bluuebunny/crossref_metadata_2025_split huggingface dataset:
An interactive power analysis tool for microarray hypothesis testing and generation
Authors: Seo Jinwook , Gordish-Dressman Heather , Hoffman Eric P. 
Published: January 2006

Abstract
Motivation: Human clinical projects typically require a priori statistical power analyses. Towards this end, we sought to build a flexible and interactive power analysis tool for microarray studies integrated into our public domain HCE 3.5 software package. We then sought to determine if probe set algorithms or organism type strongly influenced power analysis results.
Results: The HCE 3.5 power analysis tool was designed to import any pre-existing Affymetrix microarray project, and interactively test the effects of user-defined definitions of α (significance), β (1 − power), sample size and effect size. The tool generates a filter for all probe sets or more focused ontology-based subsets, with or without noise filters that can be used to limit analyses of a future project to appropriately powered probe sets. We studied projects from three organisms (Arabidopsis, rat, human), and three probe set algorithms (MAS5.0, RMA, dChip PM/MM). We found large differences in power results based on probe set algorithm selection and noise filters. RMA provided high sensitivity for low numbers of arrays, but this came at a cost of high false positive results (24% false positive in the human project studied). Our data suggest that a priori power calculations are important for both experimental design in hypothesis testing and hypothesis generation, as well as for the selection of optimized data analysis parameters.
Availability: The Hierarchical Clustering Explorer 3.5 with the interactive power analysis functions is available at or .
Contact: jseo@cnmcresearch.org
Panta rhei (QAlign2): an open graphical environment for sequence analysis
Authors: Sammeth Michael , Griebel Thasso , Tille Felix , Stoye Jens 
Published: January 2006

Abstract
Motivation: The first version of the graphical multiple sequence alignment environment QAlign was published in 2003. Heavy response from the molecular-biological user community clearly demonstrated the need for such a platform.
Results: Panta rhei extends QAlign by several features. Major redesigns on the user interface, for instance, allow users to flexibily compose views for multiple projects. The new sequence viewer handles datasets with arbitrarily many and arbitrarily large sequences that may still be edited by guided block moving. More distance-based algorithms are available to interactively reconstruct phylogenetic trees which can now also be zoomed and navigated graphicaly.
Availability: Executables and the JAVA source code are available under the Apache license at
Contact: qalign@cebitec.uni-bielefeld.de
Epidemiology of Helicobacter pylori Infection in the Czech Republic
Authors: Bureš Jan , Kopáčová Marcela , Koupil Ilona , Voříšek Viktor , Rejchrt Stanislav , Beránek Martin , Seifert Bohumil , Pozler Oldřich , Živný Pavel , Douda Tomáš , Kolesárová Martina , Pintér Michal , Palička Vladimír , Holčík Jan ,   the European Society for Primary Care Gastroenterology
Published: January 2006

AbstractBackground:  Prevalence of Helicobacter pylori infection has been estimated to range from 60 to 95% in the former communist countries of Central and Eastern Europe. The aim of this study was to evaluate H. pylori infection prevalence in a representative sample of the Czech population. The second objective was to describe difference of H. pylori prevalence between different social groups of children and adults.Materials and Methods:  A total of 2509 persons aged 5–100 years, randomly selected out of 30,012 persons of the general population, took part in the study. H. pylori infection was investigated by means of 13C‐urea breath test. Breath samples were analyzed by isotope ratio mass spectrometry. Social and demographic characteristics were based on data from self‐completed questionnaires.Results:  Using the total Czech population as a standard, we estimated the age‐standardized prevalence of H. pylori in males aged 5+ years at 41.9% (95% CI 39.0%, 44.8%) and in females aged 5+ years at 41.4% (95% CI 38.6%, 44.3%) in 2001. Prevalence of H. pylori increased with age but was not related to gender. Children of mothers with basic or lower education, living in crowded accommodations, without access to running warm water, and residing in smaller towns appear to be at the highest risk. Low education and heavy smoking are most strongly associated with prevalence of H. pylori positivity in adults and adolescents.Conclusions:  This is a unique study based on a representative sample of the general population in a Central European country. The overall prevalence of H. pylori is lower than previously assumed and could partly reflect a substantial recent decrease in H. pylori prevalence in the Czech Republic. Consistent with earlier studies, H. pylori infection is strongly influenced by socioeconomic conditions and childhood poverty.
Helicobacter pylori has Stimulatory Effects on Naive T Cells
Authors: Malfitano Anna Maria , Cahill Rachel , Mitchell Peter , Frankel Gad , Dougan Gordon , Bifulco Maurizio , Lombardi Giovanna , Lechler Robert I. , Bamford Kathleen B. 
Published: January 2006

AbstractBackground:  Despite an apparently active host response, Helicobacter pylori infection can persist for life. Unexpectedly, T cells from apparently uninfected individuals respond to H. pylori antigen by proliferating. Also, the T‐cell proliferative response appears to be less in infected compared with uninfected individuals.Materials and Methods:  We have investigated the T‐cell response of isolated human peripheral blood, naive, and memory CD4+ T cells to H. pylori antigen in infected and uninfected subjects.Results:  In agreement with previous findings, the peripheral blood proliferative response was higher in uninfected compared with infected subjects. Interestingly, there was a response in CD4+CD45RO+ (memory) and CD4+CD45RA+ (naive) subsets. The RO/RA ratio of the response to H. pylori antigen was 0.8–2.1 in both H. pylori‐positive and H. pylori‐negative subjects, which was similar to that of a known superantigen (2.5 and 2.2 in Helicobacter‐positive and ‐negative subjects, respectively) whereas the RO/RA response ratio to a recall antigen (tetanus toxoid) was 9.8 and 18.7 in Helicobacter‐positive and ‐negative subjects, respectively. Mononuclear cells isolated from cord blood also responded to H. pylori antigen, whereas there was no response to tetanus toxoid. The cord blood response and CD4+CD45RA+ cell response to H. pylori antigen were inhibited predominantly by anti‐HLA‐DR and to some extent by anti‐HLA‐DQ antibodies. Investigation of the response to five different recombinant H. pylori antigens identified two that produced a response in naive T cells.Conclusions:  These data suggest that H. pylori possesses molecules that cause higher than expected proliferation of naive T cells.
Determinants of the elimination of methotrexate and 7‐hydroxy‐methotrexate following high‐dose infusional therapy to cancer patients
Authors: Joerger M. , Huitema A. D. R. , Van Den Bongard H. J. G. D. , Baas P. , Schornagel J. H. , Schellens J. H. M. , Beijnen J. H. 
Published: January 2006

AimsTo characterize determinants of the elimination of methotrexate (MTX) and 7‐hydroxy‐methotrexate (7‐OH‐MTX) in patients receiving high‐dose MTX therapy (HDMTX).Methods24 and 48‐h blood samples from 76 patients receiving HDMTX (dose range 300 mg m−2 to 12 g m−2) were analysed, and concentration‐time data were subjected to population pharmacokinetic and covariate analysis using nonlinear mixed‐effect modelling (NONMEM).ResultsTreatment‐related mortality was 1.3% (one patient with renal failure). Values for MTX clearance (CLMTX) and 7‐OH‐MTX clearance (CL7‐OH‐MTX) were estimated at 8.85 and 2 L−1, respectively. Baseline creatinine clearance correlated with CLMTX and CL7‐OH‐MTX. Concurrent administration of benzimidazoles led to a 27% decrease in CLMTX and a 39% decrease in CL7‐OH‐MTX. Prior administration of nonsteroidal anti‐inflammatory drugs (NSAIDs) resulted in a 16% decrease in CLMTX and a 38% decrease in CL7‐OH‐MTX. Plasma MTX concentrations were significantly higher in patients also receiving benzimidazoles at 24 h (2.01 µmol L−1vs. 0.66 µmol L−1, P < 10−4) and at 48 h (0.25 µmol L−1vs. 0.12 µmol L−1, P < 10−4). 7‐OH‐MTX plasma concentrations were also significantly higher in patients with concurrent benzimidazoles as compared with patients without benzimidazoles at 24 h (4.47 µmol L−1vs. 2.52 µmol L−1, P = 0.0009) and at 48 h (1.11 µmol L−1vs. 0.72 µmol L−1, P = 0.031).ConclusionsIn patients receiving HDMTX, concurrent administration of benzimidazoles was associated with a significant decrease of CLMTX and CL7‐OH‐MTX, resulting in significantly higher plasma concentrations of MTX and 7‐OH‐MTX. The data suggest that benzimidazole treatment should be seen as a relative contraindication for HDMTX.
Phylogeography of Iurus dufoureius (Brullé, 1832) (Scorpiones, Iuridae)
Authors: Parmakelis A. , Stathi I. , Spanos L. , Louis C. , Mylonas M. 
Published: January 2006

AbstractAim  This study uses molecular data in conjunction with palaeogeography to infer the most plausible biogeographical scenario accounting for the current distributional pattern of Iurus dufoureius.Location  North‐eastern Mediterranean region.Methods  Sequencing of a 441‐bp segment of the mitochondrial 16S rRNA gene in seven populations covering the whole distributional range of the species. Phylogenetic analyses performed included neighbour joining, maximum parsimony and Bayesian inference.Results  The molecular phylogeny showed that two Iurus clades are strongly supported. These clades correspond to the two subspecies Iurus dufoureius dufoureius and Iurus dufoureius asiaticus, currently recognized within the genus. The assumption of a clock‐like evolution could not be rejected, and this enabled us to estimate an approximation of the local rate of evolution for the I. dufoureius lineages. Based on the estimated evolutionary rate (0.79 ± 0.17 Myr−1), the split between the two Iurus clades occurred c. 8 Ma.Main conclusions  Contrary to what was believed in the past, the genus Iurus is an old north‐eastern Mediterranean genus that has been differentiating in southern Greece and south‐west Turkey at least from the middle Miocene. According to the phylogenetic trees obtained and the dating of the divergence times of lineages, the genus dispersed into the Aegean Archipelago when the Aegean was still a uniform land mass. Although the phylogenetic relationships of I. d. dufoureius populations have been shaped by the most recent vicariant events, the phylogenetic relationships of I. d. asiaticus populations are mostly attributable to older palaeoevents occurring in the area.
Land hermit crab (Coenobita clypeatus) densities and patterns of gastropod shell use on small Bahamian islands
Authors: Morrison Lloyd W. , Spiller David A. 
Published: January 2006

AbstractAim  To examine patterns of abundance, density, size and shell use in land hermit crabs, Coenobita clypeatus (Herbst), occurring on three groups of small islands, and to determine how these variables change among islands.Location  Small islands in the Central Exuma Cays and near Great Exuma, Bahamas.Methods  Land hermit crabs were captured in baited pitfall traps and were separately attracted to baits. A mark–recapture technique was used in conjunction with some pitfall traps monitored for three consecutive days. The size of each crab and the type of adopted gastropod shell were recorded, along with physical island variables such as total island area, vegetated area, island perimeter, elevation and distance to the nearest mainland island.Results  Relative abundances, densities and sizes of crabs differed significantly among the three island groups. Densities of land hermit crabs were as high as 46 m−2 of vegetated island area. In simple and multiple linear regressions, the only variable that was a significant predictor of the abundance of hermit crabs was the perimeter to area ratio of the island. Patterns of gastropod shell use varied significantly among the island groups, and the vast majority of adopted shells originated from gastropod species that inhabit the high intertidal and supratidal shorelines of the islands.Main conclusions  Although densities of land hermit crabs varied, they were relatively high on many islands, and land hermit crabs may play an important role in these insular food webs. Patterns of shell use may be strongly restricted by island geomorphology: irregular shorelines provide relatively more habitat for the gastropod species that account for the majority of adopted shells and the steep sides of the islands prevent the accumulation of marine gastropod shells. The size of adult hermit crabs appears to be limited by the relatively small gastropod shells available, while the abundance of hermit crabs may be limited by the number of shells available.
Hypothalamic Pro‐GnRH‐GAP, GnRH‐I and GnRH‐II During the Onset of Photorefractoriness in the White‐Crowned Sparrow (Zonotrichia leucophrys gambelii)
Authors: Meddle S. L. , Bush S. , Sharp P. J. , Millar R. P. , Wingfield J. C. 
Published: January 2006

AbstractGambel's white‐crowned sparrow is a long distance migrant that undergoes spontaneous gonadal regression as a result of long day exposure. This termination of breeding is caused by the development of photorefractoriness and the birds become insensitive to long days, including continuous light. The present study investigated its possible mechanisms by examining the activity of the gonadotrophin‐releasing hormone (GnRH) system under different photoperiodic regimes. We investigated the localisation and distribution of GnRH‐I, its precursor pro‐GnRH‐GAP and GnRH‐II in Gambel's white‐crowned sparrow brain using immunocytochemistry with specific antibodies during photostimulation and the development of photorefractoriness. The study revealed that photoperiodic treatment, including the onset of photorefractoriness, had no significant effect on the size or number of GnRH‐I, pro‐GnRH‐GAP or GnRH II immunoreactive cells, or the density of the GnRH‐I, pro‐GnRH‐GAP immunoreactive fibres at the median eminence. GnRH‐II was not found in the median eminence, suggesting that it does not regulate pituitary gonadotrophin secretion. GnRH‐I measurement in hypothalamic extracts by radioimmunoassay did not reveal any significant difference between birds that were photostimulated or in the early stages of photorefractoriness. Furthermore, the action of the excitatory amino acid glutamate agonist N‐methyl‐D‐aspartate on GnRH neurones in photorefractory birds was demonstrated by the significant blockade of luteinising hormone release with a specific GnRH antagonist. Taken together, these results suggest that, in Gambel's white‐crowned sparrow, a decrease in GnRH‐I secretion is the initial step for the onset of photorefractoriness and not a decrease in GnRH‐I biosynthesis.
The electrocardiographic and hemodynamic effect of metohexital and propofol with and without esmolol
Authors: Korpinen R. , Klemola U‐M. , Simola M. , Toivonen H. 
Published: January 2006

Background:  Metohexital and propofol are short‐acting induction agents, which have a tendency to prolong the QTc interval of the ECG. We studied whether this increase could be prevented by combining a beta‐blocking agent, esmolol, with these drugs. Simultaneously, we studied the hemodynamic effects of these combinations.Methods:  In a randomized, double‐blind study, 80 ASA I–II young adults were premedicated with oxycodone and atropin and allocated to one of four groups: propofol (P), propofol + esmolol (P + E), metohexital (E) or metohexital + esmolol (M + E). The doses were 2 mg/kg propofol/metohexital and 1 mg/kg esmolol. Alfentanil 15 µg/kg was used in all groups. The hemodynamic parameters were measured non‐invasively and the electrocardiographic parameters using the signal processing method.Result:  The highest QTc values, which often exceeded the normal upper limit of 440 ms, were recorded at the baseline or immediately after the administration of the induction drugs. The intervals were significantly shorter if esmolol was co‐administered with either propofol or metohexital. The heart rate increased in the group M and decreased in the group P + E but remained unchanged in the groups P and M + E. Systolic and diastolic arterial pressures decreased during the study in all groups, most prominently in group P + E.Conclusions:  During the anesthesia induction, the QTc interval was significantly shorter when esmolol was co‐administered with either propofol or metohexital. The hemodynamic responses were properly controlled with the combination of metohexital and esmolol as well as with propofol alone, but the combination of propofol and esmolol tended to cause hemodynamic depression.
Isobaric bupivacaine via spinal catheter for hip replacement surgery: ED50 and ED95 dose determination
Authors: Sell A. , Olkkola K. T. , Jalonen J. , Aantaa R. 
Published: January 2006

Background:  Continuous spinal anaesthesia with spinal catheters allows incremental dosing of the local anaesthetic and, consequently, less haemodynamic change. However, little is known about the required doses. Therefore, we designed a study to assess the local anaesthetic doses of isobaric bupivacaine which were effective in 50% (ED50) and 95% (ED95) of patients undergoing hip replacement surgery.Methods:  Forty‐eight patients undergoing hip replacement surgery were randomly allocated to one of six possible groups of eight patients to receive 6, 7, 8, 9, 10 or 12 mg of isobaric bupivacaine in a double‐blind manner. The ED50 and ED95 values were calculated by a logistic regression model. The position of the spinal catheter tip was confirmed by X‐rays.Results:  The ED50 and ED95 values were 7.1 mg (95% confidence interval, 6.0–8.4) and 12.3 mg (95% confidence interval, 8.9–15.7), respectively. The location of the tip of the intrathecal catheter had no effect on local anaesthetic requirements. Eight patients required ephedrine after anaesthesia induction and a further 11 patients required ephedrine for correction of hypotension during surgery.Conclusion:  The observed ED50 and ED95 values may guide us to use small doses of isobaric bupivacaine for hip replacement surgery. Hypotension is still possible even if low doses of isobaric bupivacaine are used.
Effect of low‐dose dexmedetomidine or clonidine on the characteristics of bupivacaine spinal block
Authors: Kanazi G. E. , Aouad M. T. , Jabbour‐Khoury S. I. , Al Jazzar M. D. , Alameddine M. M. , Al‐Yaman R. , Bulbul M. , Baraka A. S. 
Published: January 2006

Background: The purpose of this study was to compare the onset and duration of sensory and motor block, as well as the hemodynamic changes and level of sedation, following intrathecal bupivacaine supplemented with either dexmedetomidine or clonidine.Methods: In a prospective, double‐blind study, 60 patients undergoing transurethral resection of prostate or bladder tumor under spinal anesthesia were randomly allocated to one of three groups. Group B received 12 mg of hyperbaric bupivacaine, group D received 12 mg of bupivacaine supplemented with 3 µg of dexmedetomidine and group C received 12 mg of bupivacaine supplemented with 30 µg of clonidine. The onset times to reach peak sensory and motor levels, and the sensory and motor regression times, were recorded. Hemodynamic changes and the level of sedation were also recorded.Results: Patients in groups D and C had a significantly shorter onset time of motor block and significantly longer sensory and motor regression times than patients in group B. The mean time of sensory regression to the S1 segment was 303 ± 75 min in group D, 272 ± 38 min in group C and 190 ± 48 min in group B (B vs. D and B vs. C,P < 0.001). The regression of motor block to Bromage 0 was 250 ± 76 min in group D, 216 ± 35 min in group C and 163 ± 47 min in group B (B vs. D and B vs. C,P < 0.001). The onset and regression times were not significantly different between groups D and C. The mean arterial pressure, heart rate and level of sedation were similar in the three groups intra‐operatively and post‐operatively.Conclusions: Dexmedetomidine (3 µg) or clonidine (30 µg), when added to intrathecal bupivacaine, produces a similar prolongation in the duration of the motor and sensory block with preserved hemodynamic stability and lack of sedation.
Analgesic effects of intrathecally administered celecoxib, a cyclooxygenase‐2 inhibitor, in the tail flick test and the formalin test in rats
Authors: Nishiyama T. 
Published: January 2006

Background:  The analgesic effects of celecoxib, a cyclooxygenase‐2 (COX‐2) inhibitor, on formalin‐induced pain are still controversial. The purpose of this study was to examine the analgesic effects of intrathecally administered celecoxib on inflammatory induced pain, thermal‐induced pain and hemodynamics.Methods:  Male Sprague‐Dawley rats with lumbar intrathecal catheters were tested via their tail withdrawal response to thermal stimulation (tail flick test) and via their paw flinching and shaking response to subcutaneous formalin injection into the hind paw (formalin test) after intrathecal administration of celecoxib. The blood pressure, pulse rate and behavioral side‐effects were also examined.Results:  Even the maximum available dose of celecoxib (200 µg/20 µl) had little effect in the tail flick test. In the formalin test, celecoxib induced a dose‐dependent decrease in the flinch response in both phases 1 and 2. The 50% effective doses were 0.025 µg (95% confidence interval, 0.007–0.082 µg) in phase 1, 0.026 µg (0.010–0.045 µg) in phase 2a and 0.001 µg (0.00009–0.010 µg) in phase 2b. With the doses used in this study, the blood pressure and pulse rate did not change and no motor disturbance or behavioral side‐effects were observed.Conclusion:  Intrathecal administration of celecoxib decreased inflammatory acute and facilitated pain without any hemodynamic or behavioral side‐effects, but had no effect on acute thermal pain.
Changes in magnesium concentration in the serum and cerebrospinal fluid of neuropathic rats
Authors: Jeong S. M. , Hahm K. D. , Shin J. W. , Leem J. G. , Lee C. , Han S. M. 
Published: January 2006

Background:  Central sensitization of neuropathic pain is associated with an influx of extracellular calcium via the opening of N‐methyl‐d‐aspartate (NMDA) receptor‐gated ion channels, which are usually blocked by magnesium plugs. As magnesium‐deficient rats develop a mechanical hyperalgesia and intrathecal or intraperitoneal magnesium suppresses neuropathic pain, the magnesium concentrations in serum and cerebrospinal fluid may be altered in neuropathic pain. We therefore compared the magnesium concentrations in serum and cerebrospinal fluid of neuropathic rats with those in injured rats without symptoms of neuropathic pain and normal rats.Methods:  Mechanical allodynia was induced in male Sprague‐Dawley rats by tight ligature of the left lumbar fifth and sixth spinal nerves. The threshold of paw withdrawal was evaluated by the up–down method using withdrawal response to stimulus with a von Frey filament on the third, seventh and 14th days. Rats with a threshold of less than 4 g were selected as the symptomatic group and compared with an asymptomatic group, an unoperated control group and a sham‐operated group. On the 16th day, the Mg2+ concentrations in serum and cerebrospinal fluid were measured.Results:  The magnesium concentrations in the serum and cerebrospinal fluid of symptomatic neuropathic rats did not differ from those in the injured rats without symptoms of neuropathic pain, sham‐operated rats and normal rats.Conclusion:  Our results suggest that physiologic homeostasis is maintained by active transport through the blood–brain barrier despite the activation of NMDA receptor‐gated ion channels. However, rats with neuropathic pain may be in a magnesium‐deficient condition at the effector site, such that magnesium treatment can decrease neuropathic pain.