bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytokeratin 20 and vascular endothelial growth factor as molecular markers in Egyptian patients with colorectal cancer
Authors: Auf Fatma A , El-Eibdy Gamal K , Mosaad Youssef M , El-Ghannam Doaa M , El-Masry Emad E 
Published: April 2010

Purpose. To investigate the expression of cytokeratin 20 (CK20) and vascular endothelial growth factor (VEGF) in the peripheral blood of colorectal cancer (CRC) patients, and correlate the findings with the pathologic data of the patients. Methods. This study was carried out on 50 subjects, 40 patients with histologically confirmed colorectal carcinoma undergoing elective surgery and 10 healthy individuals matched for age and sex. Total RNA extraction followed by real time quantitative RT-PCR and real time TaqMan quantitative assay for peripheral blood expression of CK20 and VEGF was done for both patients and controls. Results. (1) Statistically significant high levels of CK20,VEGF, CEA (p = 0.000 each) and CA19-9 (p = 0.002) in CRC patients when compared with controls; (2) Statistically significant increase in the expression of CK20 in advancing CRC stage C (p = 0.001) and with LN metastasis (p = 0.000); (3) Statistically significant increase in the expression of VEGF in advancing CRC stage C (p = 0.002), pathologic grade (p = 0.038), and with LN metastasis (p = 0.004); and (4) statistically positive correlation between CK20 and VEGF expressions, and also between these markers and CEA level. Conclusion. CK20 and VEGF expressions in peripheral blood of CRC patients are promising molecular markers for CRC progression and metastasis.
The development of a competency framework for pharmacists providing cancer services
Authors: Carrington Christine , Weir Janet , Smith Peter 
Published: April 2010

Background: Health practitioners should possess relevant, up to date skills and be able to perform within their required scope of practice to ensure that they are competent. Maintaining the competency of health care professionals is a key principle of clinical governance and risk management. The aim of this project was to develop a competency framework for pharmacists providing pharmaceutical care to cancer patients. Methodology: An initial draft framework was developed based on existing documentation and adapted to the needs of Queensland Health (QH) facilities. Pharmacists in QH and interstate were asked to review the framework for content and applicability. Cancer care pharmacists in QH were invited to evaluate and score the usefulness and relevance of the final framework. Results: The framework consists of competency clusters, which describe core activities within three areas: patient care competencies, knowledge competencies, and advanced level competencies. The characteristics of the levels of practice at foundation, advanced, and consultant are defined. Twelve pharmacists evaluated the framework by self-assessing their own practice. Respondents reported that the framework was very to somewhat reflective of what they usually do and gave overall support for the content and applicability to practice. Discussion: The framework has been developed using national and international documents and the input of experienced practitioners across Australia. It represents a set of key competencies for the pharmaceutical delivery of cancer care. The next essential step of the competency framework is to implement and integrate the framework into practice and to develop accompanying training tools.
Laparoendoscopic single-site surgery in urology
Authors: Berkowitz Jared R. , Allaf Mohamad E. 
Published: April 2010

Background: Since its introduction, the role of laparoscopic surgery has grown and it has now become the standard approach for many surgical procedures. The benefits of smaller incisions, improved pain and convalescence, and shorter hospital stays have greatly improved patient care and satisfaction. In an effort to further minimize the morbidity of surgery, laparoendoscopic single-site (LESS) or single-incision laparoscopic surgery (SILS) has emerged. We review the collective experience with this novel technique and share our initial observations and early results. Methods: We performed a literature search to review the published experience with this new technique including the breadth of applications and perioperative outcomes associated with LESS in urology. We also analysed the experience with this emerging technique at our institution. Results: There are numerous variations with regards to nomenclature as well as types of access to the abdominal cavity as it pertains to LESS. Urologic procedures involving single-port access have acceptable operating room time, blood loss, and postoperative pain, which are in line with standard laparoscopic surgical outcomes with the added benefit of improved cosmesis and smaller incisions. Conclusions: Further studies and larger cohorts are needed to assess the real benefit of LESS procedures. The additional learning curve needed to master these techniques may be a barrier to wider acceptance, although improvements in instrumentation are likely to bridge this gap.
Self-association mediated by the Ras association 1 domain of AF6 activates the oncogenic potential of MLL-AF6
Authors: Liedtke Michaela , Ayton Paul M. , Somervaille Tim C. P. , Smith Kevin S. , Cleary Michael L. 
Published: April 2010

AbstractMLL is a common target for chromosomal translocations associated with acute leukemia resulting in its fusion with a large variety of nuclear or cytoplasmic proteins that may activate its oncogenic properties by distinct but poorly understood mechanisms. The MLL-AF6 fusion gene represents the most common leukemogenic fusion of mixed lineage leukemia (MLL) to a cytoplasmic partner protein. Here, we identified a highly conserved Ras association (RA1) domain at the amino-terminus of AF6 as the minimal region sufficient for MLL-AF6 mediated myeloid progenitor immortalization in vitro and short latency leukemogenesis in vivo. Moreover, the ability of RA1 to activate MLL oncogenesis is conserved with its Drosophila ortholog, Canoe. Although the AF6 RA1 domain has previously been defined as an interaction surface for guanosine triphosphate–bound Ras, single amino acid substitutions known to abolish the AF6-Ras interaction did not abrogate MLL-AF6–mediated oncogenesis. Furthermore, fusion of MLL to heterologous RA domains of c-Raf1 or RalGDS, or direct fusion of MLL to constitutively active K-RAS, H-RAS, or RAP1 was not sufficient for oncogenic activation of MLL. Rather, the AF6 RA1 domain efficiently mediated self-association, suggesting that constitutive MLL self-association is a more common pathogenic mechanism for MLL oncogenesis than indicated by previous studies of rare MLL fusion partners.
Comprehensive analysis of lymph node stroma-expressed Ig superfamily members reveals redundant and nonredundant roles for ICAM-1, ICAM-2, and VCAM-1 in lymphocyte homing
Authors: Boscacci Rémy T. , Pfeiffer Friederike , Gollmer Kathrin , Sevilla Ana Isabel Checa , Martin Ana Maria , Soriano Silvia Fernandez , Natale Daniela , Henrickson Sarah , von Andrian Ulrich H. , Fukui Yoshinori , Mellado Mario , Deutsch Urban , Engelhardt Britta , Stein Jens V. 
Published: April 2010

AbstractAlthough it is well established that stromal intercellular adhesion molecule-1 (ICAM-1), ICAM-2, and vascular cell adhesion molecule-1 (VCAM-1) mediate lymphocyte recruitment into peripheral lymph nodes (PLNs), their precise contributions to the individual steps of the lymphocyte homing cascade are not known. Here, we provide in vivo evidence for a selective function for ICAM-1 > ICAM-2 > VCAM-1 in lymphocyte arrest within noninflamed PLN microvessels. Blocking all 3 CAMs completely inhibited lymphocyte adhesion within PLN high endothelial venules (HEVs). Postarrest extravasation of T cells was a 3-step process, with optional ICAM-1–dependent intraluminal crawling followed by rapid ICAM-1– or ICAM-2–independent diapedesis and perivascular trapping. Parenchymal motility of lymphocytes was modestly reduced in the absence of ICAM-1, while ICAM-2 and α4-integrin ligands were not required for B-cell motility within follicles. Our findings highlight nonredundant functions for stromal Ig family CAMs in shear-resistant lymphocyte adhesion in steady-state HEVs, a unique role for ICAM-1 in intraluminal lymphocyte crawling but redundant roles for ICAM-1 and ICAM-2 in lymphocyte diapedesis and interstitial motility.
Interaction of connexin43 and protein kinase C-delta during FGF2 signaling
Authors: Niger Corinne , Hebert Carla , Stains Joseph P 
Published: April 2010

Abstract

Background
We have recently demonstrated that modulation of the gap junction protein, connexin43, can affect the response of osteoblasts to fibroblast growth factor 2 in a protein kinase C-delta-dependent manner. Others have shown that the C-terminal tail of connexin43 serves as a docking platform for signaling complexes. It is unknown whether protein kinase C-delta can physically interact with connexin43.

Results
In the present study, we investigate by immunofluorescent co-detection and biochemical examination the interaction between Cx43 and protein kinase C-delta. We establish that protein kinase C-delta physically interacts with connexin43 during fibroblast growth factor 2 signaling, and that protein kinase C delta preferentially co-precipitates phosphorylated connexin43. Further, we show by pull down assay that protein kinase C-delta associates with the C-terminal tail of connexin43.

Conclusions
Connexin43 can serve as a direct docking platform for the recruitment of protein kinase C-delta in order to affect fibroblast growth factor 2 signaling in osteoblasts. These data expand the list of signal molecules that assemble on the connexin43 C-terminal tail and provide a critical context to understand how gap junctions modify signal transduction cascades in order to impact cell function.
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
Authors: Nagarajan Niranjan , Cook Christopher , Di Bonaventura MariaPia , Ge Hong , Richards Allen , Bishop-Lilly Kimberly A , DeSalle Robert , Read Timothy D , Pop Mihai 
Published: April 2010

Abstract
While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take many months and hence the time and effort can only be justified for high-priority genomes and in large sequencing centers. In this work, we revisit this issue in light of our own experience in producing finished and nearly-finished genomes for a range of microbial species in a small-lab setting. These genomes were finished with surprisingly little investments in terms of time, computational effort and lab work, suggesting that the increased access to sequencing might also eventually lead to a greater proportion of finished genomes from small labs and genomics cores.
Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data
Authors: Nishito Yukari , Osana Yasunori , Hachiya Tsuyoshi , Popendorf Kris , Toyoda Atsushi , Fujiyama Asao , Itaya Mitsuhiro , Sakakibara Yasubumi 
Published: April 2010

Abstract

Background

Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Although re-sequencing whole genomes of several laboratory domesticated B. subtilis 168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, B. subtilis natto, from very short read data is more challenging, particularly with our aim to assemble one fully connected scaffold from short reads around 35 bp in length.

Results
We applied a comparative genome assembly method, which combines de novo assembly and reference guided assembly, to one of the B. subtilis natto strains. We successfully assembled 28 scaffolds and managed to avoid substantial fragmentation. Completion of the assembly through long PCR experiments resulted in one connected scaffold for B. subtilis natto. Based on the assembled genome sequence, our orthologous gene analysis between natto BEST195 and Marburg 168 revealed that 82.4% of 4375 predicted genes in BEST195 are one-to-one orthologous to genes in 168, with two genes in-paralog, 3.2% are deleted in 168, 14.3% are inserted in BEST195, and 5.9% of genes present in 168 are deleted in BEST195. The natto genome contains the same alleles in the promoter region of degQ and the coding region of swrAA as the wild strain, RO-FF-1.
These are specific for γ-PGA production ability, which is related to natto production. Further, the B. subtilis natto strain completely lacked a polyketide synthesis operon, disrupted the plipastatin production operon, and possesses previously unidentified transposases.

Conclusions
The determination of the whole genome sequence of Bacillus subtilis natto provided detailed analyses of a set of genes related to natto production, demonstrating the number and locations of insertion sequences that B. subtilis natto harbors but B. subtilis 168 lacks. Multiple genome-level comparisons among five closely related Bacillus species were also carried out. The determined genome sequence of B. subtilis natto and gene annotations are available from the Natto genome browser http://natto-genome.org/.
Bacterial diversity at different stages of the composting process
Authors: Partanen Pasi , Hultman Jenni , Paulin Lars , Auvinen Petri , Romantschuk Martin 
Published: April 2010

Abstract

Background
Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA.

Results
Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts.

Conclusions
Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.
Excellent superiority and specificity of COBAS TaqMan HCV assay in an early viral kinetic change during pegylated interferon alpha-2b plus ribavirin treatment
Authors: Ogawa Eiichi , Furusyo Norihiro , Toyoda Kazuhiro , Taniai Hiroaki , Otaguro Shigeru , Kainuma Mosaburo , Murata Masayuki , Sawayama Yasunori , Hayashi Jun 
Published: April 2010

Abstract

Background
An early virological response (EVR) after the start of interferon (IFN) treatment for chronic hepatitis C leads to a successful virological outcome. To analyze an association between sustained virological response (SVR) and EVR by comparing TaqMan with Amplicor assays in HCV genotype 1-infected patients treated with pegylated (PEG)-IFN alpha-2b plus ribavirin (RBV).

Methods
We retrospectively analyzed a total of 80 HCV genotype 1 patients (39 SVR and 41 non-SVR patients), who received an enough dosage and a complete 48-week treatment of PEG-IFN alpha-2b plus RBV. Serum HCV RNA levels were measured by both TaqMan and Amplicor assays for each patients at Weeks 2, 4, 8 and 12 after the start of the antiviral treatment.

Results
Of the 80 patients with undetectable HCV RNA by Amplicor, 17 (21.3%) patients were positive for HCV RNA by TaqMan at Weeks 12. The quantification results showed that no significant difference in the decline of HCV RNA level between TaqMan and Amplicor 10-fold method assays within the initial 12 weeks of the treatment was found. However, the qualitative analysis showed significant differences of the positive predictive rates for SVR were found between TaqMan (100% at weeks 4 and 100% at weeks 8) and Amplicor (80.0% and 69.6%, respectively).

Conclusions
The COBAS TaqMan HCV assay is very useful for monitoring HCV viremia during antiviral treatment to predict a SVR in HCV genotype 1 patients.
Diversity in anopheline larval habitats and adult composition during the dry and wet seasons in Ouagadougou (Burkina Faso)
Authors: Fournet Florence , Cussac Maud , Ouari Ali , Meyer Pierre-Erwann , Toé Hyacinthe K , Gouagna Louis-Clément , Dabiré Roch K 
Published: April 2010

Abstract

Background
Several cases of malaria are frequently recorded during the dry period in Ouagadougou town (Burkina Faso). This has led to the design of a series of studies focusing on both parasitological and entomological investigations intended to provide relevant health data on the risk of local malaria transmission according to the way of urbanisation.

Methods
A cross-sectional entomological survey was carried out in various districts of Ouagadougou in April and October 2006. Adult malaria vectors were collected using CDC traps and indoor insecticide spraying performed in four houses during four consecutive days/nights. Intensive larval sampling was also done in available water ponds throughout the study sites.

Results
In April, the anopheline breeding sites consisted only of semi-permanent or permanent swamps located mainly in the two peripheral districts. Despite the presence of anopheline larvae in these breeding sites, less than five Anopheles gambiae s.l. adults were caught by CDC traps and indoor insecticide spraying. In October, additionally to the permanent breeding sites reported in April, some rainfall swamps were also found positive to anophelines. The number of adults' mosquitoes was higher than that collected in April (2 vs 159 in October). Out of 115 larvae of An. gambiae s.l. analysed by PCR in April, 59.1% (68/115) were identified as Anopheles arabiensis, 39.1% (45/115) as An. gambiae M while the S form represented less than 2%. Overall 120 larvae and 86 females were identified by PCR in October as An. gambiae M form (51%) and An. arabiensis (42.2%). The S form represented only 6.8%. The global sporozoite rate recorded was high (6.8%) and did not differ between the districts except in the central district where no positive mosquito was detected.

Conclusion
Although only few adults' mosquitoes were actively caught during the driest month, malaria vectors persisted all year long that increases the risk of urban malaria transmission. The distribution of breeding sites and especially the occurrence of malaria vectors were more abundant in the periphery, which is more like that of a rural settlement. The evolution of malaria prevalence and the factors sustaining the risk of transmission in Ouagadougou as well in many African cities during the dry season are discussed.
The expression of syndecan-1, syndecan-4 and decorin in healthy human breast tissue during the menstrual cycle
Authors: Hallberg Gunilla , Andersson Eva , Naessén Tord , Ordeberg Gunvor Ekman 
Published: April 2010

Abstract

Background
In order to unravel the interactions between the epithelium and the extra cellular matrix (ECM) in breast tissue progressing to cancer, it is necessary to understand the relevant interactions in healthy tissue under normal physiologic settings. Proteoglycans in the ECM play an important role in the signaling between the different tissue compartments. The proteoglycan decorin is abundant in the breast stroma. Decreased expression in breast cancer tissue is a sign of a poor tumor prognosis. The heparane sulphate proteoglycans syndecan-1 and syndecan-4 promote the integration of cellular adhesion and proliferation. The aim of this study was to investigate the gene expression and location of decorin, syndecan-1 and syndecan-4 in the healthy breast during the menstrual cycle.

Methods
Tissue from healthy women undergoing breast reduction plastic surgery was examined using immunohistochemistry (n = 38) and Real-Time RT-PCR (n = 20). Both parous and nulliparous women were eligible and the mean age of the women was 34(+/- 10 years) with regular menstrual cycles (28 +/- 7 days). None of the women had used hormonal treatment the last three months. The women were randomized to needle biopsy two months before the operation in the follicular or luteal menstrual phase and for another biopsy at the operation in the opposite phase. Serum samples were obtained to characterize the menstrual phase. The Wilcoxon signed rank test and Mann Whitney test were used for statistical analyses.

Results
By real time-RT-PCR the gene signal for all three proteoglycans; decorin (p = 0.02) and syndecan-1 (p = 0.03) and syndecan-4 (p = 0.02) was significantly lower among parous women in the luteal phase than in the follicular phase. Immunohistochemistry confirmed the identification of the proteins but no significant difference between menstrual phases was observed. Serum samples verified the menstrual phase.

Conclusions
Our study shows, for the first time in the healthy breast, a significantly lower expression of the genes for the three proteoglycans, decorin, syndecan-1 and syndecan-4 in the luteal phase during the menstrual cycle. These changes were registered under normal physiologic conditions. Since ECM molecules appear to be involved in tumor progression, these findings in the normal breast could constitute a base for further studies in women receiving hormonal therapy or those with breast cancer.