bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation of modified sorbents from rehydrated clay materials
Authors: Lhotka M. , Machovič V. , Doušová B. 
Published: June 2012

AbstractThe use of clay materials as selective sorbents for different contaminants requires very efficient methods. A natural kaolinite was calcined to metakaolinite and than rehydrated at different temperatures to produce a highly porous sorbent. The kinetics of this process were measured, with subsequent IR characterization of the phases formed. The surface and pore distribution of new phases were also assigned. In addition, the kaolinite obtained was pre-treated with Fe3+ ions to improve its sorption affinity for anionic particles. The rehydrated kaolinite and its Fe-modification were used for the adsorption of toxic cations (Zn, Cd, Pb) and anions (As, Se). Adsorption capacities depending on the physical chemical properties of the initial solution (pH, concentration of toxic ions) and the surface properties of the sorbent (specific surface area, modification method) were investigated. The adsorption properties of the sorbents were defined by the Langmuir model.
Mineralogy and microfabrics of claybearing sediments of NE Peloponnese (Greece): indices for physical behaviour in civil engineering works
Authors: Rathossi C. E. , Lampropoulou P. G. , Skourlis K. C. , Katagas C. G. 
Published: June 2012

AbstractThe mineralogical composition, microfabrics and geochemistry of a set of eight samples derived from a narrow area of NE Peloponnese (Greece), where engineering works are presently in progress, were investigated in this study. No important mineralogical differences were observed between the samples other than a variation in the proportions of the participating phases. Analyses reveal that these sediments consist mainly of carbonates (calcite, dolomite), quartz and feldspars (albite, orthoclase). Carbonate minerals exhibit a micritic texture and a high degree of cementation bonding. Phyllosilicates and clay minerals are also common, with smectite and mixed-layer smectite-chlorite being the prevailing phases, followed by chlorite and white mica (muscovite, illite). According to the physical properties measured on bulk samples, the samples were found to exhibit a low to medium expansion, low to intermediate plasticity, normal activity and brittle behaviour. The porosity does not exceed 46% and the organic matter ranges between 3.80 and 5.00%. The high degree of cementation, the dispersed appearance of clays, the small pores (<10 μm) and the common occurrence of smectite in a mixed-layer with chlorite are all favourable characteristics, positively influencing the sediment's stability for engineering constructions.
Additional chromosomal abnormalities in Philadelphia-positive clone: adverse prognostic influence on frontline imatinib therapy: a GIMEMA Working Party on CML analysis
Authors: Luatti Simona , Castagnetti Fausto , Marzocchi Giulia , Baldazzi Carmen , Gugliotta Gabriele , Iacobucci Ilaria , Specchia Giorgina , Zanatta Lucia , Rege-Cambrin Giovanna , Mancini Marco , Abruzzese Elisabetta , Zaccaria Alfonso , Grimoldi Maria Grazia , Gozzetti Alessandro , Ameli Gaia , Capucci Maria Adele , Palka Giandomenico , Bernasconi Paolo , Palandri Francesca , Pane Fabrizio , Saglio Giuseppe , Martinelli Giovanni , Rosti Gianantonio , Baccarani Michele , Testoni Nicoletta 
Published: June 2012

AbstractAdditional chromosomal abnormalities (ACAs) in Philadelphia-positive cells have been reported in ∼ 5% of patients with newly diagnosed chronic myeloid leukemia (CML) in chronic phase (CP). Few studies addressing the prognostic significance of baseline ACAs in patients treated with imatinib have been published previously. The European LeukemiaNet recommendations suggest that the presence of ACAs at diagnosis is a “warning” for patients in early CP, but there is not much information about their outcome after therapy with tyrosine kinase inhibitors. To investigate the role of ACAs in early CP CML patients treated with imatinib mesylate, we performed an analysis in a large series of 559 patients enrolled in 3 prospective trials of the Gruppo Italiano Malattie Ematologiche dell'Adulto Working Party on CML: 378 patients were evaluable and ACAs occurred in 21 patients (5.6%). The overall cytogenetic and molecular response rates were significantly lower and the time to response was significantly longer in patients with ACAs. The long-term outcome of patients with ACAs was inferior, but the differences were not significant. The prognostic significance of each specific cytogenetic abnormality was not assessable. Therefore, we confirm that ACAs constitute an adverse prognostic factor in CML patients treated with imatinib as frontline therapy. This study was registered with clinicaltrials.gov as NCT00514488 and NCT00510926.
Horizontal transfer of expressed genes in a parasitic flowering plant
Authors: Xi Zhenxiang , Bradley Robert K , Wurdack Kenneth J , Wong KM , Sugumaran M , Bomblies Kirsten , Rest Joshua S , Davis Charles C 
Published: June 2012

Abstract

Background
Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association between the parasite and its host. HGT in these systems has been invoked when a DNA sequence obtained from a parasite is placed phylogenetically very near to its host rather than with its closest relatives. Studies of HGT in parasitic plants have relied largely on the fortuitous discovery of gene phylogenies that indicate HGT, and no broad systematic search for HGT has been undertaken in parasitic systems where it is most expected to occur.

Results
We analyzed the transcriptomes of the holoparasite Rafflesia cantleyi Solms-Laubach and its obligate host Tetrastigma rafflesiae Miq. using phylogenomic approaches. Our analyses show that several dozen actively transcribed genes, most of which appear to be encoded in the nuclear genome, are likely of host origin. We also find that hundreds of vertically inherited genes (VGT) in this parasitic plant exhibit codon usage properties that are more similar to its host than to its closest relatives.

Conclusions
Our results establish for the first time a substantive number of HGTs in a plant host-parasite system. The elevated rate of unidirectional host-to- parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesia for maintaining these genes. Finally, a similar convergence in codon usage of VGTs has been shown in microbes with high HGT rates, which may help to explain the increase of HGTs in these parasitic plants.
Genomic characterization of two Staphylococcus epidermidis bacteriophages with anti-biofilm potential
Authors: Gutiérrez Diana , Martínez Beatriz , Rodríguez Ana , García Pilar 
Published: June 2012

Abstract

Background

Staphylococcus epidermidis is a commensal bacterium but can colonize the hospital environment due to its ability to form biofilms favouring adhesion to host tissues, medical devices and increasing resistance to antibiotics. In this context, the use of phages to destroy biofilms is an interesting alternative.

Results
The complete genomes of two Staphylococcus epidermidis bacteriophages, vB_SepiS-phiIPLA5 and vB_SepiS-phiIPLA7, have been analyzed. Their genomes are 43,581 bp and 42,123 bp, and contain 67 and 59 orf s. Bioinformatic analyses enabled the assignment of putative functions to 36 and 29 gene products, respectively, including DNA packaging and morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, regulation, modification and replication. A point mutation in vB_SepiS-phiIPLA5 lysogeny control-associated genes explained its strictly lytic behaviour. Comparative analysis of phi-IPLA5 and phi-IPLA7 genome structure resembled those of S. epidermidis ϕPH15 and ϕCNPH82 phages. A mosaic structure of S. epidermidis prophage genomes was revealed by PCR analysis of three marker genes (integrase, major head protein and holin). Using these genes, high prevalence (73%) of phage DNA in a representative S. epidermidis strain collection consisting of 60 isolates from women with mastitis and healthy women was determined. Putative pectin lyase-like domains detected in virion-associated proteins of both phages could be involved in exopolysaccharide (EPS) depolymerization, as evidenced by both the presence of a clear halo surrounding the phage lysis zone and the phage-mediated biofilm degradation.

Conclusions

Staphylococcus epidermidis bacteriophages, vB_SepiS-phiIPLA5 and vB_SepiS-phiIPLA7, have a mosaic structure similar to other widespread S. epidermidis prophages. Virions of these phages are provided of pectin lyase-like domains, which may be regarded as promising anti-biofilm tools.
Anatomy and evolution of telomeric and subtelomeric regions in the human protozoan parasite Trypanosoma cruzi
Authors: Moraes Barros Roberto R , Marini Marjorie M , Antônio Cristiane Regina , Cortez Danielle R , Miyake Andrea M , Lima Fábio M , Ruiz Jeronimo C , Bartholomeu Daniella C , Chiurillo Miguel A , Ramirez José Luis , da Silveira José Franco 
Published: June 2012

Abstract

Background
The subtelomeres of many protozoa are highly enriched in genes with roles in niche adaptation. T. cruzi trypomastigotes express surface proteins from Trans-Sialidase (TS) and Dispersed Gene Family-1 (DGF-1) superfamilies which are implicated in host cell invasion. Single populations of T. cruzi may express different antigenic forms of TSs. Analysis of TS genes located at the telomeres suggests that chromosome ends could have been the sites where new TS variants were generated. The aim of this study is to characterize telomeric and subtelomeric regions of T. cruzi available in TriTrypDB and connect the sequences of telomeres to T. cruzi working draft sequence.

Results
We first identified contigs carrying the telomeric repeat (TTAGGG). Of 49 contigs identified, 45 have telomeric repeats at one end, whereas in four contigs the repeats are located internally. All contigs display a conserved telomeric junction sequence adjacent to the hexamer repeats which represents a signature of T. cruzi chromosome ends. We found that 40 telomeric contigs are located on T. cruzi chromosome-sized scaffolds. In addition, we were able to map several telomeric ends to the chromosomal bands separated by pulsed-field gel electrophoresis.
The subtelomeric sequence structure varies widely, mainly as a result of large differences in the relative abundance and organization of genes encoding surface proteins (TS and DGF-1), retrotransposon hot spot genes (RHS), retrotransposon elements, RNA-helicase and N-acetyltransferase genes. While the subtelomeric regions are enriched in pseudogenes, they also contain complete gene sequences matching both known and unknown expressed genes, indicating that these regions do not consist of nonfunctional DNA but are instead functional parts of the expressed genome. The size of the subtelomeric regions varies from 5 to 182 kb; the smaller of these regions could have been generated by a recent chromosome breakage and telomere healing event.

Conclusions
The lack of synteny in the subtelomeric regions suggests that genes located in these regions are subject to recombination, which increases their variability, even among homologous chromosomes. The presence of typical subtelomeric genes can increase the chance of homologous recombination mechanisms or microhomology- mediated end joining, which may use these regions for the pairing and recombination of free ends.
Cholecystokinin receptor-1 mediates the inhibitory effects of exogenous cholecystokinin octapeptide on cellular morphine dependence
Authors: Wen Di , Ma Chun-ling , Zhang Ya-jing , Meng Yan-xin , Ni Zhi-yu , Li Shu-jin , Cong Bin 
Published: June 2012

Abstract

Background
Cholecystokinin octapeptide (CCK-8), the most potent endogenous anti-opioid peptide, has been shown to regulate the processes of morphine dependence. In our previous study, we found that exogenous CCK-8 attenuated naloxone induced withdrawal symptoms. To investigate the precise effect of exogenous CCK-8 and the role of cholecystokinin (CCK) 1 and/or 2 receptors in morphine dependence, a SH-SY5Y cell model was employed, in which the μ-opioid receptor, CCK1/2 receptors, and endogenous CCK are co-expressed.

Results
Forty-eight hours after treating SH-SY5Y cells with morphine (10 μM), naloxone (10 μM) induced a cAMP overshoot, indicating that cellular morphine dependence had been induced. The CCK receptor and endogenous CCK were up-regulated after chronic morphine exposure. The CCK2 receptor antagonist (LY-288,513) at 1–10 μM inhibited the naloxone-precipitated cAMP overshoot, but the CCK1 receptor antagonist (L-364,718) did not. Interestingly, CCK-8 (0.1-1 μM), a strong CCK receptor agonist, dose-dependently inhibited the naloxone-precipitated cAMP overshoot in SH-SY5Y cells when co-pretreated with morphine. The L-364,718 significantly blocked the inhibitory effect of exogenous CCK-8 on the cAMP overshoot at 1–10 μM, while the LY-288,513 did not. Therefore, the CCK2 receptor appears to be necessary for low concentrations of endogenous CCK to potentiate morphine dependence in SH-SY5Y cells. An additional inhibitory effect of CCK-8 at higher concentrations appears to involve the CCK1 receptor.

Conclusions
This study reveals the difference between exogenous CCK-8 and endogenous CCK effects on the development of morphine dependence, and provides the first evidence for the participation of the CCK1 receptor in the inhibitory effects of exogenous CCK-8 on morphine dependence.
Effect of fibrin glue as an adjuvant to hang-back surgery
Authors: Park Jihyun , Lee Jung Jin , Lim Eun Hye , Lee Joon H , Jin Kyung Hyun , Kim Ungsoo Samuel 
Published: June 2012

Abstract

Background
The hang-back surgery is a useful technique in the field of strabismus surgery. The aim of this study is to determine the stabilizing effects of fibrin glue as an adjuvant to hang-back surgery.

Materials and methods
Four (4)-mm hang-back recessions of the superior rectus muscle was performed in 32 eyes of 16 rabbits. Only in the left eye of the 16 rabbits, fibrin glue was applied between the recessed muscle bed and the sclera at the end of hang-back surgery (fibrin glue group). After 6 weeks, we compared the stability of the recessed rectus muscle between the fibrin glue group and the control group by evaluating the displacement of the muscle.

Results
The frequency of stable insertion of the recessed muscle at the intended site was greater in the fibrin glue group (9 eyes) compared to the control group (3 eyes) (p = 0.028). In the control group, 5 eyes showed anterior displacement and 8 eyes showed posterior displacement and in the fibrin glue group, 1 eye showed anterior displacement, and 6 eyes showed posterior displacement. Anterior displacement was more common in the control group (6.3% Vs 31.3%). The control group and the fibrin glue group showed similar histological findings on microscopic examination.

Conclusions
Fibrin glue is effective in stabilizing the new rectus muscle insertion and decreasing the displacement in the hang-back surgery.
Involving expert patients in antiretroviral treatment provision in a tertiary referral hospital HIV clinic in Malawi
Authors: Tenthani Lyson , Cataldo Fabian , Chan Adrienne K , Bedell Richard , Martiniuk Alexandra LC , van Lettow Monique 
Published: June 2012

Abstract

Background
Current antiretroviral treatment (ART) models in Africa are labour intensive and require a high number of skilled staff. In the context of constraints in human resources for health, task shifting is considered a feasible alternative for ART service delivery. In 2006, Dignitas International in partnership with the Malawi Ministry of Health trained a cadre of expert patients at the HIV Clinic at a tertiary referral hospital in Zomba, Malawi. Expert patients were trained to assist with clinic tasks including measurement of vital signs, anthropometry and counseling.

Methods
A descriptive observational study using mixed methods was conducted two years after the start of program implementation. Semi-structured interviews were conducted with 20 patients, seven expert patients and six formal health care providers to explore perceptions towards the expert patients’ contributions in the clinic. Structured exit interviews with 81 patients, assessed whether essential ART information was conveyed during counseling sessions. Vital signs and anthropometry measurements performed by expert patients were repeated by a nurse to assess accuracy of measurements. Direct observations quantified the time spent with each patient.

Results
There were minor differences in measurement of patients’ weight, height and temperature between the expert patients and the nurse. The majority of patients exiting a counseling session reported, without prompting, at least three side effects of ART, correct actions to be taken on observing a side-effect, and correct consequences of non-adherence to ART. Expert patients carried out 368 hours of nurse tasks each month, saving two and a half full-time nurse equivalents per month. Formal health care workers and patients accept and value expert patients’ involvement in ART provision and care. Expert patients felt valued by patients for being a ‘role model’, or a ‘model of hope’, promoting positive living and adherence to ART.

Conclusions
Expert patients add value to the ART services at a tertiary referral HIV clinic in Malawi. Expert patients carry out shifted tasks acceptably, saving formal health staff time, and also act as ‘living testimonies’ of the benefits of ART and can be a means of achieving greater involvement of People Living with HIV in HIV treatment programs.
Microparticle conferred microRNA profiles - implications in the transfer and dominance of cancer traits
Authors: Jaiswal Ritu , Luk Frederick , Gong Joyce , Mathys Jean-Marie , Grau Georges Emile Raymond , Bebawy Mary 
Published: June 2012

Abstract

Background
Microparticles (MPs) are membrane vesicles which are released from normal and malignant cells following a process of budding and detachment from donor cells. MPs contain surface antigens, proteins and genetic material and serve as vectors of intercellular communication. MPs comprise the major source of systemic RNA including microRNA (miRNA), the aberrant expression of which appears to be associated with stage, progression and spread of many cancers. Our previous study showed that MPs carry both transcripts and miRNAs associated with the acquisition of multidrug resistance in cancer.

Results
Herein, we expand on our previous finding and demonstrate that MPs carry the transcripts of the membrane vesiculation machinery (floppase and scramblase) as well as nucleic acids encoding the enzymes essential for microRNA biogenesis (Drosha, Dicer and Argonaute). We also demonstrate using microarray miRNA profiling analysis, the selective packaging of miRNAs (miR-1228*, miR-1246, miR-1308, miR-149*, miR-455-3p, miR-638 and miR-923) within the MP cargo upon release from the donor cells.

Conclusions
These miRNAs are present in both haematological and non-haematological cancer cells and are involved in pathways implicated in cancer pathogenesis, membrane vesiculation and cascades regulated by ABC transporters. Our recent findings reinforce our earlier reports that MP transfer ‘re-templates’ recipient cells so as to reflect donor cell traits. We now demonstrate that this process is likely to occur via a process of selective packaging of nucleic acid species, including regulatory nucleic acids upon MP vesiculation. These findings have significant implications in understanding the cellular basis governing the intercellular acquisition and dominance of deleterious traits in cancers.
Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer
Authors: Nelson Laura D , Bender Christian , Mannsperger Heiko , Buergy Daniel , Kambakamba Patryk , Mudduluru Giridhar , Korf Ulrike , Hughes Dennis , Van Dyke Michael W , Allgayer Heike 
Published: June 2012

AbstractBackgroundTri- and tetra-nucleotide repeats in mammalian genomes can induce formation of alternative non-B DNA structures such as triplexes and guanine (G)-quadruplexes. These structures can induce mutagenesis, chromosomal translocations and genomic instability. We wanted to determine if proteins that bind triplex DNA structures are quantitatively or qualitatively different between colorectal tumor and adjacent normal tissue and if this binding activity correlates with patient clinical characteristics.MethodsExtracts from 63 human colorectal tumor and adjacent normal tissues were examined by gel shifts (EMSA) for triplex DNA-binding proteins, which were correlated with clinicopathological tumor characteristics using the Mann-WhitneyU, Spearman’s rho, Kaplan-Meier and Mantel-Cox log-rank tests. Biotinylated triplex DNA and streptavidin agarose affinity binding were used to purify triplex-binding proteins in RKO cells. Western blotting and reverse-phase protein array were used to measure protein expression in tissue extracts.ResultsIncreased triplex DNA-binding activity in tumor extracts correlated significantly with lymphatic disease, metastasis, and reduced overall survival. We identified three multifunctional splicing factors with biotinylated triplex DNA affinity: U2AF65 in cytoplasmic extracts, and PSF and p54nrb in nuclear extracts. Super-shift EMSA with anti-U2AF65 antibodies produced a shifted band of the major EMSA H3 complex, identifying U2AF65 as the protein present in the major EMSA band. U2AF65 expression correlated significantly with EMSA H3 values in all extracts and was higher in extracts from Stage III/IV vs. Stage I/II colon tumors (p = 0.024). EMSA H3 values and U2AF65 expression also correlated significantly with GSK3 beta, beta-catenin, and NF- B p65 expression, whereas p54nrb and PSF expression correlated with c-Myc, cyclin D1, and CDK4. EMSA values and expression of all three splicing factors correlated with ErbB1, mTOR, PTEN, and Stat5. Western blots confirmed that full-length and truncated beta-catenin expression correlated with U2AF65 expression in tumor extracts.ConclusionsIncreased triplex DNA-binding activityin vitrocorrelates with lymph node disease, metastasis, and reduced overall survival in colorectal cancer, and increased U2AF65 expression is associated with total and truncated beta-catenin expression in high-stage colorectal tumors.