bluuebunny/crossref_metadata_2025 huggingface dataset:
Biophysical Effects Of Ion Concenteration On The Affinity Between Nanopore, OmpF Lumen and Passing Nucleotide
Authors: Hadi Saeid , Mobasheri Hamid
Published: October 2010

OmpF an outer-membrane porin channel of E. Coli posses beta-barrel structure, whose conductivity and gating phenomena are affected by changes in pH, salt concentration and so on. The distribution of amino acids in OmpF induces a non homologous electric potential in channel lumen. The intrinsic charge distribution caused be amino acid may be affected by lipid bilayer, extra and intra cellular ion concentration, and other physico-chemical condition of environment including, pH, temperature, polyelectrolytes etc. Nucleotides are considered as one of most important metabolite in the cell that have pass through membrane whenever necessary. The experimental study of translocation of such a molecules through channels have provided invaluable information However, due to the instrument limitation in monitoring ontime submolecular motions occurring during the translocation, theoretical studies attractive, modeling and simulation are inevitable. In this study we calculated the changes in the affinity of OmpF towards pyrimidin at molecular level within channel lumen by Delphi 4, and monitored by VMD 1.8.5. A non-linear Poisson-Boltzmann calculator with definite element integrator found to be appropriate choice to calculate the net energy of OmpF nucleotide interactions at different ion concentration. Our results indicate that upon increasing the ion concentration the OmpF affinity to pyrimidin decreases along the channel axis showing a minimum at the inner mouth of the channel. These observations shed lights to understand the selective molecular translocation means involved in the OmpF.
Octanol/water distribution coefficients of the C~1~ through C~7~ perfluoro-n-alkyl sulfonates: Comparison of the IEFPCM-UFF, CPCM, and SMD solvation models
Authors: Rayne Sierra , Forest Kaya
Published: October 2010

The octanol/water distribution coefficients (log D~ow~) of the C~1~ through C~7~ perfluoro-n-alkyl sulfonates (PFSAs) were calculated using the M062X/6-311++G(d,p) and MP2/6-311++G(d,p)//M062X/6-311++G(d,p) levels of theory and the IEFPCM-UFF, CPCM, and SMD solvation models. At both levels of theory with all solvation models, absolute log D~ow~ calculated for the straight chain C~1~ through C~7~ PFSAs display a substantial negative bias against available experimental data and expected trends by several log units. However, the SMD solvation model achieves accurate relative log D~ow~ accuracy, yielding fragmental contributions of a -CF~2~- group towards the log D~ow~ of 0.51+/-0.02 to 0.54+/-0.01 units (-3.0+/-0.1 to -3.1+/-0.1 kJ/mol), in good agreement with the experimental value of 0.61 units (-3.4+/-0.1 kJ/mol). In contrast, the IEFPCM-UFF and CPCM solvation models exhibit either invariant log D~ow~ with increasing perfluoro-n-alkyl chain length (CPCM) or a modestly decreasing trend (IEFPCM-UFF).
neXtProt, a new knowledgebase on human proteins
Authors: Lane Lydie
Published: October 2010

In September 2008, the UniProt/Swiss-Prot group achieved a major milestone: the first complete manual annotation of what is believed to be the full set of human proteins (derived from ~20'300 genes). This corpus of data is already quite rich in information pertinent to modern biomolecular medical research, but made us realize how large is the gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions, subcellular locations, etc). This gap resides not only in the available experimental information, but also in the way this information has been stored, which is far from being sufficient to help researchers making sense of what all these human proteins do in our bodies! Therefore, in the framework of CALIPHO, a new interdisciplinary group from the University of Geneva and the SIB, we are developing neXtProt, a human-centric protein knowledge resource.We aim to help researchers answer pertinent questions relevant to human proteins. This requires answering three different challenges: 1) Add to the corpus of data on human proteins that is already in Swiss-Prot, a lot of additional information. We will import in neXtProt data originating from a variety of highthroughput approaches such as proteomics, microarray, antibodies, siRNAs, interactomics, etc. All of these data sets must be carefully selected so as to only provide high-quality data as we want to avoid creating a noisy and dirty compendium.2) Organize the data in such a way that it is possible to make powerful queries in the most user-friendly environment. Here also, it is necessary to be able to capture the complexity and the heterogeneity of the data that will be available in neXtProt, yet make it easy for the user to forget this complexity!3) Build a software platform that will allows tools ranging from sequence analysis to text and data mining to be integrated in various research environments so as to answer specific needs of academic and industrial users.Finally, we also aim in enabling researchers to collaborate and share data and ideas through the use of the neXtProt platform. neXtProt is a common development of the SIB and of GeneBio SA. We hope you will enjoy working with it and will help us making it evolve by telling us of your specific needs.
Functional annotation of bacterial sugars
Authors: Lisacek Frederique
Published: October 2010

Glyco-bioinformatics means different things to different people. It ranges, for example, from the mining of the genome for glycosylation pathway enzymes, through to analysis of microarray expression of glycosyltransferases, to glycoprotein identification data, to the development of tools that facilitate the interpretation of mass spectra and to the construction of structural glycan databases. Lastly, these data need to be mined so that the function of the glycan structures attached to the range of glycoconjugates in nature can be determined. The quality of the data in these databases needs to be maintained for this work to be meaningful.For easier analysis, glycan structures are often characterised independent of the protein on which these sugars were originally attached. GlycosuiteDB ("http://glycosuitedb.expasy.org/glycosuite/glycodb":http://glycosuitedb.expasy.org/glycosuite/glycodb) is a freely accessible resource that has annotated this glycan structural data with protein and tissue information that sets the basis of functional interpretation. Information on cellular interactions associated with changes in glycosylation structures is essential for the understanding of the functional role of sugars and needs to be collected in order to exploit the knowledge of these posttranslational additions to proteins. One such database is SugarBind ("http://sugarbind.expasy.org/sugarbind":http://sugarbind.expasy.org/sugarbind), which collates the known glycan binding sites of human pathogens. These structural glycan epitopes occur on both proteins and lipids and will add to the knowledgebase of glycosylation function and expand the structural data contained in GlycoSuiteDB. In this presentation, the knowledge obtained on the function of glycosylation by linking the information between two databases will be highlighted as an example of the value to be gained from manual curation of literature-extracted knowledge.
ENA as an Information Hub
Authors: ten Hoopen Petra , Akhtar Ruth , Gibson Richard , Vaughan Bob , Faruque Nadeem , Cochrane Guy
Published: October 2010

The 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.
Time‐course changes in arteriolar and venular portions of capillary in young treadmill‐trained rats
Authors: Suzuki J. , Kobayashi T. , Uruma T. , Koyama T.
Published: October 2010

This study was designed to examine the time‐course changes in capillarity, especially the distribution of arteriolar and venular capillaries, in skeletal muscles during endurance training by running in young female Wistar rats. Exercise training by running started at the age of 5 weeks and lasted for 5 weeks at 25 m min–1 on a 25% gradient, 10–60 min day–1, 5 days per week. Morphological findings were obtained from the soleus (SOL) and deep portions of the medial gastrocnemius (GASd) muscles. In SOL, the training significantly increased the capillary‐to‐fibre ratio (C:F), total capillary density, and density of venular capillaries at Week 1. Significant increases in the C:F and total capillary density were also observed at Weeks 4 and 5. The capillary domain area (CDA) values for total capillary and arteriolar and venular capillaries were significantly decreased after 4 weeks of training. In GASd, the training significantly increased the C:F at Week 1 and from Week 3 onwards. It also significantly increased cross‐sectional area of all fibre types. Total capillary density and the CDA values showed no significant difference between control and training groups at all points of time. Significant increases in succinate dehydrogenase (SDH) activity were first noted after 2 weeks in GASd and after 3 weeks in SOL. These findings suggest that, in young growing rats, adaptive changes in the oxygen transport system occurred within 1 week after the onset of training mainly in highly oxidative muscles. The changes in arteriolar and venular capillary densities may help to clarify the growth pattern of the capillary network associated with endurance running training.
Rate‐dependent electrical, contractile and restitution properties of isolated left ventricular myocytes in guinea‐pig hypertrophy
Authors: Davey P. , Bryant S. , Hart G.
Published: October 2010

Left ventricular hypertrophy predisposes to sudden cardiac death (SCD) and studies of human SCD suggest that the antecedent heart rate (HR) is usually <100 beats min–1. This is surprising in view of the known association between adrenergic receptor stimulation and SCD which by itself would suggest that it is more likely to occur from high rather than low HR. We therefore hypothesized that there may be electrical or mechanical abnormalities present in myocytes isolated from animals with left ventricular hypertrophy that predispose to SCD at low stimulation frequencies but which may not be present at high HR. Mild left ventricular hypertrophy was induced in guinea‐pigs by infra‐renal aortic banding. Electrical and mechanical properties of isolated myocytes were studied at different stimulation frequencies between 0.1 and 3 Hz. Action potential duration (APD) is prolonged in hypertrophy at stimulation frequencies <1 Hz but not at faster rates. Contraction size, time‐to‐peak contraction (TTPC) and half‐relaxation time are greatly enhanced in hypertrophy at all frequencies between 0.1 and 3 Hz. Electrical (50.3 ± 5.2 ms in hypertrophy and 78.4 ± 12.1 ms in control, P < 0.03) and mechanical (205 ± 16 ms for hypertrophy and 266 ± 24 ms for control cells, P < 0.03) restitution time constants are quicker in hypertrophy. The finding of APD prolongation at low but not at high frequencies is consistent with the finding that SCD arises from low and not high HR. This data supports the role of abnormal repolarization in SCD.
Effects of losartan, prazosin and a vasopressin V1‐receptor antagonist on renal and femoral blood flow in conscious sheep
Authors: Ullman J. , Eriksson S. , Rundgren M.
Published: October 2010

The regulation of blood flow to different organs is determined by the autonomic nervous system and systemic and/or local vasoactive substances. Although the cardiovascular effects of the renin‐angiotensin system (RAS), the sympathoadrenal system and vasopressin (AVP) have been thoroughly studied, there are relatively few investigations on these systems with concomitant measurements of systemic haemodynamics and regional blood flow in conscious unstressed individuals. We therefore studied effects of pharmacological blockade of AVP V1‐, angiotensin II (ANG II) AT1‐and adrenergic α‐receptors on central and regional (renal and femoral blood flow) haemodynamics in adult conscious ewes. Eight adult cross‐bred ewes were chronically intrumented with peri‐vascular ultrasonic flow probes implanted unilaterally around the renal and the femoral artery. While standing in their habitual environment, systemic and regional haemodynamics were measured before and after the following treatments as single intravenous injections. Animals in group A (n=6) were given isotonic saline (NaCl) followed by the AT1‐receptor blocker losartan (LOS, 10 mg kg–1) 30 min later; group B (n=6) animals were given the α‐adrenoceptor blocker prazosin (PRAZ, 0.2 mg kg–1); and group C (n=6) the vasopressin V1 receptor antagonist [d(CH2)5Tyr(Me)AVP] (AVP‐a, 10 μg kg–1). PRAZ reduced mean arterial pressure (MAP) by 11% concomitant with an increase in heart rate (HR) (32%), whereas the other substances where without effect on those variables. Femoral blood flow (FBF) was enhanced (increased by 82%) by injection of PRAZ only. Administration of LOS increased the renal blood flow (RBF) by 11% while the other drugs were without effect on that parameter. We conclude that basal renal vascular tone in conscious unstressed sheep is dependent on angiotensinergic mechanism and that blockade of this influence causes a local increase in flow without concomitant effects on systemic haemodynamics.
Changes in electromyographic activity, muscle fibre and force production characteristics during heavy resistance/power strength training in middle‐aged and older men and women
Authors: Häkkinen K. , Kraemer W. J. , Newton R. U. , Alen M.
Published: October 2010

The effects of a 6‐month resistance training (2 day/week) designed to develop both strength and power on neural activation by electromyographic activity (EMG) of the agonist and antagonist knee extensors, muscle fibre proportion and areas of type I, IIa, and IIb of the vastus lateralis (VL) as well as maximal concentric one repetition maximum (1 RM) strength and maximal and explosive isometric strength of the knee extensors were examined. A total of 10 middle‐aged men (M40; 42 ± 2), 11 middle‐aged women (W40; 39 ± 3), 11 elderly men (M70; 72 ± 3) and 10 elderly women (W70; 67 ± 3) served as subjects. Maximal and explosive strength values remained unaltered during a 1‐month control period. After the 6‐month training maximal isometric and 1RM strength values increased in M40 by 28 ± 14 and 27 ± 7% (P < 0.001), in M70 by 27 ± 17 and 21 ± 9% (P < 0.001), in W40 by 27 ± 19 and 35 ± 14% (P < 0.001) and in W70 by 26 ± 14 and 31 ± 14% (P < 0.001), respectively. Explosive strength improved in M40 by 21 ± 41% (P < 0.05), in M70 by 21 ± 24% (P < 0.05), in W40 by 32 ± 45% (NS) and in W70 by 22 ± 28% (P < 0.05). The iEMGs of the VL and vastus medialis (VM) muscles increased during the training in M40 (P < 0.001 and 0.05), in M70 (P < 0.001 and 0.05), in W40 (P < 0.001 and 0.05) and in W70 (P < 0.001 and 0.05). The antagonist biceps femoris (BF) activity during the isometric knee extension remained unaltered in M40, in W40, and in M70 but decreased in W70 (from 42 ± 34 to 32 ± 26%; P < 0.05) during the first 2 months of training. Significant increases occurred during the training in the mean fibre areas of type I in W70 (P < 0.05) and of overall type II along with a specific increase in IIa in both W40 (P < 0.05) and in W70 (P < 0.05), while the changes in the male groups were not statistically significant. The individual percentage values for type II fibres at pretraining correlated with the individual values for 1 RM strength in both W70 (r=0.80; P < 0.05) and M70 (r=0.61; P < 0.05) and also at post‐training for maximal isometric torque in W70 (r=0.77, P < 0.05). The findings support the concept of the important role of neural adaptations in strength and power development in middle‐aged and older men and women. The muscle fibre distribution (percentage type II fibres) seems to be an important contributor on muscle strength in older people, especially older women. Women of both age groups appear to be hypertrophically responsive to the total body strength training protocol performed two times a week including heavier and lower (for fast movements) loads designed for both maximal strength and power development, while such a programme has limited effects on muscle hypertrophy in men.
Effects of hypovolaemia on acid‐induced duodenal mucosal damage in the rat
Authors: Johansson B. , Casselbrant A. , Holm M. , Von Bothmer C. , Johansson B. R. , Fändriks L.
Published: October 2010

Modest acute hypovolaemia in rats markedly decreases the duodenal mucosal alkaline secretion via neurohumoral links. The present study was undertaken to investigate if such a procedure influences the morphological changes observed following an acid challenge of the duodenal mucosa. Experiments were performed on anaesthetized male Sprague–Dawley rats. HCl (10 or 100 mM) was infused during 15 min into the duodenum via a luminally situated catheter. Time controls were compared with animals bled 10% of total blood volume. Mucosal damage was evaluated by light microscopic morphometry on transverse sections and by scanning electron microscopy of the luminal surface. Perfusion with either 10 mM or 100 mM HCl reduced villus length by about 30%. The villus area was unaffected by 10 mM HCl, but was reduced significantly by 10% by 100 mM HCl as compared with NaCl time controls. Hypovolaemia did not influence the morphometrical changes induced by 10 mM HCl but reduced significantly both villus length (–28%) and villus area (–10%) as compared with the unbled 100 mM HCl group. Scanning electrone microscopy (SEM)‐based visual damage score was not influenced by the hypovolaemia procedure in any of the acidities. Morphological changes of the duodenal mucosa, induced by moderate intra‐luminal acidity (10 mM HCl), is not influenced by hypovolaemia. However, at higher acidities (100 mM HCl) the hypovolaemia contributes to more severe mucosal damage.
Fossilized glycolipids reveal past oceanic N
2
fixation by heterocystous cyanobacteria
Authors: Bauersachs Thorsten , Speelman Eveline N. , Hopmans Ellen C. , Reichart Gert-Jan , Schouten Stefan , Damsté Jaap S. Sinninghe
Published: October 2010

N
2
-fixing cyanobacteria play an essential role in sustaining primary productivity in contemporary oceans and freshwater systems. However, the significance of N
2
-fixing cyanobacteria in past nitrogen cycling is difficult to establish as their preservation potential is relatively poor and specific biological markers are presently lacking. Heterocystous N
2
-fixing cyanobacteria synthesize unique long-chain glycolipids in the cell envelope covering the heterocyst cell to protect the oxygen-sensitive nitrogenase enzyme. We found that these heterocyst glycolipids are remarkably well preserved in (ancient) lacustrine and marine sediments, unambiguously indicating the (past) presence of N
2
-fixing heterocystous cyanobacteria. Analysis of Pleistocene sediments of the eastern Mediterranean Sea showed that heterocystous cyanobacteria, likely as epiphytes in symbiosis with planktonic diatoms, were particularly abundant during deposition of sapropels. Eocene Arctic Ocean sediments deposited at a time of large
Azolla
blooms contained glycolipids typical for heterocystous cyanobacteria presently living in symbiosis with the freshwater fern
Azolla
, indicating that this symbiosis already existed in that time. Our study thus suggests that heterocystous cyanobacteria played a major role in adding “new” fixed nitrogen to surface waters in past stratified oceans.
Klotho is associated with VEGF receptor-2 and the transient receptor potential canonical-1 Ca
2+
channel to maintain endothelial integrity
Authors: Kusaba Tetsuro , Okigaki Mitsuhiko , Matui Akihiro , Murakami Manabu , Ishikawa Kazuhiko , Kimura Taikou , Sonomura Kazuhiro , Adachi Yasushi , Shibuya Masabumi , Shirayama Takeshi , Tanda Shuji , Hatta Tsuguru , Sasaki Susumu , Mori Yasukiyo , Matsubara Hiroaki
Published: October 2010

Klotho is a circulating protein, and Klotho deficiency disturbs endothelial integrity, but the molecular mechanism is not fully clarified. We report that vascular endothelium in Klotho-deficient mice showed hyperpermeability with increased apoptosis and down-regulation of vascular endothelial (VE)-cadherin because of an increase in VEGF-mediated internal calcium concentration ([Ca
2+
]i) influx and hyperactivation of Ca
2+
-dependent proteases. Immunohistochemical analysis, the pull-down assay using Klotho-fixed agarose, and FRET confocal imaging confirmed that Klotho protein binds directly to VEGF receptor 2 (VEGFR-2) and endothelial, transient-receptor potential canonical Ca
2+
channel 1 (TRPC-1) and strengthens the association to promote their cointernalization. An in vitro mutagenesis study revealed that the second hydrolase domain of Klotho interacts with sixth and seventh Ig domains of VEGFR-2 and the third extracellular loop of TRPC-1. In Klotho-deficient endothelial cells, VEGF-mediated internalization of the VEGFR-2/TRPC-1 complex was impaired, and surface TRPC-1 expression increased 2.2-fold; these effects were reversed by supplementation of Klotho protein. VEGF-mediated elevation of [Ca
2+
]i was sustained at higher levels in an extracellular Ca
2+
-dependent manner, and normalization of TRCP-1 expression restored the abnormal [Ca
2+
]i handling. These findings provide evidence that Klotho protein is associated with VEGFR-2/TRPC-1 in causing cointernalization, thus regulating TRPC-1–mediated Ca
2+
entry to maintain endothelial integrity.
Epigenetic regulation of promiscuous gene expression in thymic medullary epithelial cells
Authors: Tykocinski Lars-Oliver , Sinemus Anna , Rezavandy Esmail , Weiland Yanina , Baddeley David , Cremer Christoph , Sonntag Stephan , Willecke Klaus , Derbinski Jens , Kyewski Bruno
Published: October 2010

Thymic central tolerance comprehensively imprints the T-cell receptor repertoire before T cells seed the periphery. Medullary thymic epithelial cells (mTECs) play a pivotal role in this process by virtue of promiscuous expression of tissue-restricted autoantigens. The molecular regulation of this unusual gene expression, in particular the involvement of epigenetic mechanisms is only poorly understood. By studying promiscuous expression of the mouse casein locus, we report that transcription of this locus proceeds from a delimited region (“entry site”) to increasingly complex patterns along with mTEC maturation. Transcription of this region is preceded by promoter demethylation in immature mTECs followed upon mTEC maturation by acquisition of active histone marks and local locus decontraction. Moreover, analysis of two additional gene loci showed that promiscuous expression is transient in single mTECs. Transient gene expression could conceivably add to the local diversity of self-antigen display thus enhancing the efficacy of central tolerance.
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.
Method for Automated Monitoring of Hand Hygiene Adherence without Radio-Frequency Identification
Authors: Polgreen Philip M. , Hlady Christopher S. , Severson Monica A. , Segre Alberto M. , Herman Ted
Published: October 2010

Many efforts to automatically measure hand hygiene activity depend on radio-frequency identification equipment or similar technology that can be expensive to install. We have developed a method for automatically tracking the use of hand hygiene dispensers before healthcare workers enter (or after they exit) patient rooms that is easily and quickly deployed without permanent hardware.
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

Aims  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: 50–63

Background  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.
Sustained Delayed Gastric Emptying During Repeated Restraint Stress in Oxytocin Knockout Mice
Authors: Babygirija R. , Zheng J. , Bülbül M. , Cerjak D. , Ludwig K. , Takahashi T.
Published: October 2010

We have recently shown that impaired gastric motility observed in acute restraint stress was restored following repeated restraint stress in mice. Repeated restraint stress up‐regulates oxytocin mRNA expression and down‐regulates corticotrophin‐releasing factor (CRF) mRNA expression at the hypothalamus. Oxytocin knockout mice (OXT‐KO) have been widely used to study the central oxytocin signalling pathways in response to various stressors. We studied the effects of acute and repeated restraint stress on solid gastric emptying and hypothalamic CRF mRNA expression in wild‐type (WT) and OXT‐KO mice. Heterozygous (HZ) parents (B6; 129S‐Oxttm1Wsy/J mice) were bred in our animal facility. Male OXT‐KO, WT and HZ littermates were used for the study. Solid gastric emptying was measured following acute restraint stress (for 90 min) or repeated restraint stress (for five consecutive days). Expression of CRF mRNA in the paraventricular nucleus (PVN) was measured by real‐time reverse transcriptase‐polymerase chain reaction. There were no significant differences of gastric emptying in WT (68.4 ± 4.1%, n = 6), HZ (71.8 ± 3.1%, n = 6) and OXT‐KO (70.6 ± 3.1%, n = 6) mice in nonstressed conditions. Acute stress significantly delayed gastric emptying in OXT‐KO mice (33.10 ± 2.5%, n = 6) WT (39.1 ± 1.1%, n = 6) and HZ mice (35.8 ± 1.2%, n = 6). Following repeated restraint stress loading, gastric emptying was significantly restored in WT (68.3 ± 4.5%, n = 6) and HZ mice (63.1 ± 2.6%, n = 6). By contrast, gastric emptying was still delayed in OXT‐KO mice (34.7 ± 1.3%, n = 6) following repeated restraint stress. The increase in CRF mRNA expression at the PVN was much pronounced in OXT‐KO mice compared to WT or HZ mice following repeated restraint stress. These findings suggest that central oxytocin plays a pivotal role in mediating the adaptation mechanism following repeated restraint stress in mice.
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

Grobman 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

Tolppanen 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

Genetic 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

Natural 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

To 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

Abstract

The 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 1b

What'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.