration

Australian & New Zealand Clinical Trials Registry: ACTRN12613000234718
Use of weeds as traditional vegetables in Shurugwi District, Zimbabwe
Authors: Maroyi Alfred
Published: August 2013

Background

Most agricultural weeds are usually regarded as undesirable and targeted for eradication. However, weeds are useful to human beings as food and traditional medicines. Few studies have been done to document the uses of weeds as traditional vegetables. This study was therefore, done to document indigenous knowledge related to the diversity and use of agricultural weeds as traditional vegetables in Shurugwi District, Zimbabwe, emphasizing their role in food security and livelihoods of the local people.

Materials and methods

Semi-structured interviews, observation and guided field walks with 147 participants were employed between December 2011 and January 2012 to obtain ethnobotanical data on the use of edible weeds as traditional vegetables. Based on ethnobotanical information provided by the participants, botanical specimens were collected, numbered, pressed and dried for identification.

Results

A total of 21 edible weeds belonging to 11 families and 15 genera, mostly from Amaranthaceae (19%), Asteraceae and Tiliaceae (14.3%), Capparaceae, Cucurbitaceae and Solanaceae (9.5% each) were identified. Of the documented edible weeds, 52.4% are indigenous while 47.6% are exotic to Zimbabwe; either semi-cultivated or growing naturally as agricultural weeds in farmlands, fallow land and home gardens. Among the main uses of edible weeds were leafy vegetables (81%), followed by edible fruits (19%), edible corms (9.5%), edible flowers and seeds (4.8% each). The most important edible weeds wereCleome gynandra, cited by 93.9% of the participants,Cucumis metuliferus(90.5%),Cucumis anguria(87.8%),Corchorus tridens(50.3%) andAmaranthus hybridus(39.5%). All edible weeds were available during rainy and harvest period withCleome gynandra,Corchorus tridens, Cucumis anguria, Cucumis metuliferusandMoringa oleiferaalso available during the dry season, enabling households to obtain food outputs in different times of the year. The importance of edible weeds for local livelihoods was ubiquitously perceived, with all participants reporting their contribution towards food security and nutrition.

Conclusion

The present study confirm findings from similar studies conducted elsewhere that rural households engage in harvesting of wild edible vegetables and other non-timber forest products (NTFPs) as a survival strategy. Based on their potential nutritional and medicinal value, edible weeds could contribute in a major way to food security, basic primary health care and balanced diets of rural households and possibly urban households as well.
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

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

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

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

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

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

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

The 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

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.
Oral l-Arginine Stimulates GLP-1 Secretion to Improve Glucose Tolerance in Male Mice
Authors: Clemmensen Christoffer , Smajilovic Sanela , Smith Eric P. , Woods Stephen C. , Bräuner-Osborne Hans , Seeley Randy J. , D'Alessio David A. , Ryan Karen K.
Published: August 2013

Pharmacological and surgical interventions that increase glucagon-like peptide 1 (GLP-1) action are effective to improve glucose homeostasis in type 2 diabetes mellitus. In light of this, nutritional strategies to enhance postprandial GLP-1 secretion, particularly in the context of diet-induced obesity, may provide an alternative therapeutic approach. Importantly, recent evidence suggests the amino acid l-arginine, a well-known insulin secretagogue, can also stimulate release of GLP-1 from isolated rat intestine. Here we tested the hypothesis that oral l-arginine acts as a GLP-1 secretagogue in vivo, to augment postprandial insulin secretion and improve glucose tolerance. To test this, we administered l-arginine or vehicle by oral gavage, immediately prior to an oral glucose tolerance test in lean and diet-induced obese mice. In both lean and obese mice oral l-arginine increased plasma GLP-1 and insulin and substantially improved glucose clearance. To directly assess the contribution of GLP-1 receptor (GLP-1R)-signaling to these improvements, l-arginine was given to Glp1r knockout mice and their wild-type littermates. In this experiment oral l-arginine significantly augmented insulin secretion and improved glucose clearance in WT mice, but not in Glp1r knockout littermates. Taken together these findings identify l-arginine as a GLP-1 secretagogue in vivo and demonstrate that improvement of glucose tolerance by oral l-arginine depends on GLP-1R-signaling. These findings raise the intriguing possibility that l-arginine-based nutritional and/or pharmaceutical therapies may benefit glucose tolerance by improving the postprandial GLP-1 response in obese individuals.
Autophagy Deficiency by Hepatic FIP200 Deletion Uncouples Steatosis From Liver Injury in NAFLD
Authors: Ma Di , Molusky Matthew M. , Song Jianrui , Hu Chun-Rui , Fang Fang , Rui Crystal , Mathew Anna V. , Pennathur Subramaniam , Liu Fei , Cheng Ji-Xin , Guan Jun-Lin , Lin Jiandie D.
Published: August 2013

Nonalcoholic fatty liver disease is a metabolic disorder commonly associated with obesity. A subset of nonalcoholic fatty liver disease patients further develops nonalcoholic steatohepatitis that is characterized by chronic liver injury, inflammation, and fibrosis. Recent work has implicated the autophagy pathway in the mobilization and oxidation of triglycerides from lipid droplets. However, whether impaired autophagy in hepatocytes drives excess fat accumulation in the liver remains controversial. In addition, the role of autophagy in protecting the liver from gut endotoxin-induced injury has not been elucidated. Here we generated mice with liver-specific autophagy deficiency by the conditional deletion of focal adhesion kinase family kinase-interacting protein of 200 kDa (also called Rb1cc1), a core subunit of the mammalian autophagy related 1 complex. To our surprise, mice lacking FIP200 in hepatocytes were protected from starvation- and high-fat diet-induced fat accumulation in the liver and had decreased expression of genes involved in lipid metabolism. Activation of the de novo lipogenic program by liver X receptor was impaired in FIP200-deficient livers. Furthermore, liver autophagy was stimulated by exposure to low doses of lipopolysaccharides and its deficiency-sensitized mice to endotoxin-induced liver injury. Together these studies demonstrate that hepatocyte-specific autophagy deficiency per se does not exacerbate hepatic steatosis. Instead, autophagy may play a protective role in the liver after exposure to gut-derived endotoxins and its blockade may accelerate nonalcoholic steatohepatitis progression.
E. P. Thompson's The Making of the English Working Class: Assessments After a Half Century
Authors: Arnesen Eric
Published: August 2013

This issue's Bookmark section revisits E. P. Thompson's path-breaking The Making of the English Working Class upon its fiftieth anniversary. Their commentaries, introduced by Eric Arnesen, signal a variety of appreciations and critical reevaluations of the original text and, by extension, reflect the current state of history and politics.
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.
OM Forum—Operations Management Challenges for Some “Cleantech” Firms
Authors: Plambeck Erica L.
Published: August 2013

A “cleantech” firm is one with an innovative technology and/or business model for serving an existing market with dramatically reduced environmental impact. This paper describes operations management (OM) challenges faced by five cleantech companies, and a few questions that these raise for OM and multidisciplinary research. It aims to fuel readers' motivation to identify and pursue others. The OM community has fundamental roles to play in the creation of an environmentally sustainable economy.
Austrian Books Online: Die Public Private Partnership der Österreichischen Nationalbibliothek mit Google
Authors: Kaiser Max , Majewski Stefan
Published: August 2013

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

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

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

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

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

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.