bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tomato root transcriptome response to a nitrogen-enriched soil patch
Authors: Ruzicka Daniel R , Barrios-Masias Felipe H , Hausmann Natasha T , Jackson Louise E , Schachtman Daniel P 
Published: April 2010

AbstractBackgroundNitrogen (N), the primary limiting factor for plant growth and yield in agriculture, has a patchy distribution in soils due to fertilizer application or decomposing organic matter. Studies in solution culture over-simplify the complex soil environment where microbial competition and spatial and temporal heterogeneity challenge roots' ability to acquire adequate amounts of nutrients required for plant growth. In this study, various ammonium treatments (as15N) were applied to a discrete volume of soil containing tomato (Solanum lycopersicum) roots to simulate encounters with a localized enriched patch of soil. Transcriptome analysis was used to identify genes differentially expressed in roots 53 hrs after treatment.ResultsThe ammonium treatments resulted in significantly higher concentrations of both ammonium and nitrate in the patch soil. The plant roots and shoots exhibited increased levels of15N over time, indicating a sustained response to the enriched environment. Root transcriptome analysis identified 585 genes differentially regulated 53 hrs after the treatments. Nitrogen metabolism and cell growth genes were induced by the high ammonium (65 μg NH4+-N g-1soil), while stress response genes were repressed. The complex regulation of specific transporters following the ammonium pulse reflects a simultaneous and synergistic response to rapidly changing concentrations of both forms of inorganic N in the soil patch. Transcriptional analysis of the phosphate transporters demonstrates cross-talk between N and phosphate uptake pathways and suggests that roots increase phosphate uptake via the arbuscular mycorrhizal symbiosis in response to N.ConclusionThis work enhances our understanding of root function by providing a snapshot of the response of the tomato root transcriptome to a pulse of ammonium in a complex soil environment. This response includes an important role for the mycorrhizal symbiosis in the utilization of an N patch.
Kocuria varians infection associated with brain abscess: A case report
Authors: Tsai Cheng-Yu , Su Shou-hsin , Cheng Yu-Hsin , Chou Yu-lin , Tsai Tai-Hsin , Lieu Ann-Shung 
Published: April 2010

Abstract

Background

Kocuria, established by Stackebrandt et al., previously was classified into Micrococcus. Only two species, K. rosea and K. kristinae are reported to be associated as pathogenic and found with catheter-related bacteremia and acute cholecystitis.

Case presentation
We herein report the first case of brain abscess caused by Kocuria varians, a gram-positive microorganism, in a 52-year-old man. Hematogenous spread is the probable pathogenesis.

Conclusions
This report presents a case of Kocuria varians brain abscess successfully treated with surgical excision combined with antimicrobial therapy. In addition, Vitek 2 system has been used to identify and differentiate between coagulase-negative staphylococcus.
Epidermal growth factor induces HCCR expression via PI3K/Akt/mTOR signaling in PANC-1 pancreatic cancer cells
Authors: Xu Zekuan , Zhang Yi , Jiang Jiakai , Yang Yang , Shi Ruihua , Hao Bo , Zhang Zhihong , Huang Zuhu , Kim Jin W , Zhang Guoxin 
Published: April 2010

Abstract

Background
Human cervical cancer oncoprotein 1 (HCCR-1), reported as a negative regulator of p53, is over-expressed in a variety of human cancers. However, it is yet unknown whether HCCR-1 plays any role in pancreatic cancer development. The aim of this study was to investigate the effect of epidermal growth factor on the expression of HCCR in pancreatic cancer cells, and to explore if PI3K/Akt/mTOR signaling pathway mediated this expression.

Methods
A polyclonal antibody against HCCR protein was raised by immunizing Balb/c mice with the purified recombinant protein pMBPc-HCCR. Tissue samples were constructed on a tissue chip, and the expression of HCCR was investigated by immunohistochemistry assay and Western blotting. Pancreatic cell line, PANC-1 cells were stably transfected with plasmids containing sense-HCCR-1 fragment and HCCR siRNA fragment. MTT and transwell assay were used to investigate the proliferation and invasion of stable tansfectants. The specific inhibitor of PI3K and mTOR was used to see if PI3K/mTOR signal transduction was involved in the induction of HCCR gene expression. A Luciferase assay was used to see if Akt can enhance the HCCR promoter activity.

Results
HCCR was up-regulated in pancreatic tumor tissues (mean Allred score 4.51 ± 1.549 vs. 2.87 ± 2.193, P < 0.01), especially with high expression in poorly differentiated pancreatic cancer. The growth of cells decreased in HCCR-1 siRNA transfected cells compared with vector transfectants. The number of invasion cells was significantly lower in HCCR-1 siRNA transfected cells (24.4 ± 9.9) than that in vector transfectants (49.1 ± 15.4). Treatment of PANC-1 cells with epidermal growth factor increased HCCR protein level in a dose- and time-dependent manner. However, application of LY294002 and rapamycin caused a dramatic reduction of epidermal growth factor-induced HCCR expression. Over-expression of exogenous constitutively active Akt increased the HCCR promoter activity; in contrast, dominant negative Akt decreased the promoter activity.

Conclusions
EGF-induced HCCR-1 over-expression is mediated by PI3K/AKT/mTOR signaling which plays a pivotal role in pancreatic tumor progression, suggesting that HCCR-1 could be a potential target for cancer therapeutics.
Prediction of posttraumatic stress disorder among adults in flood district
Authors: Huang Peng , Tan Hongzhuan , Liu Aizhong , Feng Shuidong , Chen Mengshi 
Published: April 2010

AbstractBackgroundFlood is one of the most common and severe forms of natural disasters. Posttraumatic stress disorder (PTSD) is a common disorder among victims of various disasters including flood. Early prediction for PTSD could benefit the prevention and treatment of PTSD. This study aimed to establish a prediction model for the occurrence of PTSD among adults in flood districts.MethodsA cross-sectional survey was carried out in 2000 among individuals who were affected by the 1998 floods in Hunan, China. Multi-stage sampling was used to select subjects from the flood-affected areas. Data was collected through face-to-face interviews using a questionnaire. PTSD was diagnosed according to DSM-IV criteria. Study subjects were randomly divided into two groups: group 1 was used to establish the prediction model and group 2 was used to validate the model. We first used the logistic regression analysis to select predictive variables and then established a risk score predictive model. The validity of model was evaluated by using the model in group 2 and in all subjects. The area under the receiver operation characteristic (ROC) curve was calculated to evaluate the accuracy of the prediction model.ResultsA total of 2336 (9.2%) subjects were diagnosed as probable PTSD-positive individuals among a total of 25,478 study subjects. Seven independent predictive factors (age, gender, education, type of flood, severity of flood, flood experience, and the mental status before flood) were identified as key variables in a risk score model. The area under the ROC curve for the model was 0.853 in the validation data. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of this risk score model were 84.0%, 72.2%, 23.4%, and 97.8%, respectively, at a cut-off value of 67.5 in the validation data.ConclusionsA simple risk score model can be used to predict PTSD among victims of flood.
Analysis of post-operative changes in serum protein expression profiles from colorectal cancer patients by MALDI-TOF mass spectrometry: a pilot methodological study
Authors: Liao Christopher CL , Mehta Anuja , Ward Nicholas J , Marsh Simon , Arulampalam Tan , Norton John D 
Published: April 2010

Abstract

Background
Mass spectrometry-based protein expression profiling of blood sera can be used to discriminate colorectal cancer (CRC) patients from unaffected individuals. In a pilot methodological study, we have evaluated the changes in protein expression profiles of sera from CRC patients that occur following surgery to establish the potential of this approach for monitoring post-surgical response and possible early prediction of disease recurrence.

Methods
In this initial pilot study, serum specimens from 11 cancer patients taken immediately prior to surgery and at approximately 6 weeks following surgery were analysed alongside 10 normal control sera by matrix-assisted laser desorption ionisation time of-flight-mass spectrometry (MALDI-TOF MS). Using a two-sided t-test the top 20 ranked protein peaks that discriminate normal from pre-operative sera were identified. These were used to classify post-operative sera by hierarchical clustering analysis (Spearman's Rank correlation) and, as an independent 'test' dataset, by k-nearest neighbour and weighted voting supervised learning algorithms.

Results
Hierarchical cluster analysis classified post-operative sera from all six early Dukes' stage (A and B) patients as normal. The remaining five post-operative sera from more advanced Dukes' stages (C1 and C2) were classified as cancer. Analysis by supervised learning algorithms similarly grouped all advanced Dukes' stages as cancer, with four of the six post-operative sera from early Dukes' stages being classified as normal (P = 0.045; Fisher's exact test).

Conclusions
The results of this pilot methodological study illustrate the proof-of-concept of using protein expression profiling of post-surgical blood sera from individual patients to monitor disease course. Further validation on a larger patient cohort and using an independent post-operative sera dataset would be required to evaluate the potential clinical relevance of this approach. Prospective data, including follow-up on patient survival, could in the future, then be evaluated to inform decisions on individualised treatment modalities.
On the identification of sensory information from mixed nerves by using single-channel cuff electrodes
Authors: Raspopovic Stanisa , Carpaneto Jacopo , Udina Esther , Navarro Xavier , Micera Silvestro 
Published: April 2010

Abstract

Background
Several groups have shown that the performance of motor neuroprostheses can be significantly improved by detecting specific sensory events related to the ongoing motor task (e.g., the slippage of an object during grasping). Algorithms have been developed to achieve this goal by processing electroneurographic (ENG) afferent signals recorded by using single-channel cuff electrodes. However, no efforts have been made so far to understand the number and type of detectable sensory events that can be differentiated from whole nerve recordings using this approach.

Methods
To this aim, ENG afferent signals, evoked by different sensory stimuli were recorded using single-channel cuff electrodes placed around the sciatic nerve of anesthetized rats. The ENG signals were digitally processed and several features were extracted and used as inputs for the classification. The work was performed on integral datasets, without eliminating any noisy parts, in order to be as close as possible to real application.

Results
The results obtained showed that single-channel cuff electrodes are able to provide information on two to three different afferent (proprioceptive, mechanical and nociceptive) stimuli, with reasonably good discrimination ability. The classification performances are affected by the SNR of the signal, which in turn is related to the diameter of the fibers encoding a particular type of neurophysiological stimulus.

Conclusions
Our findings indicate that signals of acceptable SNR and corresponding to different physiological modalities (e.g. mediated by different types of nerve fibers) may be distinguished.
A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway
Authors: Yan Han , Zhang Bo , Li Shao , Zhao Qianchuan 
Published: April 2010

AbstractBackgroundDrug combination therapy is commonly used in clinical practice. Many methods including Bliss independence method have been proposed for drug combination design based on simulations models or experiments. Although Bliss independence method can help to solve the drug combination design problem when there are only a small number of combinations, as the number of combinations increases, it may not be scalable. Exploration of system structure becomes important to reduce the complexity of the design problem.ResultsIn this paper, we deduced a mathematical model which can simplify the serial structure and parallel structure of biological pathway for synergy evaluation of drug combinations. We demonstrated in steady state the sign of the synergism assessment factor derivative of the original system can be predicted by the sign of its simplified system. In addition, we analyzed the influence of feedback structure on survival ratio of the serial structure. We provided a sufficient condition under which the combination effect could be maintained. Furthermore, we applied our method to find three synergistic drug combinations on tumor necrosis factor α-induced NFκB pathway and subsequently verified by the cell experiment.ConclusionsWe identified several structural properties underlying the Bliss independence criterion, and developed a systematic simplification framework for drug combiation desgin by combining simulation and system reaction network topology analysis. We hope that this work can provide insights to tackle the challenging problem of assessment of combinational drug therapy effect in a large scale signaling pathway. And hopefully in the future our method could be expanded to more general criteria.
Duration of First Off-Treatment Interval Is Prognostic for Time to Castration Resistance and Death in Men With Biochemical Relapse of Prostate Cancer Treated on a Prospective Trial of Intermittent Androgen Deprivation
Authors: Yu Evan Y. , Gulati Roman , Telesca Donatello , Jiang Peter , Tam Stephen , Russell Kenneth J. , Nelson Peter S. , Etzioni Ruth D. , Higano Celestia S. 
Published: April 2010

Purpose This was an exploratory analysis of a trial of intermittent androgen deprivation (IAD) in men with biochemical relapse (BR) to establish first cycle characteristics prognostic for progression to castration-resistant prostate cancer (CRPC) and death. Patients and Methods Men with BR of prostate cancer after radical prostatectomy (RP) or radiation (RT) were treated with androgen deprivation therapy (ADT) comprised of leuprolide and flutamide. After 9 months on treatment, ADT was stopped, and monthly prostate-specific antigen (PSA) levels were observed during the off-treatment interval. When the PSA reached a threshold value (1 ng/mL for RP, 4 ng/mL for RT), ADT was resumed in a new cycle. Patients were treated intermittently in this manner until CRPC, which was defined as ≥ two consecutive increasing PSA values while on ADT with castrate testosterone levels. Results Seventy-two of 100 patients enrolled onto the study met criteria for this analysis. The duration of the first off-treatment interval (≤ v > 40 weeks) was associated with shorter time to CRPC (hazard ratio = 2.9; 95% CI, 1.1 to 7.7; P = .03) and death (hazard ratio = 3.8; 95% CI, 1.1 to 13.6; P = .04) after adjusting for age, stage, grade, and PSA at diagnosis. Conclusion In patients who completed the first cycle of IAD, a duration of the first off-treatment interval of ≤ 40 weeks defines a subset of patients at higher risk of CRPC and death. Conversely, patients with an off-treatment interval of more than 40 weeks have a significantly better long-term prognosis.
A Study of Experimental Syringomyelia by Scanning Electron Microscopy
Authors: Hall Peter , Godersky John , Muller Jans , Muller Robert , Kalsbeck John 
Published: April 2010

Abstract
Experimental hydromyelia and syringomyelia, induced by kaolin in dogs, has been investigated by scanning electron microscopy. This study demonstrated that communication between the 4th ventricle and the spinal central canal is normally occluded by a plug of acellular material lying within the central canal. This plug is broken down following the onset of hydrocephalus and communication is rapidly established between the ventricles and the central canal. The canal distends and ruptures dorsally into the spinal gray matter with the development of extensive intramedullary cavities, lined by glial and neuronal elements. The morphological changes demonstrated are consistent with a physical destructive process of the cord resulting from CSF dissection.
An evaluation of measured and calculated serum free cortisol in a group of patients with known adrenal suppression
Authors: Barlow Nicola L , Holme Jayne , Stockley Robert A , Clark Penelope M 
Published: April 2010

Background Since more than 90% of cortisol is bound to protein, serum free cortisol (SFC) may be a more appropriate marker of adrenal status than total cortisol. However, measurement of SFC is technically difficult and calculated SFC may offer a more practical alternative. Methods SFC, measured by equilibrium dialysis coupled with immunoassay, and calculated using Coolens' equation from total cortisol and corticosteroid binding globulin (CBG) concentrations, was compared in short Synacthen test (SST) serum from 42 patients, of whom 20 demonstrated a suppressed adrenal response. Results Considering the patient group as a whole, calculated SFC was found to be significantly lower than measured SFC, pre- and post-Synacthen ( P < 0.05 and <0.001, respectively). Upon classifying the patients as pass or fail based on total cortisol response to Synacthen, the difference in calculated and measured SFC only reached statistical significance for post-Synacthen concentrations in the pass group ( P < 0.01), suggesting a greater discrepancy at higher cortisol concentrations. There was no difference in CBG levels between the pass and fail groups and both measured and calculated SFC gave a diminished 30 min response in subjects deemed to have failed the SST. Conclusion Coolens' equation was found to underestimate measured SFC in this cohort of outpatients, as has been previously demonstrated, particularly in patients with a pronounced acute phase response. Although calculated SFC gave a diminished response in individuals deemed to have failed the SST, the concentration-dependent nature of the discrepancy may limit the usefulness of this method for assessing adrenal status.
Anthropometric and gynaecological history according to the socioeconomic status of postmenopausal women: poverty and the menopause
Authors: Navarro Manuel Carmen , Sosa Manuel , Saavedra Pedro , Gil-Antullano Santiago Palacios , Castro Rosa , Bonet Mario , Travesí Isabel , de Miguel Emilio 
Published: April 2010

Background Less advantaged social classes usually have unhealthier lifestyles and have more difficult access to health resources. In this work we study the possible association between poverty and the prevalence of obesity and oophorectomy in a population of postmenopausal women. Design Cross-sectional observational study. Objective To study in a population of postmenopausal women in poverty the possible differences in the prevalence of obesity and oophorectomy, and to compare some other gynaecological data: age at menarche, age at menopause, fertile years, number of pregnancies, breastfeeding and the use of hormonal replacement therapy (HRT). Method All patients were interviewed personally. A questionnaire was used to find out about their lifestyles and the medication they were taking. Their medical records were reviewed to confirm the existence of some diseases. A complete physical examination was performed with every patient. Weight and height were measured with the patient dressed in light clothes. Blood was obtained in a fasting state in order to carry out some analyses. Poverty was defined according to the Spanish National Institute of Statistics criteria. Results We enrolled 1225 postmenopausal women; 449 (36.6%) were under the threshold of poverty, defined by the Spanish National Institute of Statistics. Postmenopausal women in poverty had higher body mass index (29.2 ± 4.8 versus 27.0 ± 4.7 kg/m2 P < 0.001), and a higher prevalence of obesity than postmenopausal women not in poverty (44.2% versus 24.3%, P = 0.001). The prevalence of oophorectomy was also higher in women in poverty (32.7% versus 27.2%, P < 0.04). Women in poverty had had a greater number of pregnancies (3 versus 2, P = 0.001). They also showed a higher rate of breastfeeding than women in medium and high social classes (65% versus 59%, P = 0.037). There were no statistically significant differences between the groups in either the age of menopause or fertile years, nor in the use of HRT. Conclusions Postmenopausal women in poverty have higher levels of obesity, and also a greater prevalence of oophorectomy than women of medium and high social classes. They also presented a higher rate of breastfeeding and a greater number of pregnancies than those women not in poverty.
Everyday Memory and Working Memory in Adolescents With Mild Intellectual Disability
Authors: Van der Molen M. J. , Van Luit J. E. H. , Van der Molen Maurits W. , Jongmans Marian J. 
Published: April 2010

AbstractEveryday memory and its relationship to working memory was investigated in adolescents with mild intellectual disability and compared to typically developing adolescents of the same age (CA) and younger children matched on mental age (MA). Results showed a delay on almost all memory measures for the adolescents with mild intellectual disability compared to the CA control adolescents. Compared to the MA control children, the adolescents with mild intellectual disability performed less well on a general everyday memory index. Only some significant associations were found between everyday memory and working memory for the mild intellectual disability group. These findings were interpreted to suggest that adolescents with mild intellectual disability have difficulty in making optimal use of their working memory when new or complex situations tax their abilities.
Pathways Through Services for Offenders With Intellectual Disability: A One- and Two-Year Follow-Up Study
Authors: Lindsay William R. , Holland Tony , Wheeler Jessica R. , Carson Derek , O'Brien Gregory , Taylor John L. , Steptoe Lesley , Middleton Claire , Price Karen , Johnston Susan , Young Steven J. 
Published: April 2010

Abstract
The pathways through services for offenders with intellectual disability were reviewed. Participants were 197 offenders with intellectual disability accepted into three types of community and three types of secure forensic intellectual disability services. They were first compared with 280 participants referred but not accepted into services and were then followed-up for 2 years to review pathways through services. Those accepted into services had a higher charge rate than did those who were referred (46% and 25%, respectively). The greatest diversity in pathway was seen in participants in community forensic intellectual disability and inpatient services. Individuals in secure settings showed the least diversity over time, and, similarly, a relatively high percentage of those accepted into generic community services remained in these services.