bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of 12 EST libraries and characterization of a 12,226 EST dataset for chicory (Cichorium intybus) root, leaves and nodules in the context of carbohydrate metabolism investigation
Authors: Dauchot Nicolas , Mingeot Dominique , Purnelle Bénédicte , Muys Céline , Watillon Bernard , Boutry Marc , Van Cutsem Pierre 
Published: March 2009

Abstract

Background
The industrial chicory, Cichorium intybus, is a member of the Asteraceae family that accumulates fructan of the inulin type in its root. Inulin is a low calories sweetener, a texture agent and a health promoting ingredient due to its prebiotic properties. Average inulin chain length is a critical parameter that is genotype and temperature dependent. In the context of the study of carbohydrate metabolism and to get insight into the transcriptome of chicory root and to visualize temporal changes of gene expression during the growing season, we obtained and characterized 10 cDNA libraries from chicory roots regularly sampled in field during a growing season. A leaf and a nodule libraries were also obtained for comparison.

Results
Approximately 1,000 Expressed Sequence Tags (EST) were obtained from each of twelve cDNA libraries resulting in a 12,226 EST dataset. Clustering of these ESTs returned 1,922 contigs and 4,869 singlets for a total of 6,791 putative unigenes. All ESTs were compared to public sequence databases and functionally classified. Data were specifically searched for sequences related to carbohydrate metabolism. Season wide evolution of functional classes was evaluated by comparing libraries at the level of functional categories and unigenes distribution.

Conclusion
This chicory EST dataset provides a season wide outlook of the genes expressed in the root and to a minor extent in leaves and nodules. The dataset contains more than 200 sequences related to carbohydrate metabolism and 3,500 new ESTs when compared to other recently released chicory EST datasets, probably because of the season wide coverage of the root samples. We believe that these sequences will contribute to accelerate research and breeding of the industrial chicory as well as of closely related species.
Self-reported smoking cessation activities among Swiss primary care physicians
Authors: Jacot Sadowski Isabelle , Ruffieux Christiane , Cornuz Jacques 
Published: March 2009

Abstract

Background
Individual counselling, pharmacotherapy, and group therapy are evidence-based interventions that help patients stop smoking. Acupuncture, hypnosis, and relaxation have no demonstrated efficacy on smoking cessation, whereas self-help material may only have a small benefit. The purpose of this study is to assess physicians' current clinical practice regarding smokers motivated to stop smoking.

Methods
The survey included 3385 Swiss primary care physicians. Self-reported use of nine smoking cessation interventions was scored. One point was given for each positive answer about practicing interventions with demonstrated efficacy, i.e. nicotine replacement therapy, bupropion, counselling, group therapy, and smoking cessation specialist. No points were given for the recommendation of acupuncture, hypnosis, relaxation, and self-help material. Multivariable logistic analysis was performed to identify factors associated with a good practice score, defined as ≥ 2.

Results
The response rate was 55%. Respondents were predominately over the age of 40 years (88%), male (79%), and resided in urban areas (74%). Seventeen percent reported being smokers. Most of the physicians prescribed nicotine replacement therapy (84%), bupropion (65%), or provided counselling (70%). A minority of physicians recommended acupuncture (26%), hypnosis (8%), relaxation (7%), or self-help material (24%). A good practice score was obtained by 85% of respondents. Having attended a smoking cessation-training program was the only significant predictor of a good practice score (odds ratio: 6.24, 95% CI 1.95–20.04).

Conclusion
The majority of respondents practice recommended smoking cessation interventions. However, there is room for improvement and implementing an evidence-based smoking cessation-training program could provide additional benefit.
Identification of novel Cyclooxygenase-2-dependent genes in Helicobacter pylori infection in vivo
Authors: Walduck Anna K , Weber Matthias , Wunder Christian , Juettner Stefan , Stolte Manfred , Vieth Michael , Wiedenmann Bertram , Meyer Thomas F , Naumann Michael , Hoecker Michael 
Published: March 2009

AbstractBackgroundHelicobacter pyloriis a crucial determining factor in the pathogenesis of benign and neoplastic gastric diseases. Cyclooxygenase-2 (Cox-2) is the inducible key enzyme of arachidonic acid metabolism and is a central mediator in inflammation and cancer. Expression of theCox-2gene is up-regulated in the gastric mucosa duringH. pyloriinfection but the pathobiological consequences of this enhanced Cox-2 expression are not yet characterized. The aim of this study was to identify novel genes down-stream of Cox-2 in anin vivomodel, thereby identifying potential targets for the study of the role of Cox- 2 inH. pyloripathogenesis and the initiation of pre- cancerous changes.ResultsGene expression profiles in the gastric mucosa of mice treated with a specific Cox-2 inhibitor (NS398) or vehicle were analysed at different time points (6, 13 and 19 wk) afterH. pyloriinfection.H. pyloriinfection affected the expression of 385 genes over the experimental period, including regulators of gastric physiology, proliferation, apoptosis and mucosal defence. Under conditions of Cox-2 inhibition, 160 target genes were regulated as a result ofH. pyloriinfection. The Cox-2 dependent subset included those influencing gastric physiology (Gastrin, Galr1), epithelial barrier function (Tjp1, connexin45, Aqp5), inflammation (Icam1), apoptosis (Clu) and proliferation (Gdf3, Igf2). Treatment with NS398 alone caused differential expression of 140 genes, 97 of which were unique, indicating that these genes are regulated under conditions of basal Cox-2 expression.ConclusionThis study has identified a panel of novel Cox-2 dependent genes influenced under both normal and the inflammatory conditions induced byH. pyloriinfection. These data provide important new links between Cox-2 and inflammatory processes, epithelial repair and integrity.
Pathogenesis of swine influenza virus (Thai isolates) in weanling pigs: an experimental trial
Authors: Sreta Donruethai , Kedkovid Roongtham , Tuamsang Sophon , Kitikoon Pravina , Thanawongnuwech Roongroje 
Published: March 2009

Abstract

Background
The objective of this study is to investigate the pathogenesis of swine influenza virus (SIV) subtype H1N1 and H3N2 (Thai isolates) in 22-day-old SPF pigs.

Results
The study found that all pigs in the infected groups developed typical signs of flu-like symptoms on 1–4 days post- infection (dpi). The H1N1-infected pigs had greater lung lesion scores than those of the H3N2-infected pigs. Histopathological lesions related to swine influenza-induced lesions consisting of epithelial cells damage, airway plugging and peribronchial and perivascular mononuclear cell infiltration were present in both infected groups. Immunofluorescence and immunohistochemistry using nucleoprotein specific monoclonal antibodies revealed positive staining cells in lung sections of both infected groups at 2 and 4 dpi. Virus shedding was detected at 2 dpi from both infected groups as demonstrated by RT-PCR and virus isolation.

Conclusion
The results demonstrated that both SIV subtypes were able to induce flu-like symptoms and lung lesions in weanling pigs. However the severity of the diseases with regards to lung lesions both gross and microscopic lesions was greater in the H1N1-infected pigs. Based on phylogenetic analysis, haemagglutinin gene of subtype H1N1 from Thailand clustered with the classical H1 SIV sequences and neuraminidase gene clustered with virus of avian origin, whereas, both genes of H3N2 subtype clustered with H3N2 human-like SIV from the 1970s.
A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family
Authors: Varsani Arvind , Shepherd Dionne N , Dent Kyle , Monjane Aderito L , Rybicki Edward P , Martin Darren P 
Published: March 2009

Abstract

Background
We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera.

Results
Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses. Similarly, while ECSV has the same unusual TAAGATTCC virion strand replication origin nonanucleotide found in another recently described divergent geminivirus, Beet curly top Iran virus (BCTIV), the rest of the transcription and replication origin is structurally more similar to those found in begomoviruses and curtoviruses than it is to those found in BCTIV and mastreviruses. ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions.

Conclusion
Although it superficially resembles a chimaera of geminiviruses from different genera, the ECSV genome is not obviously recombinant, implying that the features it shares with other geminiviruses are those that were probably present within the last common ancestor of these viruses. In addition to inferring how the ancestral geminivirus genome may have looked, we use the discovery of ECSV to refine various hypotheses regarding the recombinant origins of the major geminivirus lineages.
Effects of alpha-linolenic acid vs. docosahexaenoic acid supply on the distribution of fatty acids among the rat cardiac subcellular membranes after a short- or long-term dietary exposure
Authors: Brochot Amandine , Guinot Marine , Auchere Daniel , Macaire Jean-Paul , Weill Pierre , Grynberg Alain , Rousseau-Ralliard Delphine 
Published: March 2009

Abstract

Background
Previous work showed that the functional cardiac effect of dietary alpha-linolenic acid (ALA) in rats requires a long feeding period (6 months), although a docosahexaenoic (DHA) acid-supply affects cardiac adrenergic response after 2 months. However, the total cardiac membrane n-3 polyunsaturated fatty acid (PUFA) composition remained unchanged after 2 months. This delay could be due to a specific reorganization of the different subcellular membrane PUFA profiles. This study was designed to investigate the evolution between 2 and 6 months of diet duration of the fatty acid profile in sarcolemmal (SL), mitochondrial (MI), nuclear (NU) and sarcoplasmic reticulum (SR) membrane fractions.

Methods
Male Wistar rats were randomly assigned to 3 dietary groups (n = 10/diet/period), either n-3 PUFA-free diet (CTL), or ALA or DHA-rich diets. After 2 or 6 months, the subcellular cardiac membrane fractions were separated by differential centrifugations and sucrose gradients. Each membrane profile was analysed by gas chromatography (GC) after lipid extraction.

Results
As expected the n-3 PUFA-rich diets incorporated n-3 PUFA instead of n-6 PUFA in all the subcellular fractions, which also exhibited individual specificities. The diet duration increased SFA and decreased PUFA in SL, whereas NU remained constant. The SR and MI enriched in n-3 PUFA exhibited a decreased DHA level with ageing in the DHA and CTL groups. Conversely, the n-3 PUFA level remained unchanged in the ALA group, due to a significant increase in docosapentaenoic acid (DPA). N-3 PUFA rich diets lead to a better PUFA profile in all the fractions and significantly prevent the profile modifications induced by ageing.

Conclusion
With the ALA diet the n-3 PUFA content, particularly in SR and SL kept increasing between 2 and 6 months, which may partly account for the delay to achieve the modification of adrenergic response.
Increased Peripheral Nerve Excitability and Local Nav1.8 RNA Up-Regulation in Painful Neuropathy
Authors: Thakor Devang Kashyap , Lin Audrey , Matsuka Yoshizo , Meyer Edward M , Ruangsri Supanigar , Nishimura Ichiro , Spigelman Igor 
Published: March 2009

Background Neuropathic pain caused by peripheral nerve injury is a chronic disorder that represents a significant clinical challenge because the pathological mechanisms have not been fully elucidated. Several studies have suggested the involvement of various sodium channels, including tetrodotoxin-resistant NaV1.8, in affected dorsal root ganglion (DRG) neurons. We have hypothesized that altered local expression of NaV1.8 in the peripheral axons of DRG neurons could facilitate nociceptive signal generation and propagation after neuropathic injury. Results After unilateral sciatic nerve entrapment injury in rats, compound action potential amplitudes were increased in both myelinated and unmyelinated fibers of the ipsilateral sciatic nerve. Tetrodotoxin resistance of both fiber populations and sciatic nerve NaV1.8 immunoreactivity were also increased. Further analysis of NaV1.8 distribution revealed that immunoreactivity and mRNA levels were decreased and unaffected, respectively, in the ipsilateral L4 and L5 DRG; however sciatic nerve NaV1.8 mRNA showed nearly an 11-fold ipsilateral increase. Nav1.8 mRNA observed in the sciatic nerve was likely of axonal origin since it was not detected in non-neuronal cells cultured from nerve tissue. Absence of changes in NaV1.8 mRNA polyadenylation suggests that increased mRNA stability was not responsible for the selective peripheral mRNA increase. Furthermore, mRNA levels of NaV1.3, NaV1.5, NaV1.6, NaV1.7, and NaV1.9 were not significantly different between ipsilateral and contralateral nerves. We therefore propose that selective NaV1.8 mRNA axonal transport and local up-regulation could contribute to the hyperexcitability of peripheral nerves in some neuropathic pain states. Conclusion Cuff entrapment injury resulted in significantly elevated axonal excitability and increased NaV1.8 immunoreactivity in rat sciatic nerves. The concomitant axonal accumulation of NaV1.8 mRNA may play a role in the pathogenesis of this model of neuropathic pain.
Lisdexamfetamine for Treatment of Attention-Deficit/Hyperactivity Disorder
Authors: Cowles Brian J 
Published: March 2009

Objective: To review the pharmacology, pharmacokinetics, efficacy, and safety of the prodrug lisdexamfetamine for the treatment of attention-deficit/hyperactivity disorder (ADHD) in children and adults and describe its potential place in therapy. Data Sources: Primary literature published between January 1, 1990, and August 1, 2008, was selected from PubMed using the search key words lisdexamfetamine, Vyvanse, and NRP104. References of selected publications were also reviewed. Posters and abstracts of research presented at national meetings were reviewed when available. The product labeling for Vyvanse was also used. Study Selection and Data Extraction: Preference was given to published, randomized, and controlled research describing the pharmacokinetics, efficacy, and safety of lisdexamfetamine. Noncontrolled studies, postmarketing reports, and poster presentations were considered secondly. All published studies were included. Data Synthesis: Lisdexamfetamine is a prodrug of dextroamphetamine covatently bound to Hysine, which is activated during first-pass metabolism. The unique pharmacokinetic profile owing to lisdexamfetamine's prodrug design and rate-limited enzymatic biotransformation allows for once-daily dosing with a duration of activity of approximately 12 hours. Lisdexamfetamine has been proven to reduce the symptoms of ADHD both in children aged 6–12 years and adults aged 18–55 years, decreasing ADHD rating scale scores by approximately 27 and 19 points, respectively. Adverse effects with an incidence greater than 10% during preclinical trials included appetite suppression, insomnia, and headache. Lisdexamfetamine's unique pharmacokinetic properties may provide additional safety with regard to reducing abuse potential. As with other central nervous system (CNS) stimulants, concerns regarding sudden cardiac death and adverse effects on growth also apply to lisdexamfetamine. Conclusions: Lisdexamfetamine provides another amphetamine-based CNS stimulant option for treatment of children and adults with ADHD. However, its use may be limited by a lack of significant differentiation when compared with cunently used stimulants and a lack of evidence to support its use in adolescents.
Key Principles to Guide Development of Consumer Medicine Information—Content Analysis of Information Design Texts
Authors: Raynor David K , Dickinson David 
Published: March 2009

Background: Effective written consumer medicines information is essential to support safe and effective medicine taking, but the wording and layout of currently provided materials do not meet patients' needs. Objective: To identify principles from the wider discipline of information design for use by health professionals when developing or assessing written drug information for patients. Methods: Six experts in information design nominated texts on best practice in information design applicable to consumer medicines information. A content analysis identified key principles that were tabulated to bring out key themes. Results: Six texts that met the Inclusion criteria, were Identified, and content analysis indentified 4 themes: words, type, lines, and layout. Within these main themes, there were 24 subthemes. Selected principles relating to these subthemes were: use short familiar words, short sentences, and short headings that stand out from the text; use a conversational tone of voice, addressing the reader as “you”; use a large type size while retaining sufficient white space; use bullet points to organize lists; use unjustified text (ragged right) and bold, lower-case text for emphasis. Pictures or graphics do not necessarily improve a document. Conclusions: Applying the good information design principles identified to written consumer medicines information could support health professionals when developing and assessing drug information for patients.
Cyclosporine-Induced Pain Syndrome in a Child Undergoing Hematopoietic Stem Cell Transplant
Authors: Lavoratore Sara R , Navarro Oscar M , Grunebaum Eyal , Ali Muhammad , Koo Alicia , Schechter Tal , Gassas Adam , Doyle John J , Dupuis L Lee 
Published: March 2009

Objective: To report a case of calcineurin-induced pain syndrome (CIPS) in a child undergoing his second hematopoietic stem cell transplant (HSCT). Case Summary: A 6.1-year-old child received cyclosporine and methotrexate for acute graft-versus-host disease (aGVHD) prophylaxis after his first HSCT for acute myeloblastic leukemia. Amlodipine was given for the treatment of hypertension. Symptoms of CIPS were not observed. After the second HSCT at the age of 6.7 years, the child received cyclosporine (target trough whole blood cyclosporine concentration range 150–200 μg/L). starting on day −3, and mycophenolate mofetil for aGVHD prophylaxis. With the first cyclosporine dose, the patient complained of leg pain that was most severe during the cyclosporine infusion. Analgesic agents and a change from intravenous to oral administration of cyclosporine were Ineffective In controlling the pain. Magnetic resonance imaging findings on day 10 showed periosteal soft tissue changes and mild bone marrow edema of the femora and tibiae. Tacrolimus was substituted for cyclosporine on day 20; on day 21 amlodipine was initiated to manage hypertension. Trough whole blood tacrolimus concentrations ranged from 1.7 to 6.2 μg/L. Pain was reduced in seventy by day 29 and completely resolved once tacrolimus was discontinued on day 42. In this case, CIPS was considered to be probably associated with cyclosporine according to the Naranjo probability scale. Discussion: CIPS is hypothesized to result from calcineurin-induced vascular changes that disturb bone perfusion and permeability, leading to intraosseous vasoconstriction and bone manow edema. In our patient, symptoms were most acute during the infusion, when whole blood cyclosporine concentrations were likely to be the highest. Our patient's symptoms were resolved when tacrolimus was substituted for cyclosporine and amlodipine was initiated. Conclusions: interventions aimed at reducing pain associated with CIPS may include the initiation of calcium-channel blocker therapy and conversion to an alternative calcineurin inhibitor.
Trials and trails: Do HE design students need museum learning resources?
Authors: Reynolds Rebecca , Speight Catherine 
Published: March 2009

There is a lack of collaboration between universities and museums in supporting design students' learning and a corresponding lack of targeted learning resources.
This paper focuses on the iGuides from StreetAccess project, which has involved the creation of twenty web-based trails
for design students to access on personalized digital assistants (PDAs) at the Victoria and Albert Museum. It reports initial findings from the evaluation of two trails, detailing aspects of trail design and their possible usefulness to students.
It suggests that such materials can encourage
students to develop object-based learning skills skills which design tutors may perceive as innate or best left to develop with the minimum of direction. It concludes that museums can usefully supply HE design students with guidance and suggest ways of engaging with their collections.
A Revised Contact Filter Paper Method
Authors: Power Kenton C. , Vanapalli Sai K. , Garga Vinod K. 
Published: March 2009

Abstract
The filter paper method, ASTM Standard D5298-03 is generally accepted to be an inexpensive, technically simple, and reasonably accurate method that could be used to measure a wide range of soil suction. The method, however, is dependent upon the accuracy of the calibration curve that relates filter paper water content to soil suction. Additionally, applying a contact stress to the filter papers significantly influences this calibration curve. The effect of five separate contact stresses, namely, 0, 0.4, 1, 2, and 4 kPa on the calibration curve of Whatman 42 filter paper were examined. The study demonstrates that a contact stress of 1 kPa will ensure direct contact between the filter papers and the pore-water of the test specimens without significantly altering the ASTM calibration curve. The contact filter paper method was used to measure the matric suction of compacted Indian Head till specimens over a range of 20 to 300 kPa. This range was chosen to understand the performance and sensitivity of the filter paper method in the low suction range. A comparison of published calibration equations was then undertaken to show the drastically different matric suction estimates that can be obtained by the improper selection of published calibration equations.