bluuebunny/crossref_metadata_2025_split huggingface dataset:
ENA as an Information Hub
Authors: ten Hoopen Petra , Akhtar Ruth , Gibson Richard , Vaughan Bob , Faruque Nadeem , Cochrane Guy 
Published: October 2010

AbstractThe European Nucleotide Archive (ENA; "http://www.ebi.ac.uk/ena/":http://www.ebi.ac.uk/ena/) is a comprehensive repository for public nucleotide sequence data from nearly four hundred thousand taxonomic nodes. Together with partners in the International Nucleotide Sequence Database Collaboration (INSDC; EBI, NCBI and DDBJ) we provide a broad spectrum of sequences, from raw reads (Sequence Read Archive data class), assembled contigs (Whole Genome Shotgun data class), assemblies of EST transcripts (Transcriptome Shotgun Assembly data set), to partial or complete assembled nucleic acid molecules with functional annotation derived from direct and third party experimental evidence (Standard and TPA data classes, respectively). Resources beyond ENA, such as RNA and protein databases, genome collections and model organism services, use data stored and presented at ENA as both source and underlying supporting evidence for their records. Integration of the growing wealth of molecular information is a great challenge that brings opportunities for ENA to serve as a bioinformatics data information hub, allowing, through its provision of permanent identifiers for sequence and project records, community-recognized identifiers for navigation across databases.As a comprehensive repository of directly sequenced nucleic acid molecules we have the unique opportunity to obtain exact provenance information directly from the submitting researchers. Our pre-publication biocuration efforts are focused on obtaining rich and accurate information on the sample that has been sequenced and on the methodology surrounding its preparation for sequencing. We present here an insight into data flow in the archive and a straightforward biologist-orientated submission system with a rule-based validator for smaller sets of sequences.
Structurally conserved five nucleotide bulge determines the overall topology of the core domain of human telomerase RNA
Authors: Zhang Qi , Kim Nak-Kyoon , Peterson Robert D. , Wang Zhonghua , Feigon Juli 
Published: October 2010

Telomerase is a unique ribonucleoprotein complex that catalyzes the addition of telomeric DNA repeats onto the 3′ ends of linear chromosomes. All vertebrate telomerase RNAs contain a catalytically essential core domain that includes the template and a pseudoknot with extended helical subdomains. Within these helical regions is an asymmetric 5-nt internal bulge loop (J2a/b) flanked by helices (P2a and P2b) that is highly conserved in its location but not sequence. NMR structure determination reveals that J2a/b forms a defined S-shape and creates an ∼90 ° bend with a surprisingly low twist (∼10 °) between the flanking helices. A search of RNA structures revealed only one other example of a 5-nt bulge, from hepatitis C virus internal ribosome entry site, with a different sequence but the same structure. J2a/b is intrinsically flexible but the interhelical motions across the loop are remarkably restricted. Nucleotide substitutions in J2a/b that affect the bend angle, direction, and interhelical dynamics are correlated with telomerase activity. Based on the structures of P2ab (J2a/b and flanking helices), the conserved region of the pseudoknot (P2b/P3, previously determined) and the remaining helical segment (P2a.1–J2a.1 refined using residual dipolar couplings and the modeling program MC-Sym) we have calculated an NMR-based model of the full-length pseudoknot. The model and dynamics analysis show that J2a/b serves as a dominant structural and dynamical element in defining the overall topology of the core domain, and suggest that interhelical motions in P2ab facilitate nucleotide addition along the template and template translocation.
Anxiety diagnoses in smokers seeking cessation treatment: relations with tobacco dependence, withdrawal, outcome and response to treatment
Authors: Piper Megan E. , Cook Jessica W. , Schlam Tanya R. , Jorenby Douglas E. , Baker Timothy B. 
Published: October 2010

ABSTRACTAims  To understand the relations among anxiety disorders and tobacco dependence, withdrawal symptoms, response to smoking cessation pharmacotherapy and ability to quit smoking.Design  Randomized placebo‐controlled clinical trial. Participants received six 10‐minute individual counseling sessions and either: placebo, bupropion SR, nicotine patch, nicotine lozenge, bupropion SR + nicotine lozenge or nicotine patch + nicotine lozenge.Setting  Two urban research sites.Participants  Data were collected from 1504 daily smokers (>9 cigarettes per day) who were motivated to quit smoking and did not report current diagnoses of schizophrenia or psychosis or bupropion use.Measurements  Participants completed baseline assessments, the Composite International Diagnostic Interview and ecological momentary assessments for 2 weeks.Findings  A structured clinical interview identified participants who ever met criteria for a panic attack (n = 455), social anxiety (n = 199) or generalized anxiety disorder (n = 99), and those who qualified for no anxiety diagnosis (n = 891). Smokers with anxiety disorders reported higher levels of nicotine dependence and pre‐quit withdrawal symptoms. Those ever meeting criteria for panic attacks or social anxiety disorder showed greater quit‐day negative affect. Smokers ever meeting criteria for anxiety disorders were less likely to be abstinent at 8 weeks and 6 months post‐quit and showed no benefit from single‐agent or combination‐agent pharmacotherapies.Conclusions  Anxiety diagnoses were common among treatment‐seeking smokers and were related to increased motivation to smoke, elevated withdrawal, lack of response to pharmacotherapy and impaired ability to quit smoking. These findings could guide treatment assignment algorithms and treatment development for smokers with anxiety diagnoses.
Randomised clinical trial: the effects of perioperative probiotic treatment on barrier function and post‐operative infectious complications in colorectal cancer surgery – a double‐blind study
Authors: Liu Z. , Qin H. , Yang Z. , Xia Y. , Liu W. , Yang J. , Jiang Y. , Zhang H. , Yang Z. , Wang Y. , Zheng Q. 
Published: October 2010

Aliment Pharmacol Ther 2011; 33: 50–63SummaryBackground  Infection following abdominal operation remains a major factor affecting the morbidity of patients after surgery.Aim  To determine the effects of perioperative administration of probiotics on the gut barrier function and the surgical outcome in patients undergoing elective colorectal surgery.Methods  One hundred patients with colorectal carcinoma were randomly divided into the control group (n = 50) and the probiotics group (n = 50). The probiotics were given orally for 6 days preoperatively and 10 days post‐operatively. Outcomes were measured by bacterial translocation, gut permeability, the effect on the faecal microbiota, and the clinical outcomes such as infectious‐related complications and gut defecation function.Results  Compared with the control group, probiotics group had increased transepithelial resistance (P < 0.05), reduced transmucosal permeation of horseradish peroxidase and lactulose/mannitol ratio, reduced bacterial translocation (P < 0.05), decreased ileal‐bile acid binding protein (P < 0.05) and positive rate of blood bacterial DNA (P < 0.05) and an enhanced mucosal tight junction protein expression. They had decreased blood enteropathogenic bacteria and increased faecal bacterial variety. The post‐operative recovery of peristalsis, incidence of diarrhoea, and infectious‐related complications were also improved.Conclusion  Probiotics can improve the integrity of gut mucosal barrier by benefiting the faecal microbiota, and decreasing infectious complications in patients with colorectal cancer undergoing colorectomy.
The effects of increasing doses of MK‐467, a peripheral alpha2‐adrenergic receptor antagonist, on the cardiopulmonary effects of intravenous dexmedetomidine in conscious dogs
Authors: HONKAVAARA J. M. , RESTITUTTI F. , RAEKALLIO M. R. , KUUSELA E. K. , VAINIO O. M. 
Published: October 2010

Honkavaara, J. M., Restitutti, F., Raekallio, M. R., Kuusela, E. K., Vainio, O. M. The effects of increasing doses of MK‐467, a peripheral alpha2‐adrenergic receptor antagonist, on the cardiopulmonary effects of intravenous dexmedetomidine in conscious dogs.J. vet. Pharmacol. Therap.34, 332–337.Different doses of MK‐467, a peripheral alpha2‐adrenergic receptor antagonist, with or without dexmedetomidine were compared in conscious dogs. Eight animals received either dexmedetomidine (10 μg/kg [D]), MK‐467 (250 μg/kg [M250] or dexmedetomidine (10 μg/kg) with increasing doses of MK‐467 (250 μg/kg [DM250], 500 μg/kg [DM500] and 750 μg/kg [DM750], respectively). Treatments were given intravenously (i.v.) in a randomized, crossover design with a 14‐day washout period. Systemic hemodynamics and arterial blood gas analyses were recorded at baseline and at intervals up to 90 min after drugs administration. Dexmedetomidine alone decreased heart rate, cardiac index and tissue oxygen delivery and increased mean arterial pressure and systemic vascular resistance 5 min after administration. DM250 did not completely prevent these early effects, while DM750 induced a decrease in mean arterial pressure. With DM500, systemic hemodynamics remained stable throughout the observational period. MK‐467 alone increased cardiac index and tissue oxygen delivery and had no deleterious adverse effects. No differences in arterial blood gases were observed between treatments that included dexmedetomidine. It was concluded that MK‐467 attenuated or prevented dexmedetomidine’s systemic hemodynamic effects in a dose‐dependent manner when given simultaneously i.v. but had no effect on the pulmonary outcome in conscious dogs. A 50:1 dose ratio (MK‐467:dexmedetomidine) induced the least alterations in cardiovascular function.
The change in the rate of vaginal birth after caesarean section
Authors: Grobman William A. , Lai Yinglei , Landon Mark B. , Spong Catherine Y. , Rouse Dwight J. , Varner Michael W. , Caritis Steve N. , Harper Margaret , Wapner Ronald J. , Sorokin Yoram 
Published: October 2010

SummaryGrobman WA, Lai Y, Landon MB, Spong CY, Rouse DJ, Varner MW, Caritis SN, Harper M, Wapner RJ, Sorokin Y. The change in the rate of vaginal birth after caesarean section. Paediatric and Perinatal Epidemiology 2010.The objective of this study was to determine whether, and to what degree, the change in the vaginal birth after caesarean section (VBAC) rate is due to a change in the characteristics of the obstetric population, the undertaking of a trial of labour (TOL), or the tendency to abandon a TOL once it has been initiated. All women with one prior low transverse caesarean section (CS) and a vertex singleton gestation at term were identified in a registry of CS deliveries occurring at eight academic centres during a 4‐year period (1999–2002). Women were classified by their predicted chance of VBAC and year‐to‐year differences were analysed. Of the 9643 women who met criteria for analysis, 5334 (55.3%) underwent a TOL. From 1999 to 2002, the VBAC rate underwent a steady decline: 51.8% to 45.1% to 37.4% to 29.8% (P < 0.001). Although there were some changes in the characteristics of the population that predispose to successful VBAC, as well as some reduction in the chance that a VBAC is successful once a TOL is undertaken, the most pervasive reason for this decline was that women became increasingly likely to forego a TOL, regardless of their likelihood of vaginal delivery. Based on these results, it appears that the change over time in the VBAC rate is multifactorial, although the greatest change has been a decrease in the frequency with which women undertake a TOL, and this change is observed in all categories of the chance of a successful TOL.
The association of circulating 25‐hydroxyvitamin D and calcium with cognitive performance in adolescents: cross‐sectional study using data from the third National Health and Nutrition Examination Survey
Authors: Tolppanen Anna‐Maija , Williams Dylan , Lawlor Debbie A. 
Published: October 2010

SummaryTolppanen A‐M, Williams D, Lawlor DA. The association of circulating 25‐hydroxyvitamin D and calcium with cognitive performance in adolescents: cross‐sectional study using data from the third National Health and Nutrition Examination Survey. Paediatric and Perinatal Epidemiology 2010.Studies in middle‐ and older‐aged adults have shown positive associations between serum levels of 25‐hydroxyvitamin D [25(OH)D] and cognitive function. Higher serum calcium levels have been associated with greater cognitive decline in older adults. There have been relatively few studies of the associations of 25(OH)D and calcium with cognitive function in adolescents. We investigated the cross sectional association between circulating levels of 25(OH)D and pH‐normalised calcium with different domains of cognitive function (block design and digit span components from Wechsler Intelligence Scale for Children‐revised and reading and mathematics subtests of Wide‐range Achievement Test‐revised) in adolescents (age 12–16.9 years) of the third National Health and Nutrition Examination Survey (NHANES III).Serum 25(OH)D was positively associated with performance in all four cognitive tests (e.g. 1standard deviation (SD) change in digit span score per 1SD in 25(OH)D was 0.10 [95% confidence interval 0.03, 0.16]), but the association was attenuated to the null after adjusting for ethnicity/race and language used in test (1SD change in digit span per 1SD in 25(OH)D after adjusting for self‐reported race/ethnicity and language used in test was 0.01[−0.06, 0.09]). pH‐normalised calcium levels were not associated with any of the cognitive domains and adjustment for serum calcium levels did not alter the association between 25(OH)D and cognitive function. Thus, we found no evidence that the serum levels of 25(OH)D or calcium were associated with cognitive function in adolescents. A positive association of 25(OH)D with cognitive function was completely explained by confounding due to race/ethnicity.
Comparison of genetic variation and differentiation using microsatellite markers among three rare threatened and one widespread toad lily species of Tricyrtis section Flavae (Convallariaceae) in Japan
Authors: TAKAHASHI YASUHIRO , TAKAHASHI HIROSHI , MAKI MASAYUKI 
Published: October 2010

AbstractGenetic diversities were examined using six microsatellite markers amplifiable in three rare and one widespread species of Tricyrtis section Flavae, which are endemic to Japan. Contrary to a general expectation, the three rare species, Tricyrtis flava, Tricyrtis ohsumiensis and Tricyrtis perfoliata, have comparable genetic variation at the species level to that of the widespread Tricyrtis nana. This is probably because T. nana has not sufficiently recovered genetic diversity from the bottleneck at speciation or because recent range contractions have occurred in the three rare species. Genetic diversity at the population level was smaller in the putative selfing species T. nana than in the other three outcrossing species. Compared with a preceding study using allozyme markers, the genetic diversity in microsatellite loci was considerably larger, probably resulting from higher mutation rates at the microsatellite loci. Owing to the high genetic diversity of the microsatellite markers, genetic differentiation among populations could be estimated even in T. nana with little allozyme polymorphism.
Clarification of the genetic component of hybrids betweenPhyllodoce caeruleaandPhyllodoce aleutica(Ericaceae) in Hokkaido, northern Japan
Authors: KAMEYAMA YOSHIAKI , KUDO GAKU 
Published: October 2010

AbstractNatural hybridization provides great opportunities to understand the interaction of genetics and ecology in determining species boundaries. We examined the genetic relationships ofPhyllodocetaxa and revealed that most hybrids were fertile F1s and an extremely small number of backcross and no F2plants were established in natural conditions. Because this trend was irrespective of regions, we conclude that negative endogenous selection may act after the germination of F1seeds and prevent the establishment of later‐generation hybrids. Based on these results, we discuss the ecological and evolutionary significance of natural hybridization inPhyllodocetaxa.
Tissue engineering and stem cells: Basic principles and applications in urology
Authors: Shokeir Ahmed A , Harraz Ahmed M , El‐Din Ahmed B Shehab 
Published: October 2010

AbstractTo overcome problems of damaged urinary tract tissues and complications of current procedures, tissue engineering (TE) techniques and stem cell (SC) research have achieved great progress. Although diversity of techniques is used, urologists should know the basics. We carried out a literature review regarding the basic principles and applications of TE and SC technologies in the genitourinary tract. We carried out MEDLINE/PubMed searches for English articles until March 2010 using a combination of the following keywords: bladder, erectile dysfunction, kidney, prostate, Peyronie's disease, stem cells, stress urinary incontinence, testis, tissue engineering, ureter, urethra and urinary tract. Retrieved abstracts were checked, and full versions of relevant articles were obtained. Scientists have achieved great advances in basic science research. This is obvious by the tremendous increase in the number of publications. We divided this review in two topics; the first discusses basic science principles of TE and SC, whereas the second part delineates current clinical applications and advances in urological literature. TE and SC applications represent an alternative resource for treating complicated urological diseases. Despite the paucity of clinical trials, the promising results of animal models and continuous work represents the hope of treating various urological disorders with this technology.
Repair of blowout orbital floor fracture by periosteal suturing
Authors: Noda Mika , Noda Kousuke , Ideta Shinji , Nakamura Yasuhisa , Ishida Susumu , Inoue Makoto , Tsubota Kazuo 
Published: October 2010

AbstractThe study objective was to evaluate the outcome of a periosteal suturing technique in eyes with orbital blowout fractures. Fifteen orbital floor fractures were classified into: type 1, linear fracture; type 2, middle fracture; and type 3, posterior fracture extending two‐thirds into the orbit. The feasibility of periosteal suturing without silicone plates or one of minimal size was determined. The improvement of ocular movements and surgical complications were evaluated. A complete suture of the torn periosteum without implanting a silicone plate was achieved in 2/2 (100%) type 1 cases, 5/7 (71%) type 2 cases and 0/6 (0%) type 3 cases. A partial fixation was achieved in 3/6 (50%) type 3 cases with an implantation of a silicone plate of approximate one‐third of the usual size in one case. Conventional surgery with silicone plates after failed periosteal suture was required in 2/7 (29%) type 2 cases and 3/6 (50%) type 3 cases. Eye movements were improved postoperatively in all eyes, and a complete range of eye movements was achieved in 6/7 (86%) cases with complete periosteal closure, 1/3 (33%) of cases with partial closure and 2/5 (40%) cases without closure. In conclusion, periosteal suturing can minimize the need for silicone plates especially for anterior or middle orbital floor factures.
Prospective randomized trial of three different methods of nephrostomy tract closure after percutaneous nephrolithotripsy
Authors: Li Roger , Louie Michael K. , Lee Hak J. , Osann Kathryn , Pick Donald L. , Santos Rosanne , McDougall Elspeth M. , Clayman Ralph V. 
Published: October 2010

Study Type – Therapy (RCT)  Level of Evidence 1bWhat's known on the subject? and What does the study add?Percutaneous nephrolithotripsy is a common procedure throughout the world, but the optimal technique for closure of the percutaneous tract is unknown. This is important for two reasons, the first is that the access tract may bleed after removal of the instruments and access sheath, the second is that several randomized studies have shown improved patient comfort by not having any nephrostomy tubes after the procedure. Our study is the first to compare three common methods of access tract closure in a randomized study.OBJECTIVE
To evaluate the safety and efficacy of ‘tubeless’ nephrostomy tract closure in reducing postoperative morbidity after percutaneous nephrolithotomy (PCNL).
MATERIALS AND METHODS
In all, 31 patients undergoing PCNL were randomized into three groups, each with a different method of nephrostomy tract closure: using either a gelatin matrix haemostatic sealant (FloSeal), fascial stitch or Cope loop nephrostomy tube.
We compared operative time, estimated blood loss (EBL), postoperative stay, analgaesics use, changes in creatinine and haemoglobin levels, and stone clearance rate, as well as postoperative short‐form (SF)‐36 quality‐of‐life and pain analogue scores at five different time points after surgery.
All data were analysed using a one‐way anova test.
A repeated measures anova test was used selectively to assess the progression of SF‐36 and pain analogue scores.
RESULTS
The preoperative variables operative time, EBL, postoperative stay (P= 0.45), analgaesia use (P= 0.79), changes in creatinine (P= 0.28) and haemoglobin (P= 0.09) levels, and postoperative SF‐36 scores were not significantly different.
In contrast, the differences in analogue pain scales at 1 week after surgery (P= 0.02) and the trends of analogue pain score progression (P= 0.03) were statistically significant.
Three patients underwent second‐look procedures for residual stones and there was one case of postoperative pyelonephritis in a multiple sclerosis patient.
CONCLUSIONS
The Cope loop closure patients recovered fastest, while FloSeal closure patients experienced initial increase in pain followed by resolution at 1 month.
As a result of the small study group sizes, it is difficult to show any significant difference in postoperative pain, especially in long‐term follow‐up; further clinical evaluation is necessary.
Suppression of hippocampal epileptic seizures in the kainate rat by Poisson distributed stimulation
Authors: Wyckhuys Tine , Boon Paul , Raedt Robrecht , Van Nieuwenhuyse Bregt , Vonck Kristl , Wadman Wytse 
Published: October 2010

SummaryPurpose:  Hippocampal deep brain stimulation (DBS) is an experimental therapy for patients with pharmacoresistant temporal lobe epilepsy (TLE). Despite the successful clinical application of DBS, the optimal stimulation parameters are undetermined. We evaluate the efficacy of a new form of DBS, using continuous stimuli with Poisson distributed intervals (Poisson distributed stimulation, PDS) in the kainate (KA) rat model, a validated model for human TLE.Methods:  Status epilepticus was elicited by injection of KA (i.p.). After development of spontaneous seizures, rats were implanted with hippocampal DBS‐ and depth electroencephalography (EEG) electrodes. After baseline EEG monitoring, one group of rats (n = 13) was treated with PDS and a second (n = 11) received regular high frequency stimulation (HFS) at 130 Hz. Stimulation intensity was 100 μA below the threshold for induction of epileptiform EEG activity.Results:  Stimulation intensity was significantly lower for PDS (156 ± 20 μA) than HFS (207 ± 23 μA; p < 0.02). Seven (54%) of 13 rats treated with PDS and 5 (45%) of 11 rats treated with HFS experienced a significant reduction in seizure frequency. In PDS‐improved rats, seizure frequency was reduced to 33% (p < 0.01) of baseline value and in HFS‐improved rats to 50% (p < 0.01). After termination of PDS, seizure rate returned to baseline value.Discussion:  Continuous hippocampal PDS significantly reduces the number of spontaneous seizures. Compared to regular HFS, there is a slightly larger number of improved rats and a larger efficacy at a considerably lower stimulus intensity. The first two observations leave room for optimization, whereas a lower intensity is beneficial for battery life.