bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Prader-Willi syndrome murine imprinting center is not involved in the spatio-temporal transcriptional regulation of the Necdin gene
Authors: Watrin Françoise , Le Meur Elodie , Roeckel Nathalie , Ripoche Marie-Anne , Dandolo Luisa , Muscatelli Françoise 
Published: January 2005

Abstract
Background
The human Prader-Willi syndrome (PWS) domain and its mouse orthologue include a cluster of paternally expressed genes which imprinted expression is co-ordinately regulated by an imprinting center (IC) closely associated to the Snurf-Snrpn gene. Besides their co-regulated imprinted expression, two observations suggest that the spatio-temporal expression of these genes could also be co-regulated. First, the PWS genes have all been reported to be expressed in the mouse nervous system. Second, Snurf-Snrpn and its associated IC are the most ancient elements of the domain which later acquired additional functional genes by retrotransposition. Although located at least 1.5 megabases from the IC, these retroposons acquired the same imprinted regulation as Snurf-Snrpn. In this study, we ask whether the IC, in addition to its function in imprinting, could also be involved in the spatio-temporal regulation of genes in the PWS domain.

Results
We compared the expression pattern of Snurf-Snrpn and C/D-box small nucleolar RNAs (snoRNAs) MBII-85 and MBII-52 to the expression pattern of the two evolutionary related retroposons Ndn and Magel2, in the developing mouse embryo. We show that these genes have highly similar expression patterns in the central nervous system, suggesting that they share a common central nervous system-specific regulatory element. Among these genes, Ndn and Magel2 display the most similar expression patterns. Using transgenic mice containing the Ndn and Magel2 genes, we show that the transgenic Ndn gene whereas not imprinted is correctly expressed. Search for DNase I hypersensitive sites in the Ndn-Magel2 genomic region and comparative genomic analyses were performed in order to identify potential transcriptional cis-regulatory elements.

Conclusions
These results strongly suggest that paternally expressed genes of the PWS domain share a common central nervous system-specific regulatory element. We proposed that this regulatory element could co-localize with the IC. However, we demonstrate that the IC, if required for imprinted regulation, is not involved in the spatio-temporal regulation of distantly located retrotransposed genes such as the Ndn gene in the PWS domain.
Characterization of the chicken inward rectifier K+ channel IRK1/Kir2.1 gene
Authors: Mutai Hideki , Kenyon Lawrence C , Locke Emily , Kikuchi Nami , Oberholtzer John Carl 
Published: January 2005

Abstract
Background
Inward rectifier potassium channels (IRK) contribute to the normal function of skeletal and cardiac muscle cells. The chick inward rectifier K+ channel cIRK1/Kir2.1 is expressed in skeletal muscle, heart, brain, but not in liver; a distribution similar but not identical to that of mouse Kir2.1. We set out to explore regulatory domains of the cIRK1 promoter that enhance or inhibit expression of the gene in different cell types.

Results
We cloned and characterized the 5'-flanking region of cIRK1. cIRK1 contains two exons with splice sites in the 5'-untranslated region, a structure similar to mouse and human orthologs. cIRK1 has multiple transcription initiation sites, a feature also seen in mouse. However, while the chicken and mouse promoter regions share many regulatory motifs, cIRK1 possesses a GC-richer promoter and a putative TATA box, which appears to positively regulate gene expression. We report here the identification of several candidate cell/tissue specific cIRK1 regulatory domains by comparing promoter activities in expressing (Qm7) and non-expressing (DF1) cells using in vitro transcription assays.

Conclusion
While multiple transcription initiation sites and the combinatorial function of several domains in activating cIRK1 expression are similar to those seen in mKir2.1, the cIRK1 promoter differs by the presence of a putative TATA box. In addition, several domains that regulate the gene's expression differentially in muscle (Qm7) and fibroblast cells (DF1) were identified. These results provide fundamental data to analyze cIRK1 transcriptional mechanisms. The control elements identified here may provide clues to the tissue-specific expression of this K+ channel.
16S rRNA gene based analysis of Enterobacter sakazakii strains from different sources and development of a PCR assay for identification
Authors: Lehner Angelika , Tasara Taurai , Stephan Roger 
Published: January 2005

Abstract
Background
E. sakazakii is considered to be an opportunistic pathogen, implicated in food borne diseases causing meningitis or enteritis especially in neonates and infants. Cultural standard identification procedures for E. sakazakii include the observation of yellow pigmentation of colonies and a positive "Equation missing"glucosidase activity. Up to now, only one PCR system based on a single available 16S rRNA gene sequence has been published for E. sakazakii identification. However, in our hands a preliminary evaluation of this system to a number of target and non-target strains showed significant specificity problems of this system. In this study full-length 16S rRNA genes of thirteen E. sakazakii strains from food, environment and human origin as well as the type strain ATCC 51329 were sequenced. Based on this sequence data a new specific PCR system for E. sakazakii was developed and evaluated.

Results
By phylogenetic analysis of the new full-length 16S rRNA gene sequence data obtained we could show the presence of a second phylogenetic distinct lineage within the E. sakazakii species. The newly developed 16S rRNA gene targeting PCR system allows identification of E. sakazakii strains from both lineages. The assay's ability to correctly identify different E. sakazakii isolates as well as to differentiate E. sakazakii from other closely related Enterobacteriaceae species and other microorganisms was shown on 75 target and non-target strains.

Conclusion
By this study we are presenting a specific and reliable PCR identification system, which is able to correctly identify E. sakazakii isolates from both phylogenetic distinct lines within the E. sakazakii species. The impact of this second newly described phylogenetic line within the E. sakazakii species in view of clinical and food safety aspects need further investigation.
A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system
Authors: Greub Gilbert , Collyn François , Guy Lionel , Roten Claude-Alain 
Published: January 2005

Abstract
Background
The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs).

Results
On the residual cumulative G+C content curve, a G+C-rich 19-kb region was observed. This sequence is part of a 100-kb chromosome region, containing 100 highly co-oriented ORFs, flanked by two 17-bp direct repeats. Two identical gly-tRNA genes in tandem are present at the proximal end of this genetic element. Several mobility genes encoding transposases and bacteriophage-related proteins are located within this chromosome region. Thus, this region largely fulfills the criteria of GIs. The G+C content analysis shows that several modules compose this GI. Surprisingly, one of them encodes all genes essential for F-like conjugative DNA transfer (traF, traG, traH, traN, traU, traW, and trbC), involved in sex pilus retraction and mating pair stabilization, strongly suggesting that, similarly to the other F-like operons, the parachlamydial tra unit is devoted to DNA transfer. A close relatedness of this tra unit to F-like tra operons involved in conjugative transfer is confirmed by phylogenetic analyses performed on concatenated genes and gene order conservation. These analyses and that of gly-tRNA distribution in 140 GIs suggest a proteobacterial origin of the parachlamydial tra unit.

Conclusions
A GI of the UWE25 chromosome encodes a potentially functional F-like DNA conjugative system. This is the first hint of a putative conjugative system in chlamydiae. Conjugation most probably occurs within free-living amoebae, that may contain hundreds of Parachlamydia bacteria tightly packed in vacuoles. Such a conjugative system might be involved in DNA transfer between internalized bacteria. Since this system is absent from the sequenced genomes of Chlamydiaceae, we hypothesize that it was acquired after the divergence between Parachlamydiaceae and Chlamydiaceae, when the Parachlamydia-related symbiont was an intracellular bacteria. It suggests that this heterologous DNA was acquired from a phylogenetically-distant bacteria sharing an amoebal vacuole. Since Parachlamydiaceae are emerging agents of pneumonia, this GI might be involved in pathogenicity. In future, conjugative systems might be developed as genetic tools for Chlamydiales.
Extended-Spectrum β-lactamase (ESBL) producing Enterobacter aerogenes phenotypically misidentified as Klebsiella pneumoniae or K. terrigena
Authors: Claeys Geert , De Baere Thierry , Wauters Georges , Vandecandelaere Patricia , Verschraegen Gerda , Muylaert An , Vaneechoutte Mario 
Published: January 2005

Abstract
Background
Enterobacter aerogenes and Klebsiella pneumoniae are common isolates in clinical microbiology and important as producers of extended spectrum β-lactamases (ESBL). The discrimination between both species, which is routinely based on biochemical characteristics, is generally accepted to be straightforward. Here we report that genotypically unrelated strains of E. aerogenes can be misidentified as K. pneumoniae by routine laboratories using standard biochemical identification and using identification automates.

Results
Ten clinical isolates, identified as K. pneumoniae or K. terrigena with the routinely used biochemical tests and with API-20E, were identified as E. aerogenes by tDNA-PCR – an identification that was confirmed by 16S rRNA gene sequencing for five of these isolates. Misidentification also occurred when using the automated identification systems Vitek 2 and Phoenix, and was due to delayed positivity for ornithine decarboxylase and motility. Subculture and prolonged incubation resulted in positive results for ornithine decarboxylase and for motility. It could be shown by RAPD-analysis that the E. aerogenes strains belonged to different genotypes.

Conclusions
Clinical E. aerogenes isolates can be easily misidentified as Klebsiella due to delayed positivity for ornithine decarboxylase and motility. The phenomenon may be widespread, since it was shown to occur among genotypically unrelated strains from different hospitals and different isolation dates. A useful clue for correct identification is the presence of an inducible β-lactamase, which is highly unusual for K. pneumoniae. In several instances, the use of genotypic techniques like tDNA-PCR may circumvent problems of phenotypic identification.
Antitumor effects of two bisdioxopiperazines against two experimental lung cancer models in vivo
Authors: Lu Da-Yong , Xu Bin , Ding Jian 
Published: January 2005

Abstract
Background
Probimane (Pro), an anti-cancer agent originating in China, was derived from razoxane (ICRF-159, Raz), a drug created in Britain, specifically targeting at cancer metastasis and as a cardioprotectant of anthrocyclines. Pro and Raz are bisdioxopiperazine compounds. In this work, we evaluated the anti-tumor and anti-metastatic effects of Pro and Raz in vivo against two lung tumor models, one of murine origin (Lewis lung carcinoma, LLC) and one of human origin (LAX-83).

Results
After determining the lethal dosage of Pro and Raz, we assessed and compared the inhibitory effects of Pro and Raz against primary tumor growth and metastatic occurrences of LLC at the dosage of LD5. Pro and Raz were active against primary tumor growth and significantly inhibited pulmonary metastasis of LLC at same dose-ranges (inhibitory rates > 90 %). Both Raz and Pro were effective in 1, 5, and 9 day administration schedules. Three different schedules of Raz and Pro were effective against the primary tumor growth of LLC (35–50 %). The synergistic anticancer effect of Raz with bleomycin (Ble) (from 41.3 % to 73.3 %) was more obvious than those with daunorubicin (Dau) (from 33.1 % to 56.3 %) in the LLC tumor model. Pro was also seen to have synergistic anti-cancer effects with Ble in the LLC model. Both Raz and Pro inhibited the growth of LAX 83 in a statistically significant manner.

Conclusions
These data suggest that both Raz and Pro may have anti-tumor potentiality and Raz and Pro have combinative effects with Ble or Dau. The potential targets of bisdioxopiperazines may include lung cancers, especially on tumor metastasis. The anti-cancer effects of Raz and Pro can be increased with the help of other anticancer drugs.
Molecular cloning and functional expression of geranylgeranyl pyrophosphate synthase from Coleus forskohliiBriq
Authors: Engprasert Surang , Taura Futoshi , Kawamukai Makoto , Shoyama Yukihiro 
Published: January 2005

Abstract
Background
Isopentenyl diphosphate (IPP), a common biosynthetic precursor to the labdane diterpene forskolin, has been biosynthesised via a non-mevalonate pathway. Geranylgeranyl diphosphate (GGPP) synthase is an important branch point enzyme in terpenoid biosynthesis. Therefore, GGPP synthase is thought to be a key enzyme in biosynthesis of forskolin. Herein we report the first confirmation of the GGPP synthase gene in Coleus forskohlii Briq.

Results
The open reading frame for full-length GGPP synthase encodes a protein of 359 amino acids, in which 1,077 nucleotides long with calculated molecular mass of 39.3 kDa. Alignments of C. forskohlii GGPP synthase amino acid sequences revealed high homologies with other plant GGPP synthases. Several highly conserved regions, including two aspartate-rich motifs were identified. Transient expression of the N-terminal region of C. forskohlii GGPP synthase-GFP fusion protein in tobacco cells demonstrated subcellular localization in the chloroplast. Carotenoid production was observed in Escherichia coli harboring pACCAR25ΔcrtE from Erwinia uredovora and plasmid carrying C. forskohlii GGPP synthase. These results suggested that cDNA encoded functional GGPP synthase. Furthermore, C. forskohlii GGPP synthase expression was strong in leaves, decreased in stems and very little expression was observed in roots.

Conclusion
This investigation proposed that forskolin was synthesised via a non-mevalonate pathway. GGPP synthase is thought to be involved in the biosynthesis of forskolin, which is primarily synthesised in the leaves and subsequently accumulates in the stems and roots.
Endotracheal tube cuff pressure in three hospitals, and the volume required to produce an appropriate cuff pressure
Authors: Sengupta Papiya , Sessler Daniel I , Maglinger Paul , Wells Spencer , Vogt Alicia , Durrani Jaleel , Wadhwa Anupama 
Published: January 2005

Abstract
Background
Cuff pressure in endotracheal (ET) tubes should be in the range of 20–30 cm H2O. We tested the hypothesis that the tube cuff is inadequately inflated when manometers are not used.

Methods
With IRB approval, we studied 93 patients under general anesthesia with an ET tube in place in one teaching and two private hospitals. Anesthetists were blinded to study purpose. Cuff pressure in tube sizes 7.0 to 8.5 mm was evaluated 60 min after induction of general anesthesia using a manometer connected to the cuff pilot balloon. Nitrous oxide was disallowed. After deflating the cuff, we reinflated it in 0.5-ml increments until pressure was 20 cmH2O.

Results
Neither patient morphometrics, institution, experience of anesthesia provider, nor tube size influenced measured cuff pressure (35.3 ± 21.6 cmH2O). Only 27% of pressures were within 20–30 cmH2O; 27% exceeded 40 cmH2O. Although it varied considerably, the amount of air required to achieve a cuff pressure of 20 cmH2O was similar with each tube size.

Conclusion
We recommend that ET cuff pressure be set and monitored with a manometer.
A suite of web applications to streamline the interdisciplinary collaboration in secondary data analyses
Authors: Pietrobon Ricardo , Guller Ulrich , Martins Henrique , Menezes Andreia P , Higgins Laurence D , Jacobs Danny O 
Published: January 2005

Abstract
Background
We describe a system of web applications designed to streamline the interdisciplinary collaboration in outcomes research.

Description
The outcomes research process can be described as a set of three interrelated phases: design and selection of data sources, analysis, and output. Each of these phases has inherent challenges that can be addressed by a group of five web applications developed by our group. QuestForm allows for the formulation of relevant and well-structured outcomes research questions; Research Manager facilitates the project management and electronic file exchange among researchers; Analysis Charts facilitate the communication of complex statistical techniques to clinicians with varying previous levels of statistical knowledge; Literature Matrices improve the efficiency of literature reviews. An outcomes research question is used to illustrate the use of the system.

Conclusions
The system presents an alternative to streamline the interdisciplinary collaboration of clinicians, statisticians, programmers, and graduate students.
Caregivers' practices, knowledge and beliefs of antibiotics in paediatric upper respiratorytract infections in Trinidad and Tobago: a cross-sectional study
Authors: Parimi Neeta , Pereira Lexley M Pinto , Prabhakar P 
Published: January 2005

Abstract
Background
Antibiotic overuse and misuse for upper respiratory tract infections in children is widespread and fuelled by public attitudes and expectations. This study assessed knowledge, beliefs, and practices regarding antibiotic use for these paediatric infections among children's caregivers' in Trinidad and Tobago in the English speaking Caribbean.

Methods
In a cross-sectional observational study, by random survey children's adult caregivers gave a telephone interview from November 1998 to January 1999. On a pilot-tested evaluation instrument, respondents provided information about their knowledge and beliefs of antibiotics, and their use of these agents to treat recent episodes (< previous 30 days) of upper respiratory tract infections in children under their care. Caregivers were scored on an antibiotic knowledge test and divided based on their score. Differences between those with high and low scores were compared using the chi-square test.

Results
Of the 417 caregivers, 70% were female and between 18–40 years, 77% were educated to high school and beyond and 43% lived in urban areas. Two hundred and forty nine (60%) respondents scored high (≥ 12) on antibiotic knowledge and 149 (34%) had used antibiotics in the preceding year. More caregivers with a high knowledge score had private health insurance (33%), (p < 0.02), high school education (57%) (p < 0.002), and had used antibiotics in the preceding year (p < 0.008) and within the last 30 days (p < 0.05). Caregivers with high scores were less likely to demand antibiotics (p < 0.05) or keep them at home (p < 0.001), but more likely to self-treat with antibiotics (p < 0.001). Caregivers administered antibiotics in 241/288 (84%) self-assessed severe episodes of infection (p < 0.001) and in 59/126 (43%) cough and cold episodes without visiting a health clinic or private physician (p < 0.05).

Conclusions
In Trinidad and Tobago, caregivers scoring low on antibiotic knowledge have erroneous beliefs and use antibiotics inappropriately. Children in their care receive antibiotics for upper respiratory tract infections without visiting a health clinic or a physician. Educational interventions in the community on the consequences of inappropriate antibiotic use in children are recommended. Our findings emphasise the need to address information, training, legislation and education at all levels of the drug delivery system towards discouraging self-medication with antibiotics in children.
Duloxetine for the long-term treatment of Major Depressive Disorder in patients aged 65 and older: an open-label study
Authors: Wohlreich Madelaine M , Mallinckrodt Craig H , Watkin John G , Hay Donald P 
Published: January 2005

Abstract
Background
Late-life depression is a common, chronic and recurring disorder for which guidelines recommend long-term therapy. The safety and efficacy of duloxetine for the treatment of major depressive disorder (MDD) were evaluated using data from elderly patients (age ≥ 65 years; n = 101) who participated in a large, multinational, open-label study.

Methods
Patients meeting DSM-IV criteria for MDD received duloxetine 80 mg/d (40 mg twice daily (BID)) to 120 mg/d (60 mg BID) for up to 52 weeks. Efficacy measures included the Clinical Global Impression of Severity (CGI-S) scale, the 17-item Hamilton Rating Scale for Depression (HAMD17), the Beck Depression Inventory-II (BDI-II), the Patient Global Impression of Improvement (PGI-I) scale, and the Sheehan Disability Scale (SDS). Safety and tolerability were evaluated using discontinuation rates, spontaneously reported adverse events, and changes in vital signs, ECG, and laboratory analytes.

Results
Mean changes in HAMD17 total score at Weeks 6, 28, and 52 were -13.0, -17.4 and -17.5 (all p-values <.001). Significant improvement (p < .001) in both clinician- (CGI-S) and patient-rated (PGI-I) measures of improvement were observed at Week 1 and sustained throughout the study. Observed case response rates at Weeks 6, 28, and 52 were 62.9%, 84.9%, and 89.4%, respectively, while the corresponding rates of remission were 41.4%, 69.8%, and 72.3%. Adverse events led to discontinuation in 27 (26.7%) patients. Treatment-emergent adverse events reported by >10% of patients included dizziness, nausea, constipation, somnolence, insomnia, dry mouth, and diarrhea. Most events occurred early in the study. Mean changes at endpoint in blood pressure and body weight were less than 2.0 mm Hg, and -0.1 kg, respectively.

Conclusions
In this open-label study, duloxetine was effective, safe, and well tolerated in the long-term treatment of MDD in patients aged 65 and older.