bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carotid Intima-Media Thickness in Patients With Slow Coronary Flow and Its Association With Neutrophil-to-Lymphocyte Ratio
Authors: Cingoz Faruk , Iyisoy Atila , Demirkol Sait , Sahin Mehmet Ali , Balta Sevket , Celik Turgay , Unlu Murat , Arslan Zekeriya , Cakar Mustafa , Kucuk Ugur , Demirbas Seref , Kocak Necmettin 
Published: April 2013

Background: The slow coronary flow (SCF) is characterized by angiographically normal or near-normal coronary arteries with delayed progression of the contrast agent into distal vasculature. We aimed to investigate neutrophil-to-lymphocyte (N/L) ratio and the carotid intima-media thickness (CIMT) value in patients with SCF compared to patients with newly diagnosed coronary artery disease (CAD) and normal patients. Materials and Methods: We enrolled 60 consecutive patients with SCF, 68 patients with CAD, and 72 normal patients. The association between thrombolysis in myocardial infarction frame count, CIMT, and N/L ratio and other clinical and laboratory parameters were evaluated. Results: The N/L ratio was significantly higher not only in patients with SCF but also in patients with CAD, compared to those of controls. The N/L ratio was positively and moderately correlated with CIMT in the whole study population. Conclusions: The NL ratio is significantly associated with reduced coronary blood flow, and elevated N/L ratio might be an independent predictor for the presence of SCF.
Serum autoantibodies to myelin peptides distinguish acute disseminated encephalomyelitis from relapsing– remitting multiple sclerosis
Authors: Van Haren Keith , Tomooka Beren H , Kidd Brian A , Banwell Brenda , Bar-Or Amit , Chitnis Tanuja , Tenembaum Silvia N , Pohl Daniela , Rostasy Kevin , Dale Russell C , O’Connor Kevin C , Hafler David A , Steinman Lawrence , Robinson William H 
Published: April 2013

Background and objective: Acute disseminated encephalomyelitis (ADEM) and relapsing–remitting multiple sclerosis (RRMS) share overlapping clinical, radiologic and laboratory features at onset. Because autoantibodies may contribute to the pathogenesis of both diseases, we sought to identify autoantibody biomarkers that are capable of distinguishing them. Methods: We used custom antigen arrays to profile anti-myelin-peptide autoantibodies in sera derived from individuals with pediatric ADEM ( n = 15), pediatric multiple sclerosis (Ped MS; n = 11) and adult MS ( n = 15). Using isotype-specific secondary antibodies, we profiled both IgG and IgM reactivities. We used Statistical Analysis of Microarrays software to confirm the differences in autoantibody reactivity profiles between ADEM and MS samples. We used Prediction Analysis of Microarrays software to generate and validate prediction algorithms, based on the autoantibody reactivity profiles. Results: ADEM was characterized by IgG autoantibodies targeting epitopes derived from myelin basic protein, proteolipid protein, myelin-associated oligodendrocyte basic glycoprotein, and alpha-B-crystallin. In contrast, MS was characterized by IgM autoantibodies targeting myelin basic protein, proteolipid protein, myelin-associated oligodendrocyte basic glycoprotein and oligodendrocyte-specific protein. We generated and validated prediction algorithms that distinguish ADEM serum (sensitivity 62–86%; specificity 56–79%) from MS serum (sensitivity 40–87%; specificity 62–86%) on the basis of combined IgG and IgM anti-myelin autoantibody reactivity to a small number of myelin peptides. Conclusions: Combined profiles of serum IgG and IgM autoantibodies identified myelin antigens that may be useful for distinguishing MS from ADEM. Further studies are required to establish clinical utility. Further biological assays are required to delineate the pathogenic potential of these antibodies.
Impact of Age and Gender on the Coping Styles and Psychiatric Morbidity Faced by Informal Primary Caregivers of HIV-Infected Individuals Living in India
Authors: Pandit Lakshmi V. , Vishnuvardhan G. 
Published: April 2013

Background: Primary caregivers of HIV-infected patients face enormous burden, which if inappropriately coped, leads to psychiatric morbidity. Little is known of what role caregiver’s age and gender play in this. Purpose: To assess the socio-demographic profile and the influence of age and gender on coping strategies and psychiatric morbidity. Procedure: Sixty caregivers were assessed on a semistructured sociodemographic proforma, a coping checklist, and the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition ( DSM-IV; [SCID-I]). Main Findings: Majority of the carers were young, equally from both genders, and used the same number of coping strategies which increased with age. “Avoidance” was preferred by males and older carers. Youngsters had maximum psychiatric morbidity, majority of the depressed were females, while 90% of nicotine dependants were males. Conclusion: Gender, but not age, decided the style of coping and extent of psychiatric morbidity hence gender-specific interventions will improve the quality of life of the carers and their wards.
Bortezomib consolidation after autologous stem cell transplantation in multiple myeloma: a Nordic Myeloma Study Group randomized phase 3 trial
Authors: Mellqvist Ulf-Henrik , Gimsing Peter , Hjertner Oyvind , Lenhoff Stig , Laane Edward , Remes Kari , Steingrimsdottir Hlif , Abildgaard Niels , Ahlberg Lucia , Blimark Cecilie , Dahl Inger Marie , Forsberg Karin , Gedde-Dahl Tobias , Gregersen Henrik , Gruber Astrid , Guldbrandsen Nina , Haukås Einar , Carlson Kristina , Kvam Ann Kristin , Nahi Hareth , Lindås Roald , Andersen Niels Frost , Turesson Ingemar , Waage Anders , Westin Jan 
Published: April 2013

Key Points
Bortezomib consolidation after ASCT improves PFS in myeloma. Improvement of response is seen with bortezomib consolidation after ASCT in myeloma.
IκB kinase phosphorylation of SNAP-23 controls platelet secretion
Authors: Karim Zubair A. , Zhang Jinchao , Banerjee Meenakshi , Chicka Michael C. , Al Hawas Rania , Hamilton Tara R. , Roche Paul A. , Whiteheart Sidney W. 
Published: April 2013

Key Points
Nongenomic role for IκB kinase in platelet secretion: IKK phosphorylates SNAP-23, which affects granule-plasma membrane fusion. Pharmacologic inhibition or deletion of platelet IKK affects bleeding times.
Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia
Authors: Chandrasekharappa Settara C. , Lach Francis P. , Kimble Danielle C. , Kamat Aparna , Teer Jamie K. , Donovan Frank X. , Flynn Elizabeth , Sen Shurjo K. , Thongthip Supawat , Sanborn Erica , Smogorzewska Agata , Auerbach Arleen D. , Ostrander Elaine A. 
Published: April 2013

Key Points
Application of capturing/sequencing, copy number, and RNA analysis technologies ensures comprehensive molecular diagnosis of Fanconi anemia.
D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements
Authors: Laimer Josef , Zuzan Clemens J , Ehrenberger Tobias , Freudenberger Monika , Gschwandtner Simone , Lebherz Carina , Lackner Peter 
Published: April 2013

Abstract

Background
The binding of transcription factors to DNA plays an essential role in the regulation of gene expression. Numerous experiments elucidated binding sequences which subsequently have been used to derive statistical models for predicting potential transcription factor binding sites (TFBS). The rapidly increasing number of genome sequence data requires sophisticated computational approaches to manage and query experimental and predicted TFBS data in the context of other epigenetic factors and across different organisms.

Results
We have developed D-Light, a novel client-server software package to store and query large amounts of TFBS data for any number of genomes. Users can add small-scale data to the server database and query them in a large scale, genome-wide promoter context. The client is implemented in Java and provides simple graphical user interfaces and data visualization. Here we also performed a statistical analysis showing what a user can expect for certain parameter settings and we illustrate the usage of D-Light with the help of a microarray data set.

Conclusions

D-Light is an easy to use software tool to integrate, store and query annotation data for promoters. A public D-Light server, the client and server software for local installation and the source code under GNU GPL license are available at http://biwww.che.sbg.ac.at/dlight.
Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development
Authors: Zhang Jianxia , Wu Kunlin , Zeng Songjun , Teixeira da Silva Jaime A , Zhao Xiaolan , Tian Chang-En , Xia Haoqiang , Duan Jun 
Published: April 2013

Abstract

Background

Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. C. sinense, a high-grade traditional potted flower, is most prevalent in China and some Southeast Asian countries. The control of flowering time is a major bottleneck in the industrialized development of C. sinense. Little is known about the mechanisms responsible for floral development in this orchid. Moreover, genome references for entire transcriptome sequences do not currently exist for C. sinense. Thus, transcriptome and expression profiling data for this species are needed as an important resource to identify genes and to better understand the biological mechanisms of floral development in C. sinense.

Results
In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptome analysis assembles gene-related information related to vegetative and reproductive growth of C. sinense. Illumina sequencing generated 54,248,006 high quality reads that were assembled into 83,580 unigenes with an average sequence length of 612 base pairs, including 13,315 clusters and 70,265 singletons. A total of 41,687 (49.88%) unique sequences were annotated, 23,092 of which were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding. Furthermore, 120 flowering-associated unigenes, 73 MADS-box unigenes and 28 CONSTANS-LIKE (COL) unigenes were identified from our collection. In addition, three digital gene expression (DGE) libraries were constructed for the vegetative phase (VP), floral differentiation phase (FDP) and reproductive phase (RP). The specific expression of many genes in the three development phases was also identified. 32 genes among three sub-libraries with high differential expression were selected as candidates connected with flower development.

Conclusion
RNA-seq and DGE profiling data provided comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral development at three development phases of C. sinense. This data could be used as an important resource for investigating the genetics of the flowering pathway and various biological mechanisms in this orchid.
Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)
Authors: Zheng Hu , Qiyan Jiang , Zhiyong Ni , Hui Zhang 
Published: April 2013

Abstract

Background
Natural antisense transcripts (NATs) are a class of RNAs that contain a sequence complementary to other transcripts. NATs occur widely in eukaryotes and play critical roles in post-transcriptional regulation. Soybean NAT sequences are predicted in the PlantNATsDB, but detailed analyses of these NATs remain to be performed.

Results
A total of 26,216 NATs, including 994 cis-NATs and 25,222 trans-NATs, were predicted in soybean. Each sense transcript had 1–177 antisense transcripts. We identified 21 trans-NATs using RT-PCR amplification. Additionally, we identified 179 cis-NATs and 6,629 trans-NATs that gave rise to small RNAs; these were enriched in the NAT overlapping region. The most abundant small RNAs were 21, 22, and 24 nt in length. The generation of small RNAs was biased to one stand of the NATs, and the degradation of NATs was biased. High-throughput sequencing of the degradome allowed for the global identification of NAT small interfering RNAs (nat-siRNAs) targets. 446 target genes for 165 of these nat-siRNAs were identified. The nat-siRNA target could be one transcript of a given NAT, or from other gene transcripts. We identified five NAT transcripts containing a hairpin structure that is characteristic of pre-miRNA. We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean.

Conclusions
We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean. It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.
Cortical mapping of the infraspinatus muscle in healthy individuals
Authors: Ngomo Suzy , Mercier Catherine , Roy Jean-Sébastien 
Published: April 2013

Abstract

Background
While cortical representations of intrinsic hand muscles have been extensively studied in healthy individuals, little is known about the representation of proximal upper limb muscles. Improving our understanding of normal shoulder function is important, given that shoulder musculoskeletal disorders affect approximately 20% of the population and are suspected to involve changes in central motor representations. The purpose of the study is to describe the motor representation (motor evoked potentials (MEP) amplitude at the hotspot, map area, normalized map volume and center of gravity) of the infraspinatus muscle in healthy individuals, and to explore the potential influence of hand dominance on this representation (i.e. symmetry of the excitability and of the location of motor map between sides), as well as the effect of age and gender on motor excitability.

Results
Fifteen healthy participants took part in this study. No significant asymmetry between sides was observed for motor excitability (p = 0.14), map area (p = 0.73) and normalized map volume (p = 0.34). Moreover, no side x intensity interaction was found (p = 0.54), indicating similar stimulus response properties. No difference between sides was found in the location of infraspinatus motor representation, either in the mediolateral or anteroposterior axis (p > 0.10). Neither age nor gender influenced aMT (p > 0.58) or MEP size (p > 0.61).

Conclusions
As the cortical representation of infraspinatus muscles was found to be symmetric between sides, both in terms of excitability and location, comparisons between the intact and affected side could be performed in clinical studies, regardless of whether the dominant or non-dominant side is affected. The next step will be to characterize corticospinal excitability and map parameters in populations with shoulder disorders.
Eyebrow hairs from actinic keratosis patients harbor the highest number of cutaneous human papillomaviruses
Authors: Schneider Ines , Lehmann Mandy D , Kogosov Vlada , Stockfleth Eggert , Nindl Ingo 
Published: April 2013

AbstractBackgroundCutaneous human papillomavirus (HPV) infections seem to be associated with the onset of actinic keratosis (AK). This study compares the presence of cutaneous HPV types in eyebrow hairs to those in tissues of normal skin and skin lesions of 75 immunocompetent AK patients.MethodsBiopsies from AK lesions, normal skin and plucked eyebrow hairs were collected from each patient. DNA from these specimens was tested for the presence of 28 cutaneous HPV (betaPV and gammaPV) by a PCR based method.ResultsThe highest number of HPV prevalence was detected in 84% of the eyebrow hairs (63/75, median 6 types) compared to 47% of AK lesions (35/75, median 3 types) (p< 0.001) and 37% of normal skin (28/75, median 4 types) (p< 0.001), respectively. A total of 228 HPV infections were found in eyebrow hairs compared to only 92 HPV infections in AK and 69 in normal skin. In all three specimens HPV20, HPV23 and/or HPV37 were the most prevalent types. The highest number of multiple types of HPV positive specimens was found in 76% of the eyebrow hairs compared to 60% in AK and 57% in normal skin. The concordance of at least one HPV type in virus positive specimens was 81% (three specimens) and 88-93% of all three combinations with two specimens.ConclusionsThus, eyebrow hairs revealed the highest number of cutaneous HPV infections, are easy to collect and are an appropriate screening tool in order to identify a possible association of HPV and AK.
Cholinergic muscarinic receptor activation augments murine intestinal epithelial cell proliferation and tumorigenesis
Authors: Peng Zhongsheng , Heath Jonathon , Drachenberg Cinthia , Raufman Jean-Pierre , Xie Guofeng 
Published: April 2013

Abstract

Background
Previously, we showed that M3 muscarinic receptor (M3R; gene name Chrm3) deficiency attenuates murine intestinal neoplasia, supporting the hypothesis that muscarinic receptors play an important role in intestinal tumorigenesis.

Methods
To test this hypothesis, in the present study we treated mice with bethanechol, a non-selective muscarinic receptor agonist without nicotinic receptor activity, and examined its effects on azoxymethane (AOM)-induced colon neoplasia. Mice were provided with drinking water containing 400 μg/mL bethanechol chloride or water without additions (control) for a total of 20 weeks, a period that included the initial 6 weeks when mice received intraperitoneal injections of AOM.

Results
When euthanized at week 20, control mice had 8.0 ± 1.3 tumors per animal, whereas bethanechol-treated mice had 10.4 ± 1.5 tumors per mouse (mean ± SE; P = 0.023), a 30% increase. Strikingly, tumor volume per animal was increased 52% in bethanechol-treated compared with control mice (179.7 ± 21.0 vs. 111. 8 ± 22.4 mm3; P = 0.047). On histological examination, bethenechol-treated mice also had more adenocarcinomas per animal (8.0 ± 1.0 vs. 4.1 ± 0.6 for control mice, P = 0.0042). Cell proliferation in both normal mucosa and adenocarcinomas was increased in bethanechol-treated compared to control mice. Also, in tumors, bethanechol treatment increased expression of Chrm3, Egfr and post-Egfr signaling molecules Myc and cyclin D1. Bethanechol treatment increased the thickness of normal colonic mucosa and the expression of selected matrix metalloproteinase (Mmp) genes, including Mmp7, Mmp10 and Mmp13.

Conclusions
These findings support a prominent role for muscarinic receptors in colon neoplasia, and identify post-receptor signaling molecules as potential therapeutic targets.
Dieting status influences associations between dietary patterns and body composition in adolescents: a cross-sectional study
Authors: Howe Anna S , Black Katherine E , Wong Jyh Eiin , Parnell Winsome R , Skidmore Paula ML 
Published: April 2013

AbstractBackgroundAssociations between food choice and body composition in previous studies of adolescents have been inconsistent. This may be due to the body composition measures used, or these associations may be affected by the dieting status of adolescents. The objective of this study was to investigate the association between dietary patterns and body composition in adolescents, and determine if these associations are moderated by dieting status.MethodsInformation on food consumption and current dieting status was collected, using a web-based survey, in 681 adolescents (mean age 15.8 (SD 0.9) years) from schools in Otago, New Zealand. Non-dieters were defined as those reporting not being on a diet as they were “happy with their weight”. Principal components analysis (PCA) was used to determine dietary patterns. Body mass index (BMI), waist circumference (WC), waist-to-height ratio (WHtR), fat mass index (FMI), and fat-free mass index (FFMI) were examined as outcomes. Generalized estimating equations were used to examine associations between dietary patterns and body composition.ResultsPCA produced three dietary patterns: ‘Treat Foods’, ‘Fruits and Vegetables’, and ‘Basic Foods’. A standard deviation increase in ‘Basic Foods’ was associated with a 3.58% decrease in FMI (95%CI −6.14, -0.94) in the total sample. When separate sex analysis was undertaken significant negative associations were found in boys only, between the ‘Basic Food’ score and WC, WHtR, FMI, and FFMI, while the ‘Fruits and Vegetables’ pattern was negatively associated with FMI. Associations between ‘Treat Foods’ and BMI, WC, and WHtR in non-dieters were positive, while these associations were negative for all other participants.ConclusionsSignificant associations were found between dietary patterns and indices of both central and total adiposity, but not BMI. Therefore using only BMI measures may not be useful in this age group. Since our results were significant for boys and not girls, nutrition messages designed to prevent obesity may be particularly important for adolescent boys. As an interaction between dieting status and ‘Treat Foods’ existed, future studies should also explore the role of dieting when investigating food choice and body composition.
Expression of gamma-aminobutyric acid receptors on neoplastic growth and prediction of prognosis in non-small cell lung cancer
Authors: Zhang Xiaoxue , Zhang Rong , Zheng Yuanjie , Shen Jianfei , Xiao Dakai , Li Jin , Shi Xiaoshun , Huang Liyan , Tang Hailing , Liu Jun , He Jianxing , Zhang Haibo 
Published: April 2013

Abstract

Background
Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the adult mammalian brain, but exerts physiologic effects other than that on neurotransmitter in non-neuronal peripheral tissues and organs. GABA may affect cancer growth through activation GABA receptors. We investigated the gene expression of GABA receptors in tissue of non-small cell lung cancers (NSCLC) and non-cancerous tissues, and found that the gene expression of GABA receptor phenotypes was correlated with tumorigenesis and clinical prognosis.

Methods
Sixty-one snap-frozen human samples of NSCLC tissues and paired non-cancerous tissues (5cm away from tumor) were analyzed. Gene expression of GABA receptors was detected by Real-time quantitative PCR (RT-qPCR). Survival times in relation to the expression of GABA receptor phenotypes were analyzed. Human NSCLC cell lines H1299, A549, H520, H460 and human bronchial epithelial cell line BEAS-2B were used to determine the phenotypes of GABA inhibitory effects on cancer cell growth. The effects of exogenous administration of GABA on H1299 cell growth were examined.

Results
The gene expressions were significantly higher in NSCLC tissues than in the paired non-cancerous tissues for GABAA receptor subunit α3 (GABRA3, P = 0.030); for GABAA receptor subunit epsilon (GABRE, P = 0.036); and GABAB receptor subunit 2 (GABBR2, P = 0.005). Kaplan-Meier curves showed that patients with high expression of GABBR2 gene and low expression of GABRA3 gene had a better prognosis (P < 0.05). The administration of GABA resulted in suppressed proliferation of NSCLC cell lines in a dose- and time-dependent manner. The use of the GABA receptor antagonist CGP35348 could reverse the inhibitory effect.

Conclusions
The pattern of GABA receptor gene phenotype expression may be involved in the regulation of tumorigenesis. A high expression of GABBR2 with a low expression of GABRA3 may predict a better outcome. The treatment with GABA attenuates cancer cell growth in vitro. The expression of GABA receptor may be not only promising genetic therapeutic targets but may also serve as valuable prognostic markers for NSCLC.