bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of the oil-rich seed of the bioenergy crop Jatropha curcas L
Authors: Costa Gustavo GL , Cardoso Kiara C , Del Bem Luiz EV , Lima Aline C , Cunha Muciana AS , de Campos-Leite Luciana , Vicentini Renato , Papes Fábio , Moreira Raquel C , Yunes José A , Campos Francisco AP , Da Silva Márcio J 
Published: August 2010

Abstract

Background
To date, oil-rich plants are the main source of biodiesel products. Because concerns have been voiced about the impact of oil-crop cultivation on the price of food commodities, the interest in oil plants not used for food production and amenable to cultivation on non-agricultural land has soared. As a non-food, drought-resistant and oil-rich crop, Jatropha curcas L. fulfils many of the requirements for biofuel production.

Results
We have generated 13,249 expressed sequence tags (ESTs) from developing and germinating Jatropha seeds. This strategy allowed us to detect most known genes related to lipid synthesis and degradation. We have also identified ESTs coding for proteins that may be involved in the toxicity of Jatropha seeds. Another unexpected finding is the high number of ESTs containing transposable element-related sequences in the developing seed library (800) when contrasted with those found in the germinating seed library (80).

Conclusions
The sequences generated in this work represent a considerable increase in the number of sequences deposited in public databases. These results can be used to produce genetically improved varieties of Jatropha with increased oil yields, different oil compositions and better agronomic characteristics.
Comparative analysis of expressed sequence tags from three castes and two life stages of the termite Reticulitermes flavipes
Authors: Steller Matthew M , Kambhampati Srinivas , Caragea Doina 
Published: August 2010

Abstract

Background
Termites (Isoptera) are eusocial insects whose colonies consist of morphologically and behaviorally specialized castes of sterile workers and soldiers, and reproductive alates. Previous studies on eusocial insects have indicated that caste differentiation and behavior are underlain by differential gene expression. Although much is known about gene expression in the honey bee, Apis mellifera, termites remain relatively understudied in this regard. Therefore, our objective was to assemble an expressed sequence tag (EST) data base for the eastern subterranean termite, Reticulitermes flavipes, for future gene expression studies.

Results
Soldier, worker, and alate caste and two larval cDNA libraries were constructed, and approximately 15,000 randomly chosen clones were sequenced to compile an EST data base. Putative gene functions were assigned based on a BLASTX Swissprot search. Categorical in silico expression patterns for each library were compared using the R-statistic. A significant proportion of the ESTs of each caste and life stages had no significant similarity to those in existing data bases. All cDNA libraries, including those of non-reproductive worker and soldier castes, contained sequences with putative reproductive functions. Genes that showed a potential expression bias among castes included a putative antibacterial humoral response and translation elongation protein in soldiers and a chemosensory protein in alates.

Conclusions
We have expanded upon the available sequences for R. flavipes and utilized an in silico method to compare gene expression in different castes of an eusocial insect. The in silico analysis allowed us to identify several genes which may be differentially expressed and involved in caste differences. These include a gene overrepresented in the alate cDNA library with a predicted function of neurotransmitter secretion or cholesterol absorption and a gene predicted to be involved in protein biosynthesis and ligase activity that was overrepresented in the late larval stage cDNA library. The EST data base and analyses reported here will be a valuable resource for future studies on the genomics of R. flavipes and other termites.
Decreased Hsp90 expression in infiltrative lobular carcinoma: an immunohistochemical study
Authors: Zagouri Flora , Sergentanis Theodoros , Nonni Afrodite , Papadimitriou Christos , Pazaiti Anastasia , Michalopoulos Nikolaos V , Safioleas Panagiotis , Lazaris Andreas , Theodoropoulos George , Patsouris Effstratios , Zografos George 
Published: August 2010

Abstract

Background
Elevated Hsp90 expression has been documented in breast ductal carcinomas, whereas decreased Hsp90 expression has been reported in precursor lobular lesions. This study aims to assess Hsp90 expression in infiltrative lobular carcinomas of the breast.

Methods
Tissue specimens were taken from 32 patients with infiltrative lobular carcinoma. Immunohistochemical assessment of Hsp90 was performed both in the lesion and the adjacent normal breast ducts and lobules; the latter serving as control. Concerning Hsp90 assessment: i) the percentage of positive cells and ii) the intensity were separately analyzed. Subsequently, the Allred score was adopted and calculated. The intensity was treated as an ordinal variable-score (0: negative, low: 1, moderate: 2, high: 3). Statistical analysis followed.

Results
All infiltrative lobular carcinoma foci mainly presented with a positive cytoplasmic immunoreaction for Hsp90. Compared to the adjacent normal ducts and lobules, infiltrative lobular carcinoma exhibited a statistically significant decrease in Hsp90 expression, both in terms of Hsp90 positive cells (%) and Allred score (74.2 ± 11.2 vs. 59.1 ± 14.2 p = 0.0001; 7.00 ± 0.95 vs. 6.22 ± 1.01, p = 0.007, Wilcoxon matched-pairs signed-ranks test). Concerning the intensity of Hsp90 immunostaining only a marginal decrease was noted (2.16 ± 0.68 vs. 1.84 ± 0.63, p = 0.087, Wilcoxon matched-pairs signed-ranks test).

Conclusion
ILC lesions seem to exhibit decreased Hsp90 expression, a finding contrary to what might have been expected, given that high Hsp90 expression is a trait of invasive ductal carcinomas.
Mass spectrometry protein expression profiles in colorectal cancer tissue associated with clinico-pathological features of disease
Authors: Liao Christopher CL , Ward Nicholas , Marsh Simon , Arulampalam Tan , Norton John D 
Published: August 2010

AbstractBackgroundStudies of several tumour types have shown that expression profiling of cellular protein extracted from surgical tissue specimens by direct mass spectrometry analysis can accurately discriminate tumour from normal tissue and in some cases can sub-classify disease. We have evaluated the potential value of this approach to classify various clinico-pathological features in colorectal cancer by employing matrix-assisted laser desorption ionisation time of-flight-mass spectrometry (MALDI-TOF MS).MethodsProtein extracts from 31 tumour and 33 normal mucosa specimens were purified, subjected to MALDI-Tof MS and then analysed using the 'GenePattern' suite of computational tools (Broad Institute, MIT, USA). Comparative Gene Marker Selection with either a t-test or a signal-to-noise ratio (SNR) test statistic was used to identify and rank differentially expressed marker peaks. Thek-nearest neighbours algorithm was used to build classification models either using separate training and test datasets or else by using an iterative, 'leave-one-out' cross-validation method.Results73 protein peaks in the mass range 1800-16000Da were differentially expressed in tumourversesadjacent normal mucosa tissue (P ≤ 0.01, false discovery rate ≤ 0.05). Unsupervised hierarchical cluster analysis classified most tumour and normal mucosa into distinct cluster groups. Supervised prediction correctly classified the tumour/normal mucosa status of specimens in an independent test spectra dataset with 100% sensitivity and specificity (95% confidence interval: 67.9-99.2%). Supervised prediction using 'leave-one-out' cross validation algorithms for tumour spectra correctly classified 10/13 poorly differentiated and 16/18 well/moderately differentiated tumours (P= < 0.001; receiver-operator characteristics - ROC - error, 0.171); disease recurrence was correctly predicted in 5/6 cases and disease-free survival (median follow-up time, 25 months) was correctly predicted in 22/23 cases (P= < 0.001; ROC error, 0.105). A similar analysis of normal mucosa spectra correctly predicted 11/14 patients with, and 15/19 patients without lymph node involvement (P= 0.001; ROC error, 0.212).ConclusionsProtein expression profiling of surgically resected CRC tissue extracts by MALDI-TOF MS has potential value in studies aimed at improved molecular classification of this disease. Further studies, with longer follow-up times and larger patient cohorts, that would permit independent validation of supervised classification models, would be required to confirm the predictive value of tumour spectra for disease recurrence/patient survival.
Risk factors and obstetric complications of large for gestational age births with adjustments for community effects: results from a new cohort study
Authors: Ng Shu-Kay , Olog Adriana , Spinks Anneliese B , Cameron Cate M , Searle Judy , McClure Rod J 
Published: August 2010

Abstract

Background
High birth weight has serious adverse impacts on chronic health conditions and development in children. This study identifies the social determinants and obstetric complications of high birth weight adjusted for gestational age and baby gender.

Methods
Pregnant women were recruited from three maternity hospitals in South-East Queensland in Australia during antenatal clinic visits. A questionnaire was completed by each participant to elicit information on eco-epidemiological exposures. Perinatal information was extracted from hospital birth records. A hierarchical mixture regression model was used in the analysis to account for the heterogeneity of birth weights and identify risk factors and obstetric complications of births that were large for gestational age. A generalized linear mixed model was used to adjust for (random) "community" effects.

Results
Pre-pregnancy obesity (adjusted OR = 2.73, 95% CI = 1.49-5.01), previous pregnancy (adjusted OR = 2.03, 95% CI = 1.08-3.81), and married mothers (adjusted OR = 1.85, 95% CI = 1.00-3.42) were significantly associated with large for gestational age babies. Subsequent complications included the increased need for delivery by caesarean sections or instrumental procedures (adjusted OR = 1.98, 95% CI = 1.10-3.55), resuscitation (adjusted OR = 2.52, 95% CI = 1.33-4.79), and transfer to intensive/special care nursery (adjusted OR = 3.76, 95% CI = 1.89-7.49). Communities associated with a higher proportion of large for gestational age births were identified.

Conclusions
Pre pregnancy obesity is the principal modifiable risk factor for large for gestational age births. Large for gestational age is an important risk factor for the subsequent obstetric complications. The findings improve the evidence-base on which to base preventive interventions to reduce the impact of high birth weight on maternal and child health.
The Wnt/β-catenin pathway regulates growth and maintenance of colonospheres
Authors: Kanwar Shailender S , Yu Yingjie , Nautiyal Jyoti , Patel Bhaumik B , Majumdar Adhip PN 
Published: August 2010

Abstract

Background
Recent evidence suggests that epithelial cancers, including colorectal cancer are driven by a small sub-population of self-renewing, multi-potent cells termed cancer stem cells (CSCs) which are thought to be responsible for recurrence of cancer. One of the characteristics of CSCs is their ability to form floating spheroids under anchorage-independent conditions in a serum-free defined media. The current investigation was undertaken to examine the role of Wnt/β-catenin pathway in regulating the growth and maintenance of colonospheres. Human colon cancer cells HCT-116 (p53 wild type; K-ras mutant), HCT-116 (p53 null; K-ras mutant) and HT-29 (p53 mutant) were used.

Results
Colonospheres formed in vitro exhibited higher expression of colon CSCs markers LGR5, CD44, CD166 and Musashi-1 along with putative CSC marker EpCAM, compared to the corresponding parental cancer cells and also exhibit the ability to form spheroids under extreme limiting dilution, indicating the predominance of CSCs in colonospheres. Colonospheres formed by HCT-116 cells show over 80% of the cells to be CD44 positive, compared to ≤ 1% in the corresponding parental cells. Additionally, colonospheres showed reduced membrane bound β-catenin but had increased levels of total β-catenin, cyclin-D1 and c-myc and down regulation of axin-1 and phosphorylated β-catenin. Increased expression of β-catenin was associated with a marked transcriptional activation of TCF/LEF. The latter was greatly decreased following down regulation of β-catenin by the corresponding siRNA, leading to a marked reduction in CD44 positive cells as well as colonospheres formation. In contrast, upregulation of c-myc, a down-stream effector of TCF/LEF greatly augmented the formation of colonospheres.

Conclusion
Our data suggest that colonospheres formed by colon cancer cell lines are highly enriched in CSCs and that Wnt/β-catenin pathway plays a critical role in growth and maintenance of colonospheres.
Effect of apoA-I on cholesterol release and apoE secretion in human mature adipocytes
Authors: Bencharif Karima , Hoareau Laurence , Murumalla Ravi K , Tarnus Evelyne , Tallet Frank , Clerc Roger G , Gardes Christophe , Cesari Maya , Roche Régis 
Published: August 2010

Abstract

Background
The risk of cardiovascular disease is inversely correlated to level of plasma HDL-c. Moreover, reverse cholesterol transport (RCT) from peripheral tissues to the liver is the most widely accepted mechanism linked to the anti-atherosclerotic activity of HDL. The apolipoprotein A-I (apoA-I) and the ABC transporters play a key role in this process.
Adipose tissue constitutes the body's largest pool of free cholesterol. The adipose cell could therefore be regarded as a key factor in cholesterol homeostasis. The present study investigates the capacity of primary cultures of mature human adipocytes to release cholesterol and explores the relationships between apoA-I, ABCA1, and apoE as well as the signaling pathways that could be potentially involved.

Results
We demonstrate that apoA-I induces a strong increase in cholesterol release and apoE secretion from adipocytes, whereas it has no transcriptional effect on ABCA1 or apoE genes. Furthermore, brefeldin A (BFA), an intracellular trafficking inhibitor, reduces basal cholesterol and apoE secretion, but does not modify induction by apoA-I. The use of statins also demonstrates that apoA-I stimulated cholesterol release is independent of HMG-CoA reductase activation.

Conclusion
Our work highlights the fact that adipose tissue, and particularly adipocytes, may largely contribute to RCT via a mechanism specifically regulated within these cells. This further supports the argument that adipose tissue must be regarded as a major factor in the development of cardiovascular diseases, in particular atherosclerosis.
Columnar cell lesions and subsequent breast cancer risk: a nested case-control study
Authors: Aroner Sarah A , Collins Laura C , Schnitt Stuart J , Connolly James L , Colditz Graham A , Tamimi Rulla M 
Published: August 2010

Abstract
Introduction
Histologic and genetic evidence suggests that at least some columnar cell lesions (CCL) of the breast represent precursor lesions in the low-grade breast neoplasia pathway. However, the risk of subsequent breast cancer associated with the presence of CCL in a benign breast biopsy is poorly understood.

Methods
The authors examined the association between the presence of CCL and subsequent breast cancer risk in a nested case-control study of benign breast disease (BBD) and breast cancer within the Nurses' Health Studies (394 cases, 1,606 controls). Benign breast biopsy slides were reviewed by pathologists and CCL presence assessed. Logistic regression was used to compute odds ratios (ORs) and 95% confidence intervals (CIs) for the association between CCL and breast cancer risk.

Results
Women with CCL (140 cases, 448 controls) had an increased risk of breast cancer compared with those without CCL (OR = 1.44, 95% CI: 1.14 to 1.83), although this was attenuated and became non-significant after adjustment for the histologic category of BBD (OR = 1.20, 95% CI: 0.94 to 1.54). CCL presence was associated with the greatest risk of breast cancer for those with nonproliferative BBD (OR = 1.36, 95% CI: 0.79 to 2.37) and the lowest risk for those with atypical hyperplasia (AH) (OR = 1.10, 95% CI: 0.65 to 1.87); however, this apparent heterogeneity in risk across BBD categories was not significant (P for interaction between CCL presence and BBD category = 0.77).

Conclusions
These results provide evidence that CCL may be an important marker of breast cancer risk in women with BBD but suggest that CCL do not increase breast cancer risk independently of concurrent proliferative changes in the breast.
The influence of prior knowledge on the retrieval‐directed function of note taking in prior knowledge activation
Authors: Wetzels Sandra A. J. , Kester Liesbeth , van Merriënboer Jeroen J. G. , Broers Nick J. 
Published: August 2010

Background. Prior knowledge activation facilitates learning. Note taking during prior knowledge activation (i.e., note taking directed at retrieving information from memory) might facilitate the activation process by enabling learners to build an external representation of their prior knowledge. However, taking notes might be less effective in supporting prior knowledge activation if available prior knowledge is limited. Aims. This study investigates the effects of the retrieval‐directed function of note taking depending on learners' level of prior knowledge. It is hypothesized that the effectiveness of note taking is influenced by the amount of prior knowledge learners already possess. Sample. Sixty‐one high school students participated in this study. A prior knowledge test was used to ascertain differences in level of prior knowledge and assign participants to a low or a high prior knowledge group. Method. A 2×2 factorial design was used to investigate the effects of note taking during prior knowledge activation (yes, no) depending on learners' level of prior knowledge (low, high) on mental effort, performance, and mental efficiency. Results. Note taking during prior knowledge activation lowered mental effort and increased mental efficiency for high prior knowledge learners. For low prior knowledge learners, note taking had the opposite effect on mental effort and mental efficiency. Conclusions. The effects of the retrieval‐directed function of note taking are influenced by learners' level of prior knowledge. Learners with high prior knowledge benefit from taking notes while activating prior knowledge, whereas note taking has no beneficial effects for learners with limited prior knowledge.
Assessing pupil concerns about transition to secondary school
Authors: Rice Frances , Frederickson Norah , Seymour Joanna 
Published: August 2010

Background. The primary–secondary transition can negatively affect pupils' emotional and psychological adjustment. However, methods for assessing concerns regarding secondary school are limited. A reliable and valid measure of transition‐related concerns would be useful both in evaluating and shaping the content and delivery of universal and targeted transition support programmes. Aims. To assess the validity of a quantitative self‐report measure of school concerns as an assessment tool during the primary–secondary school transition. Sample. A UK sample of 147 Year 6 primary school pupils and 263 Year 7 secondary school pupils. Method. Self‐reports of school concerns and school liking as well as self‐reported and peer assessments on a range of psychological adjustment measures were collected. Results. The School Concerns Questionnaire (SCQ) showed good reliability at primary and secondary school. Secondary concerns reduced significantly post‐transition. Three factors emerged from an exploratory factor analysis of the SCQ and the pattern of results was replicated for post‐transition concerns. Pupils with higher school concerns at secondary school reported reduced liking of school and reduced trust and respect for teachers. The SCQ was associated with generalized anxiety and female gender both pre‐and post‐transition. Peer problems and depression were associated with pre‐ and post‐transition concerns, respectively. Conclusions. The SCQ is a simple to complete, reliable, and valid tool for assessing primary–secondary transition concerns. It could serve a valuable role in the evaluation and development of universal and targeted school‐based initiatives that aim to promote positive secondary transition.
Jaccard's heel: Radex models of criminal behaviour are rarely falsifiable when derived using Jaccard coefficient
Authors: Taylor Paul J. , Donald Ian J. , Jacques Karen , Conchie Stacey M. 
Published: August 2010

Purpose. This article considers whether the modular facet of popular ‘radex’ models of offender behaviour is falsifiable or a statistical inevitability when using Jaccard coefficient, as evidence from other domains suggests.Method. Data equivalent to that examined in previous papers, and artificial data varying on four parameters, were examined using the conventional procedure of deriving Jaccard coefficients and submitting these to a smallest space analyses (SSA‐I). The parameters were number of variables, number of cases, highest frequency of variable occurrence, and distribution of occurrences. Evidence of a modular pattern in each SSA‐I solution was assessed using one qualitative and two quantitative measures.Results. When variables were free to occur in more than 50% of cases, none of the Jaccard‐based SSA‐I solutions supported the null hypothesis of no modular facet. This contrasts equivalent analyses using Yules Q, where 95.7% of the solutions supported the null hypothesis. When variables were restricted to occur in less than 50% of cases, the number of solutions supporting the null hypothesis changes to .003 and 78%, respectively. Analyses of the artificial data found that reducing the number of variables in a Jaccard‐based solution increased the likelihood of supporting the null hypothesis, which suggests that these solutions are structured by variable occurrence (i.e., frequency) rather than variable co‐occurrence.Implications. Research using Jaccard coefficient to measure co‐occurrences among behaviours should not claim that the modular facet of their radex model is an empirical finding. Unfortunately, this is many of the existing publications.
Bevacizumab
Authors: Kazazi-Hyseni Filis , Beijnen Jos H. , Schellens Jan H. M. 
Published: August 2010

AbstractLearning ObjectivesAfter completing this course, the reader will be able to: Evaluate the clinical use of bevacizumab, both for cancer and for non-oncologic diseases, and discuss approved and investigational combination chemotherapies that include bevacizumab.Describe the pharmacology of bevacizumab and its mechanism of action in order to predict degrees of patient response.CME This article is available for continuing medical education credit at CME.TheOncologist.com.