bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the effectiveness of different tea types from various thyme kinds (Origanum onites, Thymbra spicata and Satureja cuneifolia) on anemia and anticholesterolemic activity
Authors: Akdogan Mehmet , Kisioglu Ahmet Nesimi , Ciris Metin , Koyu Ahmet 
Published: November 2012

In a study on villagers settled on the outskirts of the Taurus Mountains and whose source of living is thyme, it was revealed that the villagers excessively consumed thyme by adding it to their tea and many of their foods; high incidences of anemia was found among these villagers. In this study, 42 male adult Wistar albino rats weighing 200–250 g were used. The rats were divided to six equal groups as follows: control, cholesterol (Chol), 80 mg/kg Origanum onites Labiatae (OOL), 80 mg/kg Thymbra spicata Labiatae (TSL), 80 mg/kg Satureja cuneifolia Labiatae (SCL), and 160 mg/kg TSL, and each group consisted of seven rats. The control group was fed with normal pellet feed. The Chol group and all the other groups, except for the control group, were fed with 2% cholesterol-containing pellet feed. Physiological serum of 4 ml was given to the control and Chol group, wheile 80 mg/kg of thymes tea was given to the OOL group, TSL group, and SCL group, and 160 mg/kg of thymes tea was given to the TSL group by means of a gavage for 30 days. In the blood samples, the hematologic parameters and the biochemical parameters of serum glucose, blood urea nitrogen, creatinine, total protein, albumin, iron (I), total iron-binding capacity, aminotransferase aspartate, alanine aminotransferase, alkaline phosphatase, lactate dehydrogenase, total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein cholesterol, triglyceride, and oxidized LDL levels were examined. The kidney and liver tissues were examined histopathologically. The results of the study showed that different types of thymes had an antihypercholesterolemic effect. In addition to the anemic effect detected in group TSL and the mild granular degeneration found in the liver of 80 mg/kg SCL group, distinct granular degeneration was observed in 160 mg/kg TSL group.
A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings
Authors: Müller Thomas , Ensminger Ingo , Schmid Karl J 
Published: November 2012

AbstractBackgroundDouglas-fir (Pseudotsuga menziesii) extends over a wide range of contrasting environmental conditions, reflecting substantial local adaptation. For this reason, it is an interesting model species to study plant adaptation and the effects of global climate change such as increased temperatures and significant periods of drought on individual trees and the forest landscape in general. However, genomic data and tools for studying genetic variation in natural populations to understand the genetic and physiological mechanisms of adaptation are currently missing for Douglas-fir. This study represents a first step towards characterizing the Douglas-fir transcriptome based on 454 sequencing of twelve cDNA libraries. The libraries were constructed from needle and wood tissue of coastal and interior provenances subjected to drought stress experiments.ResultsThe 454 sequencing of twelve normalized cDNA libraries resulted in 3.6 million reads from which a set of 170,859 putative unique transcripts (PUTs) was assembled. Functional annotation by BLAST searches and Gene Ontology mapping showed that the composition of functional classes is very similar to other plant transcriptomes and demonstrated that a large fraction of the Douglas-fir transcriptome is tagged by the PUTs. Based on evolutionary conservation, we identified about 1,000 candidate genes related to drought stress. A total number of 187,653 single nucleotide polymorphisms (SNPs) were detected by three SNP detection tools. However, only 27,688 SNPs were identified by all three methods, indicating that SNP detection depends on the particular method used. The two alleles of about 60% of the 27,688 SNPs are segregating simultaneously in both coastal and interior provenances, which indicates a high proportion of ancestral shared polymorphisms or a high level of gene flow between these two ecologically and phenotypically different varieties.ConclusionsWe established a catalogue of PUTs and large SNP database for Douglas-fir. Both will serve as a useful resource for the further characterization of the genome and transcriptome of Douglas-fir and for the analysis of genetic variation using genotyping or resequencing methods.
A parallel genome-wide mRNA and microRNA profiling of the frontal cortex of HIV patients with and without HIV-associated dementia shows the role of axon guidance and downstream pathways in HIV-mediated neurodegeneration
Authors: Zhou Li , Pupo Gulietta M , Gupta Priyanka , Liu Bing , Tran Sieu L , Rahme Raany , Wang Bin , Rua Rejane , Rizos Helen , Carroll Adam , Cairns Murray J , Saksena Nitin K 
Published: November 2012

Abstract

Background
HIV-associated dementia (HAD) is the most common dementia type in young adults less than 40 years of age. Although the neurotoxins, oxidative/metabolic stress and impaired activity of neurotrophic factors are believed to be underlying reasons for the development of HAD, the genomic basis, which ultimately defines the virus-host interaction and leads to neurologic manifestation of HIV disease is lacking. Therefore, identifying HIV fingerprints on the host gene machinery and its regulation by microRNA holds a great promise and potential for improving our understanding of HAD pathogenesis, its diagnosis and therapy.

Results
A parallel profiling of mRNA and miRNA of the frontal cortex autopsies from HIV positive patients with and without dementia was performed using Illumina Human-6 BeadChip and Affymetrix version 1.0 miRNA array, respectively. The gene ontology and pathway analysis of the two data sets showed high concordance between miRNA and mRNAs, revealing significant interference with the host axon guidance and its downstream signalling pathways in HAD brains. Moreover, the differentially expressed (DE) miRNAs identified in this study, in particular miR-137, 153 and 218, based on which most correlations were built cumulatively targeted neurodegeneration related pathways, implying their future potential in diagnosis, prognosis and possible therapies for HIV-mediated and possibly other neurodegenerative diseases. Furthermore, this relationship between DE miRNAs and DE mRNAs was also reflected in correlation analysis using Bayesian networks by splitting-averaging strategy (SA-BNs), which revealed 195 statistically significant correlated miRNA-mRNA pairs according to Pearson’s correlation test (P<0.05).

Conclusions
Our study provides the first evidence on unambiguous support for intrinsic functional relationship between mRNA and miRNA in the context of HIV-mediated neurodegeneration, which shows that neurologic manifestation in HIV patients possibly occurs through the interference with the host axon guidance and its downstream signalling pathways. These data provide an excellent avenue for the development of new generation of diagnostic/prognostic biomarkers and therapeutic intervention strategies for HIV-associated neurodegeneration.
Cross-pollination of research findings, although uncommon, may accelerate discovery of human disease genes
Authors: Duda Marlena , Nelson Tristan , Wall Dennis P 
Published: November 2012

Abstract

Background
Technological leaps in genome sequencing have resulted in a surge in discovery of human disease genes. These discoveries have led to increased clarity on the molecular pathology of disease and have also demonstrated considerable overlap in the genetic roots of human diseases. In light of this large genetic overlap, we tested whether cross-disease research approaches lead to faster, more impactful discoveries.

Methods
We leveraged several gene-disease association databases to calculate a Mutual Citation Score (MCS) for 10,853 pairs of genetically related diseases to measure the frequency of cross-citation between research fields. To assess the importance of cooperative research, we computed an Individual Disease Cooperation Score (ICS) and the average publication rate for each disease.

Results
For all disease pairs with one gene in common, we found that the degree of genetic overlap was a poor predictor of cooperation (r2=0.3198) and that the vast majority of disease pairs (89.56%) never cited previous discoveries of the same gene in a different disease, irrespective of the level of genetic similarity between the diseases. A fraction (0.25%) of the pairs demonstrated cross-citation in greater than 5% of their published genetic discoveries and 0.037% cross-referenced discoveries more than 10% of the time. We found strong positive correlations between ICS and publication rate (r2=0.7931), and an even stronger correlation between the publication rate and the number of cross-referenced diseases (r2=0.8585). These results suggested that cross-disease research may have the potential to yield novel discoveries at a faster pace than singular disease research.

Conclusions
Our findings suggest that the frequency of cross-disease study is low despite the high level of genetic similarity among many human diseases, and that collaborative methods may accelerate and increase the impact of new genetic discoveries. Until we have a better understanding of the taxonomy of human diseases, cross-disease research approaches should become the rule rather than the exception.
Anti-inflammatory activity of cinnamon water extract in vivo and in vitro LPS-induced models
Authors: Hong Joung-Woo , Yang Ga-Eun , Kim Yoon Bum , Eom Seok Hyun , Lew Jae-Hwan , Kang Hee 
Published: November 2012

Abstract

Background
Cinnamon bark is one of the most popular herbal ingredients in traditional oriental medicine and possesses diverse pharmacological activities including anti-bacterial, anti-viral, and anti-cancer properties. The goal of this study is to investigate the in vivo and in vitro inhibitory effect of cinnamon water extract (CWE) on lipopolysaccharide (LPS)-induced tumor necrosis factor (TNF)-α and its underlying intracellular mechanisms.

Methods
CWE was orally administrated to mice for 6 days prior to intraperitoneal injection of LPS. Serum levels of TNF-α and interleukin (IL)-6 were determined 1 hour after LPS stimulation. Peritoneal macrophages from thioglycollate-injected mice were isolated and assayed for viability, cytokine expression and signaling molecules upon LPS stimulation. CWE was further fractioned according to molecular size, and the levels of total polyphenols and biological activities of each fraction were measured.

Results
The oral administration of CWE to mice significantly decreased the serum levels of TNF-α and IL-6. CWE treatment in vitro decreased the mRNA expression of TNF-α. CWE blocked the LPS-induced degradation of IκBα as well as the activation of JNK, p38 and ERK1/2. Furthermore, size-based fractionation of CWE showed that the observed inhibitory effect of CWE in vitro occurred in the fraction containing the highest level of total polyphenols.

Conclusions
Treatment with CWE decreased LPS-induced TNF-α in serum. In vitro inhibition of TNF-α gene by CWE may occur via the modulation of IκBα degradation and JNK, p38, and ERK1/2 activation. Our results also indicate that the observed anti-inflammatory action of CWE may originate from the presence of polyphenols.
Antimicrobial activities of endophytic fungi isolated from Ophiopogon japonicus (Liliaceae)
Authors: Liang Hanqiao , Xing Yongmei , Chen Juan , Zhang Dawei , Guo Shunxing , Wang Chunlan 
Published: November 2012

Abstract

Background
Drug resistance in bacteria has become a global concern and the search for new antibacterial agents is urgent and ongoing. Endophytes provide an abundant reservoir of bioactive metabolites for medicinal exploitation, and an increasing number of novel compounds are being isolated from endophytic fungi. Ophiopogon japonicus, containing compounds with antibacterial activity, is a traditional Chinese medicinal plant used for eliminating phlegm, relieving coughs, latent heat in the lungs, and alleviating diabetes mellitus. We investigated the antimicrobial activities of 30 strains of O. japonicus.

Methods
Fungal endophytes were isolated from roots and stems of O. japonicus collected from Chongqing City, southwestern China. Mycelial extracts (MC) and fermentation broth (FB) were tested for antimicrobial activity using peptide deformylase (PDF) inhibition fluorescence assays and MTT cell proliferation assays.

Results
A total of 30 endophytic strains were isolated from O. japonicus; 22 from roots and eight from stems. 53.33% of the mycelial extracts (MC) and 33.33% of the fermentation broths (FB) displayed potent inhibition of PDF. 80% of MC and 33.33% of FB significantly inhibited Staphylococcus aureus. 70% of MC and 36.67% of FB showed strong activities against Cryptococcus neoformans. None showed influence on Escherichia coli.

Conclusion
The secondary metabolites of endophytic fungi from O. japonicus are potential antimicrobial agents.
Principal component analysis reveals gender-specific predictors of cardiometabolic risk in 6th graders
Authors: Peterson Mark D , Liu Dongmei , IglayReger Heidi B , Saltarelli William A , Visich Paul S , Gordon Paul M 
Published: November 2012

Abstract

Background
The purpose of this study was to determine the sex-specific pattern of pediatric cardiometabolic risk with principal component analysis, using several biological, behavioral and parental variables in a large cohort (n = 2866) of 6th grade students.

Methods
Cardiometabolic risk components included waist circumference, fasting glucose, blood pressure, plasma triglycerides levels and HDL-cholesterol. Principal components analysis was used to determine the pattern of risk clustering and to derive a continuous aggregate score (MetScore). Stratified risk components and MetScore were analyzed for association with age, body mass index (BMI), cardiorespiratory fitness (CRF), physical activity (PA), and parental factors.

Results
In both boys and girls, BMI and CRF were associated with multiple risk components, and overall MetScore. Maternal smoking was associated with multiple risk components in girls and boys, as well as MetScore in boys, even after controlling for children’s BMI. Paternal family history of early cardiovascular disease (CVD) and parental age were associated with increased blood pressure and MetScore for girls. Children’s PA levels, maternal history of early CVD, and paternal BMI were also indicative for various risk components, but not MetScore.

Conclusions
Several biological and behavioral factors were independently associated with children’s cardiometabolic disease risk, and thus represent a unique gender-specific risk profile. These data serve to bolster the independent contribution of CRF, PA, and family-oriented healthy lifestyles for improving children’s health.
The effect of endometrial thickness and pattern measured by ultrasonography on pregnancy outcomes during IVF-ET cycles
Authors: Zhao Jing , Zhang Qiong , Li Yanping 
Published: November 2012

Abstract

Background
To study the effect of endometrial thickness and pattern measured using ultrasound upon pregnancy outcomes in patients undergoing IVF-ET.

Method
One thousand nine hundred thirty-three women undergoing IVF treatment participated in the study. We assessed and recorded endometrial patterns and thickness on the day of human chorionic gonadotropin (hCG) administration. Receiver operator curves (ROC) were used to determine the predictive accuracy of endometrial thickness. Cycles were divided into 3 groups depending on the thickness (group 1: ≤ 7 mm; group 2: > 7 mm to ≤ 14 mm; group 3: > 14 mm). Each group was subdivided into three groups according to the endometrial pattern as follows: pattern A (a triple-line pattern consisting of a central hyperechoic line surround by two hypoechoic layers); pattern B (an intermediate isoechogenic pattern with the same reflectivity as the surrounding myometrium and a poorly defined central echogenic line); and pattern C (homogenous, hyperechogenic endometrium). Clinical outcomes such as implantation and clinical pregnancy rates were analyzed.

Results
The endometrial thickness predicts pregnancy outcome with high sensitivity and specificity. The cutoff value was 9 mm. The implantation rate and clinical pregnancy rate in group 3 were 39.1% and 63.5%, respectively, which were significantly higher than those in group 2 (33.8% and 52.1%, respectively) and group 1 (13% and 25.5%, respectively). Among those with Pattern A, the implantation rate and clinical pregnancy rate were 35.3% and 55.2%, respectively, which were significantly higher than among women with Pattern B (32.1% and 50.9%, respectively) and Pattern C (23.4% and 37.4%, respectively). In groups 1 and 3, clinical pregnancy and implantation rates did not show any significant differences between different endometrial patterns (P > 0.05), whereas in group 2, the clinical pregnancy rate and implantation rate in women with pattern A were significantly higher than those with pattern B or C (P < 0.05).

Conclusions
Endometrial thickness and pattern independently affect pregnant outcomes. Combined endometrial thickness and pattern could not predict the outcome of IVF-ET when endometrial thickness was < 7 mm or >14 mm, while a triple-line pattern with a moderate endometrial thickness appeared to be associated with a good clinical outcome.
Myosin heavy chain 2A and α-Actin expression in human and murine skeletal muscles at feeding; particularly amino acids
Authors: Iresjö Britt-Marie , Lundholm Kent 
Published: November 2012

Abstract

Background
Protein dynamics during non-steady state conditions as feeding are complex. Such studies usually demand combinations of methods to give conclusive information, particularly on myofibrillar proteins with slow turnover. Therefore, time course transcript analyses were evaluated as possible means to monitor changes in myofibrillar biosynthesis in skeletal muscles in conditions with clinical nutrition; i.e. long term exposure of nutrients.

Methods
Muscle tissue from overnight intravenously fed surgical patients were used as a model combined with muscle tissue from starved and refed mice as well as cultured L6 muscle cells. Transcripts of acta 1 (α-actin), mhc2A (myosin) and slc38 a2/Snat 2 (amino acid transporter) were quantified (qPCR) as markers of muscle protein dynamics.

Results
Myosin heavy chain 2A transcripts decreased significantly in skeletal muscle tissue from overnight parenterally fed patients but did not change significantly in orally refed mice. Alpha-actin transcripts did not change significantly in muscle cells from fed patients, mice or cultured L6 cells during provision of AA. The AA transporter Snat 2 decreased in L6 cells refed by all AA and by various combinations of AA but did not change during feeding in muscle tissue from patients or mice.

Conclusion
Our results confirm that muscle cells are sensitive to alterations in extracellular concentrations of AA for induction of protein synthesis and anabolism. However, transcripts of myofibrillar proteins and amino acid transporters showed complex alterations in response to feeding with provision of amino acids. Therefore, muscle tissue transcript levels of actin and myosin do not reflect protein accretion in skeletal muscles at feeding.
Cyclic generalized contractions and fixed point results with applications to an integral equation
Authors: Nashine Hemant Kumar , Sintunavarat Wutiphol , Kumam Poom 
Published: November 2012

Abstract
We set up a new variant of cyclic generalized contractive mappings for a map in a metric space and present existence and uniqueness results of fixed points for such mappings. Our results generalize or improve many existing fixed point theorems in the literature. To illustrate our results, we give some examples. At the same time as applications of the presented theorems, we prove an existence theorem for solutions of a class of nonlinear integral equations.

MSC:47H10, 54H25.
Bioinformatics clouds for big data manipulation
Authors: Dai Lin , Gao Xin , Guo Yan , Xiao Jingfa , Zhang Zhang 
Published: November 2012

AbstractAs advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.ReviewersThis article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.
IMP3 can predict aggressive behaviour of lung adenocarcinoma
Authors: Beljan Perak Renata , Durdov Merica Glavina , Capkun Vesna , Ivcevic Veljka , Pavlovic Antonia , Soljic Violeta , Peric Mari 
Published: November 2012

Abstract

Background
Lung cancer most often presents as an inoperable tumour and the diagnosis is usually performed on a small biopsy/cytology specimen. In the group of non small cell lung cancer - not otherwise specified, adenocarcinoma phenotype can be determined immunohistochemically using TTF-1 and Napsin A. Expression of oncofetal protein IMP3 in human cancer is associated with poor differentiation and aggressive behaviour. In the present study expression of IMP3 was correlated with expression of TTF-1 and Napsin A, histological subtype and clinical stage of lung adenocarcinoma. We were interested whether distant metastases are associated with IMP3 overexpression, regardless of the histologic subtype of adenocarcinoma.

Methods
In retrospective study, consecutive series of 105 patients with advanced lung adenocarcinoma diagnosed from 2006 to 2009 in Clinical Hospital Center Split, Croatia, were analysed. Clinical data were collected from the Pulmology Department and time of death from the Mortality Registry. Paraffin blocks of bronchoscopic biopsies were collected from the Institute of Pathology and 15 cases excluded from the analysis due to insufficient material. Expression of IMP3, Napsin A and TTF-1 were analysed by indirect enzyme immunohistochemistry. Statistical analysis was performed and P values less than 0.05 considered significant.

Results
Of 90 patients, 71 (78%) were males and 19 (22%) females. Median age for males was 61.5 years (min-max 43–83) and for females 61 years (min-max 44–86). Pleural effusion was found in 15 (16.6%) and distant metastases in 45 (50%) cases. According to histological subtypes, there were 34 acinar, 2 lepidic, 2 papillary and 52 solid subtypes. IMP3 overexpression was found in 63 cases (70%) and was correlated with solid subtype (P = 0.002) and negative/weak Napsin A expression (P = 0.004). Strong Napsin A expression correlated with TTF-1 expression (P = 0.003) and lower histological grades (P = 0.031). Patients with IMP3 overexpression more often had distant metastases than patients with negative IMP3, 55.5% versus 33.3% (P = 0.033). Non solid subtypes with IMP3 overexpression developed distant metastasis more common than non solid subtypes with negative IMP3, 72% versus 35% (P = 0.028).

Conclusions
Expression of IMP3 correlates with solid subtype and with distant metastases regardless of histological subtype of lung adenocarcinoma.

Virtual slides

http://www.diagnosticpathology.diagnomx.eu/vs/1966211581795258