bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study
Authors: Wu Tao , Zhang Zhigang , Liu Bin , Hou Dezhi , Liang Yun , Zhang Jie , Shi Peng 
Published: October 2013

Abstract

Background
Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gallstone patients as well as the gut of 38 normal individuals, examining and analyzing some 299, 217 bacterial 16S rRNA gene sequences from 120 samples.

Results
First, as compared with normal individuals, in gallstone patients there were significant (P < 0.001) increases of gut bacterial phylum Proteobacteria and decreases of three gut bacterial genera, Faecalibacterium, Lachnospira, and Roseburia. Second, about 70% of gut bacterial operational taxonomic units (OTUs) from gallstone patients were detectable in the biliary tract and bacteria diversity of biliary tract was significantly (P < 0.001) higher than that of gut. Third, analysis of the biliary tract core microbiome (represented by 106 bacteria OTUs) among gallstone patients showed that 33.96% (36/106) of constituents can be matched to known bacterial species (15 of which have publicly available genomes). A genome-wide search of MDR, BSH, bG, and phL genes purpotedly associated with the formation of cholesterol gallstones showed that all 15 species with known genomes (e.g., Propionibacterium acnes, Bacteroides vulgates, and Pseudomonas putida) contained at least contained one of the four genes. This finding could potentially provide underlying information needed to explain the association between biliary tract microbiota and the formation of cholesterol gallstones.

Conclusions
To the best of our knowledge, this is the first study to discover gut microbiota dysbiosis among gallstone patients, the presence of which may be a key contributor to the complex bacteria community assembly linked with the presence of cholesterol gallstones. Likewise, this study also provides the first large-scale glimpse of biliary tract microbiota potentially associated with cholesterol gallstones. Such a characterization of the biliary tract core microbiome has potentially important biological and medical implications regarding the role of bacteria in the formation cholesterol gallstones.
An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome
Authors: Ferrarini Marco , Moretto Marco , Ward Judson A , Šurbanovski Nada , Stevanović Vladimir , Giongo Lara , Viola Roberto , Cavalieri Duccio , Velasco Riccardo , Cestaro Alessandro , Sargent Daniel J 
Published: October 2013

Abstract

Background
Second generation sequencing has permitted detailed sequence characterisation at the whole genome level of a growing number of non-model organisms, but the data produced have short read-lengths and biased genome coverage leading to fragmented genome assemblies. The PacBio RS long-read sequencing platform offers the promise of increased read length and unbiased genome coverage and thus the potential to produce genome sequence data of a finished quality containing fewer gaps and longer contigs. However, these advantages come at a much greater cost per nucleotide and with a perceived increase in error-rate. In this investigation, we evaluated the performance of the PacBio RS sequencing platform through the sequencing and de novo assembly of the Potentilla micrantha chloroplast genome.

Results
Following error-correction, a total of 28,638 PacBio RS reads were recovered with a mean read length of 1,902 bp totalling 54,492,250 nucleotides and representing an average depth of coverage of 320× the chloroplast genome. The dataset covered the entire 154,959 bp of the chloroplast genome in a single contig (100% coverage) compared to seven contigs (90.59% coverage) recovered from an Illumina data, and revealed no bias in coverage of GC rich regions. Post-assembly the data were largely concordant with the Illumina data generated and allowed 187 ambiguities in the Illumina data to be resolved. The additional read length also permitted small differences in the two inverted repeat regions to be assigned unambiguously.

Conclusions
This is the first report to our knowledge of a chloroplast genome assembled de novo using PacBio sequence data. The PacBio RS data generated here were assembled into a single large contig spanning the P. micrantha chloroplast genome, with a higher degree of accuracy than an Illumina dataset generated at a much greater depth of coverage, due to longer read lengths and lower GC bias in the data. The results we present suggest PacBio data will be of immense utility for the development of genome sequence assemblies containing fewer unresolved gaps and ambiguities and a significantly smaller number of contigs than could be produced using short-read sequence data alone.
Functional analysis of the omega-6 fatty acid desaturase (CaFAD2) gene family of the oil seed crop Crambe abyssinica
Authors: Cheng Jihua , Zhu Li-Hua , Salentijn Elma MJ , Huang Bangquan , Gruber Jens , Dechesne Annemarie C , Krens Frans A , Qi Weicong , Visser Richard GF , van Loo Eibertus N 
Published: October 2013

Abstract

Background

Crambe abyssinica produces high erucic acid (C22:1, 55-60%) in the seed oil, which can be further increased by reduction of polyunsaturated fatty acid (PUFA) levels. The omega-6 fatty acid desaturase enzyme (FAD2) is known to be involved in PUFA biosynthesis. In crambe, three CaFAD2 genes, CaFAD2-C1, CaFAD2-C2 and CaFAD2-C3 are expressed.

Results
The individual effect of each CaFAD2 gene on oil composition was investigated through studying transgenic lines (CaFAD2-RNAi) for differential expression levels in relation to the composition of seed-oil. Six first generation transgenic plants (T1) showed C18:1 increase (by 6% to 10.5%) and PUFA reduction (by 8.6% to 10.2%). The silencing effect in these T1-plants ranged from the moderate silencing (40% to 50% reduction) of all three CaFAD2 genes to strong silencing (95% reduction) of CaFAD2-C3 alone. The progeny of two T1-plants (WG4-4 and WG19-6) was further analysed. Four or five transgene insertions are characterized in the progeny (T2) of WG19-6 in contrast to a single insertion in the T2 progeny of WG4-4. For the individual T2-plants of both families (WG19-6 and WG4-4), seed-specific silencing of CaFAD2-C1 and CaFAD2-C2 was observed in several individual T2-plants but, on average in both families, the level of silencing of these genes was not significant. A significant reduction in expression level (P < 0.01) in both families was only observed for CaFAD2-C3 together with significantly different C18:1 and PUFA levels in oil.

Conclusions

CaFAD2-C3 expression is highly correlated to levels of C18:1 (r = -0.78) and PUFA (r = 0.75), which suggests that CaFAD2-C3 is the most important one for changing the oil composition of crambe.
Exploration of experiences in therapeutic groups for patients with severe mental illness: development of the Ferrara group experiences scale (FE- GES)
Authors: Caruso Rosangela , Grassi Luigi , Biancosino Bruno , Marmai Luciana , Bonatti Luciano , Moscara Maria , Rigatelli Marco , Carr Catherine , Priebe Stefan 
Published: October 2013

Abstract

Background
Group therapies are routinely provided for patients with severe mental illness. The factors important to the group experience of patients are still poorly understood and are rarely measured. To support further research and practice, we aimed to develop a questionnaire that captures how patients experience groups within a community mental health context.

Methods
An initial pool of 39 items was conceptually generated to assess different aspects of group experiences. Items were completed by 166 patients with severe mental illness attending group therapies in community mental health services in Italy. Patients with different psychiatric diagnoses who attended at least 5 group sessions were included. An exploratory factor analysis was used to identify different dimensions of group experiences and to reduce the number of items for each dimension.

Results
The resulting questionnaire has five subscales: 1) sharing of emotions and experiences, 2) cognitive improvement, 3) group learning, 4) difficulties in open expression and 5) relationships. Each subscale has 4 items. The scale and sub-scales have good internal consistency.

Conclusions
The Ferrara Group Experiences Scale is conceptually derived and assesses dimensions of group experience that are theoretically and practically relevant. It is brief, easy to use and has good psychometric properties. After further validation, the scale may be used for research into patient experiences across different group therapy modalities and for evaluation in routine care.
Growth-Inhibiting and morphostructural effects of constituents identified in Asarum heterotropoides root on human intestinal bacteria
Authors: Perumalsamy Haribalan , Jung Moon Young , Hong Seung Min , Ahn Young-Joon 
Published: October 2013

Abstract

Background
The growth-inhibiting and morphostructural effects of seven constituents identified in Asarum heterotropoides root on 14 intestinal bacteria were compared with those of the fluoroquinolone antibiotic ciprofloxacin.

Method
A microtiter plate-based bioassay in sterile 96-well plates was used to evaluate the minimal inhibitory concentrations (MICs) of the test materials against the organisms.

Results
δ-3-Carene (5) exhibited the most potent growth inhibition of Gram-positive bacteria (Clostridium difficile ATCC 9689, Clostridium paraputrificum ATCC 25780, Clostridium perfringens ATCC 13124, and Staphylococcus aureus ATCC 12600) and Gram-negative bacteria (Escherichia coli ATCC 11775 and Bacteroides fragilis ATCC 25285) (minimal inhibitory concentrations (MIC), 0.18–0.70 mg/mL) except for Salmonella enterica serovar Typhimurium ATCC 13311 (MIC, 2.94 mg/mL). The MIC of methyleugenol (2), 1,8-cineole (3), α-asarone (4), (−)-asarinin (6), and pellitorine (7) was between 1.47 and 2.94 mg/mL against all test bacteria (except for compound 2 against C. difficile (0.70 mg/mL); compounds 1 (23.50 mg/mL) and 4 (5.80 mg/mL) against C. paraputricum; compounds 2 (5.80 mg/mL), 4 (12.0 mg/mL), and 7 (0.70 mg/mL) against C. perfringens); compound 1 against E. coli (7.20 mg/mL) and S. enterica serovar Typhimurium (12.0 mg/mL). Overall, all of the constituents were less potent at inhibiting microbial growth than ciprofloxacin (MIC, 0.063–0.25 mg/ mL). The lactic acid-producing bacteria (four bifidobacteria and two lactobacilli) and one acidulating bacterium Clostridium butyricum ATCC 25779 were less sensitive and more susceptible than the five harmful bacteria and two nonpathogenic bacteria (B. fragilis and E. coli) to the constituents and to ciprofloxacin, respectively. Beneficial Gram-positive bacteria and harmful and nonpathogenic Gram-negative bacteria were observed to have different degrees of antimicrobial susceptibility to the constituents, although the antimicrobial susceptibility of the harmful Gram-positive bacteria and the harmful and nonpathogenic Gram-negative bacteria was not observed. Scanning electron microscopy observations showed different degrees of physical damage and morphological alteration to both Gram-positive and Gram-negative bacteria treated with α-asarone, δ-3-carene, pellitorine, or ciprofloxacin, indicating that they do not share a common mode of action.

Conclusion

A. heterotropoides root-derived materials described merit further study as potential antibacterial products or lead molecules for the prevention or eradication from humans from diseases caused by harmful intestinal bacteria.
VRK2 identifies a subgroup of primary high-grade astrocytomas with a better prognosis
Authors: Rodríguez-Hernández Irene , Vázquez-Cedeira Marta , Santos-Briz Angel , García Juan L , Fernández Isabel F , Gómez-Moreta Juan A , Martin-Vallejo Javier , González-Sarmiento Rogelio , Lazo Pedro A 
Published: October 2013

Abstract

Background
Malignant astrocytomas are the most common primary brain tumors and one of the most lethal among human cancers despite optimal treatment. Therefore, the characterization of molecular alterations underlying the aggressive behavior of these tumors and the identification of new markers are thus an important step towards a better patient stratification and management.

Methods and results
VRK1 and VRK2 (Vaccinia-related kinase-1, -2) expression, as well as proliferation markers, were determined in a tissue microarray containing 105 primary astrocytoma biopsies. Kaplan Meier and Cox models were used to find clinical and/or molecular parameters related to overall survival. The effects of VRK protein levels on proliferation were determined in astrocytoma cell lines. High levels of both protein kinases, VRK1 or VRK2, correlated with proliferation markers, p63 or ki67. There was no correlation with p53, reflecting the disruption of the VRK-p53-DRAM autoregulatory loop as a consequence of p53 mutations. High VRK2 protein levels identified a subgroup of astrocytomas that had a significant improvement in survival. The potential effect of VRK2 was studied by analyzing the growth characteristics of astrocytoma cell lines with different EGFR/VRK2 protein ratios.

Conclusion
High levels of VRK2 resulted in a lower growth rate suggesting these cells are more indolent. In high-grade astrocytomas, VRK2 expression constitutes a good prognostic marker for patient survival.
Quantitative proteomic analysis in HCV-induced HCC reveals sets of proteins with potential significance for racial disparity
Authors: Dillon Simon T , Bhasin Manoj K , Feng Xiaoxing , Koh David W , Daoud Sayed S 
Published: October 2013

AbstractBackgroundThe incidence and mortality of hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) is higher in African Americans (AA) than other racial/ethnic groups in the U.S., but the reasons for this disparity are unknown. There is an urgent need for the discovery of novel molecular signatures for HCV disease progression to understand the underlying biological basis for this cancer rate disparity to improve the clinical outcome.MethodsWe performed differential proteomics with isobaric labeling tags for relative and absolute quantitation (iTRAQ) and MS/MS analysis to identify proteins differentially expressed in cirrhotic (CIR) and HCC as compared to normal tissues of Caucasian American (CA) patients. The raw data were analyzed using the ProteinPilot v3.0. Searches were performed against all known sequences populating the Swiss-Prot, Refseq, and TrEMBL databases. Quality control analyses were accomplished using pairwise correlation plots, boxplots, principal component analysis, and unsupervised hierarchical clustering. Supervised analysis was carried out to identify differentially expressed proteins. Candidates were validated in independent cohorts of CA and AA tissues by qRT-PCR or Western blotting.ResultsA total of 238 unique proteins were identified. Of those, around 15% were differentially expressed between normal, CIR & HCC groups. Target validation demonstrates racially distinct alteration in the expression of certain proteins. For example, the mRNA expression levels of transferrin (TF) were 2 and18-fold higher in CIR and HCC in AA as compared to CA. Similarly; the expression of Apolipoprotein A1 (APOA1) was 7-fold higher in HCC of AA. This increase was mirrored in the protein expression levels. Interestingly, the level of hepatocyte nuclear factor4α (HNF4α) protein was down regulated in AA, whereas repression of transcription is seen more in CA compared to AA. These data suggest that racial disparities in HCC could be a consequence of differential dysregulation of HNF4α transcriptional activity.ConclusionThis study identifies novel molecular signatures in HCV-induced HCC using iTRAQ-based tissue proteomics. The proteins identified will further enhance a molecular explanation to the biochemical mechanism(s) that may play a role in HCC racial disparities.
Astragalus injection protects cerebral ischemic injury by inhibiting neuronal apoptosis and the expression of JNK3 after cerebral ischemia reperfusion in rats
Authors: Liu Guangyi , Song Jinming , Guo Yunliang , Wang Tingting , Zhou Zhen 
Published: October 2013

Abstract

Background
Astragalus is a widely used traditional Chinese medicine and has been proven beneficial for many aspects of human health. It is important to explore the neuroprotective effect and mechanism of astragalus injection in cerebral ischemia reperfusion injury.

Methods
The focal cerebral ischemic model with middle cerebral artery occlusion (MCAO) reperfusion was established by Longa’s method in healthy adult male Wistar rats, and treated by injecting intraperitoneally astragalus injection (3 ml/kg). The neurobehavioral function of rats was evaluated by Longa’s test. The cerebral blood flow (CBF) was measured by laser Doppler flowmetry and the cerebral infarct volume was calculated by tetrazolium chloride (TTC) stain. The shape and structure of neurons in parahippocampal area was observed by HE stain and the neuronal apoptosis was detected by terminal deoxynucleotidyl transferase mediated dUTP nick end labeling (TUNEL) and flow cytometry. The expressions of c-jun N-terminal kinase 3 (JNK3) mRNA and protein were determined by RT-PCR and immunohistochemical assay and Western blotting respectively.

Results
After treatment with astragalus injection, the expressions of JNK3 mRNA and protein reduced significantly, the number of neuronal apoptosis minus, the cerebral infarct volume shrink, the neuronal shape-structure and animal neurobehavioral function improved significantly than those in model rats.

Conclusions
It is suggested that astragalus injection could inhibit neuronal apoptosis, reduce infarct volume and improve neurobehavioral function by down-regulating the expression of JNK3 gene after cerebral ischemia reperfusion injury in rats.
Clozapine antipsychotic polypharmacy: audit of use and patient monitoring
Authors: Wilson Sam , Hamilton Ross , Callender John , MacManus Angela , Howitt Sheila , Okpo Blessing 
Published: October 2013

Aims and methodWe audited prescribing within our area to ascertain how widespread the practice of antipsychotic polypharmacy using clozapine was, and whether it was being carried out within existing standards, including those of high-dose monitoring when required.ResultsData on 169 patients were reviewed in year one, rising to 193 in year three. Around 30% of patients on clozapine received additional antipsychotic medication. A disturbingly low proportion of patients on clozapine whose antipsychotic polypharmacy brought them into the high-dose range were being monitored appropriately after three audit cycles (the proportion rose from 10% in cycle 1 to 28% in cycle 3). A wide range of additional antipsychotic medications was used.Clinical implicationsClozapine antipsychotic polypharmacy was prevalent at just below a third of all patients in this review. Prescribers should be alert to the fact that clozapine antipsychotic polypharmacy can push patients into the high-dose range and ensure appropriate monitoring.
Gestational Diabetes and Type 2 Diabetes in Reproductive-Aged Women With Polycystic Ovary Syndrome
Authors: Joham A. E. , Ranasinha S. , Zoungas S. , Moran L. , Teede H. J. 
Published: October 2013

Context:
Polycystic ovary syndrome (PCOS) affects 6%–21% of women. PCOS has been associated with an increased risk of dysglycemia including gestational diabetes mellitus (GDM) and type 2 diabetes mellitus (T2DM).

Objective:
The objective of the study was to assess the prevalence of dysglycemia and the impact of obesity in young reproductive-aged women with and without PCOS in a community-based cohort.

Design:
This was a cross-sectional analysis of data from a large longitudinal study (the Australian Longitudinal Study on Women's Health).

Setting:
The setting for the study was the general community.

Participants:
Women were randomly selected from the national health insurance database. Standardized data collection occurred at five survey time points (years 1996, 2000, 2003, 2006, and 2009). Data from survey 4 (2006, n = 9145, 62% of original cohort aged 18–23 y) were examined for this study.

Main Outcome Measures:
Self-reported PCOS, GDM, and T2DM were measured.

Results:
In women aged 28–33 years, PCOS prevalence was 5.8% [95% confidence interval (CI) 5.3%–6.4%]. The prevalence of GDM (in women reporting prior pregnancy) and T2DM was 11.2% and 5.1% in women with PCOS and 3.8% and 0.3% in women without PCOS, respectively (P for both &lt; .001). PCOS was associated with an increased odds of GDM and T2DM. After adjusting for age, body mass index, hypertension, smoking, and demographic factors, the odds of GDM (odds ratio 2.1, 95% CI 1.1–3.9, P = .02) and T2DM (odds ratio 8.8, 95% CI 3.9–20.1, P &lt; .001) remained increased in women reporting PCOS.

Conclusions:
In a large community-based cohort of reproductive-aged women, PCOS was independently associated with a higher risk of GDM and T2DM, independent of body mass index. Aggressive screening, prevention, and management of dysglycemia is clearly warranted in women with PCOS.
Update in Adrenocortical Carcinoma
Authors: Fassnacht Martin , Kroiss Matthias , Allolio Bruno 
Published: October 2013

Adrenocortical carcinoma (ACC) is an orphan malignancy that has attracted increasing attention during the last decade. Here we provide an update on advances in the field since our last review published in this journal in 2006.The Wnt/β-catenin pathway and IGF-2 signaling have been confirmed as frequently altered signaling pathways in ACC, but recent data suggest that they are probably not sufficient for malignant transformation. Thus, major players in the pathogenesis are still unknown.For diagnostic workup, comprehensive hormonal assessment and detailed imaging are required because in most ACCs, evidence for autonomous steroid secretion can be found and computed tomography or magnetic resonance imaging (if necessary, combined with functional imaging) can differentiate benign from malignant adrenocortical tumors. Surgery is potentially curative in localized tumors. Thus, we recommend a complete resection including lymphadenectomy by an expert surgeon. The pathology report should demonstrate the adrenocortical origin of the lesion (eg, by steroidogenic factor 1 staining) and provide Weiss score, resection status, and quantitation of the proliferation marker Ki67 to guide further treatment. Even after complete surgery, recurrence is frequent and adjuvant mitotane treatment improves outcome, but uncertainty exists as to whether all patients benefit from this therapy.In advanced ACC, mitotane is still the standard of care. Based on the FIRM-ACT trial, mitotane plus etoposide, doxorubicin, and cisplatin is now the established first-line cytotoxic therapy. However, most patients will experience progress and require salvage therapies. Thus, new treatment concepts are urgently needed. The ongoing international efforts including comprehensive “-omic approaches” and next-generation sequencing will improve our understanding of the pathogenesis and hopefully lead to better therapies.