bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment
Authors: Guo Yufan , Korhonen Anna , Liakata Maria , Silins Ilona , Hogberg Johan , Stenius Ulla 
Published: March 2011

Abstract

Background
Many practical tasks in biomedicine require accessing specific types of information in scientific literature; e.g. information about the results or conclusions of the study in question. Several schemes have been developed to characterize such information in scientific journal articles. For example, a simple section-based scheme assigns individual sentences in abstracts under sections such as Objective, Methods, Results and Conclusions. Some schemes of textual information structure have proved useful for biomedical text mining (BIO-TM) tasks (e.g. automatic summarization). However, user-centered evaluation in the context of real-life tasks has been lacking.

Methods
We take three schemes of different type and granularity - those based on section names, Argumentative Zones (AZ) and Core Scientific Concepts (CoreSC) - and evaluate their usefulness for a real-life task which focuses on biomedical abstracts: Cancer Risk Assessment (CRA). We annotate a corpus of CRA abstracts according to each scheme, develop classifiers for automatic identification of the schemes in abstracts, and evaluate both the manual and automatic classifications directly as well as in the context of CRA.

Results
Our results show that for each scheme, the majority of categories appear in abstracts, although two of the schemes (AZ and CoreSC) were developed originally for full journal articles. All the schemes can be identified in abstracts relatively reliably using machine learning. Moreover, when cancer risk assessors are presented with scheme annotated abstracts, they find relevant information significantly faster than when presented with unannotated abstracts, even when the annotations are produced using an automatic classifier. Interestingly, in this user-based evaluation the coarse-grained scheme based on section names proved nearly as useful for CRA as the finest-grained CoreSC scheme.

Conclusions
We have shown that existing schemes aimed at capturing information structure of scientific documents can be applied to biomedical abstracts and can be identified in them automatically with an accuracy which is high enough to benefit a real-life task in biomedicine.
The dChip survival analysis module for microarray data
Authors: Amin Samir B , Shah Parantu K , Yan Aimin , Adamia Sophia , Minvielle Stéphane , Avet-Loiseau Hervé , Munshi Nikhil C , Li Cheng 
Published: March 2011

Abstract

Background
Genome-wide expression signatures are emerging as potential marker for overall survival and disease recurrence risk as evidenced by recent commercialization of gene expression based biomarkers in breast cancer. Similar predictions have recently been carried out using genome-wide copy number alterations and microRNAs. Existing software packages for microarray data analysis provide functions to define expression-based survival gene signatures. However, there is no software that can perform survival analysis using SNP array data or draw survival curves interactively for expression-based sample clusters.

Results
We have developed the survival analysis module in the dChip software that performs survival analysis across the genome for gene expression and copy number microarray data. Built on the current dChip software's microarray analysis functions such as chromosome display and clustering, the new survival functions include interactive exploring of Kaplan-Meier (K-M) plots using expression or copy number data, computing survival p-values from the log-rank test and Cox models, and using permutation to identify significant chromosome regions associated with survival.

Conclusions
The dChip survival module provides user-friendly way to perform survival analysis and visualize the results in the context of genes and cytobands. It requires no coding expertise and only minimal learning curve for thousands of existing dChip users. The implementation in Visual C++ also enables fast computation. The software and demonstration data are freely available at http://dchip-surv.chenglilab.org.
Differential Role of Poly(ADP-ribose) polymerase in D. discoideum growth and development
Authors: Rajawat Jyotika , Mir Hina , Begum Rasheedunnisa 
Published: March 2011

Abstract

Background
Poly(ADP-ribose) polymerase is evolutionarily conserved as a responder to various forms of stress. Though PARP's role in cell death is well addressed, its role in development and multicellularity is still an enigma. We have previously reported the role of PARP in oxidative stress induced delayed development of D. discoideum.

Results
In the current study we highlight the involvement of PARP during D. discoideum development. Oxidative stress affects expression of aca and cAR1 thus affecting aggregation. Although parp expression is not affected during oxidative stress but it is involved during normal development as confirmed by our PARP down-regulation studies. Constitutive PARP down-regulation resulted in blocked development while no effect was observed on D. discoideum growth. Interestingly, stage specific PARP down-regulation arrested development at the slug stage.

Conclusion
These results emphasize that PARP is essential for complex differentiation and its function may be linked to multicellularity. This is the first report where the involvement of PARP during normal multicellular development in D. discoideum, an ancient eukaryote, is established which could be of evolutionary significance. Thus our study adds one more role to the multitasking function of PARP.
Quinolone resistance in Escherichia coli from Accra, Ghana
Authors: Namboodiri Sreela S , Opintan Japheth A , Lijek Rebeccah S , Newman Mercy J , Okeke Iruka N 
Published: March 2011

Abstract

Background
Antimicrobial resistance is under-documented and commensal Escherichia coli can be used as indicator organisms to study the resistance in the community. We sought to determine the prevalence of resistance to broad-spectrum antimicrobials with particular focus on the quinolones, which have recently been introduced in parts of Africa, including Ghana.

Results
Forty (13.7%) of 293 E. coli isolates evaluated were nalidixic acid-resistant. Thirteen (52%) of 2006 and 2007 isolates and 10 (66.7%) of 2008 isolates were also resistant to ciprofloxacin. All but one of the quinolone-resistant isolates were resistant to three or more other antimicrobial classes. Sequencing the quinolone-resistance determining regions of gyrA and parC, which encode quinolone targets, revealed that 28 quinolone-resistant E. coli harboured a substitution at position 83 of the gyrA gene product and 20 of these isolates had other gyrA and/or parC substitutions. Horizontally-acquired quinolone-resistance genes qnrB1, qnrB2, qnrS1 or qepA were detected in 12 of the isolates. In spite of considerable overall diversity among E. coli from Ghana, as evaluated by multilocus sequence typing, 15 quinolone-resistant E. coli belonged to sequence type complex 10. Five of these isolates carried qnrS1 alleles.

Conclusions
Quinolone-resistant E. coli are commonly present in the faecal flora of Accra residents. The isolates have evolved resistance through multiple mechanisms and belong to very few lineages, suggesting clonal expansion. Containment strategies to limit the spread of quinolone-resistant E. coli need to be deployed to conserve quinolone effectiveness and promote alternatives to their use.
Mapping and functional characterization of the murine Smoothelin-like 1 promoter
Authors: Ulke-Lemée Annegret , Turner Sara R , Mughal Saad H , Borman Meredith A , Winkfein Robert J , MacDonald Justin A 
Published: March 2011

Abstract

Background
Smoothelin-like 1 (SMTNL1, also known as CHASM) plays a role in promoting relaxation as well as adaptive responses to exercise, pregnancy and sexual development in smooth and skeletal muscle. Investigations of Smtnl1 transcriptional regulation are still lacking. Thus, in this study, we identify and characterize key regulatory elements of the mouse Smtnl1 gene.

Results
We mapped the key regulatory elements of the Smtnl1 promoter region: the transcriptional start site (TSS) lays -44 bp from the translational start codon and a TATA-box motif at -75 bp was conserved amongst all mammalian Smtnl1 promoters investigated. The Smtnl1 proximal promoter enhances expression up to 8-fold in smooth muscle cells and a second activating region lays 500 bp further upstream. Two repressing motifs were present (-118 to -218 bp and -1637 to -1869 bp). The proximal promoter is highly conserved in mammals and contains a mirror repeat sequence. In silico analysis suggests many transcription factors (notably MyoD) could potentially bind within the Smtnl1 proximal promoter sequence.

Conclusion

Smtnl1 transcript was identified in all smooth muscle tissues examined to date, albeit at much lower levels than found in skeletal muscle. It is unlikely that multiple SMTNL1 isoforms exist since a single Smtnl1 transcription start site was identified in both skeletal and intestinal smooth muscle. Promoter studies suggest restrictive control of Smtnl1 expression in non-muscle cells.
Characterisation of the legume SERK-NIKgene superfamily including splice variants: Implications for development and defence
Authors: Nolan Kim E , Kurdyukov Sergey , Rose Ray J 
Published: March 2011

Abstract

Background

SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) genes are part of the regulation of diverse signalling events in plants. Current evidence shows SERK proteins function both in developmental and defence signalling pathways, which occur in response to both peptide and steroid ligands. SERKs are generally present as small gene families in plants, with five SERK genes in Arabidopsis. Knowledge gained primarily through work on Arabidopsis SERKs indicates that these proteins probably interact with a wide range of other receptor kinases and form a fundamental part of many essential signalling pathways. The SERK1 gene of the model legume, Medicago truncatula functions in somatic and zygotic embryogenesis, and during many phases of plant development, including nodule and lateral root formation. However, other SERK genes in M. truncatula and other legumes are largely unidentified and their functions unknown.

Results
To aid the understanding of signalling pathways in M. truncatula, we have identified and annotated the SERK genes in this species. Using degenerate PCR and database mining, eight more SERK-like genes have been identified and these have been shown to be expressed. The amplification and sequencing of several different PCR products from one of these genes is consistent with the presence of splice variants. Four of the eight additional genes identified are upregulated in cultured leaf tissue grown on embryogenic medium. The sequence information obtained from M. truncatula was used to identify SERK family genes in the recently sequenced soybean (Glycine max) genome.

Conclusions
A total of nine SERK or SERK-like genes have been identified in M. truncatula and potentially 17 in soybean. Five M. truncatula SERK genes arose from duplication events not evident in soybean and Lotus. The presence of splice variants has not been previously reported in a SERK gene. Upregulation of four newly identified SERK genes (in addition to the previously described MtSERK1) in embryogenic tissue cultures suggests these genes also play a role in the process of somatic embryogenesis. The phylogenetic relationship of members of the SERK gene family to closely related genes, and to development and defence function is discussed.
Diffusion tensor imaging differences relate to memory deficits in diffuse traumatic brain injury
Authors: Palacios Eva M , Fernandez-Espejo Davinia , Junque Carme , Sanchez-Carrion Rocio , Roig Teresa , Tormos Jose M , Bargallo Nuria , Vendrell Pere 
Published: March 2011

Abstract

Background
Memory is one of the most impaired functions after traumatic brain injury (TBI). We used diffusion tensor imaging (DTI) to determine the structural basis of memory deficit. We correlated fractional anisotropy (FA) of the fasciculi connecting the main cerebral regions that are involved in declarative and working memory functions.

Methods
Fifteen patients with severe and diffuse TBI and sixteen healthy controls matched by age and years of education were scanned. The neuropsychological assessment included: Letter-number sequencing test (LNS), 2-back task, digit span (forwards and backwards) and the Rivermead profilet. DTI was analyzed by a tract-based spatial statics (TBSS) approach.

Results
Whole brain DTI analysis showed a global decrease in FA values that correlated with the 2-back d-prime index, but not with the Rivermead profile. ROI analysis revealed positive correlations between working memory performance assessed by 2-back d-prime and superior longitudinal fasciculi, corpus callosum, arcuate fasciculi and fornix. Declarative memory assessed by the Rivermead profile scores correlated with the fornix and the corpus callosum.

Conclusions
Diffuse TBI is associated with a general decrease of white matter integrity. Nevertheless deficits in specific memory domains are related to different patterns of white matter damage.
Nutritional status of iodine in pregnant women in Catalonia (Spain): study on hygiene-dietetic habits and iodine in urine
Authors: Prieto Gemma , Torres Maria Teresa , Francés Lidia , Falguera Gemma , Vila Lluis , Manresa Josep María , Casamitjana Roser , Barrada Juan Ramón , Acera Amèlia , Guix Dolors , Torrent Anna , Grau Josep , Torán Pere ,   the IODEGEST study group
Published: March 2011

Abstract

Background
It is a priority to achieve an adequate nutritional status of iodine during pregnancy since iodine deficiency in this population may have repercussions on the mother during both gestation and post partum as well as on the foetus, the neonate and the child at different ages. According to the WHO, iodine deficiency is the most frequent cause of mental retardation and irrreversible cerebral lesions around the world. However, few studies have been published on the nutritional status of iodine in the pregnant population within the Primary Care setting, a health care level which plays an essential role in the education and control of pregnant women. Therefore, the aim of the present study is: 1.- To know the hygiene-dietetic habits related to the intake of foods rich in iodine and smoking during pregnancy. 2.- To determine the prevalence of iodine deficiency and the factors associated with its appearance during pregnancy.

Methods/design
We will perform a cluster randomised, controlled, multicentre trial. Randomisation unit: Primary Care Team. Study population: 898 pregnant women over the age of 17 years attending consultation to a midwife during the first trimester of pregnancy in the participating primary care centres. Outcome measures: consumption of iodine-rich foods and iodine deficiency. Points of assessment: each trimester of the gestation. Intervention: group education during the first trimester of gestation on healthy hygiene-dietetic habits and the importance of an adequate iodine nutritional status. Statistical analysis: descriptive analysis of all variables will be performed as well as multilevel logistic regression. All analyses will be done carried out on an intention to treat basis and will be fitted for potential confounding factors and variables of clinical importance.

Discussion
Evidence of generalised iodine deficiency during pregnancy could lead to the promotion of interventions of prevention such as how to improve and intensify health care educational programmes for pregnant women.

Trial Registration
ClinicalTrials.gov: NCT01301768
Psychometric properties of the Chinese craving beliefs questionnaire for heroin abusers in methadone treatment
Authors: Chang Chun-Wei , Huang Chun-Wei , Wu Wei-Hsin , Wang Bo-En , Liu Yi-Lien , Shen Hsi-Che , Lee Tony Szu-Hsien 
Published: March 2011

Abstract

Background
This paper reports the psychometric properties of the Chinese version of Craving Beliefs Questionnaire (CCBQ), an easy-to-administer assessment instrument of measurement of craving beliefs for heroin abusers.

Methods
Participants were 445 heroin abusers from four methadone clinics in Northern Taiwan. Fifty-one of the participants were tested twice within a two-week period at a different hospital to examine test-retest reliability.

Results
Three-factor solution using principal component analysis was identified in the CCBQ: will power, compulsive behavior, and negative coping, accounting for 54.6% of the variance. Internal consistency analysis indicated that the three factors have strong reliability, with Cronbach alphas ranging from .81 to .92. The test-retest ICC coefficient is .80. The test-retest coefficients for the subscales will power, compulsive behavior, and negative coping are .76, .51, and .64, respectively. Overall, the data show that the CCBQ has acceptable reliability and validity, demonstrating that it can be a research instrument for assessing heroin craving beliefs.

Conclusions
The psychometric properties of the CCBQ seem promising for both research and clinical purposes, and the scale thus deserves further refinement and validation with heroin abusers.
Demographic and microbial characteristics of extrapulmonary tuberculosis cases diagnosed in Malatya, Turkey, 2001-2007
Authors: Gunal Selami , Yang Zhenhua , Agarwal Mansi , Koroglu Mehmet , Arıcı Zeynep Kazgan , Durmaz Riza 
Published: March 2011

Abstract

Background
Extrapulmonary tuberculosis (EPTB) has an increasing rate in Turkey. The reason remains largely unknown. A better understanding of the demographic and microbial characteristics of EPTB in the Turkish population would extend the knowledgebase of EPTB and allow us to develop better strategies to control tuberculosis (TB).

Methods
We retrospectively evaluated clinical and laboratory data of 397 bacteriologically-confirmed TB cases diagnosed during an eight year-period using by chi-square analysis and multivariate logistic regression model.

Results
Of the 397 study patients, 103 (25.9%) had EPTB and 294 (74.1%) had pulmonary tuberculosis (PTB). The most commonly seen two types of EPTB were genitourinary TB (27.2%) and meningeal TB (19.4%). TB in bone/joints, pleural cavity, lymph nodes, skin, and peritoneal cavity occurred at a frequency ranging from 9.7% to 10.7%. The age distribution was significantly different (P < 0.01) between PTB and EPTB, with patients older than 45 years tending to have an increased risk of EPTB. Furthermore, the distribution of different types of EPTB differed significantly among age groups (P = 0.03). Meningeal and bone and/or joint TB were more commonly observed among the male patients, while lymphatic, genitourinary, and peritoneal TB cases were more frequently seen among females. Unique strain infection was statistically significantly associated with EPTB (OR: 2.82, 95% CI [1.59, 5.00])

Conclusions
EPTB accounted for a significant proportion of TB cases in Malatya, Turkey between 2001 and 2007. The current study has provided an insight into the dynamics of EPTB in Malatya, Turkey. However, the risk factors for having EPTB in Malatya, Turkey remain to be assessed in future studies using population-based or randomly selected sample.
Evaluation of a social marketing intervention promoting oral rehydration salts in Burundi
Authors: Kassegne Sethson , Kays Megan B , Nzohabonayo Jerome 
Published: March 2011

Abstract

Background
Diarrhea is the second leading cause of death for children under five in Burundi; however, use of oral rehydration salts (ORS), the recommended first-line treatment, remains low. In 2004, PSI/Burundi launched a social marketing intervention to promote ORASEL among caregivers of children under five; the product was relaunched in 2006 with a new flavor. This study evaluates the intervention after the ORASEL relaunch, which included mass media and interpersonal communication activities. The study looks at trends in ORASEL use in Burundi and in behavioral determinants that may be related to its use.

Methods
In 2006 and 2007, PSI conducted household surveys among Burundian females of reproductive age (15-49). Both surveys used a two-stage sampling process to select 30 households in each of 115 rural and urban collines throughout the nation. Survey respondents were asked about diarrhea treatment-related behavior; key behavioral determinants; and exposure to the ORASEL intervention. Data were analyzed to identify trends over time, characteristics of ORASEL users, and associations between exposure to the intervention and changes in ORASEL use and related behavioral determinants.

Results
ORASEL use among caregivers at their children's last diarrheal episode increased significantly from 20% in 2006 to 30% in 2007, and there were also desirable changes in several behavioral determinants associated with ORASEL use. Evaluation analysis showed that a higher level of exposure to the social marketing campaign was associated with greater use of ORASEL and with significant improvements in perceived availability, knowledge of the signs of diarrhea and dehydration, social support, and self-efficacy.

Conclusions
ORS use can be improved through social marketing and educational campaigns that make the public aware of the availability of the product, encourage dialogue about its use, and increase skills and confidence relating to correct product preparation and administration. Further interventions in Burundi and elsewhere should promote ORS through a variety of mass media and interpersonal communication channels, and should be rigorously evaluated in the context of the total market for diarrhea treatment products.
Ethical issues of unrelated hematopoietic stem cell transplantation in adult thalassemia patients
Authors: Caocci Giovanni , La Nasa Giorgio , d'Aloja Ernesto , Vacca Adriana , Piras Eugenia , Pintor Michela , Demontis Roberto , Pisu Salvatore 
Published: March 2011

Abstract

Background
Beta thalassemia major is a severe inherited form of hemolytic anemia that results from ineffective erythropoiesis. Allogenic hematopoietic stem cell transplantation (HSCT) remains the only potentially curative therapy. Unfortunately, the subgroup of adult thalassemia patients with hepatomegaly, portal fibrosis and a history of irregular iron chelation have an elevated risk for transplantation-related mortality that is currently estimated to be about 29 percent.

Discussion
Thalassemia patients may be faced with a difficult choice: they can either continue conventional transfusion and iron chelation therapy or accept the high mortality risk of HSCT in the hope of obtaining complete recovery.
Throughout the decision making process, every effort should be made to sustain and enhance autonomous choice. The concept of conscious consent becomes particularly important. The patient must be made fully aware of the favourable and adverse outcomes of HSCT. Although it is the physician's duty to illustrate the possibility of completely restoring health, considerable emphasis should be put on the adverse effects of the procedure. The physician also needs to decide whether the patient is eligible for HSCT according to the "rule of descending order". The patient must be given full details on self-care and fundamental lifestyle changes and be fully aware that he/she will be partly responsible for the outcome.

Summary
Only if all the aforesaid conditions are satisfied can it be considered reasonable to propose unrelated HSCT as a potential cure for high risk thalassemia patients.