bluuebunny/crossref_metadata_2025_split huggingface dataset:
DockAnalyse: an application for the analysis of protein-protein interactions
Authors: Amela Isaac , Delicado Pedro , Gómez Antonio , Bonàs Sílvia , Querol Enrique , Cedano Juan 
Published: November 2010

Abstract

Background
Is it possible to identify what the best solution of a docking program is? The usual answer to this question is the highest score solution, but interactions between proteins are dynamic processes, and many times the interaction regions are wide enough to permit protein-protein interactions with different orientations and/or interaction energies. In some cases, as in a multimeric protein complex, several interaction regions are possible among the monomers. These dynamic processes involve interactions with surface displacements between the proteins to finally achieve the functional configuration of the protein complex. Consequently, there is not a static and single solution for the interaction between proteins, but there are several important configurations that also have to be analyzed.

Results
To extract those representative solutions from the docking output datafile, we have developed an unsupervised and automatic clustering application, named DockAnalyse. This application is based on the already existing DBscan clustering method, which searches for continuities among the clusters generated by the docking output data representation. The DBscan clustering method is very robust and, moreover, solves some of the inconsistency problems of the classical clustering methods like, for example, the treatment of outliers and the dependence of the previously defined number of clusters.

Conclusions

DockAnalyse makes the interpretation of the docking solutions through graphical and visual representations easier by guiding the user to find the representative solutions. We have applied our new approach to analyze several protein interactions and model the dynamic protein interaction behavior of a protein complex. DockAnalyse might also be used to describe interaction regions between proteins and, therefore, guide future flexible dockings. The application (implemented in the R package) is accessible.
Laxative effects of agarwood on low-fiber diet-induced constipation in rats
Authors: Kakino Mamoru , Tazawa Shigemi , Maruyama Hiroe , Tsuruma Kazuhiro , Araki Yoko , Shimazawa Masamitsu , Hara Hideaki 
Published: November 2010

Abstract

Background
Agarwood (Aquilaria sinensis), well known as incense in Southeast Asia, has been used as a digestive in traditional medicine. We investigated the laxative effects of an ethanol extract of agarwood leaves (EEA) in a rat model of low-fiber diet-induced constipation.

Methods
A set of rats was bred on a normal diet while another set was placed on a low-fiber diet to induce constipation. The laxative effect of agarwood was then investigated on both sets of rats.

Results
Pretreatment of normal rats with single dose of EEA (600 mg/kg, p.o.) significantly increased frequency and weight of stools. Also, treatments with EEA (300 and 600 mg/kg, p.o.) for 14 days caused a significant increase in stool frequency and weight. Feeding of the animals with a low-fiber diet resulted in a decrease in stool weight, frequency, and water content and also delayed carmine egestion. A single treatment with EEA (600 mg/kg) or senna (150 and 300 mg/kg) significantly increased stool frequency, weight, and water content and also accelerated carmine egestion in the model rats. Once daily administrations of EEA (150 mg/kg), for 14 days, caused a significant increase in water content of stools. The higher doses of EEA (300 and 600 mg/kg) significantly increased frequency, weight, and water content of the stools while accelerating carmine egestion in the constipated rats. Senna (150 and 300 mg/kg) produced similar effect as the higher doses of EEA but, in addition, induced severe diarrhea.

Conclusion
These findings indicate that EEA has a laxative effect, without causing diarrhea, in a rat model of low-fiber diet-induced constipation. These findings suggest that EEA may be highly effective on constipation as a complementary medicine in humans suffering from life style-induced constipation.
Evaluation of computerized health management information system for primary health care in rural India
Authors: Krishnan Anand , Nongkynrih Baridalyne , Yadav Kapil , Singh Satyavir , Gupta Vivek 
Published: November 2010

AbstractBackgroundThe Comprehensive Rural Health Services Project Ballabgarh, run by All India Institute of Medical Sciences (AIIMS), New Delhi has a computerized Health Management Information System (HMIS) since 1988. The HMIS at Ballabgarh has undergone evolution and is currently in its third version which uses generic and open source software. This study was conducted to evaluate the effectiveness of a computerized Health Management Information System in rural health system in India.MethodsThe data for evaluation were collected by in-depth interviews of the stakeholders i.e. program managers (authors) and health workers. Health Workers from AIIMS and Non-AIIMS Primary Health Centers were interviewed to compare the manual with computerized HMIS. A cost comparison between the two methods was carried out based on market costs. The resource utilization for both manual and computerized HMIS was identified based on workers' interviews.ResultsThere have been no major hardware problems in use of computerized HMIS. More than 95% of data was found to be accurate. Health workers acknowledge the usefulness of HMIS in service delivery, data storage, generation of workplans and reports. For program managers, it provides a better tool for monitoring and supervision and data management. The initial cost incurred in computerization of two Primary Health Centers was estimated to be Indian National Rupee (INR) 1674,217 (USD 35,622). Equivalent annual incremental cost of capital items was estimated as INR 198,017 (USD 4213). The annual savings is around INR 894,283 (USD 11,924).ConclusionThe major advantage of computerization has been in saving of time of health workers in record keeping and report generation. The initial capital costs of computerization can be recovered within two years of implementation if the system is fully operational. Computerization has enabled implementation of a good system for service delivery, monitoring and supervision.
Insect cells are superior to Escherichia coli in producing malaria proteins inducing IgG targeting PfEMP1 on infected erythrocytes
Authors: Victor Michala E , Bengtsson Anja , Andersen Gorm , Bengtsson Dominique , Lusingu John P , Vestergaard Lasse S , Arnot David E , Theander Thor G , Joergensen Louise , Jensen Anja TR 
Published: November 2010

AbstractBackgroundThe PFD1235wPlasmodium falciparumerythrocyte membrane protein 1 (PfEMP1) antigen is associated with severe malaria in children and can be expressed on the surface of infected erythrocytes (IE) adhering to ICAM1. However, the exact three-dimensional structure of this PfEMP1 and its surface-exposed epitopes are unknown. An insect cell andEscherichia colibased system was used to express single and double domains encoded by thepfd1235w vargene. The resulting recombinant proteins have been evaluated for yield and purity and their ability to induce rat antibodies, which react with the native PFD1235w PfEMP1 antigen expressed on 3D7PFD1235w-IE. Their recognition by human anti-malaria antibodies from previously infected Tanzanian donors was also analysed.MethodsThe recombinant proteins were run on SDS-PAGE and Western blots for quantification and size estimation. Insect cell andE. coli-produced recombinant proteins were coupled to a bead-based Luminex assay to measure the plasma antibody reactivity of 180 samples collected from Tanzanian individuals. The recombinant proteins used for immunization of rats and antisera were also tested by flow cytometry for their ability to surface label 3D7PFD1235w-IE.ResultsAll seven pAcGP67A constructs were successfully expressed as recombinant protein in baculovirus-infected insect cells and subsequently produced to a purity of 60-97% and a yield of 2-15 mg/L. By comparison, only three of seven pET101/D-TOPO constructs expressed in theE. colisystem could be produced at all with purity and yield ranging from 3-95% and 6-11 mg/L. All seven insect cell, but only two of theE. coliproduced proteins induced antibodies reactive with native PFD1235w expressed on 3D7PFD1235w-IE. The recombinant proteins were recognized in an age- and transmission intensity-dependent manner by antibodies from 180 Tanzanian individuals in a bead-based Luminex assay.ConclusionsThe baculovirus based insect cell system was distinctly superior to theE. coliexpression system in producing a larger number of different recombinant PFD1235w protein domains and these were significantly easier to purify at a useful yield. However, proteins produced in both systems were able to induce antibodies in rats, which can recognize the native PFD1235w on the surface of IE.
Augmented plasma microparticles during acute Plasmodium vivax infection
Authors: Campos Fernanda MF , Franklin Bernardo S , Teixeira-Carvalho Andréa , Filho Agnaldo LS , de Paula Sálua CO , Fontes Cor J , Brito Cristiana F , Carvalho Luzia H 
Published: November 2010

Abstract

Background
In the last few years, the study of microparticles (MPs) - submicron vesicles released from cells upon activation or apoptosis - has gained growing interest in the field of inflammation and in infectious diseases. Their role in the human malaria parasite Plasmodium vivax remains unexplored. Because acute vivax malaria has been related to pro-inflammatory responses, the main hypothesis investigated in this study was that Plasmodium vivax infection is associated with elevated levels of circulating MPs, which may play a role during acute disease in non-immune patients.

Methods
Plasma MPs were analysed among thirty-seven uncomplicated P. vivax infections from an area of unstable malaria transmission in the Brazilian Amazon. The MP phenotype was analysed by flow cytometry using the classical MP marker, annexin, and fluorochrome-labeled monoclonal antibodies against specific cell surface markers. The frequencies of plasma MPs in P. vivax patients (n = 37) were further compared to malaria-unexposed controls (n = 15) and ovarian carcinoma patients (n = 12), a known MPs-inducing disease non-related to malaria.

Results
The frequencies of plasma circulating MPs were markedly increased in P. vivax patients, as compared to healthy age-matched malaria-unexposed controls. Although platelets, erythrocytes and leukocytes were the main cellular sources of MPs during vivax malaria, platelet derived-MPs (PMPs) increased in a linear fashion with the presence of fever at the time of blood collection (β = 0.06, p < 0.0001) and length of acute symptoms (β = 0.36, p < 0.0001). Finally, the results suggest that plasma levels of PMPs diminish as patient experience more episodes of clinical malaria (β = 0.07, p < 0.003).

Conclusions
Abundant circulating MPs are present during acute P. vivax infection, and platelet derived-MPs may play a role on the acute inflammatory symptoms of malaria vivax.
Motivation and job satisfaction among medical and nursing staff in a Cyprus public general hospital
Authors: Lambrou Persefoni , Kontodimopoulos Nick , Niakas Dimitris 
Published: November 2010

Abstract

Background
The objective of this study was to investigate how medical and nursing staff of the Nicosia General Hospital is affected by specific motivation factors, and the association between job satisfaction and motivation. Furthermore, to determine the motivational drive of socio-demographic and job related factors in terms of improving work performance.

Methods
A previously developed and validated instrument addressing four work-related motivators (job attributes, remuneration, co-workers and achievements) was used. Two categories of health care professionals, medical doctors and dentists (N = 67) and nurses (N = 219) participated and motivation and job satisfaction was compared across socio-demographic and occupational variables.

Results
The survey revealed that achievements was ranked first among the four main motivators, followed by remuneration, co-workers and job attributes. The factor remuneration revealed statistically significant differences according to gender, and hospital sector, with female doctors and nurses and accident and emergency (A+E) outpatient doctors reporting greater mean scores (p < 0.005). The medical staff showed statistically significantly lower job satisfaction compared to the nursing staff. Surgical sector nurses and those >55 years of age reported higher job satisfaction when compared to the other groups.

Conclusions
The results are in agreement with the literature which focuses attention to management approaches employing both monetary and non-monetary incentives to motivate health care professionals. Health care professionals tend to be motivated more by intrinsic factors, implying that this should be a target for effective employee motivation. Strategies based on the survey's results to enhance employee motivation are suggested.
Serosurvey for selected pathogens in Iberian roe deer
Authors: Boadella Mariana , Carta Tania , Oleaga Álvaro , Pajares Gerardo , Muñoz Marta , Gortázar Christian 
Published: November 2010

Abstract

Background
The roe deer is the most abundant and widespread wild Eurasian cervid. Its populations are expanding and increasingly in contact with livestock. This may affect the distribution of infectious diseases shared with other wild and domestic ungulates.

Methods
We investigated the antibody seroprevalence against Pestivirus, Herpesvirus, Bluetongue (BT) virus, M. avium paratuberculosis (MAP), and Brucella sp. in 519 roe deer from different regions in Spain, south-western Europe.

Results
No antibodies were detected against BT and Brucella sp. However, antibodies were detected against Pestivirus (1.5%), Herpesvirus (0.2%) and MAP (9.2%). MAP antibodies were detected in seven of the eight populations (range 5-16.4%).

Conclusions
The detection of MAP antibodies in samples from most roe deer populations suggests that contact with MAP is widespread in this wildlife species. The highest prevalence was detected in sites with abundant dairy cattle and frequent use of liquid manure on pastures. Considering the results obtained regarding exposure to different pathogens, we suggest that antibody prevalences in this non-gregarious browser are largely determined by environmental factors, potentially modulating vector populations or pathogen survival in the environment.
The Akt-inhibitor Erufosine induces apoptotic cell death in prostate cancer cells and increases the short term effects of ionizing radiation
Authors: Rudner Justine , Ruiner Carola-Ellen , Handrick René , Eibl Hans-Jörg , Belka Claus , Jendrossek Verena 
Published: November 2010

Abstract

Background and Purpose
The phosphatidylinositol-3-kinase (PI3K)/Akt pathway is frequently deregulated in prostate cancer and associated with neoplastic transformation, malignant progression, and enhanced resistance to classical chemotherapy and radiotherapy. Thus, it is a promising target for therapeutic intervention. In the present study, the cytotoxic action of the Akt inhibitor Erufosine (ErPC3) was analyzed in prostate cancer cells and compared to the cytotoxicity of the PI3K inhibitor LY294002. Moreover, the efficacy of combined treatment with Akt inhibitors and ionizing radiation in prostate cancer cells was examined.

Materials and methods
Prostate cancer cell lines PC3, DU145, and LNCaP were treated with ErPC3 (1-100 µM), LY294002 (25-100 µM), irradiated (0-10 Gy), or subjected to combined treatments. Cell viability was determined by the WST-1 assay. Apoptosis induction was analyzed by flow cytometry after staining with propidium iodide in a hypotonic citrate buffer, and by Western blotting using antibodies against caspase-3 and its substrate PARP. Akt activity and regulation of the expression of Bcl-2 family members and key downstream effectors involved in apoptosis regulation were examined by Western blot analysis.

Results
The Akt inhibitor ErPC3 exerted anti-neoplastic effects in prostate cancer cells, however with different potency. The anti-neoplastic action of ErPC3 was associated with reduced phosphoserine 473-Akt levels and induction of apoptosis. PC3 and LNCaP prostate cancer cells were also sensitive to treatment with the PI3K inhibitor LY294002. However, the ErPC3-sensitive PC3-cells were less susceptible to LY294002 than the ErPC3-refractory LNCaP cells. Although both cell lines were largely resistant to radiation-induced apoptosis, both cell lines showed higher levels of apoptotic cell death when ErPC3 was combined with radiotherapy.

Conclusions
Our data suggest that constitutive Akt activation and survival are controlled by different different molecular mechanisms in the two prostate cancer cell lines - one which is sensitive to the Akt-inhibitor ErPC3 and one which is more sensitive to the PI3K-inhibitor LY294002. Our findings underline the importance for the definition of predictive biomarkers that allow the selection patients that may benefit from the treatment with a specific signal transduction modifier.
Loss of heterozygosity and SOSTDC1 in adult and pediatric renal tumors
Authors: Blish Kimberly R , Clausen Kathryn A , Hawkins Gregory A , Garvin A Julian , Willingham Mark C , Turner Julie C , Torti Frank M , Torti Suzy V 
Published: November 2010

AbstractBackgroundDeletions within the short arm of chromosome 7 are observed in approximately 25% of adult and 10% of Wilms pediatric renal tumors. Within Wilms tumors, the region of interest has been delineated to a 2-Mb minimal region that includes ten known genes. Two of these ten candidate genes,SOSTDC1andMEOX2, are particularly relevant to tumor development and maintenance. This finding, coupled with evidence that SOSTDC1 is frequently downregulated in adult renal cancer and regulates both Wingless-Int (Wnt)- and bone morphogenetic protein (BMP)-induced signaling, points to a role for SOSTDC1 as a potential tumor suppressor.MethodsTo investigate this hypothesis, we interrogated the Oncomine database to examine the SOSTDC1 levels in adult renal clear cell tumors and pediatric Wilms tumors. We then performed single nucleotide polymorphism (SNP) and sequencing analyses ofSOSTDC1in 25 pediatric and 36 adult renal tumors. Immunohistochemical staining of patient samples was utilized to examine the impact ofSOSTDC1genetic aberrations on SOSTDC1 protein levels and signaling.ResultsWithin the Oncomine database, we found that SOSTDC1 levels were reduced in adult renal clear cell tumors and pediatric Wilms tumors. Through SNP and sequencing analyses of 25 Wilms tumors, we identified four with loss of heterozygosity (LOH) at 7p and three that affectedSOSTDC1. Of 36 adult renal cancers, we found five with LOH at 7p, two of which affectedSOSTDC1. Immunohistochemical analysis of SOSTDC1 protein levels within these tumors did not reveal a relationship between these instances ofSOSTDC1LOH and SOSTDC1 protein levels. Moreover, we could not discern any impact of these genetic alterations on Wnt signaling as measured by altered beta-catenin levels or localization.ConclusionsThis study shows that genetic aberrations nearSOSTDC1are not uncommon in renal cancer, and occur in adult as well as pediatric renal tumors. These observations ofSOSTDC1LOH, however, did not correspond with changes in SOSTDC1 protein levels or signaling regulation. Although our conclusions are limited by sample size, we suggest that an alternative mechanism such as epigenetic silencing ofSOSTDC1may be a key contributor to the reduced SOSTDC1 mRNA and protein levels observed in renal cancer.
Prevalence and predictors of loss of wild type BRCA1 in estrogen receptor positive and negative BRCA1-associated breast cancers
Authors: Tung Nadine , Miron Alexander , Schnitt Stuart J , Gautam Shiva , Fetten Katharina , Kaplan Jennifer , Yassin Yosuf , Buraimoh Ayodele , Kim Ji-Young , Szász Attila M , Tian Ruiyang , Wang Zhigang C , Collins Laura C , Brock Jane , Krag Karen , Legare Robert D , Sgroi Dennis , Ryan Paula D , Silver Daniel P , Garber Judy E , Richardson Andrea L 
Published: November 2010

Abstract
Introduction
The majority of breast cancers that occur in BRCA1 mutation carriers (BRCA1 carriers) are estrogen receptor-negative (ER-). Therefore, it has been suggested that ER negativity is intrinsic to BRCA1 cancers and reflects the cell of origin of these tumors. However, approximately 20% of breast cancers that develop in BRCA1 carriers are ER-positive (ER+); these cancers are more likely to develop as BRCA1 carriers age, suggesting that they may be incidental and unrelated to BRCA1 deficiency. The purpose of this study was to compare the prevalence of loss of heterozygosity due to loss of wild type (wt) BRCA1 in ER+ and ER- breast cancers that have occurred in BRCA1 carriers and to determine whether age at diagnosis or any pathologic features or biomarkers predict for loss of wt BRCA1 in these breast cancers.

Methods
Relative amounts of mutated and wt BRCA1 DNA were measured by quantitative polymerase chain reaction performed on laser capture microdissected cancer cells from 42 ER+ and 35 ER- invasive breast cancers that developed in BRCA1 carriers. BRCA1 gene methylation was determined on all cancers in which sufficient DNA was available. Immunostains for cytokeratins (CK) 5/6, 14, 8 and 18, epidermal growth factor receptor and p53 were performed on paraffin sections from tissue microarrays containing these cancers.

Results
Loss of wt BRCA1 was equally frequent in ER+ and ER- BRCA1-associated cancers (81.0% vs 88.6%, respectively; P = 0.53). One of nine cancers tested that retained wt BRCA1 demonstrated BRCA1 gene methylation. Age at diagnosis was not significantly different between first invasive ER+ BRCA1 breast cancers with and without loss of wt BRCA1 (mean age 45.2 years vs 50.1 years, respectively; P = 0.51). ER+ BRCA1 cancers that retained wt BRCA1 were significantly more likely than those that lost wt BRCA1 to have a low mitotic rate (odds ratio (OR), 5.16; 95% CI, 1.91 to ∞). BRCA1 cancers with loss of wt BRCA1 were more likely to express basal cytokeratins CK 5/6 or 14 (OR 4.7; 95% CI, 1.85 to ∞).

Conclusions
We found no difference in the prevalence of loss of wt BRCA1 between ER+ and ER- invasive BRCA1-associated breast cancers. Our findings suggest that many of the newer therapies for BRCA1 breast cancers designed to exploit the BRCA1 deficiency in these cancers may also be effective in ER+ cancers that develop in this population.