bluuebunny/crossref_metadata_2025_split huggingface dataset:
A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block
Authors: Breen James , Wicker Thomas , Kong Xiuying , Zhang Juncheng , Ma Wujun , Paux Etienne , Feuillet Catherine , Appels Rudi , Bellgard Matthew 
Published: May 2010

AbstractBackgroundThe complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. Thectg1034contig completed in this paper was initially studied because it was assigned to theSr2resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features.ResultsBAC shotgun sequencing of the hexaploid wheat (Triticum aestivumcv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contigctg1034into a 783,553 bp genomic sequence. Thisctg1034sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. Thectg1034gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences ofBrachypodium distachyon,Oryza sativa,Sorghum bicolorandZea mays, even though the intergenic space and introns were divergent.ConclusionWe propose thatctg1034is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containinggypsyLTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and orientation within the gene island.Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824
A dynamic estimation of the daily cumulative cases during infectious disease surveillance: application to dengue fever
Authors: Chuang Pei-Hung , Chuang Jen-Hsiang , Lin I-Feng 
Published: May 2010

Abstract

Background
In infectious disease surveillance, when the laboratory confirmation of the cases is time-consuming, there is often a time lag between the number of suspect cases and the number of confirmed cases. This study proposes a dynamic statistical model to estimate the daily number of new cases and the daily cumulative number of infected cases, which was then applied to historic dengue fever data.

Methods
The duration between the date of disease onset and date of laboratory confirmation was assumed to follow a gamma distribution or a nonparametric distribution. A conditional probability of a case being a real case among the unconfirmed cases on a given date was then calculated. This probability along with the observed confirmed cases was integrated to estimate the daily number of new cases and the cumulative number of infected cases.

Results
The distribution of the onset-to-confirmation time for the positive cases was different from that of the negative cases. The daily new cases and cumulative epidemic curves estimated by the proposed method have a lower absolute relative bias than the values estimated solely based on the available daily-confirmed cases.

Conclusion
The proposed method provides a more accurate real-time estimation of the daily new cases and daily cumulative number of infected cases. The model makes use of the most recent "moving window" of information relative to suspect cases and dynamically updates the parameters. The proposed method will be useful for the real-time evaluation of a disease outbreak when case classification requires a time-consuming laboratory process to identify a confirmed case.
Primary liposarcoma of the ascending colon: a rare case of mixed type presenting as hemoperitoneum combined with other type of retroperitoneal liposarcoma
Authors: Choi Yoon Young , Kim Yong Jin , Jin So Young 
Published: May 2010

Abstract

Background
Liposarcoma occurs most commonly in the extremities and retroperitoneum, however, it has been rarely observed in the colon.

Case Presentation
A case is reported a 41-year-old man with liposarcoma of ascending colon which was presented as hemoperitoneum and combined with a different histological type of retroperitoneal liposarcoma. He visited hospital with right lower abdominal pain and palpable mass. Laboratory data including tumor markers were within normal limits, and computed tomography revealed a 15 × 10 cm sized enhancing soft mass. Right hemicolectomy was performed, and after that, a further large retroperitoneal mass was revealed and this was also radically excised. Mixed-type colon liposarcoma and well differentiated type of retroperitoneal liposarcoma were diagnosed in pathologic report. The patient has remained free of disease for 24 months.

Conclusions
No standardized guidelines have been established for its treatment because too small a number of cases have been reported, but surgical resection was considered the treatment of choice.
Antibiotic susceptibility of coagulase-negative staphylococci isolated from very low birth weight babies: comprehensive comparisons of bacteria at different stages of biofilm formation
Authors: Qu Yue , Daley Andrew J , Istivan Taghrid S , Garland Suzanne M , Deighton Margaret A 
Published: May 2010

Abstract

Background
Coagulase-negative staphylococci are major causes of bloodstream infections in very low birth weight babies cared for in Neonatal Intensive Care Units. The virulence of these bacteria is mainly due to their ability to form biofilms on indwelling medical devices. Biofilm-related infections often fail to respond to antibiotic chemotherapy guided by conventional antibiotic susceptibility tests.

Methods
Coagulase-negative staphylococcal blood culture isolates were grown in different phases relevant to biofilm formation: planktonic cells at mid-log phase, planktonic cells at stationary phase, adherent monolayers and mature biofilms and their susceptibilities to conventional antibiotics were assessed. The effects of oxacillin, gentamicin, and vancomycin on preformed biofilms, at the highest achievable serum concentrations were examined. Epifluorescence microscopy and confocal laser scanning microscopy in combination with bacterial viability staining and polysaccharide staining were used to confirm the stimulatory effects of antibiotics on biofilms.

Results
Most coagulase-negative staphylococcal clinical isolates were resistant to penicillin G (100%), gentamicin (83.3%) and oxacillin (91.7%) and susceptible to vancomycin (100%), ciprofloxacin (100%), and rifampicin (79.2%). Bacteria grown as adherent monolayers showed similar susceptibilities to their planktonic counterparts at mid-log phase. Isolates in a biofilm growth mode were more resistant to antibiotics than both planktonic cultures at mid-log phase and adherent monolayers; however they were equally resistant or less resistant than planktonic cells at stationary phase. Moreover, for some cell-wall active antibiotics, concentrations higher than conventional MICs were required to prevent the establishment of planktonic cultures from biofilms. Finally, the biofilm-growth of two S. capitis isolates could be enhanced by oxacillin at the highest achievable serum concentration.

Conclusion
We conclude that the resistance of coagulase-negative staphylococci to multiple antibiotics initially remain similar when the bacteria shift from a planktonic growth mode into an early attached mode, then increase significantly as the adherent mode further develops. Furthermore, preformed biofilms of some CoNS are enhanced by oxacillin in a dose-dependent manner.
Modulation of HIV-1 macrophage-tropism among R5 envelopes occurs before detection of neutralizing antibodies
Authors: Richards Kathryn H , Aasa-Chapman Marlén MI , McKnight Áine , Clapham Paul R 
Published: May 2010

Abstract
HIV-1 R5 viruses vary widely in their capacity to infect primary macrophages. R5 macrophage-tropism is associated with an increased envelope:CD4 affinity that partly results from an increased exposure of CD4 contact residues on gp120 and allows the use of low levels of CD4 for infection. The selective pressures in vivo that modulate R5 macrophage-tropism are not understood. It is possible that different R5 variants adapt for replication in either T-cells (high CD4) or in macrophages (low CD4). However, other selective pressures in vivo (e.g. neutralizing antibodies) may also impact R5 tropism. Here, we measured macrophage infectivity conferred by gp120 sequences amplified sequentially from subjects in London followed from the acute stage of infection. We report wide variation in the capacity of these envelopes to confer macrophage infection in the complete absence of both autologous and heterologous neutralizing antibodies. Our data show that the variation in macrophage tropism observed at early times cannot have been influenced by neutralizing antibodies.
Vaticanol C, a resveratrol tetramer, activates PPARα and PPARβ/δ in vitro and in vivo
Authors: Tsukamoto Tomoko , Nakata Rieko , Tamura Emi , Kosuge Yukiko , Kariya Aya , Katsukawa Michiko , Mishima Satoshi , Ito Tetsuro , Iinuma Munekazu , Akao Yukihiro , Nozawa Yoshinori , Arai Yuji , Namura Shobu , Inoue Hiroyasu 
Published: May 2010

Abstract

Background
Appropriate long-term drinking of red wine is associated with a reduced risk of cardiovascular disease. Resveratrol, a well-known SIRT1 activator is considered to be one of the beneficial components contained in red wine, and also developed as a drug candidate. We previously demonstrated that resveratrol protects brain against ischemic stroke in mice through a PPARα-dependent mechanism. Here we report the different effects of the oligomers of resveratrol.

Methods
We evaluated the activation of PPARs by ε-viniferin, a resveratrol dimer, and vaticanol C, a resveratrol tetramer, in cell-based reporter assays using bovine arterial endothelial cells, as well as the activation of SIRT1. Moreover, we tested the metabolic action by administering vaticanol C with the high fat diet to wild-type and PPARα-knockout male mice for eight weeks.

Results
We show that vaticanol C activates PPARα and PPARβ/δ in cell-based reporter assays, but does not activate SIRT1. ε-Viniferin shows a similar radical scavenging activity as resveratrol, but neither effects on PPARs and SIRT-1. Eight-week intake of vaticanol C with a high fat diet upregulates hepatic expression of PPARα-responsive genes such as cyp4a10, cyp4a14 and FABP1, and skeletal muscle expression of PPARβ/δ-responsive genes, such as UCP3 and PDK4 (pyruvate dehydrogenase kinase, isoform 4), in wild-type, but not PPARα-knockout mice.

Conclusion
Vaticanol C, a resveratrol tetramer, activated PPARα and PPARβ/δ in vitro and in vivo. These findings indicate that activation of PPARα and PPARβ/δ by vaticanol C may be a novel mechanism, affording beneficial effects against lifestyle-related diseases.
Costs of relaparotomy on-demand versus planned relaparotomy in patients with severe peritonitis: an economic evaluation within a randomized controlled trial
Authors: Opmeer Brent C , Boer Kimberly R , van Ruler Oddeke , Reitsma Johannes B , Gooszen Hein G , de Graaf Peter W , Lamme Bas , Gerhards Michael F , Steller E Philip , Mahler Cecilia M , Obertop Huug , Gouma Dirk J , Bossuyt Patrick MM , de Borgie Corianne AJM , Boermeester Marja A 
Published: May 2010

Abstract
Introduction
Results of the first randomized trial comparing on-demand versus planned-relaparotomy strategy in patients with severe peritonitis (RELAP trial) indicated no clear differences in primary outcomes. We now report the full economic evaluation for this trial, including detailed methods, nonmedical costs, further differentiated cost calculations, and robustness of different assumptions in sensitivity analyses.

Methods
An economic evaluation was conducted from a societal perspective alongside a randomized controlled trial in 229 patients with severe secondary peritonitis and an acute physiology and chronic health evaluation (APACHE)-II score ≥11 from two academic and five regional teaching hospitals in the Netherlands. After the index laparotomy, patients were randomly allocated to an on-demand or a planned-relaparotomy strategy. Primary resource-utilization data were used to estimate mean total costs per patient during the index admission and after discharge until 1 year after the index operation. Overall differences in costs between the on-demand relaparotomy strategy and the planned strategy, as well as relative differences across several clinical subgroups, were evaluated.

Results
Costs were substantially lower in the on-demand group (mean, €65,768 versus €83,450 per patient in the planned group; mean absolute difference, €17,682; 95% CI, €5,062 to €29,004). Relative differences in mean total costs per patient (approximately 21%) were robust to various alternative assumptions. Planned relaparotomy consistently generated more costs across the whole range of different courses of disease (quick recovery and few resources used on one end of the spectrum; slow recovery and many resources used on the other end). This difference in costs between the two surgical strategies also did not vary significantly across several clinical subgroups.

Conclusions
The reduction in societal costs renders the on-demand strategy a more-efficient relaparotomy strategy in patients with severe peritonitis. These differences were found across the full range of healthcare resources as well as across patients with different courses of disease.

Trial Registration
ISRCTN51729393
Comparison of albicans vs. non-albicans candidemia in French intensive care units
Authors: Leroy Olivier , Mira Jean-Paul , Montravers Philippe , Gangneux Jean-Pierre , Lortholary Olivier ,   the AmarCand Study Group
Published: May 2010

Abstract
Introduction
Candidemia raises numerous therapeutic issues for intensive care physicians. Epidemiological data that could guide the choice of initial therapy are still required. This analysis sought to compare the characteristics of intensive care unit (ICU) patients with candidemia due to non-albicansCandida species with those of ICU patients with candidemia due to Candidaalbicans.

Methods
A prospective, observational, multicenter, French study was conducted from October 2005 to May 2006. Patients exhibiting candidemia developed during ICU stay and exclusively due either to one or more non-albicans Candida species or to C. albicans were selected. The data collected included patient characteristics on ICU admission and at the onset of candidemia.

Results
Among the 136 patients analyzed, 78 (57.4%) had candidemia caused by C. albicans. These patients had earlier onset of infection (11.1 ± 14.2 days after ICU admission vs. 17.4 ± 17.7, p = 0.02), higher severity scores on ICU admission (SOFA: 10.4 ± 4.7 vs. 8.6 ± 4.6, p = 0.03; SAPS II: 57.4 ± 22.8 vs. 48.7 ± 15.5, P = 0.015), and were less often neutropenic (2.6% vs. 12%, p = 0.04) than patients with candidemia due to non-albicans Candida species.

Conclusions
Although patients infected with Candida albicans differed from patients infected with non-albicans Candida species for a few characteristics, no clinical factor appeared pertinent enough to guide the choice of empirical antifungal therapy in ICU.
EphB2-mediated interactions are essential for proper migration of T cell progenitors during fetal thymus colonization
Authors: Stimamiglio Marco A , Jiménez Eva , Silva-Barbosa Suse D , Alfaro David , García-Ceca José J , Muñoz Juan J , Cejalvo Teresa , Savino Wilson , Zapata Agustín 
Published: May 2010

Abstract
Recruitment of lymphoid progenitors to the thymus is compromised by the lack of Eph/ephrin signaling in both T-cell progenitors and thymic microenvironmental cells
The ephrin-Eph ligand receptor pair is known to control the repulsion/adhesion process in different tissues, including the immune system. Herein, we evaluated the role of EphB2 receptors in T cell progenitor migration during in vitro thymus colonization and to ECM or chemokine stimuli. EphB2 and their ligands, ephrin-B1 and ephrin-B2, are expressed in BM-derived progenitors, and EphB2−/− cells had diminished thymus colonization capacity. Conversely, EphB2LacZ cells, which maintain a preserved ephrin-binding domain, were capable of colonizing WT thymuses similarly to WT progenitors, highlighting the importance of reverse signals transmitted to normal fetal thymus. However, the EphB2 receptor expressed by microenvironmental cells also drives progenitor immigration, as recolonization of EphB2-deficient fetal thymuses was compromised profoundly. Additionally, we observed lower depositions of ECM and chemokines on EphB2-deficient thymuses but no changes in their receptor expression on BM-derived progenitors and developing thymocytes. Migration of EphB2-deficient progenitors and thymocytes was also reduced through ECM or chemokine stimuli. Furthermore, ephrin-B1 costimulation also inhibited haptotaxis and chemotaxis of WT but not EphB2LacZ cells, demonstrating the specific involvement of EphB2 signaling on T cell progenitor migration. Our data suggest the relevance of a nonactivated EphB2 for regulating T cell progenitor migration and its modulation upon ephrin-B engagement.
Quantitative denaturing high performance liquid chromatography (Q-dHPLC) detection of APC long DNA in faeces from patients with colorectal cancer
Authors: Kalimutho Murugan , Blanco Giovanna Del Vecchio , Gravina Paolo , Cretella Micaela , Mannucci Liliana , Mannisi Elena , Formosa Amanda , Pallone Francesco , Federici Giorgio , Bernardini Sergio 
Published: May 2010

Abstract

Background: Colorectal cancer (CRC) is the second leading cause of cancer-related deaths. However, prevention is possible by early detection. In the present work, we have demonstrated and validated a novel quantitative method based on a DNA integrity assay and mutation in faeces of CRC patients using denaturing high performance liquid chromatography (dHPLC).

Methods: Faecal DNA (fDNA) was isolated from 28 CRC, 96 healthy and 61 patients with adenomas. Adenomatosis polyposis coli (APC)-Long-DNA and its mutations were analysed using dHPLC and the Sanger sequencing method. The diagnostic performance was assessed using receiver operating characteristic curve analysis.

Results: We detected APC-Long-DNA in 21/28 CRC subjects with a sensitivity of 75% and specificity of 91.7%. A cut-off ratio of 0.2317 was used for APC/β-actin. The Q-dHPLC detection limit was 0.02 ng/injection. The average initial fDNA presence based on a single gene of β-actin was 26.12±13.39 ng/mL for healthy, and 49.61±46.28 ng/mL for CRC subjects, with a sensitivity of 71.4% and a specificity of 84.4% at a cut-off value >29 ng/mL. We also detected a novel mutation at codon 1576 Lys/Glu using dHPLC.

Conclusions: This study highlights a novel application of Q-dHPLC in the DNA integrity assay, which demonstrates high performance, good reproducibility, and low cost for the CRC detection using faeces. Further studies in a larger population are needed to confirm these results.
Clin Chem Lab Med 2010;48:1303–11.
Determination of trace elements in iron minerals by instrumental and radiochemical neutron activation analysis
Authors: Makreski Petre , Jacimovic Radojko , Stibilj Vekoslava , Stafilov Trajče , Jovanovski Gligor 
Published: May 2010

Abstract
The method for determination of major and trace elements in iron oxide [hematite (Fe2O3)] and sulfide [pyrite (FeS2) and chalcopyrite (CuFeS2)] minerals using the k
0-method of neutron activation analysis in both forms: instrumental (k
0-INAA) and radiochemical (k
0-RNAA) was suggested. In order to avoid interferences from iron on the determination of elements present in trace levels, radiochemical separation was made. Determination of the investigated elements in the aqueous phase was performed by k
0-RNAA after extraction of iron by isoamyl acetate (IAA) and diisopropyl ether (DIPE) from hydrochloric acid solution. The distribution of 35 elements in extraction systems (with intermediate/medium and long half-lived radionuclides) present in the studied minerals was investigated.
Novel polymer vectors of 64Cu
Authors: Kozempel J. , Hrubý M. , Nováková Michaela , Kučka Jan , Lešetický Ladislav , Lebeda O. 
Published: May 2010

Abstract
We describe a preparation of novel polymer vectors of 64Cu based on co-polymers of poly- (N-isopropylacrylamide) and poly- (N-hydroxypropylmethacrylamide). DOTA, DTPA, dipicolylamine, thiosemicarbazone and Ag-ionophore-II ligands were tested to bind 64Cu in a polymer chain. Labeling yields with no-carrier-added 64Cu varied from 95 to 99% in 30 min. at laboratory temperature. Vectors were stable in vitro for 24 h in human serum and might be prospective for targeted 64Cu radio or combined radiochemotherapy.
The Stela of Dedusobek. (Cairo, CG 20596)
Authors: Stefanović Danijela 
Published: May 2010

Abstract
Publication of a Middle Kingdom stela (Cairo, CG 20596) belonging to the ‘Draftsman ddw-sbk’, found in the northern necropolis at Abydos. The stela is on display on the ground floor of the Egyptian Museum. The text of the stela was published without translation by A. Mariette. The monument can be dated by the offering formula, its respective palaeography, epigraphy, and iconography to the Late Middle Kingdom. It is well preserved and traces of colors are still visible.
Prediction of Type 1 Diabetes in the General Population
Authors: Knip Mikael , Korhonen Sari , Kulmala Petri , Veijola Riitta , Reunanen Antti , Raitakari Olli T. , Viikari Jorma , Åkerblom Hans K. 
Published: May 2010

OBJECTIVE
To evaluate the utility of GAD antibodies (GADAs) and islet antigen-2 antibodies (IA-2As) in prediction of type 1 diabetes over 27 years in the general population and to assess the 6-year rates of seroconversion.

RESEARCH DESIGN AND METHODS
A total of 3,475 nondiabetic subjects aged 3–18 years were sampled in 1980, and 2,375 subjects (68.3%) were resampled in 1986. All subjects were observed for development of diabetes to the end of 2007. GADAs and IA-2As were analyzed in all samples obtained in 1980 and 1986.

RESULTS
A total of 34 individuals (1.0%; 9 developed diabetes) initially had GADAs and 22 (0.6%; 9 developed diabetes) IA-2As. Seven subjects (0.2%) tested positive for both autoantibodies. The positive seroconversion rate over 6 years was 0.4% for GADAs and 0.2% for IA-2As, while the inverse seroconversion rates were 33 and 57%, respectively. Eighteen subjects (0.5%) developed type 1 diabetes after a median pre-diabetic period of 8.6 years (range 0.9–20.3). Initial positivity for GADAs and/or IA-2As had a sensitivity of 61% (95% CI 36–83) for type 1 diabetes. Combined positivity for GADAs and IA-2As had both a specificity and a positive predictive value of 100% (95% CI 59–100).

CONCLUSIONS
One-time screening for GADAs and IA-2As in the general childhood population in Finland would identify ∼60% of those individuals who will develop type 1 diabetes over the next 27 years, and those subjects who have both autoantibodies carry an extremely high risk for diabetes. Both positive and inverse seroconversions do occur over time reflecting a dynamic process of β-cell autoimmunity.