bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-generation DNA sequencing-based assay for measuring allelic expression imbalance (AEI) of candidate neuropsychiatric disorder genes in human brain
Authors: Xu Xiang , Wang Hao , Zhu Min , Sun Yue , Tao Yu , He Qin , Wang Jian , Chen Li , Saffen David 
Published: December 2011

AbstractBackgroundCommon genetic variants that regulate gene expression are widely suspected to contribute to the etiology and phenotypic variability of complex diseases. Although high-throughput, microarray-based assays have been developed to measure differences in mRNA expression among independent samples, these assays often lack the sensitivity to detect rare mRNAs and the reproducibility to quantify small changes in mRNA expression. By contrast, PCR-based allelic expression imbalance (AEI) assays, which use a "marker" single nucleotide polymorphism (mSNP) in the mRNA to distinguish expression from pairs of genetic alleles in individual samples, have high sensitivity and accuracy, allowing differences in mRNA expression greater than 1.2-fold to be quantified with high reproducibility. In this paper, we describe the use of an efficient PCR/next-generation DNA sequencing-based assay to analyze allele-specific differences in mRNA expression for candidate neuropsychiatric disorder genes in human brain.ResultsUsing our assay, we successfully analyzed AEI for 70 candidate neuropsychiatric disorder genes in 52 independent human brain samples. Among these genes, 62/70 (89%) showed AEI ratios greater than 1 ± 0.2 in at least one sample and 8/70 (11%) showed no AEI. Arranging log2AEI ratios in increasing order from negative-to-positive values revealed highly reproducible distributions of log2AEI ratios that are distinct for each gene/marker SNP combination. Mathematical modeling suggests that these log2AEI distributions can provide important clues concerning the number, location and contributions ofcis-acting regulatory variants to mRNA expression.ConclusionsWe have developed a highly sensitive and reproducible method for quantifying AEI of mRNA expressed in human brain. Importantly, this assay allowed quantification of differential mRNA expression for many candidate disease genes entirely missed in previously published microarray-based studies of mRNA expression in human brain. Given the ability of next-generation sequencing technology to generate large numbers of independent sequencing reads, our method should be suitable for analyzing from 100- to 200-candidate genes in 100 samples in a single experiment. We believe that this is the appropriate scale for investigating variation in mRNA expression for defined sets candidate disorder genes, allowing, for example, comprehensive coverage of genes that function within biological pathways implicated in specific disorders. The combination of AEI measurements and mathematical modeling described in this study can assist in identifying SNPs that correlate with mRNA expression. Alleles of these SNPs (individually or as sets) that accurately predict high- or low-mRNA expression should be useful as markers in genetic association studies aimed at linking candidate genes to specific neuropsychiatric disorders.
Pyrosequencing of the Camptotheca acuminata transcriptome reveals putative genes involved in camptothecin biosynthesis and transport
Authors: Sun Yongzhen , Luo Hongmei , Li Ying , Sun Chao , Song Jingyuan , Niu Yunyun , Zhu Yingjie , Dong Liang , Lv Aiping , Tramontano Enzo , Chen Shilin 
Published: December 2011

Abstract

Background

Camptotheca acuminata is a Nyssaceae plant, often called the "happy tree", which is indigenous in Southern China. C. acuminata produces the terpenoid indole alkaloid, camptothecin (CPT), which exhibits clinical effects in various cancer treatments. Despite its importance, little is known about the transcriptome of C. acuminata and the mechanism of CPT biosynthesis, as only few nucleotide sequences are included in the GenBank database.

Results
From a constructed cDNA library of young C. acuminata leaves, a total of 30,358 unigenes, with an average length of 403 bp, were obtained after assembly of 74,858 high quality reads using GS De Novo assembler software. Through functional annotation, a total of 21,213 unigenes were annotated at least once against the NCBI nucleotide (Nt), non-redundant protein (Nr), Uniprot/SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Arabidopsis thaliana proteome (TAIR) databases. Further analysis identified 521 ESTs representing 20 enzyme genes that are involved in the backbone of the CPT biosynthetic pathway in the library. Three putative genes in the upstream pathway, including genes for geraniol-10-hydroxylase (CaPG10H), secologanin synthase (CaPSCS), and strictosidine synthase (CaPSTR) were cloned and analyzed. The expression level of the three genes was also detected using qRT-PCR in C. acuminata. With respect to the branch pathway of CPT synthesis, six cytochrome P450s transcripts were selected as candidate transcripts by detection of transcript expression in different tissues using qRT-PCR. In addition, one glucosidase gene was identified that might participate in CPT biosynthesis. For CPT transport, three of 21 transcripts for multidrug resistance protein (MDR) transporters were also screened from the dataset by their annotation result and gene expression analysis.

Conclusion
This study produced a large amount of transcriptome data from C. acuminata by 454 pyrosequencing. According to EST annotation, catalytic features prediction, and expression analysis, novel putative transcripts involved in CPT biosynthesis and transport were discovered in C. acuminata. This study will facilitate further identification of key enzymes and transporter genes in C. acuminata.
Heightened inflammasome activation is linked to age-related cognitive impairment in Fischer 344 rats
Authors: Mawhinney Lana J , de Rivero Vaccari Juan Pablo , Dale Gordon A , Keane Robert W , Bramlett Helen M 
Published: December 2011

Abstract

Background
Members of the mammalian nucleotide binding domain, leucine-rich repeat (LRR)-containing receptor (NLR) family of proteins are key modulators of innate immunity regulating inflammation. Our previous work has shown that among the members of this family, NLRP1/NALP1, present in neurons, plays a crucial role in inflammasome formation and the production of the inflammatory cytokines interleukin (IL) -1β and IL-18 after various types of central nervous system injury.

Results
We investigated whether age-related cognitive decline may involve a heightened inflammatory response associated with activation of the NLRP1 inflammasome in the hippocampus. Young (3 months) and aged (18 months) male Fischer 344 rats were tested in a spatial acquisition task via Morris water maze. Following behavioral testing, hippocampal lysates were assayed for expression of NLRP1 inflammasome components and inflammatory cytokines. Hippocampal lysates from aged rats showed significantly higher levels of NLRP1 inflammasome constituents, caspase-1, caspase-11, the purinergic receptor P2X7, pannexin-1 and X-linked inhibitor of apoptosis (XIAP) than lysates from younger animals. Following treatment with probenecid, an inhibitor or pannexin-1, aged animals demonstrated reduction in inflammasome activation and improvement in spatial learning performance.

Conclusions
Our behavioral findings are consistent with increases in IL-1β and IL-18 that have been previously shown to correlate with spatial learning deficits. Probenecid reduced activated caspase-1 and ameliorated spatial learning deficits in aged rats. Thus, aging processes stimulate activation of the NLRP1 inflammasome and secretion of IL-1β and IL-18 that may contribute to age-related cognitive decline in the growing elderly population. Moreover, probenecid may be potentially useful as a therapy to improve cognitive outcomes in the aging population.
Comparative analysis of root transcriptome profiles of two pairs of drought-tolerant and susceptible rice near-isogenic lines under different drought stress
Authors: Moumeni Ali , Satoh Kouji , Kondoh Hiroaki , Asano Takayuki , Hosaka Aeni , Venuprasad Ramiah , Serraj Rachid , Kumar Arvind , Leung Hei , Kikuchi Shoshi 
Published: December 2011

AbstractBackgroundPlant roots are important organs to uptake soil water and nutrients, perceiving and transducing of soil water deficit signals to shoot. The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. We obtained gene expression profile in roots of rice NILs under different levels of drought stress help to identify genes and mechanisms involved in drought stress.ResultsGlobal gene expression analysis showed that about 55% of genes differentially expressed in roots of rice in response to drought stress treatments. The number of differentially expressed genes (DEGs) increased in NILs as the level of water deficits, increased from mild to severe condition, suggesting that more genes were affected by increasing drought stress. Gene onthology (GO) test and biological pathway analysis indicated that activated genes in the drought tolerant NILs IR77298-14-1-2-B-10 and IR77298-5-6-B-18 were mostly involved in secondary metabolism, amino acid metabolism, response to stimulus, defence response, transcription and signal transduction, and down-regulated genes were involved in photosynthesis and cell wall growth. We also observed gibberellic acid (GA) and auxin crosstalk modulating lateral root formation in the tolerant NILs.ConclusionsTranscriptome analysis on two pairs of NILs with a common genetic background (~97%) showed distinctive differences in gene expression profiles and could be effective to unravel genes involved in drought tolerance. In comparison with the moderately tolerant NIL IR77298-5-6-B-18 and other susceptible NILs, the tolerant NIL IR77298-14-1-2-B-10 showed a greater number of DEGs for cell growth, hormone biosynthesis, cellular transports, amino acid metabolism, signalling, transcription factors and carbohydrate metabolism in response to drought stress treatments. Thus, different mechanisms are achieving tolerance in the two tolerant lines.
Comparative efficacy and acceptability of methylphenidate and atomoxetine in treatment of attention deficit hyperactivity disorder in children and adolescents: a meta-analysis
Authors: Hanwella Raveen , Senanayake Madhri , de Silva Varuni 
Published: December 2011

Abstract

Background
Psychostimulants and non stimulants are effective in the treatment of ADHD. Efficacy of both methylphenidate and atomoxetine has been established in placebo controlled trials. Direct comparison of efficacy is now possible due to availability of results from several head-to-head trials of these two medications.

Methods
All published, randomized, open label or double blind trials, comparing efficacy of methylphenidate with atomoxetine, in treatment of ADHD in children, diagnosed using DSM-IV™ criteria were included. The outcome studied was ADHDRS-IVParent:Inv score. The standardized mean difference (SMD) was used as a measure of effect size.

Results
Nine randomized trials comparing methylphenidate and atomoxetine, with a total of 2762 participants were included. Meta-analysis did not find a significant difference in efficacy between methylphenidate and atomoxetine (SMD = 0.09, 95% CI -0.08-0.26) (Z = 1.06, p = 0.29). Synthesis of data from eight trials found no significant difference in response rates (RR = 0.93 95% CI 0.76-1.14, p = 0.49). Sub group analysis showed a significant standardized mean difference favouring OROS methylphenidate (SMD = 0.32, 95% CI 0.12-0.53 (Z = 3.05, p < 0.002). Immediate release methylphenidate was not superior to atomoxetine (SMD = -0.04, 95% CI -0.19-0.12) (Z = 0.46, p = 0.64). Excluding open label trials did not significantly alter the effect size (SMD = 0.08, 95% CI -0.04-0.21) (Z = 1.27, p = 0.20). All-cause discontinuation was used as a measure of acceptability. There was no significant difference in all cause discontinuation between atomoxetine and methylphenidate (RR 1.22, 95% CI 0.87-1.71). There was significant heterogeneity among the studies (p = 0.002, I
2 = 67%). Subgroup analysis demonstrated the heterogeneity to be due to the open label trials (p = 0.001, I
2 = 81%).

Conclusions
In general atomoxetine and methylphenidate have comparable efficacy and equal acceptability in treatment of ADHD in children and adolescents. However OROS methylphenidate is more effective than atomoxetine and may be considered as first line treatment in treatment of ADHD in children and adolescents.
Laparoscopic gastric pouch and remnant resection: a novel approach to refractory anastomotic ulcers after Roux-en-Y Gastric Bypass: Case report
Authors: Steinemann Daniel C , Schiesser Marc , Clavien Pierre-Alain , Nocito Antonio 
Published: December 2011

Abstract

Background
Anastomotic or marginal ulcers occur in 0.6 to 16% of patients after laparoscopic Roux-en-Y-Gastric Bypass. Initial therapy aims at eliminating known risk factors including smoking, Helicobacter pylori infection, use of non-steroidal anti-inflammatory drugs and inhibition of gastric acid secretion. While this approach is successful in 68 to 88% of the cases, up to one third of patients need a subsequent surgical revision. However, marginal ulcers still recur in up to 10% of cases after revisional surgery, thus constituting a serious challenge for bariatric surgeons.

Case presentation
We herein report a case of an insidious marginal ulcer refractory to both medical therapy with high-dosed proton pump inhibitors and sucralfate as well as surgical therapy consisting of the lengthening of a short alimentary limb and later resection of the gastroenterostomy and construction of a new tension-free anastomosis. Only after gastrectomy by laparoscopic en-bloc resection of the gastrojejunostomy, the gastric pouch and resection of the gastric remnant with reconstruction by esophagojejunostomy the patient remained free of symptoms.

Conclusion
By laparoscopic resection of the entire gastric pouch and the gastric remnant the risk to leave a suboptimally vascularised or even ischemic pouch in situ was avoided. The esophagojejunostomy was then created in healthy, good vascularised tissue. In our case this novel approach was effective in the management of a refractory anastomotic ulcer and might represent a rescue option when simple revision of the gastrojejunostomy fails.
Survey of CAM interest, self-care, and satisfaction with health care for type 2 diabetes at group health cooperative
Authors: Bradley Ryan , Sherman Karen J , Catz Sheryl , Calabrese Carlo , Jordan Luesa , Grothaus Lou , Cherkin Dan C 
Published: December 2011

Abstract

Background
Very little research has explored the factors that influence interest in complementary and alternative medicine (CAM) treatments. We surveyed persons with sub-optimally controlled type 2 diabetes to evaluate potential relationships between interest in complementary and alternative medicine (CAM) treatments, current self-care practices, motivation to improve self-care practices and satisfaction with current health care for diabetes.

Methods
321 patients from a large integrated healthcare system with type 2 diabetes, who were not using insulin and had hemoglobin A1c values between 7.5-9.5%, were telephoned between 2009-2010 and asked about their self-care behaviors, motivation to change, satisfaction with current health care and interest in trying naturopathic (ND) care for their diabetes. Responses from patients most interested in trying ND care were compared with those from patients with less interest.

Results
219 (68.5%) patients completed the survey. Nearly half (48%) stated they would be very likely to try ND care for their diabetes if covered by their insurance. Interest in trying ND care was not related to patient demographics, health history, clinical status, or self-care behaviors. Patients with greater interest in trying ND care rated their current healthcare as less effective for controlling their blood sugar (mean response 5.9 +/- 1.9 vs. 6.6 +/- 1.5, p = 0.003), and were more determined to succeed in self-care (p = 0.007). Current CAM use for diabetes was also greater in ND interested patients.

Conclusions
Patients with sub-optimally controlled type 2 diabetes expressed a high level of interest in trying ND care. Those patients with the greatest interest were less satisfied with their diabetes care, more motivated to engage in self-care, and more likely to use other CAM therapies for their diabetes.
Anticancer activity of an extract from needles and twigs of Taxus cuspidata and its synergistic effect as a cocktail with 5-fluorouracil
Authors: Shang Weihu , Qiao Jinping , Gu Chenxin , Yin Wei , Du Jinglei , Wang Wei , Zhu Meilin , Han Mei , Lu Weidong 
Published: December 2011

Abstract

Background
Botanical medicines are increasingly combined with chemotherapeutics as anticancer drug cocktails. This study aimed to assess the chemotherapeutic potential of an extract of Taxus cuspidata (TC) needles and twigs produced by artificial cuttage and its co-effects as a cocktail with 5-fluorouracil (5-FU).

Methods
Components of TC extract were identified by HPLC fingerprinting. Cytotoxicity analysis was performed by MTT assay or ATP assay. Apoptosis studies were analyzed by H & E, PI, TUNEL staining, as well as Annexin V/PI assay. Cell cycle analysis was performed by flow cytometry. 5-FU concentrations in rat plasma were determined by HPLC and the pharmacokinetic parameters were estimated using 3p87 software. Synergistic efficacy was subjected to median effect analysis with the mutually nonexclusive model using Calcusyn1 software. The significance of differences between values was estimated by using a one-way ANOVA.

Results

TC extract reached inhibition rates of 70-90% in different human cancer cell lines (HL-60, BGC-823, KB, Bel-7402, and HeLa) but only 5-7% in normal mouse T/B lymphocytes, demonstrating the broad-spectrum anticancer activity and low toxicity to normal cells of TC extract in vitro. TC extract inhibited cancer cell growth by inducing apoptosis and G2/M cell cycle arrest. Most interestingly, TC extract and 5-FU, combined as a cocktail, synergistically inhibited the growth of cancer cells in vitro, with Combination Index values (CI) ranging from 0.90 to 0.26 at different effect levels from IC50 to IC90 in MCF-7 cells, CI ranging from 0.93 to 0.13 for IC40 to IC90 in PC-3M-1E8 cells, and CI < 1 in A549 cells. In addition, the cocktail had lower cytotoxicity in normal human cell (HEL) than 5-FU used alone. Furthermore, TC extract did not affect the pharmacokinetics of 5-FU in rats.

Conclusions
The combinational use of the TC extract with 5-FU displays strong cytotoxic synergy in cancer cells and low cytotoxicity in normal cells. These findings suggest that this cocktail may have a potential role in cancer treatment.
Decrease in thyroid adenoma associated (THADA) expression is a marker of dedifferentiation of thyroid tissue
Authors: Kloth Lars , Belge Gazanfer , Burchardt Käte , Loeschke Siegfried , Wosniok Werner , Fu Xin , Nimzyk Rolf , Mohamed Salah A , Drieschner Norbert , Rippe Volkhard , Bullerdiek Jörn 
Published: December 2011

Abstract

Background

Thyroid adenoma associated (THADA) has been identified as the target gene affected by chromosome 2p21 translocations in thyroid adenomas, but the role of THADA in the thyroid is still elusive. The aim of this study was to quantify THADA gene expression in normal tissues and in thyroid hyper- and neoplasias, using real-time PCR.

Methods
For the analysis THADA and 18S rRNA gene expression assays were performed on 34 normal tissue samples, including thyroid, salivary gland, heart, endometrium, myometrium, lung, blood, and adipose tissue as well as on 85 thyroid hyper- and neoplasias, including three adenomas with a 2p21 translocation. In addition, NIS (sodium-iodide symporter) gene expression was measured on 34 of the pathological thyroid samples.

Results
Results illustrated that THADA expression in normal thyroid tissue was significantly higher (p < 0.0001, exact Wilcoxon test) than in the other tissues. Significant differences were also found between non-malignant pathological thyroid samples (goiters and adenomas) and malignant tumors (p < 0.001, Wilcoxon test, t approximation), anaplastic carcinomas (ATCs) and all other samples and also between ATCs and all other malignant tumors (p < 0.05, Wilcoxon test, t approximation). Furthermore, in thyroid tumors THADA mRNA expression was found to be inversely correlated with HMGA2 mRNA. HMGA2 expression was recently identified as a marker revealing malignant transformation of thyroid follicular tumors. A correlation between THADA and NIS has also been found in thyroid normal tissue and malignant tumors.

Conclusions
The results suggest THADA being a marker of dedifferentiation of thyroid tissue.
Expert Delphi survey on research and development into drugs for neglected diseases
Authors: Fehr Angela , Thürmann Petra , Razum Oliver 
Published: December 2011

Abstract

Background
Tropical infectious diseases are called neglected, because they are, inter alia, characterized by an R&D deficit. A similar deficit exists for rare (orphan) diseases which neither promise a sufficient return on R&D investment. To encourage the development of treatments for rare diseases, orphan drug acts were created which contain financial and non-financial incentives for the pharmaceutical industry. Similar instruments aimed exclusively at neglected diseases do not yet exist. Proposals for a regulatory approach to promote R&D for neglected diseases include the application of selected orphan drug incentives, or the implementation of a Medical Research and Development Treaty (MRDT) with national funding obligations for medical R&D. We compiled and analyzed experts' opinions on causes for the treatment deficit for neglected diseases and on desirable and feasible measures to promote neglected disease R&D. Hereby, the focus was on mechanisms contained in orphan drug regulations and in the Medical Research and Development Treaty draft (Discussion draft 4, 2005). Lastly, we solicited experts' opinions on the desirability and feasibility of a regulatory instrument to foster R&D for neglected diseases.

Methods
An international online-Delphi survey was conducted with 117 (first round) and 56 (second round) experts of different professional backgrounds and professional affiliations who formulated and ranked causes and solutions related to the treatment deficit for neglected diseases.

Results
In both rounds of survey, the majority of the participating experts (88.4% first round, 86.8% second round) advocated the development of a regulatory instrument to promote R&D for neglected diseases. Most experts (77.9% first round, 79.3% second round) also considered this to be a feasible option. With the exception of market exclusivity, which was viewed critically, key provisions contained in orphan drug regulations were judged favorably also for neglected diseases. A majority (87.1% first round, 77.2% second round) supported national funding obligations for neglected diseases which are proposed by the Medical Research and Development Treaty draft.

Conclusions
While not all features of orphan drug regulations and of the MRDT draft received equal support, the view was expressed that a regulatory instrument would be a desirable and feasible measure to promote R&D for neglected diseases.