bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial secondary succession in a chronosequence of chalk grasslands
Authors: Kuramae Eiko E , Gamper Hannes A , Yergeau Etienne , Piceno Yvette M , Brodie Eoin L , DeSantis Todd Z , Andersen Gary L , van Veen Johannes A , Kowalchuk George A 
Published: February 2010

Abstract
Although secondary succession has been studied extensively, we have little knowledge of the succession of soil-borne microbial communities. In this study, we therefore examined the structures of the microbial communities across two separate chronosequences of chalk grasslands in Limburg, the Netherlands, which are at different stages of secondary succession after being abandoned for between 17 and &gt;66 years. Arable fields were also included in the investigation as non-abandoned references. Changes in the soil-borne microbial communities, as determined by phylogenetic microarray and quantitative PCR methodologies, were correlated with the prevailing environmental conditions related to vegetation and soil biochemistry. We observed clear patterns of microbial secondary succession related to soil age, pH and phosphate status, as exemplified by the overrepresentation of Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and α-, δ- and ɛ-Proteobacteria at late successional stages. Moreover, effects of secondary succession versus changes in soil pH could be resolved, with pH significantly altering the trajectory of microbial succession.
How significant is a protein structure similarity with TM-score = 0.5?
Authors: Xu Jinrui , Zhang Yang 
Published: February 2010

Abstract
Motivation: Protein structure similarity is often measured by root mean squared deviation, global distance test score and template modeling score (TM-score). However, the scores themselves cannot provide information on how significant the structural similarity is. Also, it lacks a quantitative relation between the scores and conventional fold classifications. This article aims to answer two questions: (i) what is the statistical significance of TM-score? (ii) What is the probability of two proteins having the same fold given a specific TM-score?
Results: We first made an all-to-all gapless structural match on 6684 non-homologous single-domain proteins in the PDB and found that the TM-scores follow an extreme value distribution. The data allow us to assign each TM-score a P-value that measures the chance of two randomly selected proteins obtaining an equal or higher TM-score. With a TM-score at 0.5, for instance, its P-value is 5.5 × 10−7, which means we need to consider at least 1.8 million random protein pairs to acquire a TM-score of no less than 0.5. Second, we examine the posterior probability of the same fold proteins from three datasets SCOP, CATH and the consensus of SCOP and CATH. It is found that the posterior probability from different datasets has a similar rapid phase transition around TM-score=0.5. This finding indicates that TM-score can be used as an approximate but quantitative criterion for protein topology classification, i.e. protein pairs with a TM-score &gt;0.5 are mostly in the same fold while those with a TM-score &lt;0.5 are mainly not in the same fold.
Contact: zhng@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Spinal 5-HT7 Receptors Play an Important Role in the Antinociceptive and Antihyperalgesic Effects of Tramadol and Its Metabolite, O-Desmethyltramadol, via Activation of Descending Serotonergic Pathways
Authors: Yanarates Omer , Dogrul Ahmet , Yildirim Vedat , Sahin Altan , Sizlan Ali , Seyrek Melik , Akgül Özgür , Kozak Orhan , Kurt Ercan , Aypar Ulku 
Published: February 2010

Background
Tramadol is an analgesic drug, and its mechanism of action is believed to be mediated by the mu-opioid receptor. A further action of tramadol has been identified as blocking the reuptake of serotonin (5-HT). One of the most recently identified subtypes of 5-HT receptor is the 5-HT7 receptor. Thus, the authors aimed to examine the potential role of serotonergic descending bulbospinal pathways and spinal 5-HT7 receptors compared with that of the 5-HT2A and 5-HT3 receptors in the antinociceptive and antihyperalgesic effects of tramadol and its major active metabolite O-desmethyltramadol (M1) on phasic and postoperative pain models.

Methods
Nociception was assessed by the radiant heat tail-flick and plantar incision test in male Balb-C mice (25-30 g). The serotonergic pathways were lesioned with an intrathecal injection of 5,7-dihydroxytryptamine. The selective 5-HT7, 5-HT2, and 5-HT3 antagonists; SB-269970 and SB-258719; ketanserin and ondansetron were given intrathecally.

Results
Systemically administered tramadol and M1 produced antinociceptive and antihyperalgesic effects. The antinociceptive effects of both tramadol and M1 were significantly diminished in 5-HT-lesioned mice. Intrathecal injection of SB-269970 (10 microg) and SB-258719 (20 microg) blocked both tramadol- and M1-induced antinociceptive and antihyperalgesic effects. Ketanserin (20 mumicrog) and ondansetron (20 microg) were unable to reverse the antinociceptive and antihyperalgesic effects of tramadol and M1.

Conclusions
These findings suggest that the descending serotonergic pathways and spinal 5-HT7 receptors play a crucial role in the antinociceptive and antihyperalgesic effects of tramadol and M1.
Diabetes-associated Alterations in Volatile Anesthetic Actions on Contractile Response to Norepinephrine in Isolated Mesenteric Resistance Arteries
Authors: Yoshino Jun , Akata Takashi , Shirozu Kazuhiro , Izumi Kaoru , Hoka Sumio 
Published: February 2010

Background
Clinical concentrations of volatile anesthetics significantly influence contractile response to the sympathetic neurotransmitter norepinephrine although its precise mechanisms remain unclarified. In this study, we investigated its possible alterations in diabetes, as well as its underlying mechanisms.

Methods
Isometric force was recorded in small mesenteric arteries from streptozotocin-induced diabetic and age-matched control rats.

Results
The concentration-response curve for acetylcholine-induced endothelium-dependent relaxation was shifted to the right in diabetic arteries compared with controls. The concentration-response curve for norepinephrine-induced contraction was shifted to the left and upward by both endothelial denudation and diabetic induction. In the presence of endothelium, isoflurane or sevoflurane enhanced norepinephrine-induced contraction in control arteries but not in diabetic arteries; however, in its absence, both anesthetics identically inhibited norepinephrine-induced contraction in both groups. In control arteries, the isoflurane- or sevoflurane-induced enhancement was not affected by adrenomedullin22-52, calcitonin gene-related peptide8-37, 18beta-glycyrrhetinic acid, N-nitro l-arginine, ouabain, Ba, indomethacin, losartan, ketanserin, BQ-123, and BQ-788.

Conclusions
In diabetes, vascular responses to acetylcholine, norepinephrine, and volatile anesthetics are altered in mesenteric resistance arteries, presumably reflecting endothelial dysfunction and possibly underlying circulatory instability during administration of either anesthetic. Some endothelial mechanisms that are impaired in diabetes would be involved in the anesthetic-induced enhancement of norepinephrine-induced contraction. However, the vasoregulatory mechanism mediated by adrenomedullin, calcitonin gene-related peptide, myoendothelial gap junction, nitric oxide, endothelium-derived hyperpolarizing factor, cyclooxygenase products, angiotensin II, serotonin, or endothelin-1, all of which have been suggested to be impaired in diabetes, would not be involved in the enhancement.
Neurally Adjusted Ventilatory Assist Increases Respiratory Variability and Complexity in Acute Respiratory Failure
Authors: Schmidt Matthieu , Demoule Alexandre , Cracco Christophe , Gharbi Alexandre , Fiamma Marie-Noëlle , Straus Christian , Duguet Alexandre , Gottfried Stewart B. , Similowski Thomas 
Published: February 2010

Background
Neurally adjusted ventilatory assist (NAVA) is a partial ventilatory support mode where positive pressure is provided in relation to diaphragmatic electrical activity (EAdi). Central inspiratory activity is normally not monotonous, but it demonstrates short-term variability and complexity. The authors reasoned that NAVA should produce a more "natural" or variable breathing pattern than other modes. This study compared respiratory variability and complexity during pressure support ventilation (PSV) and NAVA.

Methods
Flow and EAdi were recorded during routine PSV (tidal volume approximately 6-8 ml/kg) and four NAVA levels (1-4 cm H2O/microVEAdi) in 12 intubated patients. Breath-by-breath variability of flow and EAdi-related variables was quantified by the coefficient of variation (CV) and autocorrelation analysis. Complexity of flow and EAdi was described using noise titration, largest Lyapunov exponent, Kolmogorov-Sinai entropy, and three-dimensional phase portraits.

Results
Switching from PSV to NAVA increased the CV and decreased the autocorrelation for most flow-related variables in a dose-dependent manner (P < 0.05, partial eta for the CV of mean inspiratory flow 0.642). The changes were less marked for EAdi. A positive noise limit was consistently found for flow and EAdi. Largest Lyapunov exponent and Kolmogorov-Sinai entropy for flow were greater during NAVA than PSV and increased with NAVA level (P < 0.05, partial eta 0.334 and 0.312, respectively). Largest Lyapunov exponent and Kolmogorov-Sinai entropy for EAdi were not influenced by ventilator mode.

Conclusions
Compared with PSV, NAVA increases the breathing pattern variability and complexity of flow, whereas the complexity of EAdi is unchanged. Whether this improves clinical outcomes remains to be determined.
Infliximab as rescue medication for patients with severe ulcerative/indeterminate colitis refractory to tacrolimus
Authors: HERRLINGER K. R. , BARTHEL D. N. , SCHMIDT K. J. , BÜNING J. , BARTHEL C. S. , WEHKAMP J. , STANGE E. F. , FELLERMANN K. 
Published: February 2010

Aliment Pharmacol Ther 31, 1036–1041SummaryBackground  The calcineurin inhibitor tacrolimus and the anti‐TNF‐antibody infliximab are established options in steroid‐refractory ulcerative colitis (UC).Aim  To evaluate the efficacy of infliximab‐salvage therapy in patients with refractory UC failing to respond to tacrolimus.Methods  Twenty‐four patients were enrolled in this evaluation. Reasons for tacrolimus therapy were steroid‐refractory disease in 19 patients and steroid‐dependency in five patients. All patients receiving infliximab had tacrolimus‐refractory active disease (Lichtiger score >10) and were treated with 5 mg/kg at weeks 0, 2 and 6 and every 8 weeks thereafter, if tolerated.Results  Six of 24 patients (25%) achieved remission following infliximab infusion and four of 24 (17%) had an initial response only, but underwent proctocolectomy later because of loss of response (3) or development of a delayed hypersensitivity reaction (1). Fourteen patients (58%) completely failed to respond with 10 undergoing colectomy. Eight patients experienced side effects under infliximab, including two infectious complications (herpes zoster and herpes pneumonia).Conclusions  Infliximab offers a therapeutic option as rescue therapy in about a quarter of patients with active UC after failing to respond to tacrolimus. This benefit has to be weighed against the risks of infectious complications.
Monitoring sedation in the critically ill child
Authors: Lamas A. , López‐Herce J. 
Published: February 2010

SummarySedation is an essential part of the management of the critically ill child, and its monitoring must be individualised and continuous in order to adjust drug doses according to the clinical state. There is no ideal method for evaluating sedation in the critically ill child. Haemodynamic variables have not been found to be useful. Clinical scales are useful when sedation is moderate, but are limited by their subjective nature, the use of stimuli, and the impossibility of evaluating profoundly sedated patients or those receiving neuromuscular blocking drugs; in addition, many of these scales have not been evaluated in children. The COMFORT scale is the most appropriate, as it was designed and validated for critically ill children requiring mechanical ventilation. Electroencephalography‐derived methods permit continuous monitoring, provide an early indication of changes in the level of sedation, and facilitate a rapid adjustment of medication. However, these methods were designed and validated for patients under anaesthesia and their results cannot be fully extrapolated to the critically ill patient; in addition, some of them have not been validated in small children and there is still little experience in critically ill children. The main indications for the use of these methods are in patients with deep sedation and/or neuromuscular blockade. The bispectral index is the most widely used method at the present time. Analysis and comparison of the efficacy of the different methods for evaluating sedation in the critically ill child is required.
Associations between over‐winter survival and resting metabolic rate in juvenile North American red squirrels
Authors: Larivée Meghan L. , Boutin Stan , Speakman John R. , McAdam Andrew G. , Humphries Murray M. 
Published: February 2010

Summary 1. Resting metabolic rate (RMR) varies considerably among and within species. Two central questions in physiological ecology are whether values of RMR are repeatable and whether an association exists between RMR and fitness. 2. First, we investigated the repeatability of RMR in food hoarding, juvenile, North American red squirrels (Tamiasciurus hudsonicus Erxleben). Second, we explored links between RMR and survival. A low RMR may enhance survival if it reduces winter expenditure costs and/or allows more energy to be allocated towards autumn food hoarding. Alternately, a high RMR may enhance survival if it enables juveniles to hoard more food by increasing the throughput of energy available for investment in hoarding activities. 3. Resting metabolic rate adjusted for body mass, was repeatable in both males and females (r = 0·77) over a short‐term (mean 24·3 days) but only among females (r = 0·72) over a long‐term interval (mean 192 days). 4. Heavier juveniles and those with a lower RMR relative to their body mass were more likely to survive over‐winter. Multiple selection models found significant selection for a decreased RMR (β′ = −0·56 ± 0·16) and increased mass (β′ = 0·69 ± 0·17). Survivors also tended to have more food stored within their hoard. 5. A low RMR relative to body mass and large body mass may have allowed individuals to minimize the expenditure costs related to a larger body mass, while maximizing thermal inertia.
Expression of lrwd1 in mouse testis and its centrosomal localization
Authors: Teng Yen‐Ni , Liao Ming‐Hui , Lin Yang‐Ben , Kuo Pao‐Lin , Kuo Ting‐Yi 
Published: February 2010

SummaryThe mouse leucine‐rich repeats and WD repeat domain containing 1 (lrwd1) gene is located on chromosome 5qG2 and spans over 13 kilobases. It encodes a novel protein of 648‐amino acid protein that shares 78.3% amino acid sequence identity with the human LRWD1 protein. We used an oligopeptide as immunogen to generate an anti‐lrwd1 antibody in rabbits. Both Northern and Western blot results indicated that the expression of lrwd1 is testis specific. Immunostaining of mouse testis sections detected high levels of lrwd1 signals in the cytoplasm of primary spermatocytes to mature spermatozoa and much weaker signals in spermatogonia. On mature spermatozoa, the anti‐lrwd1 antibody stained strongly the connection region between the head and the neck where the centrosome is located. Additional immunostaining and immunoprecipitation showed colocalization and interaction between lrwd1 and γ‐tubulin respectively, implicating lrwd1 as a candidate centrosomal protein. These results suggest that lrwd1 may play an important role in spermatogenesis.
Empirical evidence of the relationship between parental and child dental fear: a structured review and meta‐analysis
Authors: THEMESSL‐HUBER MARKUS , FREEMAN RUTH , HUMPHRIS GERRY , MacGILLIVRAY STEVE , TERZI NATHALIE 
Published: February 2010

International Journal of Paediatric Dentistry 2010; 20: 83–101 Background.  The relationship between parental and child dental fear has been studied for over a century. During this time, the concept of dental fear as well as methodological approaches to studying dental fear in children have evolved considerably.Aim.  To provide an overview of the published empirical evidence on the link between parental and child dental fear.Design.  A structured literature review and meta‐analysis.Results.  Forty‐three experimental studies from across the six continents were included in the review. The studies ranged widely with respect to research design, methods used, age of children included, and the reported link between parental and child dental fear. The majority of studies confirmed a relationship between parental and child dental fear. This relationship is most evident in children aged 8 and under. A meta‐analysis of the available data also confirmed an association between parental and child dental fear.Conclusion.  The narrative synthesis as well as the meta‐analysis demonstrate a significant relationship between parental and child dental fear, particularly in children 8 years and younger.
Pathologic paediatric conditions associated with a compromised airway
Authors: BAKER SUHER , PARICO LIA 
Published: February 2010

International Journal of Paediatric Dentistry 2010; 20: 102–111 Purpose.  The purpose was to describe pathologic paediatric conditions associated with airway compromise adversely affecting dental treatment with sedation and general anaesthesia.Methods.  A review of available literature was completed, identifying pathologic paediatric conditions predisposing to airway compromise.Results.  Airway‐related deaths are uncommon, but respiratory complication represents the greatest cause of morbidity and mortality during the administration of general anaesthesia. Differences in anatomy and physiology of the paediatric and adult airway contribute to the child’s predisposition to rapid development of airway compromise and respiratory failure; juvenile rheumatoid arthritis, cervical spine injury, morbid obesity, and prematurity represent only a few conditions contributing to potential airway compromise of which the paediatric clinician needs to be aware. In all cases, thorough physical examination prior to treatment is mandated to affect a positive treatment outcome.Conclusions.  Successful management of children and adolescents with a compromised airway begins with identification of the problem through a detailed medical history and physical examination. Due to the likely fragile nature of many of these patients, and possibility of concomitant medical conditions affecting airway management, dental treatment needs necessitating pharmacological management are best treated in a controlled setting such as the operating room, where a patent airway can be maintained.
Mutans streptococci colonization associates with the occupation of caretaker, a practise‐based study
Authors: MEURMAN PIA , PIENIHÄKKINEN KAISU , ERIKSSON ANNA‐LEENA , ALANEN PENTTI 
Published: February 2010

International Journal of Paediatric Dentistry 2010; 20: 144–150 Background.  The early mutans streptococci (MS) bacteria colonization is connected to early childhood caries. The aim of this study is to examine associations between the MS‐colonization and background factors in young children, in order to enhance the oral health program in a low caries prevalence community.Subjects and Design.  An age cohort of 512 children was screened for MS in the oral biofilm at the age of 18 months. The caretakers were, using a structured form, interviewed of demographical factors and habits connected to oral health: antibiotic treatments, child’s appetite, frequency of night feeding, use of sugary products or drinks, and maternal xylitol use. The associations were evaluated with logistic regression analysis.Results.  Mutans streptococci colonization was significantly associated with both the occupation of the caretaker and the non‐Finnish background.Conclusion.  The early MS‐colonization, in preschool children, strongly associates with the socioeconomic status of the family.
Implications of gluten exposure period, CD clinical forms, and HLA typing in the association between celiac disease and dental enamel defects in children. A case–control study
Authors: MAJORANA ALESSANDRA , BARDELLINI ELENA , RAVELLI ALBERTO , PLEBANI ALESSANDRO , POLIMENI ANTONELLA , CAMPUS GUGLIELMO 
Published: February 2010

International Journal of Paediatric Dentistry 2010; 20: 119–124 Background.  The association between coeliac disease (CD) and dental enamel defects (DED) is well known.Aim.  The aim of this study was to investigate the prevalence of DED in children with CD and to specifically find the association of DED and gluten exposure period, CD clinical forms, HLA class II haplotype.Design.  This study was designed as a matched case–control study: 250 children were enrolled (125 coeliac children – 79 female and 46 male, 7.2 ± 2.8 years and 125 healthy children). Data about age at CD diagnosis, CD clinical form, and HLA haplotype were recorded.Results.  Dental enamel defects were detected in 58 coeliac subjects (46.4%) against seven (5.6%) controls (P < 0.005). We found an association between DED and gluten exposure period, as among CD subjects the mean age at CD diagnosis was significantly (P = 0.0004) higher in the group with DED (3.41 ± 1.27) than without DED (1.26 ± 0.7). DED resulted more frequent (100%) in atypical and silent CD forms than in the typical one (30.93%). The presence of HLA DR 52‐53 and DQ7antigens significantly increased the risk of DED (P = 0.0017) in coeliac children.Conclusions.  Our results confirmed a possible correlation between HLA antigens and DED.
Trends in paediatric dental caries by poverty status in the United States, 1988–1994 and 1999–2004
Authors: DYE BRUCE A. , AREVALO OSCAR , VARGAS CLEMENCIA M. 
Published: February 2010

International Journal of Paediatric Dentistry 2010; 20: 132–143 Background.  Recent reports have suggested that dental caries among some young children is increasing in the United States.Aim.  To describe changes in paediatric caries prevalence by poverty status in the United States.Design.  National Health and Nutrition Examination Survey (NHANES) data for children aged 2–11 years for 1988–1994 and 1999–2004 were used.Results.  Caries in the primary dentition increased among poor and non‐poor boys aged 2–8 years (45–53% and 23–31%, respectively) and among non‐poor boys aged 2–5 years (13–21%) from 1988–1994 to 1999–2004. Caries experience also increased on buccal‐lingual, mesio‐distal, and occlusal primary dental surfaces among poor children aged 2–8 years and this increase may be attributed to an increase in the number of dental surfaces restored. In the mixed dentition, caries remains relatively unchanged. Caries continues to decline in the permanent dentition for many children, but is increasing among poor non‐Hispanic whites aged 6–8 years (8–22%) and poor Mexican‐Americans aged 9–11 years (38–55%).Conclusions.  For many older children, caries continues to decline or remain unchanged. Nevertheless, for a subgroup of younger children, caries is increasing and this increase is impacting some traditionally low‐risk groups of children.