bluuebunny/crossref_metadata_2025_split huggingface dataset:
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
Authors: Tesson Bruno M , Breitling Rainer , Jansen Ritsert C 
Published: October 2010

AbstractBackgroundLarge microarray datasets have enabled gene regulation to be studied through coexpression analysis. While numerous methods have been developed for identifying differentially expressed genes between two conditions, the field of differential coexpression analysis is still relatively new. More specifically, there is so far no sensitive and untargeted method to identify gene modules (also known as gene sets or clusters) that are differentially coexpressed between two conditions. Here, sensitive and untargeted means that the method should be able to constructde novomodules by grouping genes based on shared, but subtle, differential correlation patterns.ResultsWe present DiffCoEx, a novel method for identifying correlation pattern changes, which builds on the commonly used Weighted Gene Coexpression Network Analysis (WGCNA) framework for coexpression analysis. We demonstrate its usefulness by identifying biologically relevant, differentially coexpressed modules in a rat cancer dataset.ConclusionsDiffCoEx is a simple and sensitive method to identify gene coexpression differences between multiple conditions.
(Not) Keeping the stem straight: a proteomic analysis of maritime pine seedlings undergoing phototropism and gravitropism
Authors: Herrera Raul , Krier Catherine , Lalanne Celine , Ba ElHadji Maodo , Stokes Alexia , Salin Franck , Fourcaud Thierry , Claverol Stéphane , Plomion Christophe 
Published: October 2010

Abstract

Background
Plants are subjected to continuous stimuli from the environment and have evolved an ability to respond through various growth and development processes. Phototropism and gravitropism responses enable the plant to reorient with regard to light and gravity.

Results
We quantified the speed of maritime pine seedlings to reorient with regard to light and gravity over 22 days. Seedlings were inclined at 15, 30 and 45 degrees with vertical plants as controls. A lateral light source illuminated the plants and stem movement over time was recorded. Depending on the initial angle of stem lean, the apical response to the lateral light source differed. In control and 15° inclined plants, the apex turned directly towards the light source after only 2 h. In plants inclined at 30° and 45°, the apex first reoriented in the vertical plane after 2 h, then turned towards the light source after 24 h. Two-dimensional gel electrophoresis coupled with mass spectrometry was then used to describe the molecular response of stem bending involved in photo- and gravi-tropism after 22 hr and 8 days of treatment. A total of 486 spots were quantitatively analyzed using image analysis software. Significant changes were determined in the protein accumulation of 68 protein spots. Early response gravitropic associated proteins were identified, which are known to function in energy related and primary metabolism. A group of thirty eight proteins were found to be involved in primary metabolism and energy related metabolic pathways. Degradation of Rubisco was implicated in some protein shifts.

Conclusions
Our study demonstrates a rapid gravitropic response in apices of maritime pine seedlings inclined >30°. Little or no response was observed at the stem bases of the same plants. The primary gravitropic response is concomitant with a modification of the proteome, consisting of an over accumulation of energy and metabolism associated proteins, which may allow the stem to reorient rapidly after bending.
Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer
Authors: Kinoshita Yasunori , Tayama Takahiro , Kitamura Koichiro , Salimullah Md , Uchida Hidekazu , Suzuki Miho , Husimi Yuzuru , Nishigaki Koichi 
Published: October 2010

Abstract

Background
The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations.

Results
Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aβ-binding or cathepsin E-inhibition.

Conclusions
With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-μL scale have become possible.
Expression of Inwardly Rectifying Potassium Channels by an Inducible Adenoviral Vector Reduced the Neuronal Hyperexcitability and Hyperalgesia Produced by Chronic Compression of the Spinal Ganglion
Authors: Ma Chao , Rosenzweig Jason , Zhang Pu , Johns David C , LaMotte Robert H 
Published: October 2010

Background: A chronic compressed dorsal root ganglion (CCD) in rat produces pain behavior and an enhanced excitability of neurons within the compressed ganglion. Kir2.1 is an inwardly rectifying potassium channel that acts to stabilize the resting potential of certain cell types. We hypothesized that an inducible expression of Kir2.1 channels in CCD neurons might suppress neuronal excitability in the dorsal root ganglion (DRG) and reduce the associated pain behavior. Results: We delivered, by microinjection into the fourth lumbar (L4) DRG, an adenoviral vector containing a reporter gene encoding the enhanced green fluorescent protein (GFP) and a Kir2.1 channel (AdKir). At the same time the ganglion was compressed by implantation of a rod through the intervertebral foramen (CCD). The in vivo expression of the transferred gene was controlled by an ecdysone analog via an ecdysone-inducible promoter in the viral vector. In comparison with the effects of vehicle or a control vector containing only the GFP gene, AdKir significantly reduced the neuronal hyperexcitability after CCD. Electrophysiological recordings, in vivo, from nociceptive and non-nociceptive DRG neurons expressing the virally produced Kir2.1 channels revealed a hyperpolarized resting membrane potential, an increased rheobase, and lack of spontaneous activity. Inducing the Kir2.1 gene at the beginning of CCD surgery partially prevented the development of mechanical hyperalgesia. However, a delayed induction of the Kir2.1 gene (3 days after CCD surgery) produced no significant effect on the pain behavior. Conclusions: We found that an inducible expression of Kir2.1 channels in chronically compressed DRG neurons can effectively suppress the neuronal excitability and, if induced at the beginning of CCD injury, prevent the development of hyperalgesia. We hypothesize that a higher level of neuronal hyperexcitability in the DRG is required to initiate than to maintain the hyperalgesia and that the hyperexcitability contributing to neuropathic pain is best inhibited as soon as possible after injury.
Factors that influenced county system leaders to implement an evidence-based program: a baseline survey within a randomized controlled trial
Authors: Wang Wei , Saldana Lisa , Brown C Hendricks , Chamberlain Patricia 
Published: October 2010

AbstractBackgroundDespite the burgeoning number of well-validated interventions that have been shown in randomized trials to produce superior outcomes compared to usual services, it is estimated that only 10% of public systems deliver evidence-based mental health services. In California, for example, more than 15,000 children are placed in group homes or residential centers with some evidence of iatrogenic effects. The present study evaluates the willingness among county leaders of child public service systems to adopt a new evidence-based model, Multidimensional Treatment Foster Care, (MTFC), as a way to decrease the prevalence of out-of-home placements. Specifically, the study examines how county-level socio-demographic factors and child public service system leaders' perceptions of their county's organizational climate influence their decision of whether or not to consider adopting MTFC.MethodsTwo levels were examined in this study: Stable and historical factors from 40 California counties gathered from public records including population size, number of entries into out-of-home care, financing of mental health services, and percent minority population; and system leaders' perceptions of their county's organizational climate and readiness for change measured via a web-based survey. The number of days-to-consent was the primary outcome variable defined as the duration of time between being notified of the opportunity to implement MTFC and the actual signing of a consent form indicating interest in considering implementation. Survival analysis methods were used to assess the predictors of this time-to-event measure. The present study is part of a larger randomized trial comparing two methods of implementation where counties are randomized to one of three time cohorts and two implementation conditions.ResultsThe number of entries into care was the primary predictor of days-to-consent. This variable was significantly correlated to county size. System leader's perceptions of positive climate and organizational readiness for change also contributed to but did not mediate or moderate the days-to-consent.ConclusionsSystem leaders' decision to consider implementing a new evidence-based model was influenced most by their objective need for the program and next by their perception of the county's organizational climate and motivation to change. These findings highlight the importance of understanding the fit between the needs of the systems or agencies and the potential for addressing those needs with the proposed new program.
Edelfosine-induced metabolic changes in cancer cells that precede the overproduction of reactive oxygen species and apoptosis
Authors: Selivanov Vitaly A , Vizán Pedro , Mollinedo Faustino , Fan Teresa WM , Lee Paul WN , Cascante Marta 
Published: October 2010

Abstract

Background
Metabolic flux profiling based on the analysis of distribution of stable isotope tracer in metabolites is an important method widely used in cancer research to understand the regulation of cell metabolism and elaborate new therapeutic strategies. Recently, we developed software Isodyn, which extends the methodology of kinetic modeling to the analysis of isotopic isomer distribution for the evaluation of cellular metabolic flux profile under relevant conditions. This tool can be applied to reveal the metabolic effect of proapoptotic drug edelfosine in leukemia Jurkat cell line, uncovering the mechanisms of induction of apoptosis in cancer cells.

Results
The study of 13C distribution of Jukat cells exposed to low edelfosine concentration, which induces apoptosis in ≤5% of cells, revealed metabolic changes previous to the development of apoptotic program. Specifically, it was found that low dose of edelfosine stimulates the TCA cycle. These metabolic perturbations were coupled with an increase of nucleic acid synthesis de novo, which indicates acceleration of biosynthetic and reparative processes. The further increase of the TCA cycle fluxes, when higher doses of drug applied, eventually enhance reactive oxygen species (ROS) production and trigger apoptotic program.

Conclusion
The application of Isodyn to the analysis of mechanism of edelfosine-induced apoptosis revealed primary drug-induced metabolic changes, which are important for the subsequent initiation of apoptotic program. Initiation of such metabolic changes could be exploited in anticancer therapy.
Integrin α2-deficient mice provide insights into specific functions of collagen receptors in the kidney
Authors: Girgert Rainer , Martin Maria , Kruegel Jenny , Miosge Nicolai , Temme Johanna , Eckes Beate , Müller Gerhard-Anton , Gross Oliver 
Published: October 2010

Abstract

Background
Integrins are important cellular receptors for collagens. Within the glomerulus, podocytes regulate the integrity of the glomerular basement membrane (GBM) by sensing the presence of collagen and regulating collagen IV synthesis. The present study evaluates the role of integrin α2 (ITGA2) in cell-matrix interaction.

Methods and Results
ITGA2-deficient mice had normal renal function but moderate proteinuria and enhanced glomerular and tubulointerstitial matrix deposition. Electron microscopy demonstrated irregular podocyte-matrix interaction, causing pathological protrusions towards the urinary (podocyte) side of the GBM. These characteristic subepithelial bulges mimic the renal phenotype of mice, which are deficient in another collagen receptor, discoidin domain receptor (DDR)1. Using immunogold staining, ITGA2 expression was found to localize to the basolateral site of the podocyte foot processes. ITGA2-deficient mice overexpressed transforming growth factor (TGF)β and connective tissue growth factor (CTGF) compared with wild-type mice. Using in situ hybridization, tubular cells were found to be the primary site of TGFβ synthesis and podocytes the source of CTGF in ITGA2-deficient mice.

Conclusion
These findings support our hypothesis that both these collagen receptors (ITGA2 and DDR1) play a similar role within the kidney. Further, cell-matrix interaction via collagen receptors seems to be crucial for maintenance of normal GBM architecture and function. Targeting collagen receptors such as ITGA2 might be a new form of treatment for progressive fibrotic diseases.
Trend of Entamoeba histolytica infestation in Kolkata
Authors: Mukherjee Avik K , Das Kaushik , Bhattacharya Mihir K , Nozaki Tomoyoshi , Ganguly Sandipan 
Published: October 2010

Abstract

Background

Entamoeba histolytica infection is found almost all over the world and is highly endemic and a major cause of parasitic diarrhoea particularly in the developing countries.

Methods
A systemic surveillance was set up at the Infectious Disease hospital, Kolkata, India between November 2007 and October 2009 for understanding the trend of E. histolytica infection in Kolkata. Fecal samples were collected from diarrhoeal patients attending the hospital, under the surveillance system and processed for detection of E. histolytica.

Results
During the last two years about 2500 diarrhoeal samples were collected and screened for E. histolytica. About 3.6% were positive for E. histolytica. As compared to the earlier years, E. histolytica infection was observed to be less amongst patients screened during the last two years. No seasonality was observed in Kolkata although in the neighboring tropical country Bangladesh, a typical seasonality of E. histolytica infection was noticed.

Conclusion
The study indicates that the detection rate of E. histolytica infection amongst diarrhoeal patients in Kolkata is decreasing during the last two years than that of Bangladesh.
Factors associated with access to HIV care and treatment in a prevention of mother to child transmission programme in urban Zimbabwe
Authors: Muchedzi Auxilia , Chandisarewa Winfreda , Keatinge Jo , Stranix‐Chibanda Lynda , Woelk Godfrey , Mbizvo Elizabeth , Shetty Avinash K 
Published: October 2010

BackgroundThis cross‐sectional study assessed factors affecting access to antiretroviral therapy (ART) among HIV‐positive women from the prevention of mother to child transmission HIV programme in Chitungwiza, Zimbabwe.MethodsData were collected between June and August 2008. HIV‐positive women attending antenatal clinics who had been referred to the national ART programme from January 2006 until December 2007 were surveyed. The questionnaire collected socio‐demographic data, treatment‐seeking behaviours, and positive or negative factors that affect access to HIV care and treatment.ResultsOf the 147 HIV‐positive women interviewed, 95 (65%) had registered with the ART programme. However, documentation of the referral was noted in only 23 (16%) of cases. Of the 95 registered women, 35 (37%) were receiving ART; 17 (18%) had not undergone CD4 testing. Multivariate analysis revealed that participants who understood the referral process were three times more likely to access HIV care and treatment (OR = 3.21, 95% CI 1.89‐11.65) and participants enrolled in an HIV support group were twice as likely to access care and treatment (OR = 2.34, 95% CI 1.13‐4.88). Those living with a male partner were 60% less likely to access care and treatment (OR = 0.40, 95% CI 0.16‐0.99). Participants who accessed HIV care and treatment faced several challenges, including long waiting times (46%), unreliable access to laboratory testing (35%) and high transport costs (12%). Of the 147 clients surveyed, 52 (35%) women did not access HIV care and treatment. Barriers included perceived long queues (50%), competing life priorities, such as seeking food or shelter (33%) and inadequate referral information (15%).ConclusionsDespite many challenges, the majority of participants accessed HIV care. Development of referral tools and decentralization of CD4 testing to clinics will improve access to ART. Psychosocial support can be a successful entry point to encourage client referral to care and treatment programmes.
Stability of Sodium Nitroprusside and Sodium Thiosulfate 1:10 Intravenous Admixture
Authors: Schulz Lucas T. , Elder Edmund J. , Jones Karen J. , Vijayan Ashwanth , Johnson Benjamin D. , Medow Joshua E. , Vermeulen Lee 
Published: October 2010

Purpose Thiosulfate has been shown to reduce the risk of cyanide toxicity during nitroprusside administration. Admixtures containing both agents may provide a safe and effective alternative to more expensive agents used to reduce blood pressure in the critically ill patient. This study determined the physical and chemical stability of a 1:10 nitroprusside:thiosulfate admixture, stored up to 48 hours. The economic consequences of a shift toward using thiosulfate and nitroprusside, and away from higher cost alternatives, are considered. Methods Seven samples of 50 mg nitroprusside and 500 mg thiosulfate were prepared and stored away from light, at room temperature, and in a refrigerator prepared in D5W and NS. Each sample was analyzed via a novel high-performance liquid chromatographic (HPLC) method at time 0, 8, 24, and 48 hours. The method was tested and passed specifications for linearity, reproducibility, and accuracy. A visual inspection by 9 licensed pharmacists was used to demonstrate physical stability. A cost evaluation comparing nitroprusside and thiosulfate to alternative agents was completed. Results The concentration of both nitroprusside and thiosulfate remain greater than 95% of the initial concentration through 48 hours. Physical compatibility was confirmed in all samples tested through 72 hours. Conclusion The combination of nitroprusside and thiosulfate is chemically and physically stable as a single compounded dose for up to 48 hours when stored at room temperature and protected from light. The admixture represents an inexpensive option to other higher cost alternatives such as nicardipine or clevidipine.
Association Between Cancer and Immunosuppressive Therapy—Analysis of Selected Studies in Pemphigus and Pemphigoid
Authors: Mabrouk Dalia , Gürcan Hakan M , Keskin Derin B , Christen William G , Ahmed A Razzaque 
Published: October 2010

Objective: To determine whether there is an association between the use of immunosuppressive agents (ISAs) and cancer in patients with pemphigus and pemphigoid—rare, potentially fatal diseases of the skin and mucous membranes, often requiring long-term use of ISAs. Data Source: Literature was accessed through PubMed (all years available), using the search terms cancer, immunosuppressive agents, pemphigoid, and pemphigus. Study Selection and Data Extraction: A retrospective review of the literature was conducted. Inclusion criteria for studies were: (1) English language, (2) diagnosis of pemphigus and/or pemphigoid based on histology and immunopathology, (3) more than 10 patients evaluated, (4) investigators had a high index of suspicion of cancer and patients were monitored for it, (5) follow-up information was provided for at least 1 year after initiation of therapy, and (6) absence of diagnosis of cancer before initiation of an ISA. Case reports were not included in the analysis. Data Synthesis: A total of 929 patients diagnosed with either pemphigus or pemphigoid in 17 studies were identified. Patients were divided into 2 groups. Group A comprised patients treated with azathioprine, cyclophosphamide, cyclosporins, or mycophenolate mofetil in combination with prednisone. In Group A. 22 cases of cancer were reported in 21 of the 218 patients (9.6%). Group B comprised patients treated with systemic corticosteroids only. In this group, cancer was reported in 11 of the 711 patients (1.5%). In this study there was no control group (untreated patients) and the sample sizes were small. Conclusions: Preliminary data suggest a possible association between the use of azathioprine, cyclophosphamide, and cyclosporine and increased susceptibility to cancer in patients with pemphigus and pemphigoid.
The Effects of Demography and Linkage on the Estimation of Selection and Mutation Parameters
Authors: Zeng Kai , Charlesworth Brian 
Published: October 2010

Abstract
We explore the effects of demography and linkage on a maximum-likelihood (ML) method for estimating selection and mutation parameters in a reversible mutation model. This method assumes free recombination between sites and a randomly mating population of constant size and uses information from both polymorphic and monomorphic sites in the sample. Two likelihood-ratio test statistics were constructed under this ML framework: LRTγ for detecting selection and LRTκ for detecting mutational bias. By carrying out extensive simulations, we obtain the following results. When mutations are neutral and population size is constant, LRTγ and LRTκ follow a chi-square distribution with 1 d.f. regardless of the level of linkage, as long as the mutation rate is not very high. In addition, LRTγ and LRTκ are relatively insensitive to demographic effects and selection at linked sites. We find that the ML estimators of the selection and mutation parameters are usually approximately unbiased and that LRTκ usually has good power to detect mutational bias. Finally, with a recombination rate that is typical for Drosophila, LRTγ has good power to detect weak selection acting on synonymous sites. These results suggest that the method should be useful under many different circumstances.