bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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

Additional 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.
Clotting factor concentrate switching and inhibitor development in hemophilia A
Authors: Iorio Alfonso , Puccetti Paolo , Makris Mike
Published: June 2012

The development of alloantibodies or inhibitors is the most serious complication a patient with severe hemophilia can experience from treatment with clotting factor concentrates. Although common in previously untreated patients, inhibitor development is rare in multiply exposed, well-tolerized patients. There has been a nonevidence-based reluctance to change concentrate because of a perceived greater inhibitor risk after the switch, even though most patients are now likely to be using a concentrate on which they did not begin. Inhibitors in previously treated patients are observed in approximately 2 per 1000 patient/years, which makes it difficult to study and compare rates among different products. Because the baseline inhibitor risk in previously treated patients may vary over time, it is important to compare the risk in patients switching to a new product with that in a parallel control group of nonswitching patients or within a case-controlled study. The study designs imposed by regulators are suboptimal in detecting immunogenicity signals. The issue of immunogenicity of new products is likely to gain more relevance in the near future, with a call for effective postmarketing surveillance studies for all of the new engineered factor VIII concentrates with prolonged half-lives that are likely to enter clinical practice.
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

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

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

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

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

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

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

Background

Tri- 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.

Methods

Extracts 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.

Results

Increased 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.

Conclusions

Increased 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.
Identification of cyclin B1 and Sec62 as biomarkers for recurrence in patients with HBV-related hepatocellular carcinoma after surgical resection
Authors: Weng Li , Du Juan , Zhou Qinghui , Cheng Binbin , Li Jun , Zhang Denghai , Ling Changquan
Published: June 2012

Background

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. Frequent tumor recurrence after surgery is related to its poor prognosis. Although gene expression signatures have been associated with outcome, the molecular basis of HCC recurrence is not fully understood, and there is no method to predict recurrence using peripheral blood mononuclear cells (PBMCs), which can be easily obtained for recurrence prediction in the clinical setting.

Methods

According to the microarray analysis results, we constructed a co-expression network using the k-core algorithm to determine which genes play pivotal roles in the recurrence of HCC associated with the hepatitis B virus (HBV) infection. Furthermore, we evaluated the mRNA and protein expressions in the PBMCs from 80 patients with or without recurrence and 30 healthy subjects. The stability of the signatures was determined in HCC tissues from the same 80 patients. Data analysis included ROC analysis, correlation analysis, log-lank tests, and Cox modeling to identify independent predictors of tumor recurrence.

Results

The tumor-associated proteins cyclin B1, Sec62, and Birc3 were highly expressed in a subset of samples of recurrent HCC; cyclin B1, Sec62, and Birc3 positivity was observed in 80%, 65.7%, and 54.2% of the samples, respectively. The Kaplan-Meier analysis revealed that high expression levels of these proteins was associated with significantly reduced recurrence-free survival. Cox proportional hazards model analysis revealed that cyclin B1 (hazard ratio [HR], 4.762;p = 0.002) and Sec62 (HR, 2.674;p = 0.018) were independent predictors of HCC recurrence.

Conclusion

These results revealed that cyclin B1 and Sec62 may be candidate biomarkers and potential therapeutic targets for HBV-related HCC recurrence after surgery.
A dynamic plasma membrane proteome analysis of alcohol-induced liver cirrhosis
Authors: Jia Xiaofang , Yin Lin , Feng Yanling , Peng Xia , Ma Fang , Yao Yamin , Liu Xiaoqian , Zhang Zhiyong , Yuan Zhenghong , Zhang Lijun
Published: June 2012

Alcohol-induced injury has become one of the major causes for liver cirrhosis. However, the molecular mechanisms of ethanol-induced injury are not fully understood. To this end, we performed a dynamic plasma membrane proteomic research on rat model. A rat model from hepatitis to liver cirrhosis was developed. Plasma membrane from liver tissue with liver fibrosis stage of 2 and 4 (S2 and S4) was purified by sucrose density gradient centrifugation. Its purification was verified by western blotting. Proteins from plasma membrane were separated by two-dimensional electrophoresis (2DE) and differentially expressed proteins were identified by tandem mass spectrometry. 16 consistent differentially expressed proteins from S2 to S4 were identified by mass spectrometry. The expression of differentially expressed proteins annexin A6 and annexin A3 were verified by western blotting, and annexin A3 was futher verified by immunohistochemistry. Our research suggests a possible mechanism by which ethanol alters protein expression to enhance the liver fibrosis progression. These differentially expressed proteins might be new drug targets for treating alcoholic liver cirrhosis.
Apoptotic activity in Libyan breast cancer
Authors: Boder Jamela , Abdalla Fathi , Elfagieh Mohamed , Buhmeida Abdelbaset , Collan Yrjö
Published: June 2012

Background

We evaluated the relationship of the apoptotic activity index (AI) and the standardized mitotic-apoptotic ratio (SMI/AI) with clinicopathological features and prognosis in Libyan female breast cancer (BC) patients. We then compared our results with corresponding results in Finnish and Nigerian female BC patients.

Methods

Histological samples of breast carcinoma from 130 patients were retrospectively studied: an estimation of the apoptotic activity per square millimeter (expressed as apoptotic activity index (AI)), and standardized mitotic-apoptotic ratio (SMI/AI) was made, and the results compared with the clinicopathological features and the patient’s survival.

Results

There was a statistically significant correlation between the AI and most of the clinicopathological features; the strongest association was observed for clinical stage lymph node (LN) status (P = 0.005). There were also correlations between AI and histological grade (P = 0.035), large tumor size (P = 0.011) and the clinical stage (P = 0.009). There were, however, prominent AI differences between Libyan, Nigerian and Finnish populations. The mean values of AI and SMI/AI in Libyan BC patients were 12.8 apoptotic figures per square millimeter and 2.8, respectively. The Libyan AI is slightly higher than in Nigeria, but much higher than in Finland. The differences between countries are seen throughout the samples as well as being present in certain subgroups. The survival analysis indicated that short survival time was associated with high apoptotic indices values and so can identify aggressive tumors and provide significant prognostic support. The cutoff (4 and 18 apoptosis/mm2) of AI might be applied as a quantitative criterion for Libyan BC to separate the patients into good, moderate and bad prognosis groups.

Conclusions

The results indicated that the differences in AI among the three countries may be due to the known variation in the distribution of genetic markers in these populations. Improvement in health care and introduction of screening programs, however, could be very helpful in the Libyan population.
Novel preparation of PLGA/HP55 nanoparticles for oral insulin delivery
Authors: Wu Zhi Min , Ling Li , Zhou Li Ying , Guo Xin Dong , Jiang Wei , Qian Yu , Luo Kathy Qian , Zhang Li Juan
Published: June 2012

The aim of the present study was to develop the PLGA/HP55 nanoparticles with improved hypoglycemic effect for oral insulin delivery. The insulin-loaded PLGA/HP55 nanoparticles were produced by a modified multiple emulsion solvent evaporation method. The physicochemical characteristics, in vitro release of insulin, and in vivo efficacy in diabetic rats of the nanoparticles were evaluated. The insulin encapsulation efficiency was up to 94%, and insulin was released in a pH-dependent manner under simulated gastrointestinal conditions. When administered orally (50 IU/kg) to diabetic rats, the nanoparticles can decrease rapidly the blood glucose level with a maximal effect between 1 and 8 h. The relative bioavailability compared with subcutaneous injection (5 IU/kg) in diabetic rats was 11.3% ± 1.05%. This effect may be explained by the fast release of insulin in the upper intestine, where it is better absorbed by the high gradient concentration of insulin than other regions. These results show that the PLGA/HP55 nanoparticles developed in the study might be employed as a potential method for oral insulin delivery.
The first 100 patients in the SUN(^_^)D trial (strategic use of new generation antidepressants for depression): examination of feasibility and adherence during the pilot phase
Authors: Shimodera Shinji , Kato Tadashi , Sato Hirotoshi , Miki Kazuhira , Shinagawa Yoshihiro , Kondo Masaki , Fujita Hirokazu , Morokuma Ippei , Ikeda Yoshio , Akechi Tatsuo , Watanabe Norio , Yamada Mitsuhiko , Inagaki Masatoshi , Yonemoto Naohiro , Furukawa Toshi A ,   For the SUN(^_^)D Investigators
Published: June 2012

Background

Initial glitches and unexpected inconsistencies are unavoidable in the early stage of a large, multi-centre trial. Adaptive modifications of the trial’s protocol and operational procedures to ensure its smooth running are therefore imperative. We started a large pragmatic, multi-centre, assessor-blinded, 25-week trial to investigate the optimal first- and second-line treatments for untreated episodes of nonpsychotic major depression in 2010 [Strategic Use of New generation antidepressants for Depression, abbreviated SUN(^_^)D] and would like to herein report an examination of the trial’s feasibility and adherence among the first 100 participants.

Methods

We examined the participants’ characteristics, the treatments that were allocated and received during each step of the trial, and the quality of the outcome assessments among the first 100 patients enrolled in the SUN(^_^)D trial.

Results

Of the 2,743 first-visit patients who visited the two collaborating centres between December 2010 and July 2011, 382 were judged as potentially eligible, and 100 of these patients provided written informed consent. These patients represented the whole spectrum of mild to very severe depression. Of the 93 patients who had reached Week 3 of the study by the end of July 2011, one withdrew consent for both the treatment and the assessment, and eight withdrew consent for the treatment only. Altogether, the primary outcomes were successfully assessed in 90 (96.8%) of the patients at Week 3. Of the 72 patients who had reached Week 9, three withdrew consent for the treatment, but 70 were successfully interviewed (97.2%). Of the 32 patients who had reached Week 25, 29 (90.5%) were successfully followed up. The inter-rater reliability of the assessments of the primary outcomes was nearly perfect and their successful blinding was confirmed. Minor modifications and clarifications to the protocol were deemed necessary.

Discussion

Given the satisfactory feasibility and adherence to the study protocol and the minor modifications that were necessary, we conclude that the data obtained from the first 100 patients can be safely included in the main study. We now intend to accelerate the study by recruiting more collaborating centres and clinics/hospitals.

Trial registration

ClinicalTrials.gov identifier: NCT01109693
Mapping the stabilome: a novel computational method for classifying metabolic protein stability
Authors: Patrick Ralph , Cao Kim-Anh Lê , Davis Melissa , Kobe Bostjan , Bodén Mikael
Published: June 2012

Background

The half-life of a protein is regulated by a range of system properties, including the abundance of components of the degradative machinery and protein modifiers. It is also influenced by protein-specific properties, such as a protein’s structural make-up and interaction partners. New experimental techniques coupled with powerful data integration methods now enable us to not only investigate what features govern protein stability in general, but also to build models that identify what properties determine each protein’s metabolic stability.

Results

In this work we present five groups of features useful for predicting protein stability: (1) post-translational modifications, (2) domain types, (3) structural disorder, (4) the identity of a protein’s N-terminal residue and (5) amino acid sequence. We incorporate these features into a predictive model with promising accuracy. At a 20% false positive rate, the model exhibits an 80% true positive rate, outperforming the only previously proposed stability predictor. We also investigate the impact of N-terminal protein tagging as used to generate the data set, in particular the impact it may have on the measurements for secreted and transmembrane proteins; we train and test our model on a subset of the data with those proteins removed, and show that the model sustains high accuracy. Finally, we estimate system-wide metabolic stability by surveying the whole human proteome.

Conclusions

We describe a variety of protein features that are significantly over- or under-represented in stable and unstable proteins, including phosphorylation, acetylation and destabilizing N-terminal residues. Bayesian networks are ideal for combining these features into a predictive model with superior accuracy and transparency compared to the only other proposed stability predictor. Furthermore, our stability predictions of the human proteome will find application in the analysis of functionally related proteins, shedding new light on regulation by protein synthesis and degradation.
Biochemical characterization and evaluation of cytotoxicity of antistaphylococcal chimeric protein P128
Authors: George Shilpa E , Chikkamadaiah Ravisha , Durgaiah Murali , Joshi Amruta A , Thankappan Ullas P , Madhusudhana Shampur N , Sriram Bharathi
Published: June 2012

Background

Antibiotic resistant S. aureus infection is a global threat. Newer approaches are required to control this organism in the current scenario. Cell wall degrading enzymes have been proposed as antibacterial agents for human therapy. P128 is a novel antistaphylococcal chimeric protein under development against S. aureus for human use which derives its bacterial cell wall degrading catalytic endopeptidase domain from ORF56, the Phage K tail-structure associated enzyme. Lead therapeutic entities have to be extensively characterized before they are assessed in animals for preclinical safety and toxicity. P128 is effective against antibiotic resistant strains as well as against a panel of isolates of global significance. Its efficacy against S. aureus in vivo has been established in our lab. Against this background, this study describes the characterization of this protein for its biochemical properties and other attributes.

Results

We evaluated the requirement or effect of divalent cations and the metal ion chelator, EDTA upon biological activity of P128. As the protein is intended for therapeutic use, we tested its activity in presence of body fluids and antibodies specific to P128. For the same reason, we used standard human cell lines to evaluate cytotoxic effects, if any.

The divalent cations, calcium and magnesium at upto 25 mM and Zinc upto 2.5 mM neither inhibited nor enhanced P128 activity. Incubation of this protein with EDTA, human serum, plasma and blood also did not alter the antibacterial properties of the molecule. No inhibitory effect was observed in presence of hyper-immune sera raised against the protein. Finally, P128 did not show any cytotoxic effect on HEp2 and Vero cells at the highest concentration (5 mg/mL) tested.

Conclusions

The results presented here throw light on several properties of protein P128. Taken together, these substantiate the potential of P128 for therapeutic use against S. aureus. Further development of the protein and conduct of preclinical safety studies in animals is warranted.
Interrater and intrarater reliability of photoplethysmography for measuring toe blood pressure and toe‐brachial index in people with diabetes mellitus
Authors: Scanlon Christopher , Park Kris , Mapletoft David , Begg Lindy , Burns Joshua
Published: June 2012

Background

A reliable tool to measure arterial flow to the feet in people with diabetes is required given that they are particularly prone to peripheral arterial disease. Traditionally, the ankle brachial index (ABI) has been used to measure arterial circulation, but its application is limited due to calcification of larger arteries. More recently, toe pressure and the toe brachial index (TBI) has been suggested as superior to ABI measurements because they assess smaller digital arteries less prone to arterial calcification. However, reliability studies for the clinical use of photoplethysmography (PPG) in people with diabetes are lacking.

Methods

Sixty people with diabetes mellitus (35 males and 25 females, mean age 59.6 yrs) consented to take part in the study. The majority (92%) had type 2 diabetes and 8% had type 1 diabetes. Forty‐three percent were diagnosed as having peripheral neuropathy when tested using a biothesiometer and 15% were current smokers (10 – 40/day). A podiatrist and a diabetes educator measured toe and brachial blood pressure independently and in a random order using PPG. These measurements were repeated again seven days later, and subsequently analysed with intraclass correlation coefficients (ICC), 95% confidence intervals (CI) and standard error of measurement (SEM).

Results

The intrarater reliability of measuring toe pressures was excellent (ICC3,1 =0.78‐0.79, SEM 8 mmHg) and interrater reliability was also excellent (ICC2,2 = 0.93, SEM 4 mmHg). The intrarater reliability for measuring brachial pressures was generally poor (ICC3,1 = 0.40 – 0.42, SEM 19 mmHg) and interrater reliability was fair‐good (ICC2,2. 0.65, SEM 14 mmHg). The TBI intrarater reliability was fair‐good (ICC3,1 = 0.51‐0.72, SEM 0.08), whilst the interrater reliability of TBI was excellent (ICC2,2 = 0.85, SEM 0.07).

Conclusions

Based on these results, interrater and intrarater reliability of PPG is excellent for measuring toe blood pressure, good for TBI and only fair for brachial pressures in people with diabetes mellitus.
Bioinformatics insights into acute lung injury/acute respiratory distress syndrome
Authors: Fang Xiaocong , Bai Chunxue , Wang Xiangdong
Published: June 2012

Bioinformatics is the application of omics science, information technology, mathematics and statistics in the field of biomarker detection. Clinical bioinformatics can be applied for identification and validation of new biomarkers to improve current methods of monitoring disease activity and identify new therapeutic targets. Acute lung injurt (ALI)/Acute respiratory distress syndrome (ARDS) affects a large number of patients with a poor prognosis. The present review mainly focused on the progress in understanding disease heterogeneity through the use of evolving biological, genomic, and genetic approaches and the role of clinical bioinformatics in the pathogenesis and treatment of ALI/ARDS. The remarkable advances in clinical bioinformatics can be a new way for understanding disease pathogenesis, diagnosis and treatment.
Loss of vascular early response gene reduces edema formation after experimental stroke
Authors: Liu Fudong , Turtzo L Christine , Li Jun , Regard Jean , Worley Paul , Zeevi Neer , McCullough Louise D
Published: June 2012

Vascular Early Response Gene (Verge) is an immediate early gene (IEG) that is up-regulated in endothelial cells in response to a number of stressors, including ischemic stroke. Endothelial cell lines that stably express Verge show enhanced permeability. Increased Verge expression has also been associated with blood brain barrier breakdown. In this study we investigated the role of Verge in ischemic injury induced by middle cerebral artery occlusion (MCAO) in both Verge knockout (KO) and wild type (WT) mice. Verge KO mice had significantly less cerebral edema formation after MCAO compared to WT mice. However, stroke outcome (infarct size and neurological deficit scores) evaluated at either 24 or 72 hours after stroke showed no differences between the two genotypes. Verge deletion leads to decreased edema formation after ischemia; however acute stroke outcomes were unchanged.
Branching of the p-nitrophenol (PNP) degradation pathway in burkholderia sp. Strain SJ98: Evidences from genetic characterization of PNP gene cluster
Authors: Vikram Surendra , Pandey Janmejay , Bhalla Nidhi , Pandey Gunjan , Ghosh Anuradha , Khan Fazlurrahman , Jain Rakesh K , Raghava Gajendra PS
Published: June 2012

Aerobic microbial degradation of p-nitrophenol (PNP) has been classically shown to proceed via ‘Hydroquinone (HQ) pathway’ in Gram-negative bacteria, whereas in Gram-positive PNP degraders it proceed via ‘Benzenetriol (BT) pathway’. These pathways are characterized by the ring cleavage of HQ and BT as terminal aromatic intermediates respectively. Earlier reports on PNP degradation have indicated these pathways to be mutually exclusive. We report involvement of both ‘HQ’ and ‘BT’ ring cleavage pathways in PNP degradation by Burkholderia sp. strain SJ98. Genetic characterization of an ~41 Kb DNA fragment harboring PNP degradation gene cluster cloned and sequenced from strain SJ98 showed presence of multiple orfs including pnpC and pnpD which corresponded to previously characterized ‘benzenetriol-dioxygenase (BtD)’ and ‘maleylacetate reductase (MaR)’ respectively. This gene cluster also showed presence of pnpE1 and pnpE2, which shared strong sequence identity to cognate sub-units of ‘hydroquinone dioxygenase’ (HqD). Heterologous expression and biochemical characterization ascertained the identity of PnpE1 and PnpE2. In in vitro assay reconstituted heterotetrameric complex of PnpE1 and PnpE2 catalyzed transformation of hydroquinone (HQ) into corresponding hydroxymuconic semialdehyde (HMS) in a substrate specific manner. Together, these results clearly establish branching of PNP degradation in strain SJ98. We propose that strain SJ98 presents a useful model system for future studies on evolution of microbial degradation of PNP.
Polyclonal HER2-specific antibodies induced by vaccination mediate receptor internalization and degradation in tumor cells
Authors: Ren Xiu-Rong , Wei Junping , Lei Gangjun , Wang Jiangbo , Lu Jiuyi , Xia Wenle , Spector Neil , Barak Larry S , Clay Timothy M , Osada Takuya , Hamilton Erika , Blackwell Kimberly , Hobeika Amy C , Morse Michael A , Lyerly H Kim , Chen Wei
Published: June 2012

Introduction

Sustained HER2 signaling at the cell surface is an oncogenic mechanism in a significant proportion of breast cancers. While clinically effective therapies targeting HER2 such as mAbs and tyrosine kinase inhibitors exist, tumors overexpressing HER2 eventually progress despite treatment. Thus, abrogation of persistent HER2 expression at the plasma membrane to synergize with current approaches may represent a novel therapeutic strategy.

Methods

We generated polyclonal anti-HER2 antibodies (HER2-VIA) by vaccinating mice with an adenovirus expressing human HER2, and assessed their signaling effects in vitro and anti-tumor effects in a xenograft model. In addition, we studied the signaling effects of human HER2-specific antibodies induced by vaccinating breast cancer patients with a HER2 protein vaccine.

Results

HER2-VIA bound HER2 at the plasma membrane, initially activating the downstream kinases extracellular signal-regulated protein kinase 1/2 and Akt, but subsequently inducing receptor internalization in clathrin-coated pits in a HER2 kinase-independent manner, followed by ubiquitination and degradation of HER2 into a 130 kDa fragment phosphorylated at tyrosine residues 1,221/1,222 and 1,248. Following vaccination of breast cancer patients with the HER2 protein vaccine, HER2-specific antibodies were detectable and these antibodies bound to cell surface-expressed HER2 and inhibited HER2 signaling through blocking tyrosine 877 phosphorylation of HER2. In contrast to the murine antibodies, human anti-HER2 antibodies induced by protein vaccination did not mediate receptor internalization and degradation.

Conclusion

These data provide new insight into HER2 trafficking at the plasma membrane and the changes induced by polyclonal HER2-specific antibodies. The reduction of HER2 membrane expression and HER2 signaling by polyclonal antibodies induced by adenoviral HER2 vaccines supports human clinical trials with this strategy for those breast cancer patients with HER2 therapy-resistant disease.
Secretin Receptor Promotes the Proliferation of Endocrine Tumor Cells Via the PI3K/AKT Pathway
Authors: Lee Misu , Waser Beatrice , Reubi Jean-Claude , Pellegata Natalia S.
Published: June 2012

The secretin receptor (SR), a G protein-coupled receptor, mediates the effects of the gastrointestinal hormone secretin on digestion and water homeostasis. Recently, high SR expression has been observed in pancreatic ductal adenocarcinomas, cholangiocellular carcinomas, gastrinomas, and bronchopulmonary carcinoid tumors. Receptor overexpression associates with enhanced secretin-mediated signaling, but whether this molecule plays an independent role in tumorigenesis is currently unknown. We recently discovered that pheochromocytomas developing in rats affected by the MENX (multiple endocrine neoplasia-like) syndrome express at very high-level Sctr, encoding SR. We here report that SR are also highly abundant on the membranes of rat adrenal and extraadrenal pheochromocytoma, starting from early stages of tumor development, and are functional. PC12 cells, the best characterized in vitro pheochromocytoma model, also express Sctr at high level. Thus, we used them as model to study the role of SR in neoplastic transformation. Small interfering RNA-mediated knockdown of Sctr decreases PC12 cells proliferation and increases p27 levels. The proproliferative effect of SR in PC12 cells is mediated, in part, by the phosphatidylinositol 3 kinase (PI3K)/serine-threonine protein kinase (AKT) pathway. Transfection of Sctr in Y1 adrenocortical carcinoma cells, expressing low endogenous levels of Sctr, stimulates cell proliferation also, in part, via the PI3K/AKT signaling cascade. Because of the link between SR and PI3K/AKT signaling, tumor cells expressing high levels of the receptor (MENX-associated primary pheochromocytoma and NCI-H727 human bronchopulmonary carcinoid cells) respond well and in a SR-dependent manner to PI3K inhibitors, such as NVP-BEZ235. The association between SR levels and response to PI3K inhibition might open new avenues for the treatment of tumors overexpressing this receptor.