bluuebunny/crossref_metadata_2025_split huggingface dataset:
The efficacy of bismuth containing quadruple therapy as a first‐line treatment option for Helicobacter pylori
Authors: UYGUN Ahmet , KADAYIFCI Abdurrahman , SAFALI Mukerrem , ILGAN Seyfettin , BAGCI Sait 
Published: October 2007

BACKGROUND:  Helicobacter pylori eradication rates have tended to decrease recently, mostly due to increasing antibiotic‐resistance. The present study aimed to compare the efficacy of bismuth‐based quadruple regimen with proton pump inhibitor‐based triple regimen for eradication of H. pylori.METHODS:  Consecutive H. pylori‐positive patients with non‐ulcer dyspepsia were randomized into one of two regimens: (i) bismuth subsalicylate 300 mg q.i.d., lansoprazole 30 mg b.i.d., tetracycline 500 mg q.i.d. and metronidazole 500 mg t.i.d. (BLTM group) for 14 days; (ii) lansoprazole 30 mg b.i.d., amoxicillin 1 g b.i.d and clarithromycin 500 mg b.i.d. (LAC) for 14 days. Gastroscopy and 14C‐Urea breath test (UBT) were performed before enrollment, and UBT only was repeated for 6 weeks after treatment.RESULTS:  A total of 240 patients were randomized into groups and 212 of them completed the protocols. The ‘intention‐to‐treat’ (ITT) and ‘per protocol’ (PP) H. pylori eradication rates were 70% (95%CI 61–78) and 82.3% (95%CI 74–89) in the BLTM group, and 57.5% (95%CI 48–66) and 62.7% (95%CI 53–71) in the LAC group. The BLTM treatment achieved a significantly better eradication rate compared with LAC treatment in PP analysis (82.3% vs. 62.7%, P = 0.002). Mild to severe side‐effects, which were more frequent in the BLTM group, were reported in 18.2% of the patients.CONCLUSION:  The bismuth‐based quadruple regimen achieved a better eradication rate compared with proton pump inhibitor‐based triple regimens as a first‐line eradication option for H. pylori in our population.
Peritoneal mesothelioma presenting as an acute surgical abdomen due to jejunal perforation
Authors: SALEMIS Nikolaos S , TSIAMBAS Evangelos , GOURGIOTIS Stavros , MELA Ageliki , KARAMERIS Andreas , TSOHATARIDIS Efstathios 
Published: October 2007

BACKGROUND:  Peritoneal mesothelioma is a rare disease associated with poor prognosis. Acute abdomen as the first presentation is an extremely rare occurrence. We report an exceptional case of a patient who was found to have a jejunal perforation due to infiltration of peritoneal mesothelioma.METHODS:  A 62‐year‐old man was admitted with clinical signs of peritonitis. Computerized tomographic scans showed a mass distal to the ligament of Treitz, thickening of the mesentery and a small amount of ascites.RESULTS:  Emergency laparotomy revealed a perforated tumor 15 cm distal to the ligament of Treitz and diffuse peritoneal disease. Segmental small bowel resection and suboptimal cytoreduction were performed. Histopathology and immunohistochemistry showed infiltration of malignant mesothelioma. During the postoperative period pleural mesothelioma was also diagnosed. Despite adjuvant chemotherapy, the patient died of disseminated progressive disease 7 months after surgery.CONCLUSIONS:  Peritoneal mesothelioma is a rare malignancy with grim prognosis. Small bowel involvement is a poor prognostic indicator. Our case of a small bowel perforation due to direct infiltration by peritoneal mesothelioma appears to be the first reported in the English literature.
Basic research on inflammatory bowel disease in China
Authors: BAI Ai Ping , OUYANG Qin , HU Ren Wei 
Published: October 2007

OBJECTIVE:  Since the etiology and the pathogenesis of inflammatory bowel disease (IBD) are still not well known, research on IBD often focuses on these topics. Investigative science papers about IBD in Chinese medical journals from 1989 to 2003 were viewed to understand the progress of basic IBD research in China.MATERIALS AND METHODS:  The basic science investigative papers about IBD from 1989 to 2003 in Chinese periodicals (VIP and CMCC) were reviewed and analyzed; the key words used were as follows: inflammatory bowel disease, ulcerative colitis, Crohn's disease, basic science investigation, and literature review.RESULTS:  There were 3454 articles about IBD published in Chinese medical journals from 1989 to 2003, and during these 15 years, 508 papers focused on basic scientific investigations. There were 463 papers investigating the pathogenesis of IBD, 287 papers on immunological mechanisms, and 176 papers about other mechanisms. There were 142 papers investigating the mechanisms of Chinese traditional medicine on IBD from 1989 to 2003, which included 117 papers related to animal experiments and 25 papers related to clinical studies.CONCLUSIONS:  There have been relatively few investigative scientific papers on IBD published in Chinese medical journals. However, the study of IBD has been emphasized in China. Research on the immunological mechanisms of IBD has been predominant. Furthermore, a large number of the research papers were about the mechanisms and effects of Chinese traditional medicine on IBD.
Transcriptomic and Phenotypic Analyses Suggest a Network between the Transcriptional Regulators HrcA and σBinListeria monocytogenes
Authors: Hu Yuewei , Oliver Haley F. , Raengpradub Sarita , Palmer M. Elizabeth , Orsi Renato H. , Wiedmann Martin , Boor Kathryn J. 
Published: October 2007

ABSTRACTListeria monocytogenesHrcA and CtsR negatively regulate class I and III stress response genes, respectively, while σBpositively regulates the transcription of class II stress response genes. To define the HrcA regulon and identify interactions between HrcA, CtsR, and σB, we characterized newly generatedL. monocytogenesΔhrcA, ΔctsRΔhrcA, and ΔhrcAΔsigBstrains, along with previously described ΔsigB, ΔctsR, and ΔctsRΔsigBstrains, using phenotypic assays (i.e., heat resistance, acid resistance, and invasion of human intestinal epithelial cells) and performed whole-genome transcriptome analysis of the ΔhrcAstrain. ThehrcAandsigBdeletions had significant effects on heat resistance. While thehrcAdeletion had no significant effect on acid resistance or invasion efficiency in Caco-2 cells, a linear regression model revealed a significant (P= 0.0493) effect of interactions between thehrcAdeletion and thectsRdeletion on invasiveness. Microarray-based transcriptome analyses and promoter searches identified (i) 25 HrcA-repressed genes, including two operons (thegroESLanddnaKoperons, both confirmed as HrcA regulated by quantitative real-time PCR) and one gene directly repressed by HrcA, and (ii) 36 genes that showed lower transcript levels in the ΔhrcAstrain and thus appear to be indirectly upregulated by HrcA. A number of genes were found to be coregulated by either HrcA and CtsR (2 genes), HrcA and σB(31 genes), or all three regulators (5 genes, e.g.,gadCB). Combined with previous evidence that σBappears to directly regulatehrcAtranscription, our data suggest that HrcA and σB, as well as CtsR, form a regulatory network that contributes to the transcription of a number ofL. monocytogenesgenes.
Cross-Ocean Distribution of
Rhodobacterales
Bacteria as Primary Surface Colonizers in Temperate Coastal Marine Waters
Authors: Dang Hongyue , Li Tiegang , Chen Mingna , Huang Guiqiao 
Published: October 2007

ABSTRACT

Bacterial surface colonization is a universal adaptation strategy in aquatic environments. However, neither the identities of early colonizers nor the temporal changes in surface assemblages are well understood. To determine the identities of the most common bacterial primary colonizers and to assess the succession process, if any, of the bacterial assemblages during early stages of surface colonization in coastal water of the West Pacific Ocean, nonnutritive inert materials (glass, Plexiglas, and polyvinyl chloride) were employed as test surfaces and incubated in seawater off the Qingdao coast in the spring of 2005 for 24 and 72 h. Phylogenetic analysis of the 16S rRNA gene sequences amplified from the recovered surface-colonizing microbiota indicated that diverse bacteria colonized the submerged surfaces. Multivariate statistical cluster analyses indicated that the succession of early surface-colonizing bacterial assemblages followed sequential steps on all types of test surfaces. The
Rhodobacterales
, especially the marine
Roseobacter
clade members, formed the most common and dominant primary surface-colonizing bacterial group. Our current data, along with previous studies of the Atlantic coast, indicate that the
Rhodobacterales
bacteria are the dominant and ubiquitous primary surface colonizers in temperate coastal waters of the world and that microbial surface colonization follows a succession sequence. A conceptual model is proposed based on these findings, which may have important implications for understanding the structure, dynamics, and function of marine biofilms and for developing strategies to harness or control surface-associated microbial communities.
Orthopoxvirus Detection in Environmental Specimens during Suspected Bioterror Attacks: Inhibitory Influences of Common Household Products
Authors: Kurth Andreas , Achenbach John , Miller Liljia , Mackay Ian M. , Pauli Georg , Nitsche Andreas 
Published: October 2007

ABSTRACTAfter terrorists attacked the United States in 2001, the appearance of letters and other objects containing powdery substances with unknown potentials for biological threat focused attention on the speed, sensitivity, and reliability of diagnostic methods. This study summarizes the abilities and limitations of real-time PCR, electron microscopy (EM), and virus isolation when used to detect potential bioweapons. In particular, we investigated the inhibitory influences of different common household products present in environmental specimens on PCR yield, EM detection, and virus isolation. We used vaccinia virus as a model for orthopoxviruses by spiking it into specimens. In the second part of the study, we describe modifications of diagnostic methods to overcome inhibitory effects. A variety of PCR amplification enhancers, DNA extraction protocols, and applications of internal controls were evaluated to improve diagnostic simplicity, speed, and reliability. As a result, we strongly recommend using at least two different frontline techniques in parallel, e.g., EM and PCR. A positive result obtained by any one of these techniques should be followed by a biological method to confirm the putative diagnosis. Confirmatory methods include virus isolation followed by an agent-specific immunofluorescence assay to confirm the presence of replication-competent particles.
Characterization of Nucleotide Pools as a Function of Physiological State in
Escherichia coli
Authors: Buckstein Michael H. , He Jian , Rubin Harvey 
Published: October 2007

ABSTRACT

Using a modified method that involves minimal manipulation of cells, we report new information about nucleotide pool sizes and changes throughout the
Escherichia coli
growth curve. Nucleotide pool sizes are critically dependent on sample manipulation and extraction methods. Centrifugation and even short (2 min) lapses in sample preparation can dramatically affect results. The measured ATP concentration at three different growth rates is at least 3 mM, well above the 0.8 mM needed to saturate the rRNA promoter P1 in vitro. Many of the pools, including ATP, GTP, and UTP, begin to decrease while the cells are still in mid-log growth. After an almost universal drop in nucleotide concentration as the cells transition from logarithmic to stationary phase, there is a “rebound” of certain nucleotides, most notably ATP, after the cells enter stationary phase, followed by a progressive decrease. UTP, in contrast, increases as the cells transition into stationary phase. The higher UTP values might be related to elevated UDP-glucose/galactose, which was found to be at higher concentrations than expected in stationary phase. dTTP is the most abundant deoxynucleoside triphosphate (dNTP) in the cell despite the fact that its precursors, UDP and UTP, are not. All dNTPs decrease through the growth curve but do not have the abrupt drop, as seen with other nucleotides when the cells transition into stationary phase.
Mapping the Transcription Start Points of theStaphylococcus aureus eap,emp, andvwbPromoters Reveals a Conserved Octanucleotide Sequence That Is Essential for Expression of These Genes
Authors: Harraghy Niamh , Homerova Dagmar , Herrmann Mathias , Kormanec Jan 
Published: October 2007

ABSTRACTMapping the transcription start points of theeap,emp, andvwbpromoters revealed a conserved octanucleotide sequence (COS). Deleting this sequence abolished the expression ofeap,emp, andvwb. However, electrophoretic mobility shift assays gave no evidence that this sequence was a binding site for SarA or SaeR, known regulators ofeapandemp.
Broad-Host-Range
Yersinia
Phage PY100: Genome Sequence, Proteome Analysis of Virions, and DNA Packaging Strategy
Authors: Schwudke Dominik , Ergin Asgar , Michael Kathrin , Volkmar Sven , Appel Bernd , Knabner Dorothea , Konietzny Antje , Strauch Eckhard 
Published: October 2007

ABSTRACT

PY100 is a lytic bacteriophage with a broad host range within the genus
Yersinia
. The phage forms plaques on strains of the three human pathogenic species
Yersinia enterocolitica, Y. pseudotuberculosis
, and
Y. pestis
at 37°C. PY100 was isolated from farm manure and intended to be used in phage therapy trials. PY100 has an icosahedral capsid containing double-stranded DNA and a contractile tail. The genome consists of 50,291 bp and is predicted to contain 93 open reading frames (ORFs). PY100 gene products were found to be homologous to the capsid proteins and proteins involved in DNA metabolism of the enterobacterial phage T1; PY100 tail proteins possess homologies to putative tail proteins of phage AaΦ23 of
Actinobacillus actinomycetemcomitans
. In a proteome analysis of virion particles, 15 proteins of the head and tail structures were identified by mass spectrometry. The putative gene product of ORF2 of PY100 shows significant homology to the gene
3
product (small terminase subunit) of
Salmonella
phage P22 that is involved in packaging of the concatemeric phage DNA. The packaging mechanism of PY100 was analyzed by hybridization and sequence analysis of DNA isolated from virion particles. Newly replicated PY100 DNA is cut initially at a
pac
recognition site, which is located in the coding region of ORF2.
Archaeal Transcription: Function of an Alternative Transcription Factor B from
Pyrococcus furiosus
Authors: Micorescu Michael , Grünberg Sebastian , Franke Andreas , Cramer Patrick , Thomm Michael , Bartlett Michael 
Published: October 2007

ABSTRACT

The genome of the hyperthermophile archaeon
Pyrococcus furiosus
encodes two transcription factor B (TFB) paralogs, one of which (TFB1) was previously characterized in transcription initiation. The second TFB (TFB2) is unusual in that it lacks recognizable homology to the archaeal TFB/eukaryotic TFIIB B-finger motif. TFB2 functions poorly in promoter-dependent transcription initiation, but photochemical cross-linking experiments indicated that the orientation and occupancy of transcription complexes formed with TFB2 at the strong
gdh
promoter are similar to the orientation and occupancy of transcription complexes formed with TFB1. Initiation complexes formed by TFB2 display a promoter opening defect that can be bypassed with a preformed transcription bubble, suggesting a mechanism to explain the low TFB2 transcription activity. Domain swaps between TFB1 and TFB2 showed that the low activity of TFB2 is determined mainly by its N terminus. The low activity of TFB2 in promoter opening and transcription can be partially relieved by transcription factor E (TFE). The results indicate that the TFB N-terminal region, containing conserved Zn ribbon and B-finger motifs, is important in promoter opening and that TFE can compensate for defects in the N terminus through enhancement of promoter opening.
Protein kinase C isoform expression as a predictor of disease outcome on endocrine therapy in breast cancer
Authors: Assender J W , Gee J M W , Lewis I , Ellis I O , Robertson J F R , Nicholson R I 
Published: October 2007

Background:Although in vitro breast cancer models have demonstrated a role for protein kinase C (PKC) α and δ isoforms in endocrine insensitivity and resistance respectively, there is currently little clinical evidence to support these observations.Aims:To define the pattern of PKC α and δ expression using breast cancer cell lines, with and without endocrine resistance, and also breast cancer samples, where expression can be correlated with clinicopathological and endocrine therapy outcome data.Methods:PKC isoform expression was examined in tamoxifen responsive, oestrogen receptor positive (ER+), ER+acquired tamoxifen resistant (TAM-R) and oestrogen receptor negative (ER−) cell lines by western blotting and immunocytochemical analysis. PKC isoform expression was then examined by immunohistochemistry in archival breast cancer specimens from primary breast cancer patients with known clinical outcome in relation to endocrine response and survival on therapy.Results:ER+breast cancer cell lines expressed considerable PKC-δ but barely detectable levels of PKC-α, whereas ER−cell lines expressed PKC-α but little PKC-δ. ER+acquired TAM-R cell lines expressed substantial levels of both PKC-α and δ. In clinical samples, high PKC-δ expression correlated to endocrine responsiveness whereas PKC-α expression correlated to ER negativity. PKC-δ was an independent predictor of duration of response to therapy. Patients showing a PKC-δ+/PKC-α−phenotype had a six times longer endocrine response than patients with the PKC-δ+/ PKC-α+phenotype (equating to tamoxifen resistance in vitro).Conclusions:Levels of PKC-α and δ expression appear to be indicative of response to anti-oestrogen therapy and could be useful in predicting a patient’s suitability for endocrine therapy.
Intercomparison of Odin–SMR ozone profiles with ground-based millimetre-wave observations in the Arctic, the mid-latitudes, and the tropics
Authors: Kopp G , Belova A , Diez y Riega V E , Groß J , Hochschild G , Hoffmann P , Murtagh D , Raffalski U , Urban J 
Published: October 2007

The sub-millimetre radiometer (SMR) on board the Odin satellite measures signatures of ozone in two bands centred at 501.8 and 544.6 GHz. From the measurements, ozone volume mixing ratio profiles in the stratosphere and lower mesosphere are retrieved using the Optimal Estimation Method. In this paper, the ozone profiles measured by Odin–SMR (level-2 data ver. 2.1 and 2.0, respectively) are compared to measurements taken by ground-based millimetre wave radiometers in the Arctic; at Kiruna, Sweden; in the mid-latitudes on the Zugspitze, Germany; and in the tropics at Mérida, Venezuela. The Kiruna Microwave Radiometer (KIMRA) covers the frequency range 195–224 GHz, and the Millimeter Wave Radiometer MIRA 2, which was operated on the Zugspitze and at Mérida, measures in the frequency band 268–281 GHz. From the measurements, ozone profiles in the vertical range between approximately 15–65 km were retrieved using the Optimal Estimation Method. Since the ground-based measurements have a lower vertical resolution than those of Odin the latter were degraded using the averaging kernels of the ground-based retrievals. The comparison of the resulting profiles to the ground-based data enables the identification of biases in the Odin measurements and their possible latitudinal variation. In general, a good agreement between satellite and ground-based measurements for the 501.8 GHz band was found in the stratosphere except for a negative bias in the Odin data of about 10–15% in the tropical measurements. The Odin measurements taken at 544.9 GHz yielded systematically 20–30% lower ozone mixing ratios in the middle stratosphere than the ground-based measurements at all sites. PACS No.: 92.60.hd
The impact of sea-glint upon limb radiance
Authors: Degenstein D A , Bourassa A E , Llewellyn E J , Lloyd N D 
Published: October 2007

A simple radiative transfer model is developed to calculate the contribution of sea-glint to limb radiance. It is shown that the absolute sea-glint signal peaks between 70° and 80° solar zenith angle. Sea-glint can contribute 10–15% of the total limb radiance at wavelengths greater than 600 nm, which is several times brighter than an equivalent 5% reflecting Lambertian ocean surface. A test case was identified over the Arabian Sea in October 2002 and the model results compared to limb observations from the Optical Spectrograph and Infra-Red Imaging System (OSIRIS) on-board the Odin satellite. PACS Nos.: 94.10.Gb, 93.85.+q, 42.68.Ay, 42.68.Mj
Status of the Odin/OSIRIS stratospheric O3 and NO2 data products
Authors: Haley C S , Brohede S 
Published: October 2007

This paper describes the status of the stratospheric ozone and nitrogen dioxide data products from the Optical Spectrograph and InfraRed Imager System (OSIRIS) instrument on the Odin satellite. The current version of the data products is 3.0, covering the period from November 2001 to the present. The O3 and NO2 retrieval methods are reviewed along with an overview of the error analyses and geophysical validation status. PACS Nos.: 07.05.Kf, 07.87.+v, 42.68.Mj, 92.60.hd, 92.60.Ta, 92.60.Vb, 92.70.Cp, 95.75.Fg, 95.75.Rs
A stratospheric NO2 climatology from Odin/OSIRIS limb-scatter measurements
Authors: Brohede S , McLinden C A , Berthet G , Haley C S , Murtagh D , Sioris Christopher E 
Published: October 2007

A climatology of stratospheric nitrogen dioxide (NO2), in terms of mean and standard deviation, as a function of latitude (5° bins); altitude (10–46 km in 2 km bins); local solar time (24 h); and month is constructed based on the Odin/OSIRIS limb-scattering data from 2002–2005. The measured profiles, given at specific local solar times, are scaled to all 24 h using a photochemical box model. The Odin orbit gives near global coverage around the equinoxes and hemispheric coverage elsewhere, due to lack of sunlight. The mean NO2 field at a specific local solar time involves high concentrations in the polar summer, peaking at around 25 km, with a negative equatorward gradient. Distinct high levels between 40–50° latitude at 30 km in the winter/spring hemisphere are also found, associated with the so-called {Noxon-cliff}. The diurnal cycle reveals the lowest NO2 concentrations just after sunrise and steep gradients at twilight. The 1σ standard deviation is generally quite low, around 20%, except for winter and spring high latitudes, where values are well above 50% and stretch through the entire stratosphere, a phenomenon probably related to the polar vortex. It is also found that NO2 concentrations are log-normally distributed. Comparisons to a climatology based on data from a (REPROBUS) chemical transport model for the same time period reveal relative differences below 20% in general, which is comparable to the estimated OSIRIS systematic uncertainty. Clear exceptions are the polar regions in winter/spring throughout the atmosphere and equatorial regions below 25 km, where OSIRIS is relatively higher by 40% and more. These discrepancies are most likely attributable to limitations of the model, but this has to be investigated further. PACS Nos.: 92.60.hd, 95.75.Rs, 95.55.Fw, 95.40.+s